SIB-PAIR: List of subroutines and functions

Sib-pair is largely written in standard Fortran 95 (as usual, there are a few system specific routines for file handling, time and date etc).

The Sib-pair source code is distributed as a single file, with C-preprocesser macros to deal with platform specific code. The "source lines" in the tables below are the lines within that single file.

The listings below are automatically generated (by an awk script), so check the source for additional informative comments that may have been skipped.

Listing is first by position in the source code file, then alphabetically. The organization of the source is modules, main, I/O, statistical library routines, association and linkage.

fonttype {japi}

Name of routine: fonttype
Source lines: 344 - 365
Type function
Call fonttype(s)
Modulejapi
Notes




aligntype {japi}




Name of routine: aligntype 

Source lines: 367 - 390

Type function

Call aligntype(s)
Modulejapi

Notes




random {rngs}




Name of routine: random 

Source lines: 418 - 428

Type function

Call random()
Modulerngs

Notes
  
 Algorithm AS 183 Appl Stat 1982; 31:188
 Returns a pseudo-random number from U(0,1)
  
 ix,iy,iz should be "randomly" initialised to 1-30000
 eg via time
  





uniqnam {rngs}




Name of routine: uniqnam 

Source lines: 443 - 451

Type subroutine

Call uniqnam(nchar, str)
Modulerngs

Notes
 Random character string






rantri {rngs}




Name of routine: rantri 

Source lines: 455 - 458

Type function

Call rantri()
Modulerngs

Notes
  
 Triangular random number generator
  





randn {rngs}




Name of routine: randn 

Source lines: 467 - 489

Type function

Call randn()
Modulerngs

Notes
  
  The function RANDN() returns a normally distributed pseudo-random
  number with zero mean and unit variance.  Calls are made to a
  function subprogram RANDOM() which returns independent random
  numbers uniform in the interval (0,1).
  
  The algorithm uses the ratio of uniforms method of A.J. Kinderman
  and J.F. Monahan augmented with quadratic bounding curves.





permut {rngs}




Name of routine: permut 

Source lines: 493 - 506

Type subroutine

Call permut(n, ia)
Modulerngs

Notes
  
 Permute the contents of an integer array
  





handler {interrupt}




Name of routine: handler 

Source lines: 517 - 523

Type subroutine

Call handler()
Moduleinterrupt

Notes
 keyboard interrupt handler (exits after 6 interrupts, usually ctrl-C)






fgz_open {f95zlib}




Name of routine: fgz_open 

Source lines: 659 - 687

Type subroutine

Call fgz_open(path, mode, fd, ios)
Modulef95zlib

Notes
 Wrapper for gzopen
   also reinitializes gzread's buffer






fgz_rewind {f95zlib}




Name of routine: fgz_rewind 

Source lines: 691 - 700

Type subroutine

Call fgz_rewind(fd, ios)
Modulef95zlib

Notes
 Wrapper for gzrewind






fgz_read {f95zlib}




Name of routine: fgz_read 

Source lines: 705 - 788

Type subroutine

Call fgz_read(fd, lin, advance, ios)
Modulef95zlib

Notes
 Wrapper for gzread
   read one line of text from buffer






fgz_write {f95zlib}




Name of routine: fgz_write 

Source lines: 792 - 833

Type subroutine

Call fgz_write(fd, lin, advance, ios)
Modulef95zlib

Notes
 write one line of text to a gzipped textfile






fgz_close {f95zlib}




Name of routine: fgz_close 

Source lines: 837 - 845

Type subroutine

Call fgz_close(fd, ios)
Modulef95zlib

Notes
 Wrapper for gzclose






pipe_open {f95pipes}




Name of routine: pipe_open 

Source lines: 893 - 904

Type subroutine

Call pipe_open(command, fd, ios)
Modulef95pipes

Notes
 wrapper for popen
   fd%stat gives mode





pipe_rewind {f95pipes}




Name of routine: pipe_rewind 

Source lines: 907 - 913

Type subroutine

Call pipe_rewind(fd, ios)
Modulef95pipes

Notes
 rewind pipe





pipe_read {f95pipes}




Name of routine: pipe_read 

Source lines: 916 - 940

Type subroutine

Call pipe_read(fd, lin, advance, ios)
Modulef95pipes

Notes
 wrapper for fgets





pipe_write {f95pipes}




Name of routine: pipe_write 

Source lines: 943 - 963

Type subroutine

Call pipe_write(fd, lin, advance, ios)
Modulef95pipes

Notes
 wrapper for fputs





pipe_close {f95pipes}




Name of routine: pipe_close 

Source lines: 966 - 974

Type subroutine

Call pipe_close(fd, ios)
Modulef95pipes

Notes
 wrapper for pclose





newlun {fileio}




Name of routine: newlun 

Source lines: 995 - 1009

Type subroutine

Call newlun(strm)
Modulefileio

Notes
 Find a free Fortran style unit






isgzipped {fileio}




Name of routine: isgzipped 

Source lines: 1013 - 1035

Type function

Call isgzipped(filnam)
Modulefileio

Notes
 Test if gzipped file, reading magic number 31,139






open_port {fileio}




Name of routine: open_port 

Source lines: 1039 - 1105

Type subroutine

Call open_port(filnam, port, mode, ios)
Modulefileio

Notes
 Open a (plain or gzipped) file or pipe for reading or writing






rewind_port {fileio}




Name of routine: rewind_port 

Source lines: 1109 - 1125

Type subroutine

Call rewind_port(port, ios)
Modulefileio

Notes
 Reopen a file for reading or writing






readline {fileio}




Name of routine: readline 

Source lines: 1129 - 1151

Type subroutine

Call readline(port, lin, advance, ios)
Modulefileio

Notes
 Read one record from file






writeline {fileio}




Name of routine: writeline 

Source lines: 1155 - 1177

Type subroutine

Call writeline(port, lin, advance, ios)
Modulefileio

Notes
 Write one record to file






close_port {fileio}




Name of routine: close_port 

Source lines: 1182 - 1205

Type subroutine

Call close_port(port, ios)
Modulefileio

Notes
 Close file for reading -  
   if gzipped but ZLIB not available, then delete temporary file






sow {scanner}




Name of routine: sow 

Source lines: 1215 - 1226

Type function

Call sow(string)
Modulescanner

Notes
 skip leading whitespace






nextword {scanner}




Name of routine: nextword 

Source lines: 1239 - 1324

Type subroutine

Call nextword(pos, s, eos, reserved, nword, word, stat, typ)
Modulescanner

Notes
 Next token in buffer

 Need to know which word if reading pedigree or case-control data
 as slashes separate alleles in data but are allowed in ID strings

 typ  action
 1    whitespace separated
 2    whitespace separated or reserved character (id by opchar())
 3    whitespace or slash separated (so genotypes can be written a/b) ped data
 4    whitespace or slash separated (so genotypes can be written a/b) case data






args {scanner}




Name of routine: args 

Source lines: 1328 - 1358

Type subroutine

Call args(s, narg, arg, typ)
Modulescanner

Notes
 extracts narg arguments from input string s






getword {scanner}




Name of routine: getword 

Source lines: 1362 - 1386

Type subroutine

Call getword(s, which, word)
Modulescanner

Notes
 extracts the nth whitespace-separated argument from input string s






wordpos {scanner}




Name of routine: wordpos 

Source lines: 1390 - 1413

Type function

Call wordpos(s, which)
Modulescanner

Notes
 Find end of nth whitespace-separated argument in input string s






countargs {scanner}




Name of routine: countargs 

Source lines: 1417 - 1437

Type function

Call countargs(s, typ)
Modulescanner

Notes
 return count of  whitespace-separated argument from input string s






getlabel {scanner}




Name of routine: getlabel 

Source lines: 1441 - 1471

Type subroutine

Call getlabel(val, s, label)
Modulescanner

Notes
 extracts the matching value for a list of value=label pairs in a string






opchar {scanner}




Name of routine: opchar 

Source lines: 1475 - 1485

Type function

Call opchar(ch)
Modulescanner

Notes
 is a reserved character for primitives?  "()*+-/<=>^:"






opsimple {scanner}




Name of routine: opsimple 

Source lines: 1489 - 1497

Type function

Call opsimple(ch)
Modulescanner

Notes
 is a reserved character for name = value pair list?  "=:,;"






setup_hash {idhash_class}




Name of routine: setup_hash 

Source lines: 1518 - 1559

Type subroutine

Call setup_hash(keytyp, nrec, hashtab, load)
Moduleidhash_class

Notes
 Allocate an open addressed hash table
   number of buckets is prime
   probe using exponential hash following Muehlbacher 2004 JUCS 10: 1239-1249






cleanup_hash {idhash_class}




Name of routine: cleanup_hash 

Source lines: 1563 - 1572

Type subroutine

Call cleanup_hash(hashtab)
Moduleidhash_class

Notes
 release memory held by a hash table






fill_hash {idhash_class}




Name of routine: fill_hash 

Source lines: 1576 - 1593

Type subroutine

Call fill_hash(hashtab, string_array)
Moduleidhash_class

Notes
 populate hash table






find_hashtab {idhash_class}




Name of routine: find_hashtab 

Source lines: 1597 - 1616

Type subroutine

Call find_hashtab(str, string_array, hashtab, iaddress)
Moduleidhash_class

Notes
 Search hash table






string_hash {idhash_class}




Name of routine: string_hash 

Source lines: 1620 - 1631

Type function

Call string_hash(str, ibound)
Moduleidhash_class

Notes
 String hash function (that used by SRFI-64)






make_lochash {lochash_class}




Name of routine: make_lochash 

Source lines: 1639 - 1658

Type subroutine

Call make_lochash(nloci, loc, lochash)
Modulelochash_class

Notes
 Locus name hash table





insert_lochash {lochash_class}




Name of routine: insert_lochash 

Source lines: 1662 - 1681

Type subroutine

Call insert_lochash(str, nloci, loc, lochash)
Modulelochash_class

Notes
 append most recent locus to hash table






show_lochash {lochash_class}




Name of routine: show_lochash 

Source lines: 1683 - 1692

Type subroutine

Call show_lochash(nloci, loc, lochash)
Modulelochash_class

Notes
 Locus name hash table





show_one_iarray {showcomponent}




Name of routine: show_one_iarray 

Source lines: 1699 - 1711

Type subroutine

Call show_one_iarray(nam, sep, nval, isall, array)
Moduleshowcomponent

Notes
 Utilities to print arrays





show_one_carray {showcomponent}




Name of routine: show_one_carray 

Source lines: 1713 - 1725

Type subroutine

Call show_one_carray(nam, sep, nval, isall, array)
Moduleshowcomponent

Notes
 Utilities to print arrays





show_one_farray {showcomponent}




Name of routine: show_one_farray 

Source lines: 1727 - 1739

Type subroutine

Call show_one_farray(nam, sep, nval, isall, array)
Moduleshowcomponent

Notes
 Utilities to print arrays





loccode {locus_types}




Name of routine: loccode 

Source lines: 1773 - 1798

Type function

Call loccode(ch)
Modulelocus_types

Notes
 Locus types bitpatterns
 loctyp Compression_scheme Deleted Marker: Autosomal X-marker Haploid Y-chrom / Affection Quantitative
        CC D T  
 1      00 0 0 001 Autosomal marker
 2      00 0 0 010 X-chromosome marker
 4      00 0 0 100 Haploid unspecified
 5      00 0 0 101 Mitochondrial marker
 6      00 0 0 110 Y-Chromosome marker
 8      00 0 1 000 Trait unspecified
 9      00 0 1 001 Quantitative trait
 10     00 0 1 010 Binary trait
 11     00 0 1 011 Categorical trait





same_loctyp {locus_types}




Name of routine: same_loctyp 

Source lines: 1802 - 1815

Type function

Call same_loctyp(loctyp, reftyp)
Modulelocus_types

Notes
 same locus type or same class, ignoring compression type but not where dropped






isactive {locus_types}




Name of routine: isactive 

Source lines: 1817 - 1821

Type function

Call isactive(loctyp)
Modulelocus_types

Notes
 is an active variable





istrait {locus_types}




Name of routine: istrait 

Source lines: 1823 - 1827

Type function

Call istrait(loctyp)
Modulelocus_types

Notes
 trait - active





isqtrait {locus_types}




Name of routine: isqtrait 

Source lines: 1829 - 1833

Type function

Call isqtrait(loctyp)
Modulelocus_types

Notes
 quantitative trait





iscattrait {locus_types}




Name of routine: iscattrait 

Source lines: 1835 - 1839

Type function

Call iscattrait(loctyp)
Modulelocus_types

Notes
 categorical trait - active





ismarker {locus_types}




Name of routine: ismarker 

Source lines: 1841 - 1845

Type function

Call ismarker(loctyp)
Modulelocus_types

Notes
 marker - inactive or active





gencode {locus_types}




Name of routine: gencode 

Source lines: 1847 - 1851

Type function

Call gencode(loctyp)
Modulelocus_types

Notes
 genotype encoding 1=standard 2=sequence 3=compressed SNP





ishaploid {locus_types}




Name of routine: ishaploid 

Source lines: 1853 - 1857

Type function

Call ishaploid(loctyp)
Modulelocus_types

Notes
 is a haploid locus





iscompressed {locus_types}




Name of routine: iscompressed 

Source lines: 1859 - 1863

Type function

Call iscompressed(loctyp)
Modulelocus_types

Notes
 is genotype storage compact (gencode > 1)





isactdip {locus_types}




Name of routine: isactdip 

Source lines: 1865 - 1869

Type function

Call isactdip(loctyp)
Modulelocus_types

Notes
 most association/linkage procedures are for active diploid codominant markers





setup_loci {locus_data}




Name of routine: setup_loci 

Source lines: 1917 - 1933

Type subroutine

Call setup_loci(n)
Modulelocus_data

Notes
 Allocate storage for locus descriptions






cleanup_loci {locus_data}




Name of routine: cleanup_loci 

Source lines: 1937 - 1942

Type subroutine

Call cleanup_loci()
Modulelocus_data

Notes
 Deallocate storage for locus descriptions






expand_loci {locus_data}




Name of routine: expand_loci 

Source lines: 1946 - 1989

Type subroutine

Call expand_loci(nextra, plevel)
Modulelocus_data

Notes
 Expand arrays for locus descriptions






insloc {locus_data}




Name of routine: insloc 

Source lines: 1994 - 2005

Type subroutine

Call insloc(pos)
Modulelocus_data

Notes
  
 insert a locus into the locus list
 other details of the slot are left blank
  





setupmer {locus_data}




Name of routine: setupmer 

Source lines: 2009 - 2032

Type subroutine

Call setupmer(port)
Modulelocus_data

Notes
 Preallocate arrays for locus descriptions from MERLIN locus file






setup_plink {locus_data}




Name of routine: setup_plink 

Source lines: 2036 - 2056

Type subroutine

Call setup_plink(port, nmark, newsiz)
Modulelocus_data

Notes
 Allocate arrays for locus descriptions from PLINK .map file






setup_stat {locus_data}




Name of routine: setup_stat 

Source lines: 2060 - 2065

Type subroutine

Call setup_stat(comment)
Modulelocus_data

Notes
 initialize locstat (stores test statistic for each locus)






show_locus_allocation {locus_data}




Name of routine: show_locus_allocation 

Source lines: 2069 - 2085

Type subroutine

Call show_locus_allocation()
Modulelocus_data

Notes
 Diagnostics for locus structure






newloctyp {locus_data}




Name of routine: newloctyp 

Source lines: 2087 - 2100

Type subroutine

Call newloctyp()
Modulelocus_data

Notes
 Old to new locus types





matrix_create {matrix_class}




Name of routine: matrix_create 

Source lines: 2137 - 2183

Type subroutine

Call matrix_create(nr, nc, a, astat, setbufwidth)
Modulematrix_class

Notes
 Create a matrix container






matrix_zero {matrix_class}




Name of routine: matrix_zero 

Source lines: 2187 - 2206

Type subroutine

Call matrix_zero(a)
Modulematrix_class

Notes
 zero a matrix






matrix_copy {matrix_class}




Name of routine: matrix_copy 

Source lines: 2210 - 2283

Type subroutine

Call matrix_copy(a, b, iflag, newrows, newcols, setbufwidth)
Modulematrix_class

Notes
 Copy a matrix container (a -> b)






matrix_destroy {matrix_class}




Name of routine: matrix_destroy 

Source lines: 2287 - 2301

Type subroutine

Call matrix_destroy(a)
Modulematrix_class

Notes
  
 Destroy a matrix container






matrix_active {matrix_class}




Name of routine: matrix_active 

Source lines: 2305 - 2309

Type function

Call matrix_active(a)
Modulematrix_class

Notes
 Test if matrix allocated/active






matrix_size {matrix_class}




Name of routine: matrix_size 

Source lines: 2313 - 2321

Type function

Call matrix_size(a)
Modulematrix_class

Notes
  
 Size of matrix in container






matrix_nrows {matrix_class}




Name of routine: matrix_nrows 

Source lines: 2325 - 2330

Type function

Call matrix_nrows(a)
Modulematrix_class

Notes
 Number of matrix rows accessor






matrix_ncols {matrix_class}




Name of routine: matrix_ncols 

Source lines: 2334 - 2339

Type function

Call matrix_ncols(a)
Modulematrix_class

Notes
 Number of matrix cols accessor






matrix_type {matrix_class}




Name of routine: matrix_type 

Source lines: 2343 - 2348

Type function

Call matrix_type(a)
Modulematrix_class

Notes
 Matrix storage type






matrix_write {matrix_class}




Name of routine: matrix_write 

Source lines: 2352 - 2375

Type subroutine

Call matrix_write(a, stream, iflag)
Modulematrix_class

Notes
 Write a matrix






matrix_write_row {matrix_class}




Name of routine: matrix_write_row 

Source lines: 2380 - 2399

Type subroutine

Call matrix_write_row(irow, a, stream)
Modulematrix_class

Notes
 Write one row of a matrix to an open stream, 
 needed by disjoin, nuclear etc






matrix_read {matrix_class}




Name of routine: matrix_read 

Source lines: 2403 - 2422

Type subroutine

Call matrix_read(stream, a, iflag)
Modulematrix_class

Notes
 Read a matrix






matrix_read_unformatted {matrix_class}




Name of routine: matrix_read_unformatted 

Source lines: 2426 - 2444

Type subroutine

Call matrix_read_unformatted(stream, nr, nc, a, iflag)
Modulematrix_class

Notes
 Fill a matrix container from a unformatted stream






matrix_read_contents {matrix_class}




Name of routine: matrix_read_contents 

Source lines: 2448 - 2505

Type subroutine

Call matrix_read_contents(stream, a, iflag)
Modulematrix_class

Notes
 Read in actual contents of matrix






matrix_read_row {matrix_class}




Name of routine: matrix_read_row 

Source lines: 2510 - 2536

Type subroutine

Call matrix_read_row(stream, irow, a)
Modulematrix_class

Notes
 Read one row of a matrix from an open stream, 
 was written row major by matrix_write_row






matrix_set_row {matrix_class}




Name of routine: matrix_set_row 

Source lines: 2540 - 2587

Type subroutine

Call matrix_set_row(ivals, irow, a, iflag)
Modulematrix_class

Notes
 Set row






matrix_get_row {matrix_class}




Name of routine: matrix_get_row 

Source lines: 2591 - 2624

Type subroutine

Call matrix_get_row(a, irow, ivals, iflag)
Modulematrix_class

Notes
 Get row






matrix_copy_row {matrix_class}




Name of routine: matrix_copy_row 

Source lines: 2628 - 2657

Type subroutine

Call matrix_copy_row(rowa, a, rowb, b, iflag)
Modulematrix_class

Notes
 Copy row 






matrix_set_col {matrix_class}




Name of routine: matrix_set_col 

Source lines: 2661 - 2708

Type subroutine

Call matrix_set_col(ivals, icol, a, iflag)
Modulematrix_class

Notes
 Set col






matrix_get_col {matrix_class}




Name of routine: matrix_get_col 

Source lines: 2712 - 2746

Type subroutine

Call matrix_get_col(a, icol, ivals, iflag)
Modulematrix_class

Notes
 Get col: updates column buffer






matrix_set_el {matrix_class}




Name of routine: matrix_set_el 

Source lines: 2750 - 2772

Type subroutine

Call matrix_set_el(ival, irow, icol, a, iflag)
Modulematrix_class

Notes
 Set element: updates column buffer as well if current






matrix_get_el {matrix_class}




Name of routine: matrix_get_el 

Source lines: 2776 - 2810

Type subroutine

Call matrix_get_el(irow, icol, a, ival, iflag)
Modulematrix_class

Notes
 Get element: updates column buffer






matrix_print {matrix_class}




Name of routine: matrix_print 

Source lines: 2814 - 2842

Type subroutine

Call matrix_print(a)
Modulematrix_class

Notes
 Print matrix






setup_peds {ped_class}




Name of routine: setup_peds 

Source lines: 2917 - 2987

Type subroutine

Call setup_peds(nped, nobs, numloc, numcol, dataset, astat, plevel)
Moduleped_class

Notes
 allocate pedigree data






copy_peds {ped_class}




Name of routine: copy_peds 

Source lines: 2991 - 3030

Type subroutine

Call copy_peds(set1, set2)
Moduleped_class

Notes
 copy pedigree data






cleanup_peds {ped_class}




Name of routine: cleanup_peds 

Source lines: 3034 - 3065

Type subroutine

Call cleanup_peds(dataset)
Moduleped_class

Notes
 deallocate pedigree structure arrays






expand_pheno {ped_class}




Name of routine: expand_pheno 

Source lines: 3069 - 3090

Type subroutine

Call expand_pheno(newcol, dataset, astat)
Moduleped_class

Notes
 expand phenotype storage






expand_geno {ped_class}




Name of routine: expand_geno 

Source lines: 3094 - 3140

Type subroutine

Call expand_geno(newcol, dataset, astat)
Moduleped_class

Notes
 expand genotype storage






expand_sgeno {ped_class}




Name of routine: expand_sgeno 

Source lines: 3144 - 3188

Type subroutine

Call expand_sgeno(newcol, dataset, astat)
Moduleped_class

Notes
 expand SNP storage






get_geno {ped_class}




Name of routine: get_geno 

Source lines: 3192 - 3237

Type subroutine

Call get_geno(idx, gcol1, gcol2, dataset, g1, g2)
Moduleped_class

Notes
 Extract a genotype either stored as alleles or SNP genotypes






encode_geno1 {ped_class}




Name of routine: encode_geno1 

Source lines: 3242 - 3259

Type subroutine

Call encode_geno1(g1, g2, ig1, ig2) 
Moduleped_class

Notes
 Transfer genotype to internal coding
 if snptyp = 1, then one allele per byte






encode_geno2 {ped_class}




Name of routine: encode_geno2 

Source lines: 3264 - 3292

Type subroutine

Call encode_geno2(g1, g2, ig, whichpos)
Moduleped_class

Notes
 Transfer genotype to internal coding
 if snptyp = 2, then one genotype per byte






set_geno {ped_class}




Name of routine: set_geno 

Source lines: 3296 - 3319

Type subroutine

Call set_geno(idx, gcol1, gcol2, dataset, g1, g2)
Moduleped_class

Notes
 Set a genotype






observed {ped_class}




Name of routine: observed 

Source lines: 3323 - 3343

Type function

Call observed(idx, gcol, dataset)
Moduleped_class

Notes
 Test if genotype is observed






missing {ped_class}




Name of routine: missing 

Source lines: 3345 - 3370

Type function

Call missing(idx, gcol, dataset)
Moduleped_class

Notes




show_ped_allocation {ped_class}




Name of routine: show_ped_allocation 

Source lines: 3372 - 3453

Type subroutine

Call show_ped_allocation(dataset)
Moduleped_class

Notes




show_snp {ped_class}




Name of routine: show_snp 

Source lines: 3455 - 3475

Type subroutine

Call show_snp(idx, gpos, dataset)
Moduleped_class

Notes




setup_freq {alleles_class}




Name of routine: setup_freq 

Source lines: 3515 - 3522

Type subroutine

Call setup_freq(nall, allele_buffer)
Modulealleles_class

Notes
 initialize allele_data






copyfreq {alleles_class}




Name of routine: copyfreq 

Source lines: 3526 - 3547

Type subroutine

Call copyfreq(allele_buffer, allele_buffer2)
Modulealleles_class

Notes
 Copy allele frequency data from one structure to another






expand_alleles {alleles_class}




Name of routine: expand_alleles 

Source lines: 3551 - 3574

Type subroutine

Call expand_alleles(allele_buffer, nextra)
Modulealleles_class

Notes
 expand size of an allele frequency structure






cleanup_alleles {alleles_class}




Name of routine: cleanup_alleles 

Source lines: 3578 - 3596

Type subroutine

Call cleanup_alleles(allele_buffer)
Modulealleles_class

Notes
 release memory held by an allele frequency structure






genot {alleles_class}




Name of routine: genot 

Source lines: 3600 - 3614

Type subroutine

Call genot(allele_buffer, gfrq)
Modulealleles_class

Notes
  
 produce genotype frequencies for Metropolis algorithm
  





calc_gtp_freqs {alleles_class}




Name of routine: calc_gtp_freqs 

Source lines: 3617 - 3635

Type subroutine

Call calc_gtp_freqs(allele_buffer)
Modulealleles_class

Notes
 or for sequential imputation





dohash_ped_id {idhash_funs}




Name of routine: dohash_ped_id 

Source lines: 3656 - 3664

Type function

Call dohash_ped_id(idx, dataset, maxkey)
Moduleidhash_funs

Notes
 pedigree + individual ID





dohash_id {idhash_funs}




Name of routine: dohash_id 

Source lines: 3666 - 3673

Type function

Call dohash_id(idx, dataset, maxkey)
Moduleidhash_funs

Notes
 individual ID 





domatch_ped_id {idhash_funs}




Name of routine: domatch_ped_id 

Source lines: 3675 - 3683

Type function

Call domatch_ped_id(idx, iaddress, dataset)
Moduleidhash_funs

Notes
 match pedigree + individual ID





domatch_id {idhash_funs}




Name of routine: domatch_id 

Source lines: 3685 - 3691

Type function

Call domatch_id(idx, iaddress, dataset)
Moduleidhash_funs

Notes
 match individual id





domatch_string_ped_id {idhash_funs}




Name of routine: domatch_string_ped_id 

Source lines: 3693 - 3702

Type function

Call domatch_string_ped_id(pedstr, indstr, iaddress, dataset)
Moduleidhash_funs

Notes
 match search string to pedigree + individual ID





domatch_string_id {idhash_funs}




Name of routine: domatch_string_id 

Source lines: 3704 - 3711

Type function

Call domatch_string_id(idstr, iaddress, dataset)
Moduleidhash_funs

Notes
 match search string to individual ID





betacf {statfuns}




Name of routine: betacf 

Source lines: 3727 - 3762

Type function

Call betacf(a,b,x)
Modulestatfuns

Notes
  
 betacf from Numerical Recipes, 1986
  





ibeta {statfuns}




Name of routine: ibeta 

Source lines: 3770 - 3837

Type function

Call ibeta(x, p, q)
Modulestatfuns

Notes
 This function computes the beta cumulative
 distribution function at the point x.  p and q are the
 exponents of x and 1-x in the beta density.  see KL Majumder
 GP Bhattacharjee (1973). Algorithm AS 63 The incomplete beta
 integral. Appl Stat 22: 409-411.






fp {statfuns}




Name of routine: fp 

Source lines: 3841 - 3866

Type function

Call fp(x, n1, n2)
Modulestatfuns

Notes
  
 F-ratio P-values
  





tp {statfuns}




Name of routine: tp 

Source lines: 3870 - 3877

Type function

Call tp(x, df)
Modulestatfuns

Notes
 Wrap fp to give t-distribution P-values
 





chip {statfuns}




Name of routine: chip 

Source lines: 3881 - 3907

Type function

Call chip(chisq, df)
Modulestatfuns

Notes
  
 Evaluate central chi-square in FORTRAN
  





gammad {statfuns}




Name of routine: gammad 

Source lines: 3913 - 4021

Type function

Call gammad(x, p, ifault)
Modulestatfuns

Notes
  
 Algorithm AS239  Appl. Statist. (1988) Vol. 37, No. 3
  
 Computation of the Incomplete Gamma Integral
  





chi2nc {statfuns}




Name of routine: chi2nc 

Source lines: 4126 - 4189

Type function

Call chi2nc(x, f, ncp, ifault)
Modulestatfuns

Notes
 ALGORITHM AS 275 APPL.STATIST. (1992), VOL.41, NO.2

 Computes the noncentral chi-square distribution function
 with positive real degrees of freedom f and nonnegative
 noncentrality parameter theta






mvbvu {statfuns}




Name of routine: mvbvu 

Source lines: 4262 - 4359

Type function

Call mvbvu(sh, sk, r)
Modulestatfuns

Notes
     A function for computing bivariate normal probabilities;
       developed using 
         Drezner, Z. and Wesolowsky, G. O. (1989),
         On the Computation of the Bivariate Normal Integral,
         J. Stat. Comput. Simul.. 35 pp. 101-107.
       with extensive modications for double precisions by    
         Alan Genz and Yihong Ge
         Department of Mathematics
         Washington State University
         Pullman, WA 99164-3113
         Email : alangenz@wsu.edu

 BVN - calculate the probability that X is larger than SH and Y is
       larger than SK.

 Parameters

   SH  REAL, integration limit
   SK  REAL, integration limit
   R   REAL, correlation coefficient
   LG  INTEGER, number of Gauss Rule Points and Weights






chisqd {statfuns}




Name of routine: chisqd 

Source lines: 4453 - 4514

Type function

Call chisqd(p, n)
Modulestatfuns

Notes
 Richard Goldstein, Algorithm 451: Chi-Square Quantiles,
 Communications of the ACM, August 1973, Volume 16, Number 8, pages 483-484. 
 Transcribed to machine readable form by John Burkhardt






fact {statfuns}




Name of routine: fact 

Source lines: 4567 - 4584

Type function

Call fact(n)
Modulestatfuns

Notes
  
 Factorial
  





lfact {statfuns}




Name of routine: lfact 

Source lines: 4588 - 4593

Type function

Call lfact(n)
Modulestatfuns

Notes
  
 Log factorial
  





dpois {statfuns}




Name of routine: dpois 

Source lines: 4612 - 4624

Type function

Call dpois(x, mu)
Modulestatfuns

Notes
  
 Log poisson density
  





dweib {statfuns}




Name of routine: dweib 

Source lines: 4628 - 4645

Type function

Call dweib(x, mu, shap, cens)
Modulestatfuns

Notes
  
 Log Weibull density (with censoring)
  





mvndst {mftfuns}




Name of routine: mvndst 

Source lines: 4704 - 4741

Type subroutine

Call mvndst(n, lower, upper, infin, correl, maxpts,  abseps, releps, error, value, inform )
Modulemftfuns

Notes
     A subroutine for computing multivariate normal probabilities.
     This subroutine uses an algorithm given in the paper
     "Numerical Computation of Multivariate Normal Probabilities", in
     J. of Computational and Graphical Stat., 1(1992), pp. 141-149, by
          Alan Genz
          Department of Mathematics
          Washington State University
          Pullman, WA 99164-3113
          Email : AlanGenz@wsu.edu
  Parameters
     N      INTEGER, the number of variables.
     LOWER  REAL, array of lower integration limits.
     UPPER  REAL, array of upper integration limits.
     INFIN  INTEGER, array of integration limits flags:
            if INFIN(I) < 0, Ith limits are (-infinity, infinity);
            if INFIN(I) = 0, Ith limits are (-infinity, UPPER(I)];
            if INFIN(I) = 1, Ith limits are [LOWER(I), infinity);
            if INFIN(I) = 2, Ith limits are [LOWER(I), UPPER(I)].
     CORREL REAL, array of correlation coefficients; the correlation
            coefficient in row I column J of the correlation matrix
            should be stored in CORREL( J + ((I-2)*(I-1))/2 ), for J < I.
            THe correlation matrix must be positive semidefinite.
     MAXPTS INTEGER, maximum number of function values allowed. This
            parameter can be used to limit the time. A sensible
            strategy is to start with MAXPTS = 1000*N, and then
            increase MAXPTS if ERROR is too large.
     ABSEPS REAL absolute error tolerance.
     RELEPS REAL relative error tolerance.
     ERROR  REAL estimated absolute error, with 99% confidence level.
     VALUE  REAL estimated value for the integral
     INFORM INTEGER, termination status parameter:
            if INFORM = 0, normal completion with ERROR < EPS;
            if INFORM = 1, completion with ERROR > EPS and MAXPTS
                           function vaules used; increase MAXPTS to
                           decrease ERROR;
            if INFORM = 2, N > 500 or N < 1.





mvnlms {mftfuns}




Name of routine: mvnlms 

Source lines: 4834 - 4849

Type subroutine

Call mvnlms( a, b, infin, lower, upper )
Modulemftfuns

Notes
  





covsrt {mftfuns}




Name of routine: covsrt 

Source lines: 4853 - 5021

Type subroutine

Call covsrt(n, lower, upper, correl, infin, y,  infis, a, b, cov, infi)
Modulemftfuns

Notes
  
 Subroutine to sort integration limits and determine Cholesky factor.






dkswap {mftfuns}




Name of routine: dkswap 

Source lines: 5023 - 5030

Type subroutine

Call dkswap( x, y )
Modulemftfuns

Notes
 Swap elements  





rcswp {mftfuns}




Name of routine: rcswp 

Source lines: 5034 - 5066

Type subroutine

Call rcswp( p, q, a, b, infin, n, c )
Modulemftfuns

Notes
  
 Swaps rows and columns P and Q in situ, with P <= Q.






dkbvrc {mftfuns}




Name of routine: dkbvrc 

Source lines: 5117 - 5325

Type subroutine

Call dkbvrc(ndim, minvls, maxvls, functn, abseps, releps,  abserr, finest, inform )
Modulemftfuns

Notes
  ABSEPS  Required absolute accuracy.
  RELEPS  Required relative accuracy.
***** Output parameters
  MINVLS  Actual number of function evaluations used.
  ABSERR  Estimated absolute accuracy of FINEST.
  FINEST  Estimated value of integral.
  INFORM  INFORM = 0 for normal exit, when
                     ABSERR <= MAX(ABSEPS, RELEPS*ABS(FINEST))
                  and
                     INTVLS <= MAXCLS.
          INFORM = 1 If MAXVLS was too small to obtain the required
          accuracy. In this case a value FINEST is returned with
          estimated absolute accuracy ABSERR.






dksmrc {mftfuns}




Name of routine: dksmrc 

Source lines: 5327 - 5361

Type subroutine

Call dksmrc( ndim, klim, sumkro, prime, vk, functn, x )
Modulemftfuns

Notes
  





chfind {string_utilities}




Name of routine: chfind 

Source lines: 5641 - 5665

Type function

Call chfind(string, ch)
Modulestring_utilities

Notes
 
 find an unescaped character in a string
 





strfind {string_utilities}




Name of routine: strfind 

Source lines: 5670 - 5748

Type function

Call strfind(regexp, targt, nocase)
Modulestring_utilities

Notes
 
 Compare string to a search string, allowing wildcards '*.', and case
 matching
 





escape {string_utilities}




Name of routine: escape 

Source lines: 5752 - 5778

Type subroutine

Call escape(str, trget)
Modulestring_utilities

Notes
 Escape a target character, usually "






setup_mem {scheme_lang}




Name of routine: setup_mem 

Source lines: 6001 - 6068

Type subroutine

Call setup_mem(siz)
Modulescheme_lang

Notes
 Memory management





cleanup_bank {scheme_lang}




Name of routine: cleanup_bank 

Source lines: 6074 - 6088

Type subroutine

Call cleanup_bank(sta, fin)
Modulescheme_lang

Notes
 Clean up memory arrays

 Zero a block of cells, including deallocating strings 






cleanup_mem {scheme_lang}




Name of routine: cleanup_mem 

Source lines: 6092 - 6095

Type subroutine

Call cleanup_mem()
Modulescheme_lang

Notes
 Free all memory






save_scheme_image {scheme_lang}




Name of routine: save_scheme_image 

Source lines: 6098 - 6118

Type subroutine

Call save_scheme_image(strm, ios)
Modulescheme_lang

Notes
 Save memory image





read_scheme_image {scheme_lang}




Name of routine: read_scheme_image 

Source lines: 6121 - 6152

Type subroutine

Call read_scheme_image(strm, ios)
Modulescheme_lang

Notes
 Read memory image





gc_mark {scheme_lang}




Name of routine: gc_mark 

Source lines: 6158 - 6197

Type subroutine

Call gc_mark(a)
Modulescheme_lang

Notes
 Mark-sweep garbage collector

 Mark cells to be saved






gc {scheme_lang}




Name of routine: gc 

Source lines: 6202 - 6237

Type subroutine

Call gc(a, b, plevel)
Modulescheme_lang

Notes
 Copy all registers to free memory
 Reset pointers from old addresses to new addresses






getcell {scheme_lang}




Name of routine: getcell 

Source lines: 6241 - 6264

Type function

Call getcell(a, b)
Modulescheme_lang

Notes
 Get next free cell






set_type {scheme_lang}




Name of routine: set_type 

Source lines: 6269 - 6273

Type subroutine

Call set_type(p, iflag)
Modulescheme_lang

Notes
 Cell type operations

 Setting values





set_ivalue {scheme_lang}




Name of routine: set_ivalue 

Source lines: 6274 - 6279

Type subroutine

Call set_ivalue(p, ivalue)
Modulescheme_lang

Notes
 Cell type operations

 Setting values





set_value {scheme_lang}




Name of routine: set_value 

Source lines: 6280 - 6285

Type subroutine

Call set_value(p, val)
Modulescheme_lang

Notes
 Cell type operations

 Setting values





set_string {scheme_lang}




Name of routine: set_string 

Source lines: 6286 - 6299

Type subroutine

Call set_string(p, str)
Modulescheme_lang

Notes
 Cell type operations

 Setting values





set_substring {scheme_lang}




Name of routine: set_substring 

Source lines: 6300 - 6310

Type subroutine

Call set_substring(p, sta, fin, str)
Modulescheme_lang

Notes
 Cell type operations

 Setting values





set_car {scheme_lang}




Name of routine: set_car 

Source lines: 6312 - 6315

Type subroutine

Call set_car(p, icar)
Modulescheme_lang

Notes
 Miniscm





set_cdr {scheme_lang}




Name of routine: set_cdr 

Source lines: 6316 - 6319

Type subroutine

Call set_cdr(p, icdr)
Modulescheme_lang

Notes
 Miniscm





set_caar {scheme_lang}




Name of routine: set_caar 

Source lines: 6320 - 6323

Type subroutine

Call set_caar(p, icaar)
Modulescheme_lang

Notes
 Miniscm





set_cdar {scheme_lang}




Name of routine: set_cdar 

Source lines: 6324 - 6327

Type subroutine

Call set_cdar(p, icdar)
Modulescheme_lang

Notes
 Miniscm





set_syntaxnum {scheme_lang}




Name of routine: set_syntaxnum 

Source lines: 6328 - 6331

Type subroutine

Call set_syntaxnum(p, op)
Modulescheme_lang

Notes
 Miniscm





get_ivalue {scheme_lang}




Name of routine: get_ivalue 

Source lines: 6335 - 6339

Type function

Call get_ivalue(p)
Modulescheme_lang

Notes
 Getting values






get_value {scheme_lang}




Name of routine: get_value 

Source lines: 6341 - 6349

Type function

Call get_value(p)
Modulescheme_lang

Notes
 Miniscm





rvalue {scheme_lang}




Name of routine: rvalue 

Source lines: 6351 - 6359

Type function

Call rvalue(p)
Modulescheme_lang

Notes
 Miniscm





get_string {scheme_lang}




Name of routine: get_string 

Source lines: 6363 - 6373

Type function

Call get_string(p) 
Modulescheme_lang

Notes
 Strings
 





append_string {scheme_lang}




Name of routine: append_string 

Source lines: 6377 - 6400

Type subroutine

Call append_string(p, str)
Modulescheme_lang

Notes
 Append to existing string






get_substr {scheme_lang}




Name of routine: get_substr 

Source lines: 6402 - 6415

Type function

Call get_substr(p, sta, fin) 
Modulescheme_lang

Notes
 Substring





get_strlen {scheme_lang}




Name of routine: get_strlen 

Source lines: 6417 - 6421

Type function

Call get_strlen(p) 
Modulescheme_lang

Notes
 String length





get_listlen {scheme_lang}




Name of routine: get_listlen 

Source lines: 6423 - 6435

Type function

Call get_listlen(p) 
Modulescheme_lang

Notes
 Miniscm





get_var {scheme_lang}




Name of routine: get_var 

Source lines: 6441 - 6527

Type subroutine

Call get_var(string, pos, fin, istat)
Modulescheme_lang

Notes
 allowing access to Scheme environment from Sib-pair
 accessible variables are atomic
 result inserted into passed string






list_var {scheme_lang}




Name of routine: list_var 

Source lines: 6531 - 6578

Type subroutine

Call list_var(typ, ple)
Modulescheme_lang

Notes
 List Sib-pair accessible (atomic or pair) variables






isafun {scheme_lang}




Name of routine: isafun 

Source lines: 6582 - 6611

Type function

Call isafun(nam)
Modulescheme_lang

Notes
 Test if a macro function exists






procnum {scheme_lang}




Name of routine: procnum 

Source lines: 6613 - 6617

Type function

Call procnum(p)
Modulescheme_lang

Notes
 Miniscm





syntaxnum {scheme_lang}




Name of routine: syntaxnum 

Source lines: 6618 - 6622

Type function

Call syntaxnum(p)
Modulescheme_lang

Notes
 Miniscm





typeof {scheme_lang}




Name of routine: typeof 

Source lines: 6626 - 6630

Type function

Call typeof(p) 
Modulescheme_lang

Notes
 Underlying primitives for Scheme






isstring {scheme_lang}




Name of routine: isstring 

Source lines: 6631 - 6635

Type function

Call isstring(p) 
Modulescheme_lang

Notes
 Underlying primitives for Scheme






isnumber {scheme_lang}




Name of routine: isnumber 

Source lines: 6636 - 6640

Type function

Call isnumber(p) 
Modulescheme_lang

Notes
 Underlying primitives for Scheme






ispair {scheme_lang}




Name of routine: ispair 

Source lines: 6641 - 6645

Type function

Call ispair(p) 
Modulescheme_lang

Notes
 Underlying primitives for Scheme






car {scheme_lang}




Name of routine: car 

Source lines: 6649 - 6653

Type function

Call car(p) 
Modulescheme_lang

Notes
 car, cdr etc






cdr {scheme_lang}




Name of routine: cdr 

Source lines: 6654 - 6658

Type function

Call cdr(p) 
Modulescheme_lang

Notes
 car, cdr etc






caar {scheme_lang}




Name of routine: caar 

Source lines: 6660 - 6665

Type function

Call caar(p) 
Modulescheme_lang

Notes
 Miniscm





cadr {scheme_lang}




Name of routine: cadr 

Source lines: 6666 - 6671

Type function

Call cadr(p) 
Modulescheme_lang

Notes
 Miniscm





cdar {scheme_lang}




Name of routine: cdar 

Source lines: 6672 - 6677

Type function

Call cdar(p) 
Modulescheme_lang

Notes
 Miniscm





cddr {scheme_lang}




Name of routine: cddr 

Source lines: 6678 - 6683

Type function

Call cddr(p) 
Modulescheme_lang

Notes
 Miniscm





cadar {scheme_lang}




Name of routine: cadar 

Source lines: 6684 - 6690

Type function

Call cadar(p) 
Modulescheme_lang

Notes
 Miniscm





caddr {scheme_lang}




Name of routine: caddr 

Source lines: 6691 - 6697

Type function

Call caddr(p) 
Modulescheme_lang

Notes
 Miniscm





cadaar {scheme_lang}




Name of routine: cadaar 

Source lines: 6698 - 6705

Type function

Call cadaar(p) 
Modulescheme_lang

Notes
 Miniscm





cadddr {scheme_lang}




Name of routine: cadddr 

Source lines: 6706 - 6713

Type function

Call cadddr(p) 
Modulescheme_lang

Notes
 Miniscm





cddddr {scheme_lang}




Name of routine: cddddr 

Source lines: 6714 - 6721

Type function

Call cddddr(p) 
Modulescheme_lang

Notes
 Miniscm





issymbol {scheme_lang}




Name of routine: issymbol 

Source lines: 6723 - 6727

Type function

Call issymbol(p) 
Modulescheme_lang

Notes
 Miniscm





issyntax {scheme_lang}




Name of routine: issyntax 

Source lines: 6728 - 6732

Type function

Call issyntax(p) 
Modulescheme_lang

Notes
 Miniscm





isproc {scheme_lang}




Name of routine: isproc 

Source lines: 6733 - 6737

Type function

Call isproc(p) 
Modulescheme_lang

Notes
 Miniscm





isclosure {scheme_lang}




Name of routine: isclosure 

Source lines: 6738 - 6742

Type function

Call isclosure(p) 
Modulescheme_lang

Notes
 Miniscm





ismacro {scheme_lang}




Name of routine: ismacro 

Source lines: 6743 - 6747

Type function

Call ismacro(p) 
Modulescheme_lang

Notes
 Miniscm





iscontinuation {scheme_lang}




Name of routine: iscontinuation 

Source lines: 6748 - 6752

Type function

Call iscontinuation(p) 
Modulescheme_lang

Notes
 Miniscm





ispromise {scheme_lang}




Name of routine: ispromise 

Source lines: 6753 - 6757

Type function

Call ispromise(p) 
Modulescheme_lang

Notes
 Miniscm





isport {scheme_lang}




Name of routine: isport 

Source lines: 6758 - 6762

Type function

Call isport(p) 
Modulescheme_lang

Notes
 Miniscm





istrue {scheme_lang}




Name of routine: istrue 

Source lines: 6764 - 6768

Type function

Call istrue(p) 
Modulescheme_lang

Notes
 true or false value functions





isfalse {scheme_lang}




Name of routine: isfalse 

Source lines: 6769 - 6773

Type function

Call isfalse(p) 
Modulescheme_lang

Notes
 true or false value functions





isinteger {scheme_lang}




Name of routine: isinteger 

Source lines: 6777 - 6781

Type function

Call isinteger(p) 
Modulescheme_lang

Notes
 tower of numbers 






isfloat {scheme_lang}




Name of routine: isfloat 

Source lines: 6782 - 6786

Type function

Call isfloat(p) 
Modulescheme_lang

Notes
 tower of numbers 






isatom {scheme_lang}




Name of routine: isatom 

Source lines: 6790 - 6794

Type function

Call isatom(p) 
Modulescheme_lang

Notes
 Garbage collection
 





setatom {scheme_lang}




Name of routine: setatom 

Source lines: 6795 - 6798

Type subroutine

Call setatom(p) 
Modulescheme_lang

Notes
 Garbage collection
 





clratom {scheme_lang}




Name of routine: clratom 

Source lines: 6799 - 6802

Type subroutine

Call clratom(p) 
Modulescheme_lang

Notes
 Garbage collection
 





ismark {scheme_lang}




Name of routine: ismark 

Source lines: 6803 - 6807

Type function

Call ismark(p) 
Modulescheme_lang

Notes
 Garbage collection
 





setmark {scheme_lang}




Name of routine: setmark 

Source lines: 6808 - 6811

Type subroutine

Call setmark(p) 
Modulescheme_lang

Notes
 Garbage collection
 





clrmark {scheme_lang}




Name of routine: clrmark 

Source lines: 6812 - 6815

Type subroutine

Call clrmark(p) 
Modulescheme_lang

Notes
 Garbage collection
 





cons {scheme_lang}




Name of routine: cons 

Source lines: 6819 - 6826

Type function

Call cons(reg1, reg2)
Modulescheme_lang

Notes
 Cons






ceqstr {scheme_lang}




Name of routine: ceqstr 

Source lines: 6830 - 6847

Type function

Call ceqstr(cstr, reg)
Modulescheme_lang

Notes
 Contents of a Lisp string cell equal to a Fortran string






streq {scheme_lang}




Name of routine: streq 

Source lines: 6851 - 6867

Type function

Call streq(a, b)
Modulescheme_lang

Notes
 Contents of a Lisp string equal to a Lisp string 






mk_number {scheme_lang}




Name of routine: mk_number 

Source lines: 6871 - 6879

Type function

Call mk_number(num)
Modulescheme_lang

Notes
 Declare a number






mk_real {scheme_lang}




Name of routine: mk_real 

Source lines: 6883 - 6891

Type function

Call mk_real(num)
Modulescheme_lang

Notes
 Declare a real






mk_string {scheme_lang}




Name of routine: mk_string 

Source lines: 6895 - 6903

Type function

Call mk_string(str)
Modulescheme_lang

Notes
 Declare a string






mk_symbol {scheme_lang}




Name of routine: mk_symbol 

Source lines: 6907 - 6924

Type function

Call mk_symbol(nam)
Modulescheme_lang

Notes
 Declare a symbol






gensym {scheme_lang}




Name of routine: gensym 

Source lines: 6928 - 6947

Type function

Call gensym()
Modulescheme_lang

Notes
 automatically generate a unique symbol 






mk_atom {scheme_lang}




Name of routine: mk_atom 

Source lines: 6952 - 6992

Type function

Call mk_atom(str)
Modulescheme_lang

Notes
 make symbol or number atom from string






mk_const {scheme_lang}




Name of routine: mk_const 

Source lines: 6996 - 7037

Type function

Call mk_const(nam)
Modulescheme_lang

Notes
 
 Make a constant






mk_closure {scheme_lang}




Name of routine: mk_closure 

Source lines: 7041 - 7050

Type function

Call mk_closure(c, e)
Modulescheme_lang

Notes
 make closure, c is code, e is environment






mk_continuation {scheme_lang}




Name of routine: mk_continuation 

Source lines: 7054 - 7062

Type function

Call mk_continuation(d)
Modulescheme_lang

Notes
 make continuation






mk_port {scheme_lang}




Name of routine: mk_port 

Source lines: 7066 - 7076

Type function

Call mk_port(iport, nam)
Modulescheme_lang

Notes
 make a port






test_port {scheme_lang}




Name of routine: test_port 

Source lines: 7079 - 7090

Type function

Call test_port(iport)
Modulescheme_lang

Notes
 Test a port - return location in portaddress





reverse {scheme_lang}




Name of routine: reverse 

Source lines: 7094 - 7111

Type function

Call reverse(a)
Modulescheme_lang

Notes
 Reverse list






non_alloc_rev {scheme_lang}




Name of routine: non_alloc_rev 

Source lines: 7115 - 7131

Type function

Call non_alloc_rev(term, list)
Modulescheme_lang

Notes
 Reverse list -- no new cell generated






append {scheme_lang}




Name of routine: append 

Source lines: 7135 - 7151

Type function

Call append(a, b)
Modulescheme_lang

Notes
 append list -- make new cells






eqv {scheme_lang}




Name of routine: eqv 

Source lines: 7155 - 7170

Type function

Call eqv(a, b)
Modulescheme_lang

Notes
 equivalence of atoms






inchar {scheme_lang}




Name of routine: inchar 

Source lines: 7174 - 7199

Type subroutine

Call inchar(ch)
Modulescheme_lang

Notes
 get a new character from input file or stdin






clearinput {scheme_lang}




Name of routine: clearinput 

Source lines: 7203 - 7205

Type subroutine

Call clearinput()
Modulescheme_lang

Notes
 clear input buffer






flushinput {scheme_lang}




Name of routine: flushinput 

Source lines: 7209 - 7215

Type subroutine

Call flushinput()
Modulescheme_lang

Notes
 back to standard input






backchar {scheme_lang}




Name of routine: backchar 

Source lines: 7219 - 7221

Type subroutine

Call backchar()
Modulescheme_lang

Notes
 backstep one character in input buffer






skipspace {scheme_lang}




Name of routine: skipspace 

Source lines: 7225 - 7235

Type subroutine

Call skipspace()
Modulescheme_lang

Notes
 skip whitespace






token {scheme_lang}




Name of routine: token 

Source lines: 7239 - 7284

Type function

Call token()
Modulescheme_lang

Notes
 get next token






scheme_delim {scheme_lang}




Name of routine: scheme_delim 

Source lines: 7288 - 7296

Type function

Call scheme_delim(ch)
Modulescheme_lang

Notes
 read characters to delimiter  -- hard coded to work on Windows as well






readstr {scheme_lang}




Name of routine: readstr 

Source lines: 7298 - 7315

Type subroutine

Call readstr(res)
Modulescheme_lang

Notes
 Miniscm





readstrexp {scheme_lang}




Name of routine: readstrexp 

Source lines: 7319 - 7342

Type subroutine

Call readstrexp(res, reslen)
Modulescheme_lang

Notes
 read rest of a quoted string






printatom {scheme_lang}




Name of routine: printatom 

Source lines: 7346 - 7393

Type subroutine

Call printatom(l, space, ndigits)
Modulescheme_lang

Notes
 print an atom






padprint {scheme_lang}




Name of routine: padprint 

Source lines: 7397 - 7413

Type subroutine

Call padprint(str, space)
Modulescheme_lang

Notes
 Pad printing of an atom






ok_abbrev {scheme_lang}




Name of routine: ok_abbrev 

Source lines: 7415 - 7419

Type function

Call ok_abbrev(x)
Modulescheme_lang

Notes
 Miniscm





s_save {scheme_lang}




Name of routine: s_save 

Source lines: 7421 - 7426

Type subroutine

Call s_save(a, b, c)   
Modulescheme_lang

Notes
 Miniscm





s_return {scheme_lang}




Name of routine: s_return 

Source lines: 7427 - 7435

Type subroutine

Call s_return(a) 
Modulescheme_lang

Notes
 Miniscm





s_retbool {scheme_lang}




Name of routine: s_retbool 

Source lines: 7436 - 7443

Type subroutine

Call s_retbool(tf) 
Modulescheme_lang

Notes
 Miniscm





opexe0 {scheme_lang}




Name of routine: opexe0 

Source lines: 7448 - 7782

Type subroutine

Call opexe0(op, inline)
Modulescheme_lang

Notes
 Apply Scheme commands - split into opexe0 to opexe10
   load -- let*






opexe1 {scheme_lang}




Name of routine: opexe1 

Source lines: 7786 - 8004

Type subroutine

Call opexe1(op)
Modulescheme_lang

Notes
 Scheme procedures letrc -- call/cc






opexe2 {scheme_lang}




Name of routine: opexe2 

Source lines: 8008 - 8277

Type subroutine

Call opexe2(op)
Modulescheme_lang

Notes
 Scheme procedures plus -- set-cdr!






opexe3 {scheme_lang}




Name of routine: opexe3 

Source lines: 8281 - 8368

Type subroutine

Call opexe3(op)
Modulescheme_lang

Notes
 Scheme procedures not -- eqv?






opexe4 {scheme_lang}




Name of routine: opexe4 

Source lines: 8372 - 8478

Type subroutine

Call opexe4(op, plevel)
Modulescheme_lang

Notes
 Scheme procedures force -- gc -- new-segment






opexe5 {scheme_lang}




Name of routine: opexe5 

Source lines: 8482 - 8618

Type subroutine

Call opexe5(op, plevel)
Modulescheme_lang

Notes
 Scheme procedures read expression






opexe6 {scheme_lang}




Name of routine: opexe6 

Source lines: 8622 - 8677

Type subroutine

Call opexe6(op)
Modulescheme_lang

Notes
 Scheme procedures length -- macro?






opexe7 {scheme_lang}




Name of routine: opexe7 

Source lines: 8681 - 8766

Type subroutine

Call opexe7(op)
Modulescheme_lang

Notes
 Mathematical functions






opexe8 {scheme_lang}




Name of routine: opexe8 

Source lines: 8770 - 8874

Type subroutine

Call opexe8(op)
Modulescheme_lang

Notes
 A few other library functions eg min, max






opexe9 {scheme_lang}




Name of routine: opexe9 

Source lines: 8878 - 9129

Type subroutine

Call opexe9(op)
Modulescheme_lang

Notes
 string functions






getint {scheme_lang}




Name of routine: getint 

Source lines: 9133 - 9149

Type subroutine

Call getint(pos, slen, string, res)
Modulescheme_lang

Notes
 Nonstandard library additions for system interface such as system, read-line






opexe10 {scheme_lang}




Name of routine: opexe10 

Source lines: 9153 - 9529

Type subroutine

Call opexe10(op, plevel)
Modulescheme_lang

Notes
 Extensions for i/o and accessing system facilities eg inquire, time, date






opexe11 {scheme_lang}




Name of routine: opexe11 

Source lines: 9533 - 9620

Type subroutine

Call opexe11(op)
Modulescheme_lang

Notes
 Statistical library






opexe12 {scheme_lang}




Name of routine: opexe12 

Source lines: 9624 - 9885

Type subroutine

Call opexe12(op, plevel)
Modulescheme_lang

Notes
 Procedures that interact with Sib-pair






opexe13 {scheme_lang}




Name of routine: opexe13 

Source lines: 9889 - 10211

Type subroutine

Call opexe13(op, plevel)
Modulescheme_lang

Notes
 Manipulate Sib-pair dataset






alldata {scheme_lang}




Name of routine: alldata 

Source lines: 10215 - 10229

Type subroutine

Call alldata(res, extractor)
Modulescheme_lang

Notes
 pedigree data accessor






extract_ped {scheme_lang}




Name of routine: extract_ped 

Source lines: 10233 - 10239

Type function

Call extract_ped(i, res)
Modulescheme_lang

Notes
 extractors for different pedigree data fields






extract_id {scheme_lang}




Name of routine: extract_id 

Source lines: 10241 - 10247

Type function

Call extract_id(i, res)
Modulescheme_lang

Notes
 Miniscm





extract_iped {scheme_lang}




Name of routine: extract_iped 

Source lines: 10249 - 10255

Type function

Call extract_iped(i, res)
Modulescheme_lang

Notes
 Miniscm





extract_fa {scheme_lang}




Name of routine: extract_fa 

Source lines: 10257 - 10263

Type function

Call extract_fa(i, res)
Modulescheme_lang

Notes
 Miniscm





extract_mo {scheme_lang}




Name of routine: extract_mo 

Source lines: 10265 - 10271

Type function

Call extract_mo(i, res)
Modulescheme_lang

Notes
 Miniscm





extract_imztwin {scheme_lang}




Name of routine: extract_imztwin 

Source lines: 10273 - 10279

Type function

Call extract_imztwin(i, res)
Modulescheme_lang

Notes
 Miniscm





opexe14 {scheme_lang}




Name of routine: opexe14 

Source lines: 10284 - 10987

Type subroutine

Call opexe14(op)
Modulescheme_lang

Notes
 Miniscm





opexe15 {scheme_lang}




Name of routine: opexe15 

Source lines: 10993 - 11331

Type subroutine

Call opexe15(op)
Modulescheme_lang

Notes
 Miniscm





mk_syntax {scheme_lang}




Name of routine: mk_syntax 

Source lines: 11337 - 11345

Type subroutine

Call mk_syntax(op, nam)
Modulescheme_lang

Notes

 Initialization of internal keywords






mk_proc {scheme_lang}




Name of routine: mk_proc 

Source lines: 11347 - 11356

Type subroutine

Call mk_proc(op, nam)
Modulescheme_lang

Notes
 Miniscm





init_vars_global {scheme_lang}




Name of routine: init_vars_global 

Source lines: 11360 - 11367

Type subroutine

Call init_vars_global()
Modulescheme_lang

Notes
 Initiate global environment






init_syntax {scheme_lang}




Name of routine: init_syntax 

Source lines: 11371 - 11389

Type subroutine

Call init_syntax()
Modulescheme_lang

Notes
 Initiate syntax






init_procs {scheme_lang}




Name of routine: init_procs 

Source lines: 11393 - 11665

Type subroutine

Call init_procs()
Modulescheme_lang

Notes
 Initiate procedures






init_scm {scheme_lang}




Name of routine: init_scm 

Source lines: 11669 - 11824

Type subroutine

Call init_scm()
Modulescheme_lang

Notes
 Inlined init.scm






init_globals {scheme_lang}




Name of routine: init_globals 

Source lines: 11828 - 11840

Type subroutine

Call init_globals()
Modulescheme_lang

Notes
 Initiate procedures






error0 {scheme_lang}




Name of routine: error0 

Source lines: 11844 - 11850

Type subroutine

Call error0(s)
Modulescheme_lang

Notes
 Error handling






error1 {scheme_lang}




Name of routine: error1 

Source lines: 11852 - 11860

Type subroutine

Call error1(s, a)
Modulescheme_lang

Notes
 Miniscm





init_scheme {scheme_lang}




Name of routine: init_scheme 

Source lines: 11862 - 11865

Type subroutine

Call init_scheme()
Modulescheme_lang

Notes
 Miniscm





repl_scheme {scheme_lang}




Name of routine: repl_scheme 

Source lines: 11869 - 11963

Type subroutine

Call repl_scheme(inline, ple)
Modulescheme_lang

Notes
 Scheme read-eval-print loop






create_form {formula_class}




Name of routine: create_form 

Source lines: 12003 - 12146

Type subroutine

Call create_form(sta, fin, terms, nloci, loc, formula)
Moduleformula_class

Notes
 read commands and write appropriate formula structure






cleanup_form {formula_class}




Name of routine: cleanup_form 

Source lines: 12148 - 12159

Type subroutine

Call cleanup_form(formula)
Moduleformula_class

Notes
 Simple regression formula structure and parser

 formula and design matrix
 formula is:   a   b   c   a*b   a*c   b*c  a*b*c
         T1    1   2   3    1     1     2     1
         T2    .   .   .    2     3     3     2
         T3    .   .   .    .     .     .     3
    TERMDIM    1   1   1    2     2     2     3

 Effects       1    2     3
         NLEV  n1   n2    n3
         STA   1    n1+1  n1+n2+1
         FIN   n1   n1+n2 n1+n2+n3
       INFORM  1    1     1       





sumcols_form {formula_class}




Name of routine: sumcols_form 

Source lines: 12163 - 12203

Type subroutine

Call sumcols_form(formula)
Moduleformula_class

Notes
 If levels available, evaluate total number of model parameters
 





show_form {formula_class}




Name of routine: show_form 

Source lines: 12205 - 12226

Type subroutine

Call show_form(formula)
Moduleformula_class

Notes
 Simple regression formula structure and parser

 formula and design matrix
 formula is:   a   b   c   a*b   a*c   b*c  a*b*c
         T1    1   2   3    1     1     2     1
         T2    .   .   .    2     3     3     2
         T3    .   .   .    .     .     .     3
    TERMDIM    1   1   1    2     2     2     3

 Effects       1    2     3
         NLEV  n1   n2    n3
         STA   1    n1+1  n1+n2+1
         FIN   n1   n1+n2 n1+n2+n3
       INFORM  1    1     1       





setup_props {mcmc_model}




Name of routine: setup_props 

Source lines: 12383 - 12387

Type subroutine

Call setup_props(maxsiz)
Modulemcmc_model

Notes
 Allocate or deallocate work arrays






clean_props {mcmc_model}




Name of routine: clean_props 

Source lines: 12388 - 12390

Type subroutine

Call clean_props()
Modulemcmc_model

Notes
 Allocate or deallocate work arrays






setup_mix {mcmc_model}




Name of routine: setup_mix 

Source lines: 12394 - 12449

Type subroutine

Call setup_mix(ped, dataset, nchain, nqtl, nvar, family)
Modulemcmc_model

Notes
 Allocate a pedigree's data arrays






setup_ibd {ibd_class}




Name of routine: setup_ibd 

Source lines: 12488 - 12500

Type subroutine

Call setup_ibd(ped, nobs, nvar, family)
Moduleibd_class

Notes
 Allocate a pedigree's data arrays





setup_table {contingency_table}




Name of routine: setup_table 

Source lines: 12530 - 12541

Type subroutine

Call setup_table(ncat, maxcells, table)
Modulecontingency_table

Notes
 allocate space for contingency table






zero_table {contingency_table}




Name of routine: zero_table 

Source lines: 12545 - 12557

Type subroutine

Call zero_table(table)
Modulecontingency_table

Notes
 zero table for reuse






clean_table {contingency_table}




Name of routine: clean_table 

Source lines: 12561 - 12571

Type subroutine

Call clean_table(table)
Modulecontingency_table

Notes
 deallocate space






expand_table {contingency_table}




Name of routine: expand_table 

Source lines: 12575 - 12598

Type subroutine

Call expand_table(nextra, table)
Modulecontingency_table

Notes
 increase available space






insert_table {contingency_table}




Name of routine: insert_table 

Source lines: 12602 - 12661

Type subroutine

Call insert_table(ncat, values, table, iwt)
Modulecontingency_table

Notes
 insert data






search_table {contingency_table}




Name of routine: search_table 

Source lines: 12665 - 12703

Type function

Call search_table(ncat, values, table)
Modulecontingency_table

Notes
 Search table






incr_table {contingency_table}




Name of routine: incr_table 

Source lines: 12707 - 12713

Type subroutine

Call incr_table(pos, table, iwt)
Modulecontingency_table

Notes
 Increment cell count if correct address already available






print_table {contingency_table}




Name of routine: print_table 

Source lines: 12717 - 12725

Type subroutine

Call print_table(table)
Modulecontingency_table

Notes
 print a table






marginal_table {contingency_table}




Name of routine: marginal_table 

Source lines: 12729 - 12743

Type subroutine

Call marginal_table(nmargin, margin, table, martable)
Modulecontingency_table

Notes
 fill a table with marginal counts from another table






flat_table {contingency_table}




Name of routine: flat_table 

Source lines: 12748 - 12793

Type subroutine

Call flat_table(mtable1, mtable2, table, mat)
Modulecontingency_table

Notes
 Convert table counts to a R (dim1 x dim2 ..x dimN-1) x C (dimN) matrix 
 so mtable1 is marginal table for vars 1..nloc-1, mtable2 is univariate






dim_table {contingency_table}




Name of routine: dim_table 

Source lines: 12797 - 12810

Type function

Call dim_table(margin, table)
Modulecontingency_table

Notes
 get dimension of a margin






sort_table {contingency_table}




Name of routine: sort_table 

Source lines: 12814 - 12826

Type subroutine

Call sort_table(cat, table)
Modulecontingency_table

Notes
 reorder values in 1-D table to match order in table index






findlev {contingency_table}




Name of routine: findlev 

Source lines: 12830 - 12878

Type function

Call findlev(val, table)
Modulecontingency_table

Notes
 factor level based on position in (marginal) 1-D table






findrank {contingency_table}




Name of routine: findrank 

Source lines: 12882 - 12901

Type function

Call findrank(val, table)
Modulecontingency_table

Notes
 find rank based on position in 1-D table






setup_pairs {pairlist_class}




Name of routine: setup_pairs 

Source lines: 12920 - 12930

Type subroutine

Call setup_pairs(npairs, pairlist)
Modulepairlist_class

Notes
 allocate space for pairlist






clean_pairs {pairlist_class}




Name of routine: clean_pairs 

Source lines: 12934 - 12940

Type subroutine

Call clean_pairs(pairlist)
Modulepairlist_class

Notes
 deallocate space






expand_pairs {pairlist_class}




Name of routine: expand_pairs 

Source lines: 12944 - 12959

Type subroutine

Call expand_pairs(nextra, pairlist)
Modulepairlist_class

Notes
 increase available space






append_pair {pairlist_class}




Name of routine: append_pair 

Source lines: 12963 - 12977

Type subroutine

Call append_pair(key1, key2, pairlist)
Modulepairlist_class

Notes
 
 append data, testing only latest entry for uniqueness






insert_pair {pairlist_class}




Name of routine: insert_pair 

Source lines: 12981 - 13029

Type subroutine

Call insert_pair(key1, key2, pairlist)
Modulepairlist_class

Notes
 insert data






find_pair {pairlist_class}




Name of routine: find_pair 

Source lines: 13033 - 13072

Type function

Call find_pair(key1, key2, pairlist)
Modulepairlist_class

Notes
 find a pair






complete {covariate_data}




Name of routine: complete 

Source lines: 13096 - 13125

Type function

Call complete(useimp, idx, nvar, terms, locpos, loctyp, dataset)
Modulecovariate_data

Notes
  
 test if complete data for i'th individual
  





varlevels {covariate_data}




Name of routine: varlevels 

Source lines: 13130 - 13219

Type subroutine

Call varlevels(typ, gene, numal, nvar, varlist,  loc, loctyp, locpos, dataset, covariates, plevel)
Modulecovariate_data

Notes
 Collect necessary information to create dummy variables encoding a categorical trait
 allocates necessary marginal table storage






fixeff {covariate_data}




Name of routine: fixeff 

Source lines: 13226 - 13344

Type subroutine

Call fixeff(idx, designpos, interc, gene, genemod, allele_buffer, nvar, varlist, loctyp, locpos, covariates, dataset, vals)
Modulecovariate_data

Notes
 One row of the design matrix for the fixed effects part of model for varcom and segsim.
 Possibly including one marker for full dummy encoding.
 Possibly including an intercept.
 Missing x values replaced by overall mean






xmeans {covariate_data}




Name of routine: xmeans 

Source lines: 13348 - 13427

Type subroutine

Call xmeans(nvar, varlist, loctyp, locpos, dataset, covariates)
Modulecovariate_data

Notes
  
 Means for set of variables (incl dummies) in formula
  





clean_AS164 {AS164_class}




Name of routine: clean_AS164 

Source lines: 13437 - 13444

Type subroutine

Call clean_AS164()
ModuleAS164_class

Notes
 Work arrays for AS164 -- allow passing of results to other routines





varmet {optimizer}




Name of routine: varmet 

Source lines: 13466 - 13636

Type subroutine

Call varmet(fun, npar, b, f0, gradtl, toler, maxfn, ifault, plevel)
Moduleoptimizer

Notes
 Actual varmet minimizer





grad {optimizer}




Name of routine: grad 

Source lines: 13640 - 13683

Type subroutine

Call grad(fun, npar, b, f0, g, sa, er, ifault)
Moduleoptimizer

Notes
 Calculate approximate gradient






vmerr {optimizer}




Name of routine: vmerr 

Source lines: 13687 - 13703

Type subroutine

Call vmerr(ier, maxfn)
Moduleoptimizer

Notes
 varmet error messages






popgen_init {popgen_vcdata}




Name of routine: popgen_init 

Source lines: 13730 - 13735

Type subroutine

Call popgen_init()
Modulepopgen_vcdata

Notes
 Cockerham-like multi-locus variance components





popgen_summary {popgen_vcdata}




Name of routine: popgen_summary 

Source lines: 13736 - 13755

Type subroutine

Call popgen_summary(outstr, plevel)
Modulepopgen_vcdata

Notes
 Cockerham-like multi-locus variance components





popgen_homoz {popgen_vcdata}




Name of routine: popgen_homoz 

Source lines: 13756 - 13769

Type subroutine

Call popgen_homoz(outstr, plevel)
Modulepopgen_vcdata

Notes
 Cockerham-like multi-locus variance components





printmat {symmetric_matrix}




Name of routine: printmat 

Source lines: 13780 - 13791

Type subroutine

Call printmat(n, c, fstring)
Modulesymmetric_matrix

Notes
 print n rows of symmetric lower triangular matrix






postmult {symmetric_matrix}




Name of routine: postmult 

Source lines: 13797 - 13817

Type subroutine

Call postmult(n, x, c, w)
Modulesymmetric_matrix

Notes
 Evaluate S x
 where S is symmetric lower triangular matrix
       x is a vector






postmultm {symmetric_matrix}




Name of routine: postmultm 

Source lines: 13823 - 13847

Type subroutine

Call postmultm(n, m, x, c, w)
Modulesymmetric_matrix

Notes
 Evaluate S X
 where S is symmetric lower triangular matrix
       X is a full n*m matrix






sumsym {symmetric_matrix}




Name of routine: sumsym 

Source lines: 13852 - 13868

Type subroutine

Call sumsym(n, c, res)
Modulesymmetric_matrix

Notes
 Evaluate 1' S 1
 where S is symmetric lower triangular matrix






quadmult {symmetric_matrix}




Name of routine: quadmult 

Source lines: 13873 - 13894

Type subroutine

Call quadmult(typ, n, x, c, res)
Modulesymmetric_matrix

Notes
 Evaluate x' S x  or 1' S x
 where S is symmetric lower triangular matrix






quadxxm {symmetric_matrix}




Name of routine: quadxxm 

Source lines: 13901 - 13921

Type subroutine

Call quadxxm(n, m, x, c, res)
Modulesymmetric_matrix

Notes
 Evaluate X' S X
 where S is symmetric lower triangular matrix
       X n*m matrix
 result returned in lower triangular form






quadxy {symmetric_matrix}




Name of routine: quadxy 

Source lines: 13927 - 13942

Type subroutine

Call quadxy(n, x, c, y, res)
Modulesymmetric_matrix

Notes
 Evaluate x' S y
 where S is symmetric lower triangular matrix
       x, y are 1-D arrays






quadxymv {symmetric_matrix}




Name of routine: quadxymv 

Source lines: 13948 - 13964

Type subroutine

Call quadxymv(n, m, x, c, y, res)
Modulesymmetric_matrix

Notes
 Evaluate X' S y
 where S is symmetric lower triangular matrix
       X full n*m matrix, y n-vector






quadxym {symmetric_matrix}




Name of routine: quadxym 

Source lines: 13970 - 13981

Type subroutine

Call quadxym(n, m1, m2, x, c, y, res)
Modulesymmetric_matrix

Notes
 Evaluate X' S Y
 where S is symmetric lower triangular matrix
       X, Y full n*m1,n*m2 matrices






quadxy1 {symmetric_matrix}




Name of routine: quadxy1 

Source lines: 13987 - 14002

Type subroutine

Call quadxy1(n, m, c, y, res)
Modulesymmetric_matrix

Notes
 Evaluate 1' S Y
 where S is symmetric lower triangular matrix
       Y full n*m matrix






quadform {symmetric_matrix}




Name of routine: quadform 

Source lines: 14006 - 14020

Type subroutine

Call quadform(n, x, m, c, res)
Modulesymmetric_matrix

Notes
 Evaluate (y-m)' S (y-m) where S is symmetric lower triangular matrix






pre_grapheps {grapheps}




Name of routine: pre_grapheps 

Source lines: 14029 - 14363

Type subroutine

Call pre_grapheps(outstr, xbound, ybound)
Modulegrapheps

Notes
 The grapheps Postscript functions
 See http://swiss.csail.mit.edu/~jaffer/Docupage/grapheps





xy_grapheps {grapheps}




Name of routine: xy_grapheps 

Source lines: 14370 - 14484

Type subroutine

Call xy_grapheps(outstr, nvals, xvals, yvals,  xlab, ylab, title, gstyle, gratio, typ)
Modulegrapheps

Notes
 Draw simple plot

 typ 1=scatterplot 2=jittered dotplot 3=mountain 4=bargraph
     10=square Q-Q plot






scatter_grapheps {grapheps}




Name of routine: scatter_grapheps 

Source lines: 14488 - 14553

Type subroutine

Call scatter_grapheps(outstr, nvals, symbols, xvals, yvals,  slab, xlab, ylab, title, gratio)
Modulegrapheps

Notes
 Draw scatterplot with different glyphs for each category






nextcmd




Name of routine: nextcmd 

Source lines: 23606 - 23664

Type subroutine

Call nextcmd(commands, numcmd, linlen, s, more)
ModuleNone

Notes
 count number of commands on line and delineate next command 
 (using position of ";"'s) to be evaluated






ival




Name of routine: ival 

Source lines: 23668 - 23688

Type function

Call ival(string)
ModuleNone

Notes
 character to integer conversion via internal read






fval




Name of routine: fval 

Source lines: 23692 - 23719

Type function

Call fval(string)
ModuleNone

Notes
 character to float conversion via internal read






aval




Name of routine: aval 

Source lines: 23724 - 23775

Type function

Call aval(string, gcode)
ModuleNone

Notes
 read allele values either numeric or letter code
   range of legal alleles depends on storage type






locfmt




Name of routine: locfmt 

Source lines: 23779 - 23809

Type subroutine

Call locfmt(str, rep, newtyp)
ModuleNone

Notes
 Read simplified locus declaration eg 10m 10 m -> 10 autosomal markers






sow




Name of routine: sow 

Source lines: 23813 - 23823

Type function

Call sow(string)
ModuleNone

Notes
 skip leading whitespace






eow




Name of routine: eow 

Source lines: 23827 - 23836

Type function

Call eow(string)
ModuleNone

Notes
 find end of string






sclean




Name of routine: sclean 

Source lines: 23840 - 23848

Type subroutine

Call sclean(string)
ModuleNone

Notes
 scrub non-ASCII characters






ismiss




Name of routine: ismiss 

Source lines: 23852 - 23856

Type function

Call ismiss(string)
ModuleNone

Notes
  See if a string is a missing value






isint




Name of routine: isint 

Source lines: 23860 - 23881

Type function

Call isint(string)
ModuleNone

Notes
  see if a string is a valid integer






isreal




Name of routine: isreal 

Source lines: 23885 - 23904

Type function

Call isreal(string)
ModuleNone

Notes
  see if a string is a valid double precision number






iscomment




Name of routine: iscomment 

Source lines: 23908 - 23923

Type function

Call iscomment(string)
ModuleNone

Notes
  See if a string is a comment






wrsex




Name of routine: wrsex 

Source lines: 23927 - 23936

Type subroutine

Call wrsex(sex,ch)
ModuleNone

Notes
  
 write sex as character
  





wrdate




Name of routine: wrdate 

Source lines: 23940 - 23953

Type subroutine

Call wrdate(date,str,typ)
ModuleNone

Notes
 write date as character






wraff




Name of routine: wraff 

Source lines: 23957 - 23968

Type subroutine

Call wraff(value, ch, typ)
ModuleNone

Notes
  
 binary trait as character
  





wrform




Name of routine: wrform 

Source lines: 23972 - 23987

Type subroutine

Call wrform(typ, nwid, ndec, fstring)
ModuleNone

Notes
 Fortran format statement to write one number






idwidths




Name of routine: idwidths 

Source lines: 23991 - 24019

Type subroutine

Call idwidths(dataset, widths, name_formats)
ModuleNone

Notes
 Get maximum lengths of ID strings






phist




Name of routine: phist 

Source lines: 24023 - 24039

Type subroutine

Call phist(pval1, pval2, histo)
ModuleNone

Notes
  
 Write P-values as a histogram: . + * ** ***
  





pstring




Name of routine: pstring 

Source lines: 24043 - 24068

Type function

Call pstring(pval)
ModuleNone

Notes
  
 Write P-values as a string
  





corstring




Name of routine: corstring 

Source lines: 24072 - 24082

Type function

Call corstring(rval)
ModuleNone

Notes
  
 Write correlation as a 6 character string (deal nicely with -1)
  





append




Name of routine: append 

Source lines: 24086 - 24096

Type subroutine

Call append(word, note)
ModuleNone

Notes
 append one word to a string if enough room






addlet




Name of routine: addlet 

Source lines: 24101 - 24111

Type subroutine

Call addlet(old, new)
ModuleNone

Notes
  
 prepend "x" to a string if starts with an integer
 Loki and R for example do not allow variable names that start with a digit
  





shorten




Name of routine: shorten 

Source lines: 24116 - 24157

Type subroutine

Call shorten(idx, nwords, words, newlen, res)
ModuleNone

Notes
  
 create a shorter unique version of a string eg locus name
 Old versions of MENDEL for instance wants 8 character locus names
  





makeind




Name of routine: makeind 

Source lines: 24162 - 24208

Type subroutine

Call makeind(typ, idx, eos, los, string)
ModuleNone

Notes
  
 hash an integer to a two character string 01-99,A-Z,a-z,a-z...
 append to name: typ=1, appended with underscore; typ=2, appended directly
  





mktmpfil




Name of routine: mktmpfil 

Source lines: 24212 - 24234

Type subroutine

Call mktmpfil(str, filnam, wrkdir, ioerr)
ModuleNone

Notes
  
 Create a new unique temporary file 
  





wrinline




Name of routine: wrinline 

Source lines: 24239 - 24258

Type subroutine

Call wrinline(nlin, outstr)
ModuleNone

Notes
 Copy inline data to a file
 Relies on iostat=-2 as eol to use lin as a buffer






openlog




Name of routine: openlog 

Source lines: 24262 - 24292

Type subroutine

Call openlog(lstr, logfil, nhis)
ModuleNone

Notes
 Open the standard log file "sib-pair.log"






findfile




Name of routine: findfile 

Source lines: 24298 - 24327

Type subroutine

Call findfile(fil, stat)
ModuleNone

Notes
 System utilities

 Find a file along the search path -- check pwd, then HOME first






delfile




Name of routine: delfile 

Source lines: 24331 - 24348

Type subroutine

Call delfile(filnam, plevel)
ModuleNone

Notes
 Delete a file






unzipper




Name of routine: unzipper 

Source lines: 24353 - 24374

Type subroutine

Call unzipper(filnam, wrkfil, gzipped)
ModuleNone

Notes
 Flag a file as gzip compressed and 
 unzip for reading (necessary for binary files)






reclen




Name of routine: reclen 

Source lines: 24380 - 24404

Type subroutine

Call reclen(port, buffer, longest)
ModuleNone

Notes
 Return length of longest line of file
 Use lin as buffer
 Relies on iostat code for eol






filecols




Name of routine: filecols 

Source lines: 24409 - 24440

Type subroutine

Call filecols(port, buffer, testlines, nwords, plevel)
ModuleNone

Notes
 Return representative number of words per line in file
 Use lin as buffer






fchooser




Name of routine: fchooser 

Source lines: 24446 - 24498

Type subroutine

Call fchooser(fil, gui, plevel)
ModuleNone

Notes
 GUI stuff
 Uses JAPI to call AWT, or PILIB to call GTK2 if present
 else simple file picker






fpicker




Name of routine: fpicker 

Source lines: 24503 - 24609

Type subroutine

Call fpicker(fil, plevel)
ModuleNone

Notes
 Text based Windows file picker






fpicker




Name of routine: fpicker 

Source lines: 24614 - 24698

Type subroutine

Call fpicker(fil, plevel)
ModuleNone

Notes
 Text based file picker






info




Name of routine: info 

Source lines: 24703 - 24765

Type subroutine

Call info(lin, burnin, imp, iter, initix, initiy, initiz,  ix, iy, iz, mapf, mincnt, plevel, genemod,  showorig, chek, droperr, prompt, use2, gui, twintrait, sexmarker, datdir, wrkdir)
ModuleNone

Notes
 Info






help




Name of routine: help 

Source lines: 24769 - 25237

Type subroutine

Call help(typ, regexp, lin, twrk)
ModuleNone

Notes
  
 brief online help
  





shell




Name of routine: shell 

Source lines: 25241 - 25274

Type subroutine

Call shell(lin, plevel)
ModuleNone

Notes
 pass line to shell -- requires existence of fairly
                       standard routine system()





stamp




Name of routine: stamp 

Source lines: 25278 - 25298

Type subroutine

Call stamp(t0)
ModuleNone

Notes
  
 write elapsed time since first/last asked
  





proct




Name of routine: proct 

Source lines: 25302 - 25312

Type subroutine

Call proct(t1, plevel)
ModuleNone

Notes
  
 time a procedure
  





gettrait




Name of routine: gettrait 

Source lines: 25316 - 25365

Type subroutine

Call gettrait(nam, typ1, typ2, nloci, loc, lochash, loctyp, trait, plevel)
ModuleNone

Notes
  
 determine if word is name of a trait locus
  





isinuse




Name of routine: isinuse 

Source lines: 25369 - 25398

Type function

Call isinuse(string, nloci, loc)
ModuleNone

Notes
  
 check if name is not already used or reserved
  





getbin




Name of routine: getbin 

Source lines: 25402 - 25463

Type subroutine

Call getbin(sta, fin, words, nloci, loc, lochash, loctyp, trait, gt, thresh)
ModuleNone

Notes
  
 Get a single binary trait or dichotomized quantitative trait
  





loadnam




Name of routine: loadnam 

Source lines: 25473 - 25667

Type subroutine

Call loadnam(sta, fin, words, nloci, loc, lochash, loctyp, group, map, locstat, chosen, nterms, terms, filter, typ)
ModuleNone

Notes
 
 Load list of traits into an array

 allows wild cards and spans
 filter= selection must also be of class eg LOC_CODOM, LOC_ANY
 typ=1 active loci, =2 inactive loci, =3 all loci (used by ls etc)

 output both as list (terms) and as index vector (chosen)
 





actlist




Name of routine: actlist 

Source lines: 25671 - 25701

Type subroutine

Call actlist(typ, nloci, loctyp, nchosen, chosen)
ModuleNone

Notes
 All active/inactive






listloci




Name of routine: listloci 

Source lines: 25706 - 25787

Type subroutine

Call listloci(nord, locord, nloci, loc, loctyp, outpos, locnotes,  typ, plevel)
ModuleNone

Notes
 List loci using short (typ=2) or long (typ=1) form
   plevel < -1 will give a simple list of names






newlin




Name of routine: newlin 

Source lines: 25791 - 25807

Type subroutine

Call newlin(sol, eol, pos, newpos)
ModuleNone

Notes
  
 format free output






cntclasses




Name of routine: cntclasses 

Source lines: 25811 - 25848

Type subroutine

Call cntclasses(nloci, loctyp)
ModuleNone

Notes
  
 Output counts of class of loci
  





cntmark




Name of routine: cntmark 

Source lines: 25852 - 25872

Type subroutine

Call cntmark(nloci, loctyp, nmark, typ)
ModuleNone

Notes
  
 Count active codominant markers or active loci
  





findmk




Name of routine: findmk 

Source lines: 25876 - 25894

Type function

Call findmk(sta, fin, loctyp)
ModuleNone

Notes
  
 Find next active codominant marker in list
  





findml




Name of routine: findml 

Source lines: 25898 - 25914

Type function

Call findml(nord, locord, loctyp)
ModuleNone

Notes
  
 Find first codominant or haploid marker in list
  





ldlist




Name of routine: ldlist 

Source lines: 25919 - 25976

Type subroutine

Call ldlist(typ, loc1, loc2, nloci, loctyp, last)
ModuleNone

Notes
 produce next pair of markers from:
     1. named pair 2. One named 3. map order 4. all pairs 10. empty






getlin




Name of routine: getlin 

Source lines: 25980 - 25996

Type subroutine

Call getlin(port, narg, words, lin, skipbl)
ModuleNone

Notes
  
 Get a line from a port
  





rdmerloc




Name of routine: rdmerloc 

Source lines: 26000 - 26100

Type subroutine

Call rdmerloc(port, xli, lin, nloci, loc, locpos, outpos, loctyp, locnotes,  numloc, twinning, twintype, twintrait)
ModuleNone

Notes
  
 Read a MERLIN locus file
  





rdplink




Name of routine: rdplink 

Source lines: 26108 - 26188

Type subroutine

Call rdplink(port, typ, chrcode, nloci, loc, locpos, outpos, loctyp, locnotes, numloc, group, map)
ModuleNone

Notes
 Read PLINK .map file (combines locus and map information)
   typ=1: standard, one dummy trait, overwrite any existing loci
       2: no dummy trait, append
   chrcode=1: standard codes for chromosomes, number, X, Y, Mt
           2: and, 23=X 24=Y 25=PAR 26=Mit






readmap




Name of routine: readmap 

Source lines: 26193 - 26446

Type subroutine

Call readmap(port, units, lin, words, plevel)
ModuleNone

Notes
  
 Read a mapfile -- attempts to intelligently decide
 what to read
  





readnames




Name of routine: readnames 

Source lines: 26450 - 26473

Type subroutine

Call readnames(port, nloci, loc, lochash, chosen)
ModuleNone

Notes
 Read a list of locus names from a file to keep/drop/undrop






rdlinloc




Name of routine: rdlinloc 

Source lines: 26477 - 26692

Type subroutine

Call rdlinloc(port, lin, words, nord, numloc)
ModuleNone

Notes
  
 Read a Linkage locus file
  





rdfreq




Name of routine: rdfreq 

Source lines: 26699 - 26809

Type subroutine

Call rdfreq(typ, sta, fin, words, allele_buffer)
ModuleNone

Notes
 Read a set of allele frequencies from the command line, 
 making up some numbers if necessary
 typ=1 only expect list of allele frequencies
     2 check for allele names alternating with frequencies






ordvar




Name of routine: ordvar 

Source lines: 26813 - 26858

Type subroutine

Call ordvar(twrk, nloci, loc, loctyp, locpos, outpos, nord, locord, group, map, locstat, locnotes, ord)
ModuleNone

Notes
  
 Make change in order of variables
  





packer




Name of routine: packer 

Source lines: 26863 - 27005

Type subroutine

Call packer(typ, red, wrk, wrk2, nloci, loc, loctyp, locpos, group, map,  locnotes, dataset, plevel)
ModuleNone

Notes
 Pack pedigrees and loci
 Note that SNPs stored as 2 genotypes per byte cannot be packed






bonf




Name of routine: bonf 

Source lines: 27009 - 27018

Type function

Call bonf(ntest,alpha)
ModuleNone

Notes
 Calculate Bonferroni corrected P-value for given number of tests






dsort




Name of routine: dsort 

Source lines: 27023 - 27142

Type subroutine

Call dsort(n, dx)
ModuleNone

Notes
  
 SLATEC quicksort routine.  Jones, Kahaner and Wisniewski.
 double precision
  





srank




Name of routine: srank 

Source lines: 27149 - 27312

Type subroutine

Call srank(n, x, iy)
ModuleNone

Notes
  
 SLATEC quicksort routine.  Jones, Kahaner and Wisniewski.
 here allowing for a missing value indicator, and carrying an indicator along
 pulls down the missing data.  To sort test statistics retaining a pointer
 to the variable name






isort




Name of routine: isort 

Source lines: 27318 - 27563

Type subroutine

Call isort(bot, top, ix, iy, kflag)
ModuleNone

Notes
  
 SLATEC quicksort routine.  Jones, Kahaner and Wisniewski.
 The option to sort descending has been removed, the argument order
 changed, and the sort is now from bot...top, rather than 1...top.
  





iscomp




Name of routine: iscomp 

Source lines: 27708 - 27716

Type function

Call iscomp(op)
ModuleNone

Notes
  
 determine if trait being compared to a constant, for isaff
  





docomp




Name of routine: docomp 

Source lines: 27722 - 27768

Type subroutine

Call docomp(pos, words, gt, thresh)
ModuleNone

Notes
  
 parse comparison in isaff
 15='<', 16='>', 17='ge', 18='le',19='ne',20='eq'
 21='odd', 22='even'
  





defpro




Name of routine: defpro 

Source lines: 27772 - 27800

Type subroutine

Call defpro(gt, thresh)
ModuleNone

Notes
  
 Message defining proband based on comparison
  





compsign




Name of routine: compsign 

Source lines: 27804 - 27810

Type function

Call compsign(idx)
ModuleNone

Notes
 Show comparison






isaff




Name of routine: isaff 

Source lines: 27814 - 27846

Type function

Call isaff(val, thresh, gt)
ModuleNone

Notes
  
 determine if index person is affected or unaffected
  





isatwin




Name of routine: isatwin 

Source lines: 27850 - 27858

Type function

Call isatwin(twintype, twinind)
ModuleNone

Notes
 Is an MZ twin?






ismzpair




Name of routine: ismzpair 

Source lines: 27863 - 27877

Type function

Call ismzpair(i, j, dataset)
ModuleNone

Notes
 Is pair MZ?
 index i must precede j






order




Name of routine: order 

Source lines: 27881 - 27890

Type subroutine

Call order(all1, all2)
ModuleNone

Notes
 swap alleles so ordered consistently






swap




Name of routine: swap 

Source lines: 27894 - 27902

Type subroutine

Call swap(all1, all2)
ModuleNone

Notes
  
 swap alleles
  





lorder




Name of routine: lorder 

Source lines: 27914 - 27990

Type subroutine

Call lorder(typ, addummy, liab, liabclass,  nloci, loctyp, nord, locord)
ModuleNone

Notes
 Create order of loci for outputting a pedigree
  1 = as is
  2 = LINKAGE
  3 = GENEHUNTER
  4 = MENDEL
  5 = LINKAGE PPD
  6 = FBAT
  7 = MERLIN
  





isinenv




Name of routine: isinenv 

Source lines: 27994 - 28005

Type function

Call isinenv(word,nvar,envnam)
ModuleNone

Notes
 Is a bound environmental variable? and if so where?






readbin




Name of routine: readbin 

Source lines: 28016 - 28168

Type subroutine

Call readbin(strm, filnam, wrkfil, typ, numloc, dataset, red, plevel)
ModuleNone

Notes
 Read a Sib-pair binary file encoded using
 various levels of compression (currently just calls gunzip)
 Default (compress=1) is a "Fortran unformatted write" dump of the 
 locus and pedigree arrays
 typ=format version 
    1=current (2012/02) 
    2=older   (2009/08) 
    3=original (change in loctyp coding)






writebin




Name of routine: writebin 

Source lines: 28175 - 28255

Type subroutine

Call writebin(strm, compress, filnam, dataset, plevel)
ModuleNone

Notes
 Write a Sib-pair binary file
 Default is a "Fortran unformatted write" dump of the 
 locus and pedigree arrays.
 If compress=2, currently calls gzip to compress the resulting file






readhapmap




Name of routine: readhapmap 

Source lines: 28259 - 28439

Type subroutine

Call readhapmap(filnam, numloc, dataset, longnam, red, plevel)
ModuleNone

Notes
 Read in HapMap format






readgeno




Name of routine: readgeno 

Source lines: 28444 - 28532

Type subroutine

Call readgeno(port, skipline, hashtab, dataset, plevel)
ModuleNone

Notes
 Read genotyping file where one genotype per record (eg Sequenom)
   id locus_name allele1 allele2 ... [quality score etc]






readprobs




Name of routine: readprobs 

Source lines: 28546 - 28705

Type subroutine

Call readprobs(port, typ, mergekey, longest, dataset, plevel)
ModuleNone

Notes
 Read in biallelic genotypic probabilities from a file, 
 imputing the most likely genotype
 Need to have numeric variable in pedigree that matches
 column of genotypes
 Assumes that all SNPs have been declared already
 file formats 
 typ=1: (Beagle)
 marker alleleA alleleB col.3 col.3 col.3 col.5 col.5 col.5 col.7 col.7 col.7 col
 rs885550 C T 0.9846 0.0154 0.0001 0.9846 0.0154 0.0001 0.9846 0.0154 0.0001 0.98
 typ=2:
   -- rs885550 9887804 C T 0.97 0.03 0 0.97 0.03 0 0.97 0.03 0 0.97 0.03 0 0.97






readbed




Name of routine: readbed 

Source lines: 28745 - 29065

Type subroutine

Call readbed(strm, typ, filnam, hashtab, dataset, plevel)
ModuleNone

Notes
 Read PLINK .bed format
 
 The .bim and .fam files are plain ASCII and allow us to fix the
 expected number of genotypes. In the .bed file, the first 3 bytes
 have a special meaning. The first two bytes are a 'magic number'
 that enables PLINK to confirm that a BED file is really a BED
 file: that is, BED files should always start 01101100 00011011.
 The third byte indicates whether the BED file is in SNP-major or
 individual-major mode: a value of 00000001 indicates SNP-major (i.e.
 list all individuals for first SNP, all individuals for second SNP,
 etc) whereas a value of 00000000 indicates individual-major (i.e.
 list all SNPs for the first individual, list all SNPs for the second
 individual, etc). By default, all BED files are SNP-major mode.

 For the genotype data, each byte encodes up to four genotypes (2 bits
 per genotype). The coding is
             
   00  Homozygote    1/1
   01  Heterozygote  1/2
   11  Homozygote    2/2
   10  Missing       x/x
 
 The only slightly confusing wrinkle is that each byte is effectively read
 backwards. That is, if we label each of the 8 position as A to H, we would
 label backwards: 01101100
                  HGFEDCBA
                  | | | AB   00  -- homozygote (first)
                  | | CD   11  -- other homozygote
                  | EF   01  -- heterozygote
                  GH   10  -- missing genotype (fourth)
 
 Finally, when we reach the end of a SNP (or if in individual-mode, the
 end an individual) we skip to the start of a new byte (i.e. skip any
 remaining bits in that byte).
 
 Data read in is either stored as normal genotypes (typ=1) or as 4-bits per
 genotype (typ=2).






fromplink




Name of routine: fromplink 

Source lines: 29069 - 29096

Type subroutine

Call fromplink(pcode, a1, a2, snpswap, g1, g2, ngeno)
ModuleNone

Notes
 Convert PLINK .bed genotype codes to alleles






readcases




Name of routine: readcases 

Source lines: 29102 - 29357

Type subroutine

Call readcases(port, hassex, skipline, numloc, coltyp,  dataset, longnam, longest, nwarn, plevel)
ModuleNone

Notes
 Read file containing just unrelated individuals
 Duplicates (if contiguous) are combined into the same "family"
 with appended copy numbers






readpeds




Name of routine: readpeds 

Source lines: 29361 - 29864

Type subroutine

Call readpeds(port, wrk, wrk2, skipline, link, unspecified,  mztwin, gt, thresh, sexchek, hassex, nextped,   numloc, coltyp, dataset, longnam, longest, nwarn, plevel)
ModuleNone

Notes
 Read pedigree file






nextped




Name of routine: nextped 

Source lines: 29868 - 29873

Type function

Call nextped(str, pedigree)
ModuleNone

Notes
 Test if current line is next pedigree






nonextped




Name of routine: nonextped 

Source lines: 29877 - 29882

Type function

Call nonextped(str, pedigree)
ModuleNone

Notes
 Does not use pedigree IDs






processfam




Name of routine: processfam 

Source lines: 29886 - 30041

Type subroutine

Call processfam(sexchek, mztwin, gt, thresh,  wrk, wrk2, nped, pedigree, num, nfound, numloc, nobs, buffer, nid, higen, ord, key1, key2, plevel)
ModuleNone

Notes
 All members of pedigree now read in, error check and sort






tabid




Name of routine: tabid 

Source lines: 30045 - 30085

Type subroutine

Call tabid(curid, nid, indx, id, counts, incr, idpos)
ModuleNone

Notes
  
 Tabulate alphanumeric IDs in order of appearance
  





addsexes




Name of routine: addsexes 

Source lines: 30090 - 30333

Type subroutine

Call addsexes(mztwin, gt, thresh, pedigree, num, buffer,  key1, ord, nerr, plevel)
ModuleNone

Notes
 
 Check consistency of sexes
 Assign consistent sexes where missing, allowing for possible MZ twins






famsort




Name of routine: famsort 

Source lines: 30340 - 30503

Type subroutine

Call famsort(pedigree, num, nfound, nid, id, pid, fa, mo,  key1, ord, higen, nerr, plevel)
ModuleNone

Notes
 
 Work out generation number ord(), then sort family on
 founder status, generation number, parental ID,
 and personal ID giving their position in ord().
 Returns the ranking in ord(), and the depth of the pedigree in higen
 





msdsort




Name of routine: msdsort 

Source lines: 30507 - 30530

Type subroutine

Call msdsort(bot,top,key1,key2,ord)
ModuleNone

Notes
  
 MSD radix sort key1, key2
  





mkdummy




Name of routine: mkdummy 

Source lines: 30534 - 30556

Type subroutine

Call mkdummy(num, nfound, sx, numloc, buffer)
ModuleNone

Notes
 Create dummy records for added individals






asstyp




Name of routine: asstyp 

Source lines: 30560 - 30581

Type subroutine

Call asstyp(nloci, loctyp, locpos, totloc, coltyp)
ModuleNone

Notes
 Assign a locus type to every column of data file






addvar




Name of routine: addvar 

Source lines: 30585 - 30663

Type subroutine

Call addvar(wrk, wrk2, dclass, newloc, dataset, plevel) 
ModuleNone

Notes
  
 Add extra blank columns to the dataset
  





addtmpvar




Name of routine: addtmpvar 

Source lines: 30667 - 30686

Type subroutine

Call addtmpvar(tmpnam, dataset, tmppos, ifail)
ModuleNone

Notes
 Create a temporary quantitative variable






wrkout




Name of routine: wrkout 

Source lines: 30690 - 30729

Type subroutine

Call wrkout(wrk, wrk2, ped, dataset, nped, nobs) 
ModuleNone

Notes
 Write out current pedigree to a work file, updating number of records






pedin




Name of routine: pedin 

Source lines: 30735 - 30802

Type subroutine

Call pedin(wrk, wrk2, nped, nobs, numloc, numcol, dataset) 
ModuleNone

Notes
 Read pedigree back in from work files
 May allocate extra blank columns in dataset%plocus for later use
   by numcol > numloc






replacedata




Name of routine: replacedata 

Source lines: 30809 - 31072

Type subroutine

Call replacedata(port, typ, nloci, loc, lochash, loctyp, locpos, chosen, hashtab, dataset, longest, plevel)
ModuleNone

Notes
 Read in data updates from a file
 file format: ped id loc1 loc2 ... locN, with header giving locus names
 uses hash to match up ids in file and current dataset
 and to match locus names in file to current dataset






concat




Name of routine: concat 

Source lines: 31076 - 31100

Type subroutine

Call concat(dirnam, filnam)
ModuleNone

Notes
 Prefix filnam






extprefix




Name of routine: extprefix 

Source lines: 31104 - 31123

Type subroutine

Call extprefix(filnam, suffix)
ModuleNone

Notes
 Extract prefix from filnam






extpath




Name of routine: extpath 

Source lines: 31127 - 31144

Type subroutine

Call extpath(filnam)
ModuleNone

Notes
 Extract path from filnam 






slash




Name of routine: slash 

Source lines: 31149 - 31163

Type subroutine

Call slash(dirnam, lend)
ModuleNone

Notes
 Test what character used to separate directories
 and append to directory






display




Name of routine: display 

Source lines: 31167 - 31198

Type subroutine

Call display(str)
ModuleNone

Notes
 Print a string, stripping out C-style escapes






cat




Name of routine: cat 

Source lines: 31202 - 31226

Type subroutine

Call cat(fil)
ModuleNone

Notes
 Display contents of a file






head




Name of routine: head 

Source lines: 31230 - 31253

Type subroutine

Call head(fil, nlin)
ModuleNone

Notes
 Display first N lines of a file






countfields




Name of routine: countfields 

Source lines: 31258 - 31380

Type subroutine

Call countfields(fil, plevel)
ModuleNone

Notes
 Utility to count number of columns in a file
   simpler scanner than args






fprinter




Name of routine: fprinter 

Source lines: 31384 - 31543

Type subroutine

Call fprinter(nwords, words, linbuf, plevel)
ModuleNone

Notes
 Utility to extract columns from a file






sibloci




Name of routine: sibloci 

Source lines: 31547 - 31578

Type subroutine

Call sibloci(ostr, nloci, loc, loctyp, outpos, map, locnotes)
ModuleNone

Notes
 write Sib-pair locus declarations 






wrmap




Name of routine: wrmap 

Source lines: 31599 - 31874

Type subroutine

Call wrmap(ostr, typ, mapf, nloci, loc, loctyp, locnotes, nord, locord, group, map)
ModuleNone

Notes
  
 Write map
  
 10 = table for Sib-pair output
  0 = LINKAGE
  1 = LINKAGE plus dummy binary trait
  2 = GENEHUNTER plus dummy binary trait
  3 = GENEHUNTER
  4 = MENDEL
 14 = MENDEL free format
 20 = MENDEL .var file
  5 = ASPEX
  6 = MERLIN
  7 = LOKI
  8 = STRUCTURE
  9 = SOLAR
 11 = MORGAN
 12 = Haploview
 13 = PLINK    
  





pedhead




Name of routine: pedhead 

Source lines: 31879 - 31944

Type subroutine

Call pedhead(strm, typ, pedmask, name_widths, name_formats,  nwid, nloci, loc, loctyp)
ModuleNone

Notes
 
 Write out pedigree header with locus names
 either multiline (typ=1) or simple
 





onestripe




Name of routine: onestripe 

Source lines: 31948 - 31985

Type subroutine

Call onestripe(strm, linenum, totlines, width, string, truncate)
ModuleNone

Notes
 Writing a string within a given rectangle: one line






pedout




Name of routine: pedout 

Source lines: 31997 - 32200

Type subroutine

Call pedout(strm, header, pedmask, fieldsep, allsep, imp, nwid, ndec,  misval, nrc, skip, filter,  nloci, loc, loctyp, locpos, dataset)
ModuleNone

Notes
 
 Write out GAS style pedigree
 header=print variable names as header
 allsep=allele separator
 imp=show imputed genotypes
 nwid,ndec=format for quantitative trait values
 misval=missing data token
 nrc=number of records to print
 skip=number of records to skip at beginning
 filter=(1=show all) (2=flagged)






wrlink




Name of routine: wrlink 

Source lines: 32217 - 32446

Type subroutine

Call wrlink(strm, typ, imp, addummy, liabclass, renumall, twinning, twintype, nwid, ndec, nloci, loctyp, locpos, nord, locord, dataset)
ModuleNone

Notes
 
 write out Linkage type file pre- or post- Makeped style

 style     typ property
 --------- --- --------
 lin, pre  1
 ppd       2   extra pedigree pointer fields
 gh        3   MISS='-', ordering binary_trait1, marker1...markerN, quantitative traits
 asp, tcl  4   marker names prepended to file
 hap       5   SNP alleles coded ACGT 1234
 mer       6   If present, zygosity indicator in column 6: 1,3,5...for each MZ set
 
 pre: ped id fa mo sex ...
 ppd: ped.n id.n fa.n mo.n child1.n patsibid.n matsibid.n sex proband.n ...
      where ped.n, id.n are sequential numerical ID number
 





wrphe




Name of routine: wrphe 

Source lines: 32452 - 32526

Type subroutine

Call wrphe(strm, typ, nwid, ndec,  nloci, loc, loctyp, locpos, dataset)
ModuleNone

Notes
  
 write out Mapmaker-Sibs/FBAT/etc phenotype file
 whitespace delimited ped id trait1...traitN  
 write out Mapmaker-Sibs phenotype file
  





wrcsv




Name of routine: wrcsv 

Source lines: 32539 - 32789

Type subroutine

Call wrcsv(strm, typ, imp, nwid, ndec, sep, allsep, misval, twinning,  twintype, nloci, loc, loctyp, locpos, nord, locord, dataset)
ModuleNone

Notes
  
 Write out pedigree as character-delimited
 typ
 1   full pedigree
 2   id,fa,mo,sex,ped,mztwin,hhid (for SOLAR)
 3   ped, id, phenotype_data
 4   id, phenotype_data
 5   ped, id, genotype_data
 6   id, genotype_data
 10  full pedigree with mztwin, na=' ' (for MENDEL 8.0)
 11  full pedigree with mztwin, na='.' (for SAS)
  





wrmorg




Name of routine: wrmorg 

Source lines: 32796 - 32952

Type subroutine

Call wrmorg(strm, typ, nwid, ndec, nloci, loc, loctyp, locpos,  smlfreq, smlpen, dataset)
ModuleNone

Notes
  
 Write out pedigree for Morgan
 typ
 1   pedigree and traits
 2   id, markers
  





wrfish




Name of routine: wrfish 

Source lines: 32956 - 33078

Type subroutine

Call wrfish(strm, ndec, twinning, twintype, nloci, loctyp, locpos, nord, locord, dataset, fstyle, plevel)
ModuleNone

Notes
  
 write out FISHER or MENDEL type pedigree file
  





wrdot




Name of routine: wrdot 

Source lines: 33082 - 33184

Type subroutine

Call wrdot(strm, trait, gene, allsep,  trcoly, trcoln, trcolx, dataset)
ModuleNone

Notes
  
 Describe pedigree using dot graphics language
  





wrarl




Name of routine: wrarl 

Source lines: 33188 - 33337

Type subroutine

Call wrarl(strm, popind, typ, nloci, loc, loctyp, locpos, dataset)
ModuleNone

Notes
 write out Arlequin data file (haplotype or genotype data)






wrprd




Name of routine: wrprd 

Source lines: 33341 - 33385

Type subroutine

Call wrprd(strm, typ, trait, nloci, loc, loctyp, locpos, dataset)
ModuleNone

Notes
 write out data file used by Jonathon Pritchard's structure program






wrbeagle




Name of routine: wrbeagle 

Source lines: 33390 - 33506

Type subroutine

Call wrbeagle(strm, typ, dataset)
ModuleNone

Notes
 write out data file used by Browning and Browning's Beagle program
 exclude MZ cotwins






wrsnp




Name of routine: wrsnp 

Source lines: 33512 - 33586

Type subroutine

Call wrsnp(strm, trait, nloci, loc, loctyp, locpos, dataset)
ModuleNone

Notes
 Write out SNP-major data file with
 integer genotype encoding used by ROADTRIPS
   genotypes are -9,0,1,2






wrpap




Name of routine: wrpap 

Source lines: 33590 - 33717

Type subroutine

Call wrpap(trip, phen, nloci, loc, loctyp, locpos, dataset)
ModuleNone

Notes
 Write out old-style PAP pedigree






wrcri




Name of routine: wrcri 

Source lines: 33721 - 33787

Type subroutine

Call wrcri(strm, nloci, loc, loctyp, locpos, locord, dataset)
ModuleNone

Notes
  
 Write out .gen pedigree file for CRI-MAP
  





wrbed




Name of routine: wrbed 

Source lines: 33791 - 33954

Type subroutine

Call wrbed(strm, filnam, trait, allele_buffer, dataset)
ModuleNone

Notes
 Write PLINK .bed format (also used by MENDEL 10.0+)






simdata




Name of routine: simdata 

Source lines: 33958 - 34017

Type subroutine

Call simdata(strm, nped, ngen, nminoff, nmaxoff, totloc)
ModuleNone

Notes
 Write a file of simulated pedigrees






showdata




Name of routine: showdata 

Source lines: 34021 - 34148

Type subroutine

Call showdata(fped, fid, larg, words,  nloci, loc, loctyp, locpos, dataset, pedmask, nwid, ndec, misval, fieldsep, allsep, pstyle)
ModuleNone

Notes
  
 Write out data for particular pedigree or particular person
  





wrind




Name of routine: wrind 

Source lines: 34152 - 34244

Type subroutine

Call wrind(idx, nloci, loc, loctyp, locpos, dataset,  pedmask, nwid, ndec, misval, allsep, pstyle)
ModuleNone

Notes
  
 Write out data for an individual
  





wrvert




Name of routine: wrvert 

Source lines: 34248 - 34326

Type subroutine

Call wrvert(nloci, loc, loctyp, locpos,  dataset, nwid, ndec, allsep)
ModuleNone

Notes
  
 Write out data for individuals vertically
  





prgtp




Name of routine: prgtp 

Source lines: 34330 - 34344

Type subroutine

Call prgtp(idx, gene, dataset, gtp)
ModuleNone

Notes
 print one genotype from dataset






wrid




Name of routine: wrid 

Source lines: 34349 - 34369

Type subroutine

Call wrid(just, id, chid, sx)
ModuleNone

Notes
  
 Write id as justified (l,c,r) string, possibly indicating sex
 as male [101] or female (102)
  





decgtp




Name of routine: decgtp 

Source lines: 34373 - 34386

Type subroutine

Call decgtp(value, g1, g2)
ModuleNone

Notes
  
 Decode genotype code
  





encgtp




Name of routine: encgtp 

Source lines: 34390 - 34400

Type function

Call encgtp(a1, a2)
ModuleNone

Notes
 Hash a genotype
  





iencgtp




Name of routine: iencgtp 

Source lines: 34404 - 34416

Type function

Call iencgtp(a1, a2)
ModuleNone

Notes
 Hash an integer genotype
  





encchr




Name of routine: encchr 

Source lines: 34420 - 34441

Type subroutine

Call encchr(chr, val)
ModuleNone

Notes
 Hash a chromosome retaining nice collation order






decchr




Name of routine: decchr 

Source lines: 34445 - 34464

Type subroutine

Call decchr(val, chr)
ModuleNone

Notes
 Unhash a chromosome






wrpercent




Name of routine: wrpercent 

Source lines: 34468 - 34478

Type function

Call wrpercent(num, den)
ModuleNone

Notes
 Write out a percentage






wrpercentd




Name of routine: wrpercentd 

Source lines: 34480 - 34490

Type function

Call wrpercentd(num, den)
ModuleNone



wrtrait




Name of routine: wrtrait 

Source lines: 34494 - 34565

Type subroutine

Call wrtrait(value, str, typ, catlabels, nwid, ndec)
ModuleNone

Notes
  
 Write out trait value to a string
  





get_snpallele1




Name of routine: get_snpallele1 

Source lines: 34569 - 34582

Type subroutine

Call get_snpallele1(locnote, alleles)
ModuleNone

Notes
 Extract alleles from locus annotation of form "A/B" to string "AB"






get_snpallele2




Name of routine: get_snpallele2 

Source lines: 34586 - 34607

Type subroutine

Call get_snpallele2(locnote, allele_buffer)
ModuleNone

Notes
 Extract alleles from locus annotation of form "A/B" to allele data structure






wrgtp




Name of routine: wrgtp 

Source lines: 34611 - 34659

Type subroutine

Call wrgtp(all1, all2, gtp, allsep, typ)
ModuleNone

Notes
 Write out a genotype






wrall




Name of routine: wrall 

Source lines: 34663 - 34680

Type subroutine

Call wrall(iall, allel)
ModuleNone

Notes
 Write an allele 






juststr




Name of routine: juststr 

Source lines: 34684 - 34711

Type subroutine

Call juststr(just,string,length)
ModuleNone

Notes
 Justify a string of characters within a string






ascend




Name of routine: ascend 

Source lines: 34715 - 34722

Type subroutine

Call ascend(n, ia)
ModuleNone

Notes
 
 Initialize array with value of index
 





connect




Name of routine: connect 

Source lines: 34726 - 34826

Type subroutine

Call connect(num, fa, mo, set, nsub, maxgrp)
ModuleNone

Notes
 See if all members of a pedigree are connected






addlist




Name of routine: addlist 

Source lines: 34831 - 34841

Type subroutine

Call addlist(pos, idx, set)
ModuleNone

Notes
 Shift an individual from the list of ungrouped individuals
 to the appropriate group (subpedigree) nucleating around the index person.






findlist




Name of routine: findlist 

Source lines: 34845 - 34860

Type subroutine

Call findlist(trget, num, set, pos)
ModuleNone

Notes
 Find list number <target>






badloop




Name of routine: badloop 

Source lines: 34864 - 34932

Type subroutine

Call badloop(pedigree, num, id, key, fa, mo, nerr)
ModuleNone

Notes
 Find pathological loops in current pedigree






wrsubped




Name of routine: wrsubped 

Source lines: 34936 - 34974

Type subroutine

Call wrsubped(pedigree, num, id, key, set, nsub, maxgrp, plevel)
ModuleNone

Notes
 List the members of pedigree(s)






gener




Name of routine: gener 

Source lines: 34980 - 35151

Type subroutine

Call gener(pedigree, num, fa, mo, nsub, set, ord, higen, nerr, plevel)
ModuleNone

Notes
 Work out generation number ord().
 Visit every person in each subpedigree in turn.
 The missing value for generation must be a large negative value.






dogen




Name of routine: dogen 

Source lines: 35156 - 35293

Type subroutine

Call dogen(dataset, trait, typ, plevel)
ModuleNone

Notes
 Write out pedigrees as list of nuclear families plus marry-ins by
 generation number






wrgen




Name of routine: wrgen 

Source lines: 35298 - 35355

Type subroutine

Call wrgen(ped, dataset, curped, set, higen, ord)
ModuleNone

Notes
 Write out structure and generation numbers
   List of sibships by generation number






tidydata




Name of routine: tidydata 

Source lines: 35359 - 35406

Type subroutine

Call tidydata(nloci, loctyp, locpos, dataset, tottyp)
ModuleNone

Notes
 Round up allele sizes etc






duplicates




Name of routine: duplicates 

Source lines: 35410 - 35449

Type subroutine

Call duplicates(dataset, plevel)
ModuleNone

Notes
 Check for duplicate pedigrees or records






showdups




Name of routine: showdups 

Source lines: 35453 - 35481

Type subroutine

Call showdups(pos, ncopies, pedname, pedpos, dataset, plevel)
ModuleNone

Notes
 Print the duplicates for current pedigree






testhap




Name of routine: testhap 

Source lines: 35485 - 35690

Type subroutine

Call testhap(typ, nloci, loc, loctyp, locpos, dataset, inconsist, plevel)
ModuleNone

Notes
 Check haploid markers 1=Y 2=Mit






testsex




Name of routine: testsex 

Source lines: 35714 - 35972

Type subroutine

Call testsex(sexcrit, sexmarker, nloci, loc, lochash, loctyp, locpos, dataset, allele_buffer, inconsist, plevel)
ModuleNone

Notes
 Check sex using sex-linked markers assuming false het call rate z

 Male outcomes     A        AB         B
                 p(1-z)     z         q(1-z)

 Female outcomes   A        AB         BB
                pp(1-z) 2pq+z(1-2pq)  qq(1-z)

 LR(G=AB) = Pr(AB|Sex=M)/Pr(AB|Sex=Female)
                  z
          = -----------------------
               2pq+z(1-2pq)
          = z/(2pq+z(1-2pq))

 LR(G=AA) = Pr(A|Sex=M)/Pr(AA|Sex=Female)
                  p
          = -----------------------
                 p^2
          = 1/p

 Absence of Y-haplotype data can be female sex or ungenotyped






mzgtp




Name of routine: mzgtp 

Source lines: 35976 - 36134

Type subroutine

Call mzgtp(mztwin, gt, thresh, nloci, loc, loctyp, locpos, dataset, inconsist, plevel)
ModuleNone

Notes
 Test monozygotic twins






dropt2




Name of routine: dropt2 

Source lines: 36139 - 36332

Type subroutine

Call dropt2(mztwin, gt, thresh, typ,  nloci, loc, loctyp, locpos, dataset, plevel)
ModuleNone

Notes
  
 Delete MZ twin with least phenotype information out of pair
 or clean MZ genotypes
  





countmz




Name of routine: countmz 

Source lines: 36336 - 36448

Type subroutine

Call countmz(mztwin, gt, thresh, dataset, plevel)
ModuleNone

Notes
 Count up MZ twins, triplets, quads, higher






mzfind




Name of routine: mzfind 

Source lines: 36453 - 36609

Type subroutine

Call mzfind(typ, mztrait, nloci, loc, loctyp, locpos, dataset, plevel)
ModuleNone

Notes
 Find MZ twins/duplicates based on genotype concordance
 Abort pairwise comparison after <nfailure> mismatches
 





mztest




Name of routine: mztest 

Source lines: 36614 - 36651

Type subroutine

Call mztest(id1, id2, nmark, mark, dataset, nfailure, nonmatch,  typed, istwin)
ModuleNone

Notes
 Test if pair are genetically identical, aborting if
   nfailure nonmatches






testage




Name of routine: testage 

Source lines: 36655 - 36710

Type subroutine

Call testage(typ, locnam, trait, thresh, dataset, droperr)
ModuleNone

Notes
 Test ages or DOB for consistency






testpage




Name of routine: testpage 

Source lines: 36714 - 36762

Type subroutine

Call testpage(typ, trait, ped, idx, parent, thresh, dataset, droperr)
ModuleNone

Notes
 Test a parent






ckibs




Name of routine: ckibs 

Source lines: 36767 - 36871

Type subroutine

Call ckibs(nloci, loctyp, locpos, allele_buffer, dataset)
ModuleNone

Notes
 Check if multilocus ibs sharing for pairs of sibs is consistent
 with purported relationship.  Again as per Bishop et al 1990






ibskin




Name of routine: ibskin 

Source lines: 36878 - 37054

Type subroutine

Call ibskin(typ, trait, gt, thresh, nloci, loc, loctyp, locpos,  dataset, plevel)
ModuleNone

Notes
 Estimate kinship coefficients based on overall ibs sharing
 EM algorithm of Choi et al Genet Epidemiol 33:668-678
 Either founders only (typ=1), all individuals (typ=2), 
 within pedigrees (typ=3), or subsetted on a phenotype (typ=4)






ibskin_one




Name of routine: ibskin_one 

Source lines: 37059 - 37179

Type subroutine

Call ibskin_one(peri, perj, nmark, mark, locpos, alleles, dataset, useful, ibscoef)
ModuleNone

Notes
 Estimate kinship coefficients based on overall ibs sharing
 One pair of relatives






emibskin




Name of routine: emibskin 

Source lines: 37183 - 37229

Type subroutine

Call emibskin(nmark, nused, ibscoef, k0, k1, k2, plevel)
ModuleNone

Notes
 EM approach of Choi et al 2009






genmatch




Name of routine: genmatch 

Source lines: 37234 - 37373

Type subroutine

Call genmatch(tped, tid, nloci, loc, loctyp, locpos, dataset)
ModuleNone

Notes
  
 Find closest match of genotypes between index person and all other
 active individuals
  





cntibs




Name of routine: cntibs 

Source lines: 37377 - 37409

Type subroutine

Call cntibs(idx, nmark, geno, ord, locpos, dataset, nmatch, ibs)
ModuleNone

Notes
  
 IBS at specified set of markers
  





bluefreq




Name of routine: bluefreq 

Source lines: 37417 - 37562

Type subroutine

Call bluefreq(gene, filter, gt, thresh, dataset, allele_buffer, plevel)
ModuleNone

Notes
 BLUE allele frequency estimator of McPeek et al 2004

 a = (1' L^(-1) 1)^(-1) 1' L^(-1) Z
 Var(a) = 0.5 * (1' L^(-1) 1)^(-1) a(1-a)
 Z=ith allele count L=NRM
 





domqls




Name of routine: domqls 

Source lines: 37566 - 37922

Type subroutine

Call domqls(typ, trait, gt, thresh, gene, locnam, prev, dataset, allele_buffer, iter, pval, plevel)
ModuleNone

Notes
 MQLS of Bourgain et al 2003, Thornton et al 2007
 





corchi




Name of routine: corchi 

Source lines: 37927 - 38243

Type subroutine

Call corchi(trait, loctyp, gene, locnam, prev, dataset, allele_buffer, iter, pval, plevel)
ModuleNone

Notes
 WQLS association chi-square 
 extending Bourgain et al 2003 to categorical traits with more than 2 levels
 





freq




Name of routine: freq 

Source lines: 38251 - 38393

Type subroutine

Call freq(gene, loctyp, fndr, dataset, allele_buffer)
ModuleNone

Notes
  
 Count alleles in entire sample -- codominant system
 Either unweighted or weighted by number of founders in pedigree
  
 If imputation has been done and fndr=2, then return the
 count of alleles in the founders, both observed and imputed
  





tab




Name of routine: tab 

Source lines: 38398 - 38433

Type subroutine

Call tab(curr, allele_buffer, wei)
ModuleNone

Notes
  
 update table of counts of alleles -- binary search and insertion sort
 if allele_buffer too small, increase size
  





wrfreq




Name of routine: wrfreq 

Source lines: 38437 - 38689

Type subroutine

Call wrfreq(strm, locnam, group, mappos, locnote, allele_buffer, fstyle)
ModuleNone

Notes
  
 Write out frequencies in 20 different styles
  





getchr




Name of routine: getchr 

Source lines: 38694 - 38744

Type subroutine

Call getchr(locnam, locnote, chr)
ModuleNone

Notes
 Get chromosome number from a locus name of form "DnnSn" ^[Dd][0-9]+[Ss]$
 or an annotation of form "chr NN" \<[Cc][Hh][Rr][ :]*[0-9]+\>






thischr




Name of routine: thischr 

Source lines: 38748 - 38777

Type subroutine

Call thischr(string, eos, pos, chr)
ModuleNone

Notes
 Read a chromosome number from a string after the start position [1-9]|[1-4][0-9]|X|Y






chrnum




Name of routine: chrnum 

Source lines: 38781 - 38794

Type function

Call chrnum(chr)
ModuleNone

Notes
 Convert the chromosome number to an integer






precis




Name of routine: precis 

Source lines: 38799 - 38833

Type subroutine

Call precis(numal, allele_freqs, ndec)
ModuleNone

Notes
  
 remove rounding errors in allele frequencies printed out to precision ndec
 from f3.1 to f9.7
  





uninf




Name of routine: uninf 

Source lines: 38837 - 38848

Type function

Call uninf(numal, allele_freqs)
ModuleNone

Notes
  
 Frequency of uninformative matings for marker locus
  





getfreq




Name of routine: getfreq 

Source lines: 38852 - 38873

Type function

Call getfreq(allele, allele_set)
ModuleNone

Notes
 
 find allele frequency
  





getnam




Name of routine: getnam 

Source lines: 38877 - 38905

Type function

Call getnam(rall, allele_set)
ModuleNone

Notes
  
 find index for allele
  





get_namedgeno




Name of routine: get_namedgeno 

Source lines: 38909 - 38923

Type subroutine

Call get_namedgeno(idx, gene, gen2, dataset, allele_set, g1, g2)
ModuleNone

Notes
  
 find indices for i'th individual's genotype
  





match




Name of routine: match 

Source lines: 38927 - 38948

Type subroutine

Call match(ival,num,key,pos)
ModuleNone

Notes
  
 Binary search for position of value in an ascending sorted array -- integer
  





dmatch




Name of routine: dmatch 

Source lines: 38952 - 38973

Type subroutine

Call dmatch(val, num, key, pos)
ModuleNone

Notes
  
 Binary search for position of value in an ascending sorted array -- double precision
  





actped




Name of routine: actped 

Source lines: 38981 - 39141

Type subroutine

Call actped(typ, red, pedfil, nloci, loc, loctyp, locpos,  outpos, locnotes, typed, dataset, plevel)
ModuleNone

Notes
  
 summarize current pedigree file
 typ=1 as for info
     2 numbers typed at each locus
     3 numbers typed at active loci
     4 numbers missing at each locus






sumped




Name of routine: sumped 

Source lines: 39145 - 39207

Type subroutine

Call sumped(nloci, loctyp, locpos, dataset)
ModuleNone

Notes
 Summary statistics on families
    





countships




Name of routine: countships 

Source lines: 39211 - 39228

Type function

Call countships(ped, dataset)
ModuleNone

Notes
 Count matings/sibships in current family






listpeds




Name of routine: listpeds 

Source lines: 39232 - 39264

Type subroutine

Call listpeds(dataset, typ)
ModuleNone

Notes
 List all pedigree IDs






listids




Name of routine: listids 

Source lines: 39268 - 39361

Type subroutine

Call listids(dataset, ithresh, plevel)
ModuleNone

Notes
 Tabulate all active IDs






listchroms




Name of routine: listchroms 

Source lines: 39365 - 39388

Type subroutine

Call listchroms(nloci, loctyp, group)
ModuleNone

Notes
 Table of number of markers per chromosome






check




Name of routine: check 

Source lines: 39401 - 39676

Type subroutine

Call check(checkall, nloci, loc, loctyp, locpos, locnotes, dataset,  droperr, ndiscard, inconsist, plevel)
ModuleNone

Notes
 check for simple inconsistencies between child and parent
 if requested, delete any problem genotypes (up to and including
 all genotypes for a nuclear family)
  
 error                                     action if droperr
 ----------------------------------------  ----------------------------
 11=single parent-offspring inconsistency  delete child genotype
 12=Multiple p-o inconsistencies           delete all nuclear fam genos
 13=Inconsistencies between siblings       delete all nuclear fam genos
 14=More than 4 alleles segregating        delete all nuclear fam genos
  





addall




Name of routine: addall 

Source lines: 39680 - 39696

Type subroutine

Call addall(iall, nall, allmax, allele)
ModuleNone

Notes
  
 identify parental alleles in nuclear family
  





nuchek




Name of routine: nuchek 

Source lines: 39700 - 39787

Type subroutine

Call nuchek(xlinkd, ptyped, p11, p12, p21, p22,  nkids, set, xmale, nall, allele, thiserr)
ModuleNone

Notes
  
 nuclear family consistency check (untyped parents)
  





famerr




Name of routine: famerr 

Source lines: 39791 - 39827

Type subroutine

Call famerr(locnam, gene, xlinkd, ped, dataset,  currf, currm, badchild, sta, fin, errtyp, plevel)
ModuleNone

Notes
  
 Write out nuclear family error
  





inderr




Name of routine: inderr 

Source lines: 39831 - 39850

Type subroutine

Call inderr(idx, locnam, gene, gen2, dataset)
ModuleNone

Notes
  
 write genotype for an individual flagged as a Mendelian error
  





remove




Name of routine: remove 

Source lines: 39854 - 39867

Type subroutine

Call remove(idx, gene, dataset, ndiscard)
ModuleNone

Notes
  
 Remove a genotype from data 
  





remfam




Name of routine: remfam 

Source lines: 39871 - 39887

Type subroutine

Call remfam(currf, currm, sta, fin, gene, dataset, ndiscard)
ModuleNone

Notes
  
 drop a nuclear family's genotypes
  





parcon




Name of routine: parcon 

Source lines: 39893 - 39912

Type function

Call parcon(c1, c2, p11, p12, p21, p22, xmale)
ModuleNone

Notes
  
 Tests if child genotype consistent with parental genotypes:
 parcon=4*Pr(Child_genotype|Father_genotype,Mother_genotype)
 if xmale  TRUE then X-linked locus *and* male child
  





opcon




Name of routine: opcon 

Source lines: 39916 - 39923

Type function

Call opcon(c1,c2,p1,p2)
ModuleNone

Notes
  
 test if child genotype consistent with one parental genotype
  





shipcon




Name of routine: shipcon 

Source lines: 39927 - 39944

Type function

Call shipcon(pg1, pg2, mg1, mg2, nkids, set, xmale)
ModuleNone

Notes
 test consistency of a sibship with parents






couple




Name of routine: couple 

Source lines: 39949 - 39966

Type subroutine

Call couple(idx,tot,rang,i1,i2)
ModuleNone

Notes
  
 Enumerate all combinations of i ~ I(1..range) with itself
 If index=tot then return last tuple
  





whall




Name of routine: whall 

Source lines: 39970 - 39985

Type function

Call whall(iall,nall,allele)
ModuleNone

Notes
  
 Find index of allele segregating in nuclear family
  





describe




Name of routine: describe 

Source lines: 39989 - 40255

Type subroutine

Call describe(locnam, gene, xlinkd, ped, dataset,  currf, currm, sta, fin, mesg)
ModuleNone

Notes
  
 write out genotypes in nuclear family and grandparents
  





famset




Name of routine: famset 

Source lines: 40260 - 40420

Type subroutine

Call famset(ped, dataset, currf, currm, sta, fin, gene, set, gset)
ModuleNone

Notes
 Write out phenoset for a nuclear family (plus grandparents and halfsibs)
 Useful in detecting sources of long distance Mendelian inconsistencies.






indset




Name of routine: indset 

Source lines: 40424 - 40467

Type subroutine

Call indset(idx, gene, pedoffset, dataset, set, gset)
ModuleNone

Notes
 write out phenoset for an individual






allinset




Name of routine: allinset 

Source lines: 40471 - 40487

Type function

Call allinset(idx, iall, ngeno, gset)
ModuleNone

Notes
 see if particular allele in phenoset for idx person






cntbad




Name of routine: cntbad 

Source lines: 40491 - 40503

Type subroutine

Call cntbad(idx, ngeno, gset)
ModuleNone

Notes
 If phenoset contains zero legal genotypes, reconstruct last state






wroddall




Name of routine: wroddall 

Source lines: 40507 - 40527

Type subroutine

Call wroddall(pedigree, parent, child, iall, partyp)
ModuleNone

Notes
 If find an odd-allele-out, write out its location






start




Name of routine: start 

Source lines: 40532 - 40652

Type subroutine

Call start(maxtry, nloci, loc, loctyp, locpos, dataset, allele_buffer,  inconsist, plevel)
ModuleNone

Notes
  
 If Lange-Goradia algorithm not used, initialize genotypes for random walk
 algorithms via a conditional gene dropping algorithm
  





workpointers




Name of routine: workpointers 

Source lines: 40656 - 40681

Type subroutine

Call workpointers(ped, dataset, fa, mo, imztwin)
ModuleNone

Notes
 make parental pointers offset for local work array






dattoset




Name of routine: dattoset 

Source lines: 40685 - 40713

Type subroutine

Call dattoset(sta, fin, gene, dataset, allele_buffer, set)
ModuleNone

Notes
 transfer genotypes to working array






startone




Name of routine: startone 

Source lines: 40717 - 40801

Type subroutine

Call startone(maxtry, allele_buffer, num, nfound,  fa, mo, sex, set, sibd, key, failid, plevel)
ModuleNone

Notes
 start genotypes for one pedigree






genof3




Name of routine: genof3 

Source lines: 40807 - 40900

Type subroutine

Call genof3(idx, fa, mo, xmale, set, sibd, key, failid)
ModuleNone

Notes
  
 Drop ibd-alleles conditional on observed markers
 and randomly where marker genotype not observed -- restart
 if later generates inconsistency
  





fillin




Name of routine: fillin 

Source lines: 40904 - 40956

Type subroutine

Call fillin(allele_buffer, num, nfound, set, sibd, key,  sta, fin, gene, dataset)
ModuleNone

Notes
  
 infer missing genotypes based on sibd values after run of start
  





found




Name of routine: found 

Source lines: 40960 - 40971

Type subroutine

Call found(cumfrq, allele)
ModuleNone

Notes
  
 founder frequency
  





coutyp




Name of routine: coutyp 

Source lines: 40975 - 41014

Type subroutine

Call coutyp(nloci, loctyp, locpos, dataset, eligible, typed)
ModuleNone

Notes
  
 Give counts of typed individuals for each locus
  





thetaf




Name of routine: thetaf 

Source lines: 41024 - 41041

Type function

Call thetaf(het, n)
ModuleNone

Notes
  
 Xu and Fu 2004 correction for thetaf=4Nu=1/2(1/F^2-1)
 where F is the observed homozygosity for the locus is:
 1/2 (1/F^2-1) = a thetaf + b sqrt(thetaf)
 where
 thetaf <=10                        >10
    a   1.1313+3.4882/n+28.2878/n^2ltyp,  1.1675+3.3232/n+63.698/n^2
    b   0.3998                      0.2569
  





mutage




Name of routine: mutage 

Source lines: 41045 - 41057

Type subroutine

Call mutage(p, ne, r)
ModuleNone

Notes
 Age of an allele (Ohta, Nei, Rannala & Slatkin)






qtlpars




Name of routine: qtlpars 

Source lines: 41061 - 41106

Type subroutine

Call qtlpars(p,m1,m2,m3,sd1,sd2,sd3)
ModuleNone

Notes
  
 Calculate variances for a given SML model
  





ccpen




Name of routine: ccpen 

Source lines: 41112 - 41128

Type subroutine

Call ccpen(prev, pca, pco, typ)
ModuleNone

Notes
  
 Calculate penetrances for a particular prevalence and 
 case and control allele frequencies, assuming multiplicative model
 Controls are unaffected (1), or population (2)
  





grrpen




Name of routine: grrpen 

Source lines: 41132 - 41165

Type subroutine

Call grrpen(model, prev, q, grr)
ModuleNone

Notes
  
 Calculate penetrances for a particular prevalence and genotypic RR
  





recrisk




Name of routine: recrisk 

Source lines: 41169 - 41259

Type subroutine

Call recrisk(q,f1,f2,f3)
ModuleNone

Notes
  
 Calculate recurrence risks and risk ratios for given SML model
  





doito




Name of routine: doito 

Source lines: 41263 - 41315

Type subroutine

Call doito(typ, pars)
ModuleNone

Notes
  
 Calculate GPE for a relative: ITO method
  





ito




Name of routine: ito 

Source lines: 41319 - 41358

Type subroutine

Call ito(rel, q, r)
ModuleNone

Notes
 ITO calculation






tetcor




Name of routine: tetcor 

Source lines: 41362 - 41374

Type function

Call tetcor(prev, prrr)
ModuleNone

Notes
 MFT heritability






brent_tet




Name of routine: brent_tet 

Source lines: 41376 - 41384

Type function

Call brent_tet(r)
ModuleNone



dataset_uses




Name of routine: dataset_uses 

Source lines: 41389 - 41405

Type function

Call dataset_uses(dataset)
ModuleNone



dataset_uses




Name of routine: dataset_uses 

Source lines: 41407 - 41423

Type function

Call dataset_uses(dataset)
ModuleNone



macsub




Name of routine: macsub 

Source lines: 41428 - 41539

Type subroutine

Call macsub(narg, words, commands, plevel)
ModuleNone

Notes
 Perform simple macro substitutions on contents of command buffer






macloop




Name of routine: macloop 

Source lines: 41547 - 41636

Type subroutine

Call macloop(lin, nloci, loc, loctyp, commands, plevel)
ModuleNone

Notes
 Expand an iterator list of tokens in a command
 These implicit loops are signalled by a list surrounded by braces
 Implemented as a naive immediate macro expansion so:
   {1 2} + 1 -> 1 + 1; 2 + 1
   {1 2} + {1 2} -> 1 + {1 2}; 2 + {1 2} requiring further evaluation






macvar




Name of routine: macvar 

Source lines: 41641 - 41717

Type subroutine

Call macvar(lin, commands, plevel)
ModuleNone

Notes
 Perform simple macro variable substitutions on contents of command buffer
 cf macro functions which are handled by macsub






parser




Name of routine: parser 

Source lines: 41728 - 41866

Type subroutine

Call parser(nterm, wtyp, wtag, expr, error)
ModuleNone

Notes
  
 Evaluate and apply simple expressions either
  
 (1) pure arithmetic, so no effect on pedigree file
 (2) Dry run, so can test if will lead to a legal effect on pedigree file
         all variables set to MISS
 (3) Pedigree operation -- individual-wise calculation and update
  
 The parser
  





simpev




Name of routine: simpev 

Source lines: 41870 - 42103

Type subroutine

Call simpev(sta, fin, nterm, wtyp, wtag, expr, error)
ModuleNone

Notes
  
 The non-compound evaluator
  





wrans




Name of routine: wrans 

Source lines: 42107 - 42146

Type subroutine

Call wrans(prefix, nterm, expr, wtyp, wtag, val)
ModuleNone

Notes
  
 write out results of command line expression evaluation
  





legall




Name of routine: legall 

Source lines: 42150 - 42164

Type function

Call legall(xall)
ModuleNone

Notes
  
 the legal range of alleles
  





isdata




Name of routine: isdata 

Source lines: 42168 - 42173

Type function

Call isdata(idx)
ModuleNone

Notes
  
 Is a stack element a number, variable or operator
  





isenv




Name of routine: isenv 

Source lines: 42177 - 42182

Type function

Call isenv(idx)
ModuleNone

Notes
 Is a stack element an automatic variable






isvar




Name of routine: isvar 

Source lines: 42186 - 42191

Type function

Call isvar(idx)
ModuleNone

Notes
 Is a stack element data






isop




Name of routine: isop 

Source lines: 42195 - 42200

Type function

Call isop(idx)
ModuleNone

Notes
 Is a stack element an operator






isvec




Name of routine: isvec 

Source lines: 42204 - 42209

Type function

Call isvec(idx)
ModuleNone

Notes
 Is a stack element a genotype - both values of interest
  





ismis




Name of routine: ismis 

Source lines: 42213 - 42218

Type function

Call ismis(idx)
ModuleNone

Notes
  
 Is a stack element missing data
  





addcolon




Name of routine: addcolon 

Source lines: 42222 - 42257

Type subroutine

Call addcolon(nterm, wtyp, wtag, expr)
ModuleNone

Notes
 Convert (expr) (expr) to (expr : expr)






compop




Name of routine: compop 

Source lines: 42261 - 42309

Type subroutine

Call compop(pos, sta, fin, nterm, wtyp, wtag, expr, error)
ModuleNone

Notes
  
 compound operators eg <= >= == ^=
  





zerop




Name of routine: zerop 

Source lines: 42313 - 42355

Type subroutine

Call zerop(pos, wtyp, wtag, expr, error)
ModuleNone

Notes
  
 zero argument functions
  





unop




Name of routine: unop 

Source lines: 42359 - 42517

Type subroutine

Call unop(pos, sta, fin, nterm, wtyp, wtag, expr, error)
ModuleNone

Notes
  
 unary operators
  





binop




Name of routine: binop 

Source lines: 42521 - 42752

Type subroutine

Call binop(pos, sta, fin, nterm, wtyp, wtag, expr, error)
ModuleNone

Notes
  
 binary operators
  





typwords




Name of routine: typwords 

Source lines: 42771 - 42835

Type subroutine

Call typwords(farg, larg, words, nloci, loc, lochash, loctyp,  wtyp, wtag, expr, actn)
ModuleNone

Notes
  
 Evaluate type of each term in expression word(farg...larg) and actn
 actn=0 error  =1 purely arithmetic  =2 legal
  
 Types are:         wtyp     wtag        expr
                    ----     --------    --------
 tokens             0        0...TOKNUM    -
 env                1        1...ENVNUM   (value)
 constant           2                      value
 trait data         2        1...NLOCI    (value)
 constant genotype  3                      value, value
 genotype data      3        1...NLOCI    (value, value)
 MISS               4                      MISS
 missing trait      4        1...NLOCI     MISS
 MISS genotype      5                      MISS/MISS
 missing trait      5        1...NLOCI     MISS/MISS
 NUM                6                      -
  





dryrun




Name of routine: dryrun 

Source lines: 42840 - 42851

Type subroutine

Call dryrun(farg, larg, wtyp)
ModuleNone

Notes
  
 If checking arguments via dry run of parser,
 replace variable values with (generic) NUM
  





pull




Name of routine: pull 

Source lines: 42855 - 42873

Type subroutine

Call pull(pos, dec, fin, nterm, typ, tag, expr)
ModuleNone

Notes
  
 Pull up expr
  





isgeno




Name of routine: isgeno 

Source lines: 42877 - 42910

Type function

Call isgeno(string)
ModuleNone

Notes
  
  See if a string is a valid genotype
  





getgeno




Name of routine: getgeno 

Source lines: 42914 - 42957

Type subroutine

Call getgeno(string, a1, a2, wtyp)
ModuleNone

Notes
  
  Get a valid genotype
  





incpos




Name of routine: incpos 

Source lines: 42961 - 42970

Type subroutine

Call incpos(pos, minpos, maxpos)
ModuleNone

Notes
  
 Increment counter mod maxpos
  





getrelval




Name of routine: getrelval 

Source lines: 42974 - 43190

Type subroutine

Call getrelval(relate, summary, locnam, loctyp, trait,  sumval, dataset, plevel)
ModuleNone

Notes
 Get values for trait in relatives






priallval




Name of routine: priallval 

Source lines: 43194 - 43271

Type subroutine

Call priallval(summary, trait, loctyp, ped, sumval, totobs, dataset, plevel)
ModuleNone

Notes
 Output single summary value for entire pedigree
 





prirelval




Name of routine: prirelval 

Source lines: 43275 - 43449

Type subroutine

Call prirelval(relate, summary, trait, loctyp, ped,  nobs, relid, sumval, totobs, dataset, plevel)
ModuleNone

Notes
 Output values for each eligible persion
 





evalped




Name of routine: evalped 

Source lines: 43453 - 43765

Type subroutine

Call evalped(narg, words, nloci, loc, lochash, loctyp, locpos,  locnotes, wtyp, wtag, expr, allele_buffer, dataset,  chek, imp, droperr, plevel)
ModuleNone

Notes
  
 Evaluate expression for each pedigree member
  





findth




Name of routine: findth 

Source lines: 43769 - 43804

Type subroutine

Call findth(nterm, wtyp, wtag, posif, posth, posel, posen)
ModuleNone

Notes
  
 Find if/then/else
  





findend




Name of routine: findend 

Source lines: 43808 - 43839

Type subroutine

Call findend(sta, fin, nterm, wtyp, wtag, posen)
ModuleNone

Notes
 Find end of block






findwh




Name of routine: findwh 

Source lines: 43843 - 43856

Type function

Call findwh(farg, larg, narg, args)
ModuleNone

Notes
  
 Find the start of a "where" clause on command line
  





findword




Name of routine: findword 

Source lines: 43860 - 43874

Type function

Call findword(word, farg, larg, narg, args)
ModuleNone

Notes
  
 Find a keyword -- exact match
  





findbracket




Name of routine: findbracket 

Source lines: 43880 - 43902

Type subroutine

Call findbracket(lb, rb, lin, sta, fin, istat)
ModuleNone

Notes
  
 Find matching bracket in string starting at a left bracket
   if unmatched, returns to end of line
   rb may equal lb, brackets may be nested
  





loadvar




Name of routine: loadvar 

Source lines: 43909 - 44057

Type subroutine

Call loadvar(idx, nmark, nloci, loctyp, locpos, tot, nped,  dataset, sta, fin, wtyp, wtag, expr)
ModuleNone

Notes
  
 Load variable values for ith individual
 code y and n as 1 and 0
 tot records number of active records evaluated to date
 nped records number of active pedigrees evaluated to date
  





doselect




Name of routine: doselect 

Source lines: 44061 - 44199

Type subroutine

Call doselect(typ, nprob, farg, larg, words, nloci, loc, lochash, loctyp, locpos, wtyp, wtag, expr,  dataset, nobs, plevel)
ModuleNone

Notes
  
 Select pedigrees where probands meet a given criterion v2
  





edit




Name of routine: edit 

Source lines: 44203 - 44314

Type subroutine

Call edit(tped, tid, gene, loc, loctyp, all1, all2, dataset, plevel)
ModuleNone

Notes
 Edit alleles for particular gene for particular person






copydata




Name of routine: copydata 

Source lines: 44320 - 44429

Type subroutine

Call copydata(typ, ped1, id1, ped2, id2,  nloci, loc, loctyp, locpos,  dataset, hashtab, plevel)
ModuleNone

Notes
 Copy data for person A to person B
 typ=1 overwrite at B if A nonmissing for that variable
 typ=2 insert data only where B is missing for that variable






selped




Name of routine: selped 

Source lines: 44433 - 44487

Type subroutine

Call selped(typ, farg, larg, words, dataset, plevel)
ModuleNone

Notes
  
 include or exclude a list of pedigrees
  





unsel




Name of routine: unsel 

Source lines: 44491 - 44544

Type subroutine

Call unsel(dataset, rollback, plevel)
ModuleNone

Notes
  
 unselect
  





docount




Name of routine: docount 

Source lines: 44548 - 44815

Type subroutine

Call docount(typ, farg, larg, words, nloci, loc, lochash, loctyp, locpos, wtyp, wtag, expr,  dataset, pedmask, nwid, ndec, misval, fieldsep, allsep,  pstyle, plevel)
ModuleNone

Notes
  
 Count or print individuals per pedigree fulfilling criterion
  





seldel




Name of routine: seldel 

Source lines: 44819 - 44941

Type subroutine

Call seldel(nord, locord, farg, larg, words, nloci, loc, lochash, loctyp, locpos, wtyp, wtag, expr,  dataset, plevel)
ModuleNone

Notes
  
 Delete data for individuals fulfilling criterion
  





prexpr




Name of routine: prexpr 

Source lines: 44945 - 44977

Type subroutine

Call prexpr(typ, nprob, farg, larg, words)
ModuleNone

Notes
  
 Echo action to be performed
  





marshare




Name of routine: marshare 

Source lines: 44982 - 45019

Type subroutine

Call marshare(idx, nloci, loctyp, locpos, dataset, marcom)
ModuleNone

Notes
  
 Count maximum number of active markers where proband and
 any of relatives is genotyped at
  





hashids




Name of routine: hashids 

Source lines: 45023 - 45040

Type subroutine

Call hashids(typ, dataset, hashtab, load, plevel)
ModuleNone

Notes
 Hash IDs






dohashids




Name of routine: dohashids 

Source lines: 45042 - 45118

Type subroutine

Call dohashids(typ, dataset, hashtab, load,  hasher, matcher, plevel)
ModuleNone



hashprint




Name of routine: hashprint 

Source lines: 45120 - 45164

Type subroutine

Call hashprint(hashtab, dataset, loc, plevel)
ModuleNone



matchid




Name of routine: matchid 

Source lines: 45168 - 45219

Type subroutine

Call matchid(keytyp, idstr1, idstr2, dataset, hashtab, iaddress, plevel)
ModuleNone

Notes
 Search for ID using hash






findids




Name of routine: findids 

Source lines: 45223 - 45302

Type subroutine

Call findids(port, lin, hashtab, dataset, plevel)
ModuleNone

Notes
 Match list of IDs from file






sextable




Name of routine: sextable 

Source lines: 45306 - 45333

Type subroutine

Call sextable(dataset)
ModuleNone

Notes
 Tabulate sexes






xtab




Name of routine: xtab 

Source lines: 45337 - 45439

Type subroutine

Call xtab(analys, nloc, loclist, loc, locpos, loctyp,  locnotes, dataset, iter, nwid, ndec, pval, plevel)
ModuleNone

Notes
  
 N-way cross-tabulation
  





maketab




Name of routine: maketab 

Source lines: 45443 - 45494

Type subroutine

Call maketab(nloc, loclist, loc, locpos, loctyp,  dataset, nmiss, table)
ModuleNone

Notes
 Generate crosstabulation






onetab




Name of routine: onetab 

Source lines: 45498 - 45539

Type subroutine

Call onetab(loc, loctyp, locnotes, table, nmiss, nwid, ndec)
ModuleNone

Notes
  
 print summary of one-way table
  





listab




Name of routine: listab 

Source lines: 45543 - 45590

Type subroutine

Call listab(nloc, loclist, loc, loctyp, locnotes,  table, nmiss, nwid, ndec)  
ModuleNone

Notes
  
 print listwise contingency table
  





wrtab




Name of routine: wrtab 

Source lines: 45594 - 45849

Type subroutine

Call wrtab(analys, nloc, loclist, loc, loctyp, locnotes, table,  nmiss, iter, nwid, ndec, pval)  
ModuleNone

Notes
  
 print RxC contingency table
  





kwtest




Name of routine: kwtest 

Source lines: 45853 - 45934

Type subroutine

Call kwtest(nloc, loclist, loc, loctyp, locnotes,  martable1, martable2, table,  nwid, ndec, pval)  
ModuleNone

Notes
 Kruskal-Wallis test






logrank




Name of routine: logrank 

Source lines: 45938 - 46129

Type subroutine

Call logrank(typ, nloc, loclist, loc, loctyp, locpos, locnotes,  dataset, nwid, ndec, lrstat, df, pval, plevel)  
ModuleNone

Notes
 Logrank test: table 1..(nloc-2)=covariate levels (nloc-1)=time nloc=censor 






simlogrank




Name of routine: simlogrank 

Source lines: 46133 - 46449

Type subroutine

Call simlogrank(locnam, gene, onset, censor, iter, mincnt,  dataset, allele_buffer, pval, plevel)  
ModuleNone

Notes
 Logrank association test: gene time censor 






survtab




Name of routine: survtab 

Source lines: 46453 - 46477

Type subroutine

Call survtab(timelev, ngroups, table, dij, cij, nij, ni, di)
ModuleNone

Notes
 Life table logrank test






calclogrank




Name of routine: calclogrank 

Source lines: 46481 - 46536

Type subroutine

Call calclogrank(timelev, ngroups, ns2, di, ni, naff, cij, dij, nij,  ediff, vardiff, vinv, lrstat, df)
ModuleNone

Notes
 Calculate log rank statistic






pedtab




Name of routine: pedtab 

Source lines: 46540 - 46589

Type subroutine

Call pedtab(gene, loctyp, locnotes, dataset, nwid, ndec, plevel)
ModuleNone

Notes
 One-way tabulation by pedigree






fitloglin




Name of routine: fitloglin 

Source lines: 46593 - 47037

Type subroutine

Call fitloglin(sta, fin, terms, nloci, loc, loctyp, locpos, locnotes,  dataset, mlik, mpar, pval, nwid, ndec, plevel)
ModuleNone

Notes
 Fit poisson model to a contingency table






strattyp




Name of routine: strattyp 

Source lines: 47042 - 47209

Type subroutine

Call strattyp(trait, nloci, loc, loctyp, locpos, locnotes,  locord, dataset, locstat, plevel)
ModuleNone

Notes
  
 Tabulate counts of typed individuals for each locus versus 
 stratifying variables
  





dohwe




Name of routine: dohwe 

Source lines: 47213 - 47472

Type subroutine

Call dohwe(locnam, gene, loctyp, iter, mincnt, hwefnd, norder,  dataset, outp, plevel)
ModuleNone

Notes
  
 Monte-Carlo test for HWE
  





tabgen




Name of routine: tabgen 

Source lines: 47479 - 47497

Type subroutine

Call tabgen(a1, a2, xmale, ngcount, gcount)
ModuleNone

Notes
  
 Increment counts of genotypes and alleles for HWE test
 Storage of allele counts in gcount(,2) indexed from 1..nall
 Genotypes indexed from 1..ngtp by gcount(,1).
 Males contribute to allele counts but not genotype counts
  





hwep




Name of routine: hwep 

Source lines: 47501 - 47555

Type subroutine

Call hwep(numal)
ModuleNone

Notes
  
 Calculate HWE Chi-square for table entered on command line
  





hwechi




Name of routine: hwechi 

Source lines: 47559 - 47602

Type function

Call hwechi(numal, ngcount, gcount, tot, totmal)
ModuleNone

Notes
  
 Calculate Gibbs chi-square for HWE
  





hwe2




Name of routine: hwe2 

Source lines: 47607 - 47634

Type subroutine

Call hwe2(n11, n12, n22, pa, pvalue)
ModuleNone

Notes
  
 calculate hwe test for diallelic autosomal marker
  





dhwe2




Name of routine: dhwe2 

Source lines: 47638 - 47652

Type function

Call dhwe2(n11, n12, n22)
ModuleNone

Notes
  
 hypergeometric for diallelic genotypes under hwe
  





domar




Name of routine: domar 

Source lines: 47656 - 47760

Type subroutine

Call domar(gene, dataset, allele_buffer, plevel)
ModuleNone

Notes
 Do ibs sharing in parents






margen




Name of routine: margen 

Source lines: 47764 - 47856

Type subroutine

Call margen(gene, dataset, allele_buffer, iter, plevel)
ModuleNone

Notes
 Tabulate maternal v. paternal genotypes






invmap




Name of routine: invmap 

Source lines: 47860 - 47872

Type function

Call invmap(x,mapf)
ModuleNone

Notes
  
 inverse Haldane (mapf=1) or Kosambi (mapf=2) mapping x cM to r
  





doplot




Name of routine: doplot 

Source lines: 47878 - 47973

Type subroutine

Call doplot(fil, typ, xtrait, ytrait, ztrait,  xlab, ylab, zlab, pedfil, dataset)
ModuleNone

Notes
  
 Produce a scatterplot of two traits
 typ=1 scatterplot
    =2 dotplot (xtrait is categorical)
  





dohist




Name of routine: dohist 

Source lines: 47977 - 48069

Type subroutine

Call dohist(locnam, histcat, cat, table, nwid, ndec, outfil)
ModuleNone

Notes
  
 Produce a histogram with histcat intervals from sorted tabulation
  





sumucsc




Name of routine: sumucsc 

Source lines: 48073 - 48090

Type subroutine

Call sumucsc(chr)
ModuleNone

Notes
 Summarize test statistics for UCSC browser






tabstat




Name of routine: tabstat 

Source lines: 48094 - 48175

Type subroutine

Call tabstat(plevel)
ModuleNone

Notes
 Summarize test statistics






sumstat




Name of routine: sumstat 

Source lines: 48179 - 48213

Type subroutine

Call sumstat(numval, plevel)
ModuleNone

Notes
 Show ranked test statistics






rankstat




Name of routine: rankstat 

Source lines: 48217 - 48235

Type subroutine

Call rankstat(nvar)
ModuleNone

Notes
 Rank the test statistics (nvar=no. nonmissing values)






sumplot




Name of routine: sumplot 

Source lines: 48239 - 48299

Type subroutine

Call sumplot(fil)
ModuleNone

Notes
  
 Produce a plot of P-values
  





qqplot




Name of routine: qqplot 

Source lines: 48303 - 48346

Type subroutine

Call qqplot(fil)
ModuleNone

Notes
  
 Produce a Q-Q (quantile-quantile) plot of P-values
  





selstat




Name of routine: selstat 

Source lines: 48350 - 48369

Type subroutine

Call selstat(message, thresh, gt, plevel)
ModuleNone

Notes
 Select loci (wloc) based on test on value of locstat






traceplot




Name of routine: traceplot 

Source lines: 48373 - 48407

Type subroutine

Call traceplot(fil, nobs, nmult, yvals)
ModuleNone

Notes
  
 Produce a MCMC trace
  





filliben




Name of routine: filliben 

Source lines: 48415 - 48461

Type subroutine

Call filliben(table)
ModuleNone

Notes
  
 Filliben correlation here testing for normality
  
   m(i) = 1 - m(n) for i = 1
   m(i) = (i - 0.3175)/(n + 0.365) for i = 2, 3, ..., n-1
   m(i) = 0.5**(1/n) for i = n
  





symtest




Name of routine: symtest 

Source lines: 48469 - 48522

Type subroutine

Call symtest(table)
ModuleNone

Notes
  
 David & Johnson's Jr test for symmetry of a distribution
 Resek Busi Stat 1975; 546-551
 Doksum Biometrika 1977; 64: 473-487
  
 Standard error of Jr based on simulations under Gaussian true distribution
  





unidens




Name of routine: unidens 

Source lines: 48535 - 48668

Type subroutine

Call unidens(num, xvals, xmode, plevel)
ModuleNone

Notes
 Unimodal density estimation using modified PAVA algorithm
 adapted from code written by Mary Meyer
 Statistica Sinica 11(2001), 1159-1174
    AN ALTERNATIVE UNIMODAL DENSITY ESTIMATOR
         WITH A CONSISTENT ESTIMATE OF THE MODE
                                         Mary C. Meyer
                                       University of Georgia
       
 starts with unimodal interval and then does LCM and GCM on either side
 Approach is a NPMLE modified to handle the unknown mode case - with penalty on mode






evdtailp




Name of routine: evdtailp 

Source lines: 48676 - 48694

Type function

Call evdtailp(n, mm, xvals, xnew)
ModuleNone

Notes
 Tail estimation procedure of Davis and Resnick (1984; Ann Stat 12:1467-87)
 Pareto tail estimate from order statistics per extreme value theory.
 xvals(1:(m+2)) contains the ordered m highest out of n values 
 where xvals(1) is work space, xvals(2) = b = the n-m'th order statistic,
 a is the tail index, here estimated using Hill's (1975) estimator.






clcmcn




Name of routine: clcmcn 

Source lines: 48698 - 48707

Type function

Call clcmcn(b,c)
ModuleNone

Notes
  
 calculate McNemar statistic
  





binz




Name of routine: binz 

Source lines: 48711 - 48720

Type function

Call binz(x, n, e)
ModuleNone

Notes
  
 normal approx binomial deviate
  





ftdev




Name of routine: ftdev 

Source lines: 48724 - 48729

Type function

Call ftdev(o,e)
ModuleNone

Notes
 
 Freeman-Tukey deviates
 





clcpos




Name of routine: clcpos 

Source lines: 48734 - 48743

Type function

Call clcpos(i,j)
ModuleNone

Notes
  
 find index of coefficient for pair i,j in a lower triangular matrix
 stored as a 1-D array
  





copy




Name of routine: copy 

Source lines: 48747 - 48754

Type subroutine

Call copy(n, ia, ib)
ModuleNone

Notes
  
 Copy integer array A to integer array B
  





filltri




Name of routine: filltri 

Source lines: 48758 - 48777

Type subroutine

Call filltri(n, nn, a, dval, oval)
ModuleNone

Notes
  
 Load a lower triangular matrix
  





ln




Name of routine: ln 

Source lines: 48781 - 48789

Type function

Call ln(x)
ModuleNone

Notes
  
 zero-trapped log
  





logit




Name of routine: logit 

Source lines: 48793 - 48803

Type function

Call logit(p)
ModuleNone

Notes
  
 logit of p
  





alogit




Name of routine: alogit 

Source lines: 48807 - 48811

Type function

Call alogit(x)
ModuleNone

Notes
  
 Reverse logit
  





inht




Name of routine: inht 

Source lines: 48815 - 48819

Type function

Call inht(x)
ModuleNone

Notes
  
 Inverse hyperbolic tan
  





fishzse




Name of routine: fishzse 

Source lines: 48823 - 48827

Type function

Call fishzse(n)
ModuleNone

Notes
 Standard error for Fisher-Z transformed correlation coefficient






fishzci




Name of routine: fishzci 

Source lines: 48831 - 48842

Type subroutine

Call fishzci(r, n, rlo, rhi)
ModuleNone

Notes
 95%CI via Fisher-Z transform for correlation coefficient






sech




Name of routine: sech 

Source lines: 48846 - 48850

Type function

Call sech(x) 
ModuleNone

Notes
 Hyperbolic secant






cortest




Name of routine: cortest 

Source lines: 48856 - 48868

Type function

Call cortest(r1, r2, n1, n2)
ModuleNone

Notes
 Test equality of two correlation coefficients via LRTS 
 (Brandner 1933; Stuart & Ord Volume 2, Exercise 26.21)
 Direction of test is retained






rtheta




Name of routine: rtheta 

Source lines: 48872 - 48876

Type function

Call rtheta(x)
ModuleNone

Notes
  
 ibd correlation to recombination fraction
  





wrpropci




Name of routine: wrpropci 

Source lines: 48881 - 48891

Type subroutine

Call wrpropci(num, den, width)
ModuleNone

Notes
  
 Confidence intervals around a proportion: approach of Wilson (Agresti
 & Coull) -- wrapper 
  





propci




Name of routine: propci 

Source lines: 48895 - 48923

Type subroutine

Call propci(num, den, inwidth, phat, ll, ul)
ModuleNone

Notes
 Actual Wilson algorithm






binp




Name of routine: binp 

Source lines: 48927 - 48953

Type function

Call binp(np,nq)
ModuleNone

Notes
  
 Binomial probabilities for x,n-x with p=0.5
  





moment




Name of routine: moment 

Source lines: 48957 - 48967

Type subroutine

Call moment(n, x, mean, ss)
ModuleNone

Notes
  
 accumulate mean and sum-of-squares following AS41
  





dssp




Name of routine: dssp 

Source lines: 48971 - 48993

Type subroutine

Call dssp(nvar, nobs, iwt, x, mean, cov)
ModuleNone

Notes
  
 accumulate means and SSCP following AS41
  





covcor




Name of routine: covcor 

Source lines: 48997 - 49017

Type subroutine

Call covcor(nvar, nobs, cov)
ModuleNone

Notes
  
 Standardize covariance matrix (variances left on diagonal)
  





thincov




Name of routine: thincov 

Source lines: 49021 - 49052

Type subroutine

Call thincov(nfull, nreduced, active, cov)
ModuleNone

Notes
 Thin a covariance matrix
 





predmat




Name of routine: predmat 

Source lines: 49060 - 49102

Type subroutine

Call predmat(nfull, yindicator, cov, xval, yp)
ModuleNone

Notes
 Predicting values for subset (indexed by yindicator)
 given covariance matrix and values for complementary subset.
 X values are stored counting backwards in xval(nfull-ny+1:nfull)
 (the observed values for the predicted group are stored xval(1:ny)
 On output, yp contains ny (sum(active)) predicted values.






inicov




Name of routine: inicov 

Source lines: 49106 - 49111

Type subroutine

Call inicov(nter, ncov, r)
ModuleNone

Notes
  
 Initialize covariance matrix used by AS164
  





givenc




Name of routine: givenc 

Source lines: 49116 - 49196

Type subroutine

Call givenc(r, ir, nvars, x, v, ifault)
ModuleNone

Notes
  
 Algorithm AS164  Appl. Statist. (1981) vol.30, no.2
 Incorporate new row of data into R matrix
  





bsub




Name of routine: bsub 

Source lines: 49201 - 49298

Type subroutine

Call bsub(r, ir, idep, coeff, ic, ifault)
ModuleNone

Notes
  
 Algorithm AS 164.1  Appl. Statist. (1981) vol.30, no.2
 Perform back substitution to get regression coefficient estimates
  





var




Name of routine: var 

Source lines: 49303 - 49404

Type subroutine

Call var(r, ir, s, is, idep, nobs, typ, ifault)
ModuleNone

Notes
 Algorithm AS164.3  Appl. Statist. (1981) vol.30, no.2
 Estimates var/covar matrix of regression coefficients






alias




Name of routine: alias 

Source lines: 49410 - 49460

Type subroutine

Call alias(r, ir, nvars, eps, worksp, ifault)
ModuleNone

Notes
  
 Algorithm AS164.4  Appl. Statist. (1981) vol.30, no.2
 Assumes any diagonal elements of d less than eps are
 rounding errors and reduces them to zero
  





iquadmult




Name of routine: iquadmult 

Source lines: 49464 - 49498

Type subroutine

Call iquadmult(n, y, s, res)
ModuleNone

Notes
 Use AS164 to evaluate quadratic y' S~ y where S not necessarily full rank






loglin




Name of routine: loglin 

Source lines: 49502 - 49582

Type subroutine

Call loglin(ncells, totpars, npars, counts, model, offset, b, cov, lrts)
ModuleNone

Notes
  
 Use AS164 to fit a log-linear model
  





emllm




Name of routine: emllm 

Source lines: 49587 - 49703

Type subroutine

Call emllm(ncells, nfull, totpars, npars, counts, scatter, model,  ex, oldex, full, offset, b, cov, lrts, plevel)
ModuleNone

Notes
  
 Use AS164 and EM algorithm to fit a log-linear model to incomplete
 tables
  





gl




Name of routine: gl 

Source lines: 49707 - 49749

Type subroutine

Call gl(nr, nc, design, sta, levels, reps, droplev)
ModuleNone

Notes
  
 Appropriate design matrix for factor
  





logccs




Name of routine: logccs 

Source lines: 49753 - 49956

Type subroutine

Call logccs(nstrata, nobs, nv, nv1, ivar, nca, nct, z,  b, cov, chi2, st, ifault, plevel)
ModuleNone

Notes
 AS162 - Conditional logistic regression. Converted to Fortran 95






twidl




Name of routine: twidl 

Source lines: 49961 - 50008

Type subroutine

Call twidl(x, y, z, done, p, n2)
ModuleNone

Notes
 this generates all combinations of m out of n.
 CACM algorithm 382






tojulian




Name of routine: tojulian 

Source lines: 50017 - 50031

Type function

Call tojulian(gdate)
ModuleNone

Notes
  
 Julian and Gregorian from Peter Meyer's on-line notes:
 In 1968 in a letter to the editor of Communications of the ACM (CACM,
 volume 11, number 10, October 1968, p.657) Henry F. Fliegel and Thomas
 C. Van Flandern presented such conversion algorithms:
  
 gdate takes the form YYYYMMDD
  





togreg




Name of routine: togreg 

Source lines: 50035 - 50054

Type function

Call togreg(jdate)
ModuleNone

Notes
 from Julian to Gregorian
  





getyear




Name of routine: getyear 

Source lines: 50058 - 50072

Type function

Call getyear(gdate)
ModuleNone

Notes
 Gregorian date as decimal year
 





segrat




Name of routine: segrat 

Source lines: 50076 - 50323

Type subroutine

Call segrat(locnam, trait, dataset)
ModuleNone

Notes
  
 Binary trait prevalences and recurrence risks.
  





twincon




Name of routine: twincon 

Source lines: 50327 - 50534

Type subroutine

Call twincon(locnam, trait, mztwin, gt, thresh, dataset, plevel)
ModuleNone

Notes
  
 Classical twin analysis: binary trait prevalences and recurrence risks
  





concest




Name of routine: concest 

Source lines: 50538 - 50562

Type subroutine

Call concest(group, concord, npairs, prev, con, locon, hicon)
ModuleNone

Notes
 Summary statistics for recurrence risk calculation






conchi




Name of routine: conchi 

Source lines: 50566 - 50582

Type subroutine

Call conchi(a, b, c, d, lrts)
ModuleNone

Notes
 LRTS for equality of 2x2






tarone




Name of routine: tarone 

Source lines: 50586 - 50676

Type subroutine

Call tarone(trait, dataset, plevel)
ModuleNone

Notes
 Test for extrabinomial variation






davie




Name of routine: davie 

Source lines: 50680 - 50795

Type subroutine

Call davie(loc1, trait, loc2, proband, dataset, plevel)
ModuleNone

Notes
  
  Segregation ratios using Davie 1976
  





davstat




Name of routine: davstat 

Source lines: 50799 - 50831

Type subroutine

Call davstat(typ, pos, sta, npro, trait, dataset, class, j, q, t, r)
ModuleNone

Notes
  
 Accumulate counts needed for Davie formula in current family
  





davwri




Name of routine: davwri 

Source lines: 50835 - 50864

Type subroutine

Call davwri(ped, currf, currm, pos, sta, npro, trait, dataset)
ModuleNone

Notes
  
 print prop affected per sibship
  





marseg




Name of routine: marseg 

Source lines: 50877 - 51023

Type subroutine

Call marseg(gene, locnam, typ, dataset, allele_buffer, plevel) 
ModuleNone

Notes
  
 Simple segregation tabulations for a codominant marker
 Phase the genotypes if requested

 So either
   Father Mother Child
   ng     ng     na*na

 or
   mating        Child
   ng*(ng+1)/2   ng






famimp




Name of routine: famimp 

Source lines: 51028 - 51252

Type subroutine

Call famimp(locnam, trait, dataset, plevel)
ModuleNone

Notes
 Simple family based imputation of age/yob/etc
 ego ~ midparent + sibs + spouses + offspring






famcor




Name of routine: famcor 

Source lines: 51256 - 51454

Type subroutine

Call famcor(locnam, trait, dataset, jdraw, iter, plevel)
ModuleNone

Notes
  
 Quantitative trait relatives means and covariances
  





fammeans




Name of routine: fammeans 

Source lines: 51459 - 51557

Type subroutine

Call fammeans(trait, dataset, nobserved, obs_indx, plevel)
ModuleNone

Notes
 Simple descriptive statistics for a quantitative trait
 sets up dataset%untyped






famcovar




Name of routine: famcovar 

Source lines: 51561 - 51762

Type subroutine

Call famcovar(trait, dataset, npairs, mu, cvar, cov)
ModuleNone

Notes
 Pairwise correlations






sibvar




Name of routine: sibvar 

Source lines: 51766 - 51890

Type subroutine

Call sibvar(trait, dataset, plevel)
ModuleNone

Notes
 Sibship variance tests






twincor




Name of routine: twincor 

Source lines: 51894 - 52102

Type subroutine

Call twincor(locnam, trait, mztwin, gt, thresh, dataset, plevel)
ModuleNone

Notes
 Classical twin analysis contrasting monozygotic twins v. other siblings.






corr




Name of routine: corr 

Source lines: 52112 - 52134

Type subroutine

Call corr(typ, x1, x2, nclass, npairs, mean, var, cov)
ModuleNone

Notes
  
 update means and sums of squares and products
  
 1=Marital 2=Grandparent-Grandchild 3=Half-sib
 4=Parent-Offspring 5=Full-sib 6=MZ-Twin
 7=father-son 8=father-daugher 9=mother-son 10=mother-daughter
 11=brother 12=sister 13=brother-sister
 14=MZ-Males 15=MZ-Females
  





corrstd




Name of routine: corrstd 

Source lines: 52138 - 52154

Type subroutine

Call corrstd(nclass, npairs, var, cov)
ModuleNone

Notes
  
 cor to cov for classes
  





docov




Name of routine: docov 

Source lines: 52160 - 52259

Type subroutine

Call docov(typ, nterms, terms, loc, loctyp, locpos, dataset)
ModuleNone

Notes
  
 Means and covariances for multiple trait
 typ=1 means and covariances
     2 plus PCA
  





domix




Name of routine: domix 

Source lines: 52263 - 52367

Type subroutine

Call domix(locnam, trait, nmix, typ, histcat, outfil, dataset,  logl, df, nwid, ndec, plevel)
ModuleNone

Notes
 Fit mixture of distributions to quantitative trait






mixture




Name of routine: mixture 

Source lines: 52372 - 52547

Type subroutine

Call mixture(a, k, m, x, n, alpha, mean, sd, f, g, nobs, logl, ifail, plevel)
ModuleNone

Notes
 Fit mixture of distributions
 Algorithm AS 203 (Appl Stat 1984; 33:327-332)






regress




Name of routine: regress 

Source lines: 52551 - 52870

Type subroutine

Call regress(typ, nterms, terms, loc, loctyp, locpos,     gene, genemod, allele_buffer, dataset, mlik, mpar, plevel)
ModuleNone

Notes
  
 linear regression analysis of quantitative trait
  





binreg




Name of routine: binreg 

Source lines: 52875 - 53397

Type subroutine

Call binreg(ilink, nterms, terms, loc, loctyp, locpos,     offset, censor, gene, genemod, allele_buffer,  mcp, useimp, fixshape, iter, mincnt,  dataset, wshap, mlik, mpar, statval, pval, plevel)
ModuleNone

Notes
  
 Binomial (ilink=2), Poisson (ilink=3),
 Weibull (ilink=4), Exponential (ilink=5), EVD (ilink=6) regression analysis
  





fitbin




Name of routine: fitbin 

Source lines: 53401 - 53447

Type subroutine

Call fitbin(ilink, nobs, nter, ncov,  it, x2, r, b, y, v, offval, x, shap, ierr, plevel)
ModuleNone

Notes
  
 Perform binomial (ilink=2) or poisson (ilink=3) regression IRLS,
  





binirls




Name of routine: binirls 

Source lines: 53451 - 53523

Type subroutine

Call binirls(ilink, nobs, nter, nel, x2,  r, b, y, v, offval, x, shap, ierr, plevel)
ModuleNone

Notes
  
 One iteration of IRLS for binomial or poisson regression
  





glmscale




Name of routine: glmscale 

Source lines: 53527 - 53563

Type subroutine

Call glmscale(ilink, nobs, nter, b, y, offval, x, shap, scaleval)
ModuleNone

Notes
  
 Scale parameter for GLM
  





weishape




Name of routine: weishape 

Source lines: 53568 - 53601

Type subroutine

Call weishape(nobs, naff, nter, b, y, offval, x, alpha, alpha2)
ModuleNone

Notes
  
 Estimate shape for Weibull distribution
 Use relaxation methods and hard limit on step size
  





rcp




Name of routine: rcp 

Source lines: 53605 - 53634

Type subroutine

Call rcp(nr, nc, iter)
ModuleNone

Notes
  
 Simulation P for RxC contingency table
  





rctest




Name of routine: rctest 

Source lines: 53638 - 53744

Type subroutine

Call rctest(nr, nc, tble, e, iter)
ModuleNone

Notes
  
 LRTS and Permutation P for RxC contingency table
  





simchi




Name of routine: simchi 

Source lines: 53748 - 53816

Type subroutine

Call simchi(nr, rows, nc, cols, tble, e, obschi, tot, iter, pval)
ModuleNone

Notes
  
 MCMC a RxC contingency table retaining given margins
  





upchi




Name of routine: upchi 

Source lines: 53820 - 53836

Type subroutine

Call upchi(ncells, tble, e, lrts)
ModuleNone

Notes
  
 LRTS for contingency table in MCMC
  





rclrts




Name of routine: rclrts 

Source lines: 53840 - 53886

Type subroutine

Call rclrts(nr, nc, tble, e, lrts, df)
ModuleNone

Notes
 Contingency table LRTS






mkchoose




Name of routine: mkchoose 

Source lines: 53890 - 53902

Type subroutine

Call mkchoose(ni, eligible , nelig)
ModuleNone

Notes
  
 Load an array with indices of eligible choices (eg nonmissing alleles)
  





choose




Name of routine: choose 

Source lines: 53907 - 53919

Type subroutine

Call choose(nch, ni, idx)
ModuleNone

Notes
  
 Shuffle array of indices so can randomly select combination from
 as first r elements
  





uniqid




Name of routine: uniqid 

Source lines: 53923 - 53968

Type subroutine

Call uniqid(typ, dataset, plevel)
ModuleNone

Notes
 Make every individual and pedigree ID a unique number






prunep




Name of routine: prunep 

Source lines: 53972 - 54146

Type subroutine

Call prunep(wrk, wrk2, locnam, trait, gt, thresh, dataset, plevel)
ModuleNone

Notes
  
 Prune pedigree to ancestors shared by affecteds
  





relations




Name of routine: relations 

Source lines: 54150 - 54282

Type subroutine

Call relations(tped, tid, dataset, loc, loctyp, plevel)
ModuleNone

Notes
  
 Write relatives of index






prrel




Name of routine: prrel 

Source lines: 54286 - 54318

Type subroutine

Call prrel(iclass, ped, dataset, key, eop, loc, loctyp)
ModuleNone

Notes
 print list of relatives






appval




Name of routine: appval 

Source lines: 54322 - 54366

Type subroutine

Call appval(idx, loc, loctyp, dataset)
ModuleNone

Notes
 append locus value if asked






pairlink




Name of routine: pairlink 

Source lines: 54370 - 54482

Type subroutine

Call pairlink(ped, idx, dataset, plevel)
ModuleNone

Notes
 Show relationship of all pairs to ego: Djikstra's shortest path algorithm






conlen




Name of routine: conlen 

Source lines: 54486 - 54502

Type function

Call conlen(i, j, ped, dataset)
ModuleNone

Notes
 Are i and j a parent-offspring pair?






findloop




Name of routine: findloop 

Source lines: 54518 - 54724

Type subroutine

Call findloop(trait, dataset, plevel)
ModuleNone

Notes
 Find loops

 Marriage node representation
 Traverses depth-first with backtracking
 Trades time for space ;)

 Data structure:
 nodal backlink typelink

 nodal is the list of vertices 1..maxact are   individuals with edge to mating
                               maxact+1... are matings with edges to parents
 backlink contains the "thread" or point stack, and also the mark (negative)
 typelink shows direction of edge  






wricas




Name of routine: wricas 

Source lines: 54728 - 54811

Type subroutine

Call wricas(wrk, wrk2, trait, dataset)
ModuleNone

Notes
 extract unrelated individuals with information for a criterion trait






nuclear




Name of routine: nuclear 

Source lines: 54815 - 54876

Type subroutine

Call nuclear(wrk, wrk2, typ, maxsibs, dataset)
ModuleNone

Notes
 convert into nuclear families, duplicating individuals as needed






onefam




Name of routine: onefam 

Source lines: 54880 - 55009

Type subroutine

Call onefam(wrk, wrk2, typ, maxsibs, ped, dataset,  nuc, newoffset, currf, currm, sta, fin)
ModuleNone

Notes
 Write out current nuclear family -- with or without grandparents






disjoin




Name of routine: disjoin 

Source lines: 55015 - 55132

Type subroutine

Call disjoin(wrk, wrk2, dataset, plevel)
ModuleNone

Notes
 chop into disjoint subpedigrees
 note that the pointers in set(,2) do not follow the sort order of
 the pedigree, as connect() moves both up and down the generations






joinped




Name of routine: joinped 

Source lines: 55136 - 55453

Type subroutine

Call joinped(wrk, wrk2, typ, farg, larg, words,  nloci, loc, locpos, loctyp, locnotes,  dataset, chek, droperr, plevel)
ModuleNone

Notes
 join families together by duplicated individuals






pedsort




Name of routine: pedsort 

Source lines: 55457 - 55573

Type subroutine

Call pedsort(ped, dataset, nerr, plevel)
ModuleNone

Notes
 Sort a pedigree in a dataset






doanova




Name of routine: doanova 

Source lines: 55577 - 55927

Type subroutine

Call doanova(trait, locnam, gene, genetyp, iter, mincnt, norder, assfnd, conibd, dataset, freqfnd, use_fixfreq,  fixfreq_buffer, allele_buffer2, pval, plevel, typ)
ModuleNone

Notes
  
 Additive allelic model for association with a quantitative trait
  





qtdt




Name of routine: qtdt 

Source lines: 55933 - 56315

Type subroutine

Call qtdt(trait, locnam, gene, genetyp, freqfnd, iter, mincnt, use2, typ,  dataset, pval, plevel) 
ModuleNone

Notes
  
 Quantitative trait TDT following Gauderman 2003 25(4): 327-338

 E(Y_i) = a_MTi + beta Z(G_i)
  





cpganova




Name of routine: cpganova 

Source lines: 56320 - 56546

Type subroutine

Call cpganova(trait, locnam, gene, genetyp, iter, mincnt,  freqfnd, dataset, plevel) 
ModuleNone

Notes
  
 Additive allelic model for association with a quantitative trait
 Conditional on parental genotypes
  





haploid_count




Name of routine: haploid_count 

Source lines: 56552 - 56585

Type subroutine

Call haploid_count(nloc, loclist, loc, locpos, loctyp, dataset,  haplotable)
ModuleNone

Notes
 MC approach to association to haploid markers

 Enumerate haplotypes for haploid SNPs






set_hval




Name of routine: set_hval 

Source lines: 56589 - 56626

Type subroutine

Call set_hval(nloc, loclist, loc, locpos, loctyp,  haplotable, hval, dataset, plevel)
ModuleNone

Notes
 encode observed haplotypes






fillin_yha




Name of routine: fillin_yha 

Source lines: 56630 - 56678

Type subroutine

Call fillin_yha(haplotable, hval, dataset, plevel)
ModuleNone

Notes
 fill in missing haplotypes and check for mutation/error






fillin_mit




Name of routine: fillin_mit 

Source lines: 56682 - 56726

Type subroutine

Call fillin_mit(haplotable, hval, dataset, plevel)
ModuleNone

Notes
 Mitochondrial






haploid_freq




Name of routine: haploid_freq 

Source lines: 56730 - 56918

Type subroutine

Call haploid_freq(nloc, loclist, loc, locpos, loctyp,  dataset, plevel, typ)
ModuleNone

Notes
  
 Count of haplotypes from haploid markers
  





haploid_aov




Name of routine: haploid_aov 

Source lines: 56922 - 57226

Type subroutine

Call haploid_aov(trait, nloc, loclist, loc, locpos, loctyp,  iter, mincnt, dataset, pval, plevel, typ)
ModuleNone

Notes
 MC approach to association to haploid markers






haploid_ass




Name of routine: haploid_ass 

Source lines: 57230 - 57606

Type subroutine

Call haploid_ass(trait, nloc, loclist, loc, locpos, loctyp,  locnotes, iter, mincnt, dataset, pval, plevel, typ)
ModuleNone

Notes
  
 Count of marker alleles/genotypes in cases and controls -- haploid marker(s)
  





doassoc




Name of routine: doassoc 

Source lines: 57610 - 58348

Type subroutine

Call doassoc(trait, loctyp, locnotes, locnam, gene, genetyp,  iter, mincnt, norder, assfnd, gt, thresh, conibd, dataset,  freqfnd, use_fixfreq, fixfreq_buffer, allele_buffer2,  prevalence, pval, plevel, typ)
ModuleNone

Notes
  
 Count of marker alleles/genotypes in cases and controls -- codominant system
  





twobyk




Name of routine: twobyk 

Source lines: 58352 - 58373

Type function

Call twobyk(sta, fin, cntall, pexp)
ModuleNone

Notes
  
 Pearson chi-sq for 2xK table (uses only cntall(,1-3))
  





pearson




Name of routine: pearson 

Source lines: 58378 - 58405

Type function

Call pearson(sta, fin, nlev, nca, cntall)
ModuleNone

Notes
  
 Pearson chi-sq for slice of RxC table 
 (uses cntall(,1:traitlevels+1), nca(1:traitlevels))
  





rctdt




Name of routine: rctdt 

Source lines: 58418 - 58795

Type subroutine

Call rctdt(trait, locnam, gene, genetyp, iter, mincnt, gt, thresh, fbatimp, freqfnd, dataset, plevel)
ModuleNone

Notes
  
 perform sibship association permutation test
  
 Combines TDT with SDT: appropriate permutation set for each sibship
  
 If both parents genotyped, then each child can be drawn from 13,14,23,24
 If one or no parents genotyped, but may be reconstructed, then draw
 from mixture of obligate genotypes (those usable to reconstruct the missing
 parents) and 13,14,23,24.
 If cannot unequivocally reconstruct parental genotypes
 draw only from obligate (observed) genotypes among children
  





parimp




Name of routine: parimp 

Source lines: 58799 - 58917

Type subroutine

Call parimp(pg1, pg2, mg1, mg2, sta, fin, set, parall)
ModuleNone

Notes
  
 Make list of possible parental genotypes for this sibship
  





rctperm




Name of routine: rctperm 

Source lines: 58929 - 59015

Type subroutine

Call rctperm(ifam, sibships, set)
ModuleNone

Notes
  
 Simulate the null distribution of sibship genotypes
 Parental alleles imputed via the children must be transmitted
 at least once to that sibship
 Furthermore, if two imputed alleles are the same in the two parents,
 then these must be transmitted together to at least one child
 And (Jun 2008), if only A/A and A/B segregating in sibship, 
 need to also condition on total number of each type of
 genotype in sibship for -/- x -/- and A/B x -/- matings
 (sticking point is A/B x A/B possibility)
  





ranall




Name of routine: ranall 

Source lines: 59019 - 59032

Type function

Call ranall(par)
ModuleNone

Notes
  
 Randomly transmit nonmissing alleles
  





conoff




Name of routine: conoff 

Source lines: 59037 - 59050

Type subroutine

Call conoff(tr, par, imputd, off)
ModuleNone

Notes
  
 Conditional parent-offspring transmission
 Flag whether an imputed parental allele is transmitted
  





rctsim




Name of routine: rctsim 

Source lines: 59054 - 59083

Type subroutine

Call rctsim(nfam, sibships, aff, set, numal, trans)
ModuleNone

Notes
  
 One simulation of entire set of informative nuclear families
  





rctuse




Name of routine: rctuse 

Source lines: 59087 - 59137

Type function

Call rctuse(pg1, pg2, mg1, mg2, ptyped, parall, contrib, naff)
ModuleNone

Notes
  
 test if useful for RC-TDT/FBAT
  





sibass




Name of routine: sibass 

Source lines: 59142 - 59309

Type subroutine

Call sibass(trait, locnam, gene, allele_buffer, dataset, iter,  typ, pval, plevel)
ModuleNone

Notes
 Tabulate sibship affection by genotype for fast test of total
 association






whitehead




Name of routine: whitehead 

Source lines: 59313 - 59539

Type subroutine

Call whitehead(trait, locnam, gt, thresh, gene, allele_buffer,  stratvar, strattyp, stratlabels,  dataset, pval, plevel)
ModuleNone

Notes
 Random effects stratified proportional odds model of Whitehead and Whitehead






simped




Name of routine: simped 

Source lines: 59544 - 59606

Type subroutine

Call simped(ped, dataset, allele_buffer, set)
ModuleNone

Notes
  
  Simulate (gene-dropping) genotypes at a single autosomal locus
  in a pedigree of arbitrary complexity
  





xsimped




Name of routine: xsimped 

Source lines: 59611 - 59684

Type subroutine

Call xsimped(ped, dataset, allele_buffer, set)
ModuleNone

Notes
  
  Simulate (gene-dropping) genotypes at a single X-linked locus
  in a pedigree of arbitrary complexity
  





csimped




Name of routine: csimped 

Source lines: 59691 - 59754

Type subroutine

Call csimped(ped, dataset, set, xlinkd)
ModuleNone

Notes
  
 Simulate (gene-dropping) genotypes at a single codominant locus
 Conditioning on typed ``founder'' genotypes (true founders/marry-ins
 plus individuals without typed parents) heading informative
 chains of descent
  





genoff




Name of routine: genoff 

Source lines: 59758 - 59784

Type subroutine

Call genoff(idx, fa, mo, set)
ModuleNone

Notes
  
 transmit genes from parents to child
  





mumson




Name of routine: mumson 

Source lines: 59788 - 59800

Type subroutine

Call mumson(idx, mo, set)
ModuleNone

Notes
  
 Transmit single X-linked allele from mother to son
  





gencopy




Name of routine: gencopy 

Source lines: 59804 - 59809

Type subroutine

Call gencopy(idx, origin, set)
ModuleNone

Notes
 Copy genotype from MZ cotwin to ego






simhaploid




Name of routine: simhaploid 

Source lines: 59813 - 59841

Type subroutine

Call simhaploid(typ, ped, dataset, nhaps, cumhaps, hval)
ModuleNone

Notes
  
 Simulate Y or mitochondrial haplotypes 
  





fsimped




Name of routine: fsimped 

Source lines: 59846 - 59973

Type subroutine

Call fsimped(it, pedigree, num, nfound, id, fa, mo, imztwin, set, sibd,   untyped, key, plevel)
ModuleNone

Notes
  
 Simulate pedigree conditional on all founders (all must be typed) and
 typed nonfounders
  





genof4




Name of routine: genof4 

Source lines: 59980 - 60065

Type subroutine

Call genof4(idx, fa, mo, imztwin, set, sibd, untyped, key, failid)
ModuleNone

Notes
  
  Drop ibd-alleles conditional on observed markers
  and randomly where marker genotype not observed -- restart
  if later generates inconsistency
  This version assumes all founders are typed
  





fill2




Name of routine: fill2 

Source lines: 60070 - 60095

Type subroutine

Call fill2(num, set, sibd, untyped, key)
ModuleNone

Notes
  
 infer missing genotypes based on sibd values after run of fsimped
 assume all founders are typed
  





cisimped




Name of routine: cisimped 

Source lines: 60100 - 60150

Type subroutine

Call cisimped(ped, gene, allele_buffer, allele_buffer2, dataset, set)
ModuleNone

Notes
 Simulate a single marker consistent with ibd sharing at a target marker locus
 If there are missing genotypes, call should be preceded by call to newstart()






sample




Name of routine: sample 

Source lines: 60154 - 60209

Type subroutine

Call sample(trait, ped, dataset, typ)
ModuleNone

Notes
 Sample with or without replacement from the trait values within an entire pedigree
 





drop




Name of routine: drop 

Source lines: 60229 - 60454

Type subroutine

Call drop(it, ped, dataset, cntmat, numal, gfrq,  set, sibd, set2, key, iprop, plevel)
ModuleNone

Notes
 Modified random walk simulation (one iteration) of pedigree missing
 genotypes (Metropolis-Hastings algorithm) -- proposal uses founder
 allele mutations propagated throughout then pedigree conditional
 on (identity by) descent, swapping ibd origins for heterozygotes,
 alternated with a randomization of descent conditional on marker
 genotype. This procedure has the advantage of being quick,
 but the proposal probabilities are not always symmetric, so they
 are combined with additional local proposals
  
 It is alternated with a locally updating Gibbs sampler. This jointly
 simulates Untyped x Untyped founder matings genotypes conditional on
 offspring and other spouses; other genotypes individual-by-individual,
 conditional on parental, spouse and child genotypes.
  
 set and sibd (set2 and sibd2) are genotypes for current pedigree only
 only fa and mo need to be redirected







simnuc




Name of routine: simnuc 

Source lines: 60463 - 60535

Type subroutine

Call simnuc(par1, par2, num, nfound, fa, mo, numal, gfrq, set)
ModuleNone

Notes
  
  Gibbs sampler for codominant marker locus
  Simulate parental genotypes for untyped x untyped
  mating conditional on offspring genotypes
  or for untyped nonfounders conditional on offspring, spouses
  and parents. Family may be contained within larger pedigree, and
  multiple spouses are possible
  





nuclik




Name of routine: nuclik 

Source lines: 60541 - 60605

Type subroutine

Call nuclik(par1, par2, sta, fin, fa, mo, numal, gfrq, set, targt)
ModuleNone

Notes
  
 Nuclik is run twice, once to calculate the total likelihood <totlik> of the
 legal genotypes (with target=1), the second time to select a
 parental genotypes with target ~ U(0,totlik).
  





foulik




Name of routine: foulik 

Source lines: 60612 - 60659

Type subroutine

Call foulik(idx, fa, mo, sta, fin, numal, gfrq, set, targt)
ModuleNone

Notes
  
 Founder codominant locus conditional likelihood
 foulik is run twice, once to calculate the total likelihood <totlik> of the
 legal genotypes (with target=1), the second time to select a genotype,
 with target ~ U(0,totlik).
  





onelik




Name of routine: onelik 

Source lines: 60666 - 60710

Type subroutine

Call onelik(idx, fa, mo, sta, fin, set, targt)
ModuleNone

Notes
  
 nonfounder codominant locus conditional likelihood
 onelik is run twice, once to calculate the total likelihood <totlik> of the
 legal genotypes (with target=1), the second time to select a genotype,
 with target ~ U(0,totlik).
  





simpar




Name of routine: simpar 

Source lines: 60717 - 60759

Type subroutine

Call simpar(par1, par2, numal, num, nfound, fa, mo, set)
ModuleNone

Notes
  
  Propose parental genotypes for untyped x untyped
  mating conditional on offspring genotypes
  Family may be contained within larger pedigree, and
  multiple spouses are possible
  





inuclik




Name of routine: inuclik 

Source lines: 60766 - 60811

Type subroutine

Call inuclik(par1, par2, sta, fin, numal, fa, mo, set, targt, totp)
ModuleNone

Notes
  
 inuclik is an integer version of nuclik
 inuclik is run twice, once to calculate the total number <totp> of the
 legal genotypes (with target=MAXG*MAXG), the second time to select a
 parental genotype.
  





mutate




Name of routine: mutate 

Source lines: 60818 - 60861

Type subroutine

Call mutate(numal, num, nfound, set, sibd, set2, untyped)
ModuleNone

Notes
  
 Mutate 1-4 allele in untyped founders.  Can never fail, due "backmutation".
  
 (1) mutate an allele never transmitted to a typed individual
 (2) swap parent of origin if have no offspring sharing ibd-allele
  





switch




Name of routine: switch 

Source lines: 60865 - 60984

Type subroutine

Call switch(num, nfound, id, fa, mo, set, sibd, set2, untyped)
ModuleNone

Notes
  
 Do a switch of grandparent of origin of alleles = switch lineage
  





cpibd




Name of routine: cpibd 

Source lines: 60991 - 61011

Type subroutine

Call cpibd(i, j, sibd, sibd2, imiss)
ModuleNone

Notes
  
 Copy ibd for a pair of relatives.
 Person j has a typing-genotype at sibd2, person i does not.
 The typing-allele corresponding to that shared at sibd()
 is "transmitted" to person i from person j.
  





update




Name of routine: update 

Source lines: 61015 - 61028

Type subroutine

Call update(idx, all1, all2, set)
ModuleNone

Notes
  
 update new genotype
  





simibd




Name of routine: simibd 

Source lines: 61035 - 61122

Type subroutine

Call simibd(typ, pedigree, num, nfound, fa, mo, imztwin, set, sibd)
ModuleNone

Notes
  
  Given genotypes at a single locus in a pedigree of arbitrary complexity,
  generate ibd by gene dropping a perfectly informative marker a la
  John Blangero.
  Type=1 unconditional, =2, conditional on observed markers
  





genof2




Name of routine: genof2 

Source lines: 61130 - 61190

Type subroutine

Call genof2(pedigree, idx, fa, mo, imztwin, set, sibd, ifault)
ModuleNone

Notes
  
 transmit ibd-marker from parents to child,
 test if consistent with observed marker
 In this version 12/99, the sibd pairs are ordered by the collating
 order of the marker alleles they represent and
 not the collating order of the sibd allele.
  





wrhbd




Name of routine: wrhbd 

Source lines: 61194 - 61419

Type subroutine

Call wrhbd(gene, trait, iter, burnin, allele_buffer, dataset, plevel)
ModuleNone

Notes
 Monte-Carlo approach to estimating one-locus homozygosity by descent






mcgpe




Name of routine: mcgpe 

Source lines: 61423 - 61643

Type subroutine

Call mcgpe(gene, trait, iter, burnin, allele_buffer, dataset, plevel)
ModuleNone

Notes
  
 MCMC for genotype probability estimates and allele doses
  





mcfreq




Name of routine: mcfreq 

Source lines: 61647 - 61858

Type subroutine

Call mcfreq(gene, iter, emiter, dataset, allele_buffer, plevel)
ModuleNone

Notes
  
 MCEM for pedigree allele frequencies
  





newstart




Name of routine: newstart 

Source lines: 61862 - 62014

Type subroutine

Call newstart(gene, allele_buffer, dataset, plevel)
ModuleNone

Notes
 Call drop to shuffle the unobserved genotypes






cntprop




Name of routine: cntprop 

Source lines: 62018 - 62026

Type subroutine

Call cntprop(iprop, proprate, proptyp)
ModuleNone

Notes
  
 Increment counts of MCMC proposal type
  





wrprop




Name of routine: wrprop 

Source lines: 62030 - 62045

Type subroutine

Call wrprop(ilabel, proprate, proptyp)
ModuleNone

Notes
  
 Summary of MCMC proposals from drop()
  





tabmat




Name of routine: tabmat 

Source lines: 62049 - 62066

Type subroutine

Call tabmat(ped, dataset, cntmat)
ModuleNone

Notes
  
 count the untyped founder x founder matings for use by Metropolis algs
  





nucseg




Name of routine: nucseg 

Source lines: 62088 - 62325

Type subroutine

Call nucseg(trait, locnam, gene, genetyp, freqfnd,  spec_candal, dataset, pval, plevel)
ModuleNone

Notes
  
 Approach of Schaid and Sommer (1993), amplified by Knapp et al (1995)
  
 MM x MM   MM x MN   MM x NN   MN x MN    MN x NN    NN x NN
   MM      MM   MN     MN      MM MN NN   MN   NN      NN
   n1      n2   n3     n4      n5 n6 n7   n8   n9      n10
  
 a=4*n1 + 3*n2 + 3*n3 + 2*n4 + 2*n5 + 2*n6 + 2*n7 + n8 + n9
 b=n2 + n3 + 2*n4 + 2*n5 + 2*n6 + 2*n7 + 3*n8 + 3*n9 + 4*n10
 c=n1 + n2 + n5
 d=n3 + n4 + n6 + n8
  
 providing n-c-d!=0 and a-2c-d!=0 then
  
 p=(a-2*c-d)/2n
 r1= (1-p)*d/(2*p*(n-c-d))
 r2= (1-p)^2 c/(p^2*(n-c-d))
  
 Here, actually done as the log-linear model, as the closed form
 standard error formulae are ugly
  





dohomoz




Name of routine: dohomoz 

Source lines: 62329 - 62528

Type subroutine

Call dohomoz(trait, locnam, gene, genetyp, freqfnd, iter, mincnt, norder,  gt, thresh, dataset, pval, plevel)
ModuleNone

Notes
  
 marker homozygosity in all subjects or just probands -- codominant system
  





sibpair




Name of routine: sibpair 

Source lines: 62541 - 63116

Type subroutine

Call sibpair(tranam, trait, locnam, gene, mappos, typ,  sibm, sibr, sibv, mcp, iter, mincnt, weight,  dataset, allele_buffer, pval, plevel)
ModuleNone

Notes
  
 perform Haseman-Elston sib-pair regression: univariate
 using squared difference or centred cross-product
 and ibds estimated from the entire sibship
 if missing parental genotypes
  
 typ
  1   Original Haseman-Elston
  2   Haseman-Elston II
  3   Sham and Purcell
  4   Visscher and Hopper
  





sibcor




Name of routine: sibcor 

Source lines: 63120 - 63224

Type subroutine

Call sibcor(trait, typ, dataset, muy, vay, rf, rh, npairs, bigship, plevel)
ModuleNone

Notes
  
 Estimate sibling and half-sib intraclass correlations
  





nucibd




Name of routine: nucibd 

Source lines: 63236 - 63435

Type subroutine

Call nucibd(gene, setoffset, fa, mo, sta, fin, set, untyped, allele_buffer, ibd)
ModuleNone

Notes
  
 Routines to calculate ibd sharing using full sibship information
 where parent(s) untyped.
  
 ibd(1..nsib*(nsib+1)/2)
 prall(5) probs for 1..4 observed alleles plus all others
  
 1. enumerate alleles segregating among children
 2. generate short list of genotypes for parents
 3. sum up ibd sharing for each pair of sibs for each genotype freq
  





shibd




Name of routine: shibd 

Source lines: 63439 - 63490

Type function

Call shibd(c11, c12, c21, c22, p11, p12, p21, p22)
ModuleNone

Notes
  
 Calculate ibd sharing for full sibs when parental genotypes known
  





regwt




Name of routine: regwt 

Source lines: 63494 - 63509

Type function

Call regwt(weight, i, j, dataset)
ModuleNone

Notes
  
 Calculate regression weight
  





hibd




Name of routine: hibd 

Source lines: 63514 - 63572

Type function

Call hibd(c11, c12, c21, c22, p11, p12, pc1, pc2, p21, p22)
ModuleNone

Notes
  
 estimate ibd score for a pair of half-sibs -- parents known
 tabulations of number of genes expected shared ibd
  





twopoi




Name of routine: twopoi 

Source lines: 63581 - 63713

Type subroutine

Call twopoi(mark1, loc1, mark2, loc2,  allele_buffer1, allele_buffer2, dataset, plevel)
ModuleNone

Notes
  
 perform Elston & Keats sib pair linkage analysis
 between two codominant markers
  
 recombination fraction c= 0.5 (1-sqrt(r))
 where r is the correlation between mean ibd at marker1 and mean ibd at
 marker2 for all sib pairings
  





countall




Name of routine: countall 

Source lines: 63717 - 63748

Type subroutine

Call countall(p1, p2, p3, p4, nallele, nmiss)
ModuleNone

Notes
  
 Count alleles in pair of relatives or spouses
  





doasp




Name of routine: doasp 

Source lines: 63752 - 63991

Type subroutine

Call doasp(trait, locnam, gene, gt, thresh,  allele_buffer, dataset, pval, plevel)
ModuleNone

Notes
 Do ibs sharing ASP analysis as per Lange 1986 and Bishop 1990






sshare




Name of routine: sshare 

Source lines: 63995 - 64006

Type subroutine

Call sshare(g1, g2, g3, g4, zibs)
ModuleNone

Notes
  
 Return IBS sharing for relative pair 
  





dopenrose




Name of routine: dopenrose 

Source lines: 64010 - 64132

Type subroutine

Call dopenrose(loc1, trait, typ1, loc2, gene, typ2, dataset, iter, plevel)
ModuleNone

Notes
 Penrose sib pair linkage analysis






shipsiz




Name of routine: shipsiz 

Source lines: 64136 - 64163

Type subroutine

Call shipsiz(dataset, bigship)
ModuleNone

Notes
  
 Find biggest active sibship
  





doapm




Name of routine: doapm 

Source lines: 64167 - 64752

Type subroutine

Call doapm(trait, locnam, gene, typ, iter, burnin, gt, thresh,  dataset, allele_buffer, pvalout, plevel)
ModuleNone

Notes
  
 Perform Monte-Carlo based APM analysis
  





loadset




Name of routine: loadset 

Source lines: 64756 - 64800

Type subroutine

Call loadset(gene, ped, allele_buffer, dataset, set, nuntyp)
ModuleNone

Notes
 Copy genotypes from pedigree to set






pedibd




Name of routine: pedibd 

Source lines: 64804 - 64833

Type subroutine

Call pedibd(typ, ped, dataset, set, sibd)
ModuleNone

Notes
 Pedigree structure type call to simibd






makewt




Name of routine: makewt 

Source lines: 64839 - 64857

Type function

Call makewt(typ, naff, unaff, var)
ModuleNone

Notes
  
 Calculate some plausible weights to allow combination of APM statistics
 from different pedigrees
 type=1 pair=AA, 2 AU, 3 UU, 4 GPM, 5 W-H
  





clcibs




Name of routine: clcibs 

Source lines: 64861 - 64973

Type subroutine

Call clcibs(naff, unaff, aff, allele_buffer, set, z)
ModuleNone

Notes
  
 Calculate ibs statistic
  





delta




Name of routine: delta 

Source lines: 64977 - 64982

Type function

Call delta(g1,g2)
ModuleNone

Notes
  
 measure of IBS sharing
  





clcibd




Name of routine: clcibd 

Source lines: 64986 - 65050

Type subroutine

Call clcibd(naff, unaff, aff, sibd, zibd)
ModuleNone

Notes
  
 calculate ibd sharing statistic based on simulated ibd
  





share




Name of routine: share 

Source lines: 65054 - 65068

Type subroutine

Call share(g1, g2, g3, g4, zibd)
ModuleNone

Notes
  
 Return IBD sharing for relative pair based on ibd-alleles
  





simil




Name of routine: simil 

Source lines: 65090 - 65151

Type function

Call simil(nfound, naff, aff, sibd, key)
ModuleNone

Notes
  
 Whittemore's & Halpern's (Biometrics 1994; 50:118-127) measure
 of ibd sharing for multiple relatives
  
 for a set of N individuals, enumerate 2**N vectors containing
 one ibd-allele from each person.  For each such set u_i, calculate
 a measure of overall similarity as the number of [additional] "nontrivial"
 permutations of that set that leave u unchanged.  For example, if
 3 individuals are {1/2} {1/3} {1/2}, there are 8 u's, which give a total
 abc  Legal permutations (excl obs)   of 10 possible permutations, with
 111  5    acb, bac, bca, cab, cba    a mean of 10/8.  If a 4th relative
 112  1    bac                        was ibd-genotype {4/5}, the mean
 131  1    cba                        would be 10/16.  The mean score (S)
 132  0                               is used to derive a standardized
 211  1    acb                        score [S-E(S)]/SD(S), as in the APM
 212  1    cba                        method, although direct enumeration
 231  0                               is of course feasible for small N.
 232  1    cba
  
 Randomized version
  





clreg




Name of routine: clreg 

Source lines: 65156 - 65447

Type subroutine

Call clreg(typ, styp, nterms, terms, loc, loctyp, locpos,     gene, genemod, allele_buffer,  dataset, mlik, mpar, statval, pval, plevel)
ModuleNone

Notes
  
 Conditional logistic regression
 Stratum variable is either pedigree or sibship
  





getstrata




Name of routine: getstrata 

Source lines: 65451 - 65483

Type subroutine

Call getstrata(styp, ped, dataset, nstrata, strata)
ModuleNone

Notes
 Locate beginnings and ends of strata 






dohrr




Name of routine: dohrr 

Source lines: 65487 - 65808

Type subroutine

Call dohrr(trait, locnam, gene, iter, mincnt, gt, thresh, dataset, allele_buffer, pval, plevel)
ModuleNone

Notes
 Haplotype Relative Risk






dotdt




Name of routine: dotdt 

Source lines: 65812 - 66243

Type subroutine

Call dotdt(trait, locnam, gene, genetyp, freqfnd, iter, mincnt,  use2, typ, cutoff, gt, thresh, dataset, pval, plevel)
ModuleNone

Notes
 Monte-Carlo approach to various TDTs






tdtuse




Name of routine: tdtuse 

Source lines: 66247 - 66266

Type function

Call tdtuse(pg1, pg2, mg1, mg2, naff, use2, xlinkd)
ModuleNone

Notes
 test if useful for TDT






shuffle




Name of routine: shuffle 

Source lines: 66272 - 66333

Type subroutine

Call shuffle(nallele, cntall, tot, cutoff, tdt, mxiter, mincnt, pvalue)
ModuleNone

Notes
 randomization test for allelic TDT -- shuffle table ITER times
 using TOT swaps per shuffle
 Genotype counts: all1, all2, #all1 trans, #all2 trans






clctdt




Name of routine: clctdt 

Source lines: 66337 - 66356

Type function

Call clctdt(ngcount, gcount, cutoff)
ModuleNone

Notes
 calculate symmetry pearson chi-square






clcchi




Name of routine: clcchi 

Source lines: 66360 - 66381

Type function

Call clcchi(ngcount, gcount, cutoff)
ModuleNone

Notes
 calculate g.o.f. LR chi-square






trans




Name of routine: trans 

Source lines: 66386 - 66475

Type subroutine

Call trans(pg1, pg2, mg1, mg2, cg1, cg2, tr1, tr2, nt1, nt2, typ)
ModuleNone

Notes
 Test the 4 possible unions of gametes 1 2 3 4 -> 13 14 23 24
 if typ=0 return both parental contributions, else 2=pat, 1=mat






xtrans




Name of routine: xtrans 

Source lines: 66479 - 66499

Type subroutine

Call xtrans(mg1, mg2, cg1, cg2, tr1, tr2, nt1, nt2)
ModuleNone

Notes
 Transmission of X-linked marker to a male






incpo




Name of routine: incpo 

Source lines: 66503 - 66525

Type subroutine

Call incpo(tr, nt, nall, cntall)
ModuleNone

Notes
 Increment counts of transmitted and nontransmitted alleles: parentwise






incr




Name of routine: incr 

Source lines: 66530 - 66556

Type subroutine

Call incr(tr1, tr2, nt1, nt2, ngcount, gcount)
ModuleNone

Notes
 Increment counts of transmitted and expected genotypes
 Revised after reading Thomas 1999






insgen




Name of routine: insgen 

Source lines: 66561 - 66605

Type subroutine

Call insgen(a1, a2, ngcount, gcount, typ, haplo)
ModuleNone

Notes
 update counts of genotypes or haplotypes for cases or controls --
 binary search and insertion sort






ldp




Name of routine: ldp 

Source lines: 66609 - 66667

Type subroutine

Call ldp(numal, numal2, plevel)
ModuleNone

Notes
 Do LD analysis for unphased data






cubicld




Name of routine: cubicld 

Source lines: 66671 - 66841

Type subroutine

Call cubicld(loc1, loc2, typ, counts, pval, sumtyp, plevel)
ModuleNone

Notes
 Two SNPs, unphased and phased data






cubiclik




Name of routine: cubiclik 

Source lines: 66845 - 66915

Type subroutine

Call cubiclik(typ, nunph, nph, praw, counts, h1, h2, h3, h4, ex, lik, eh)
ModuleNone

Notes
 Likelihood for pairwise SNP LD table under given level of LD






ld2




Name of routine: ld2 

Source lines: 66919 - 67228

Type subroutine

Call ld2(loc1, numal, name1, loc2, numal2, name2, typ, ngcat, nhcat, nxcat, counts, pval, sumtyp, plevel)
ModuleNone

Notes
 Do LD analysis for unphased and phased data






haptogen




Name of routine: haptogen 

Source lines: 67232 - 67279

Type subroutine

Call haptogen(numal, numal2, scatter, typ, xlinkd)
ModuleNone

Notes
 Map haplotypes to genotypes 1=phase unknown 2=phase KNOWN






twohwe




Name of routine: twohwe 

Source lines: 67283 - 67335

Type subroutine

Call twohwe(numal, numal2, nfull, totpars, model, typ, xlinkd)
ModuleNone

Notes
 Double HWE






twofrq




Name of routine: twofrq 

Source lines: 67339 - 67413

Type subroutine

Call twofrq(numal, numal2, ncells, counts, typ, xlinkd)
ModuleNone

Notes
 Marginal allele frequencies two loci






ldtab




Name of routine: ldtab 

Source lines: 67417 - 67484

Type subroutine

Call ldtab(numal, numal2, counts, ex, typ, xlinkd)
ModuleNone

Notes
 Show table of genotypes and haplotypes






twold




Name of routine: twold 

Source lines: 67489 - 67823

Type subroutine

Call twold(zrec, maxhap, gene1, loc1, ltyp1, gene2, loc2, ltyp2, allele_buffer1, allele_buffer2, dataset, iter, pval,  sumtyp, plevel)
ModuleNone

Notes
 Two locus linkage disequilibrium: autosomal or X-linked loci
 identify typed founders or nonfounders who have untyped parents






inchap




Name of routine: inchap 

Source lines: 67828 - 67866

Type subroutine

Call inchap(g11, g12, g21, g22, ngcat, npg,  allele_buffer1, allele_buffer2, counts, typ)
ModuleNone

Notes
 increment count of phased or unphased genotype, haplotype
 contingency table is partitioned 1..ngcat...ngcat+npg...






tabhap




Name of routine: tabhap 

Source lines: 67870 - 67886

Type subroutine

Call tabhap(g1, g2, allele_buffer1, allele_buffer2, tble)
ModuleNone

Notes
 straight haplotype count






useld




Name of routine: useld 

Source lines: 67890 - 67914

Type function

Call useld(c1, c2, c3, c4, f1, f2, f3, f4, m1, m2, m3, m4)
ModuleNone

Notes
 Check if useful triad for haplotype inference






ldtest




Name of routine: ldtest 

Source lines: 67918 - 68035

Type subroutine

Call ldtest(loc1, allele_buffer1, loc2, allele_buffer2, tble,  iter, pval, plevel)
ModuleNone

Notes
  
 LRTS and Permutation P for haplotype table
  





compld




Name of routine: compld 

Source lines: 68039 - 68145

Type subroutine

Call compld(gene1, gene2, newgene, cutoff, allele_buffer1, allele_buffer2, dataset)
ModuleNone

Notes
 Infer haplotypes for SNPs in complete LD






moskvina




Name of routine: moskvina 

Source lines: 68150 - 68256

Type subroutine

Call moskvina(window, alpha, maxhap, nloci, loc, loctyp,  locpos, locord, map, dataset, plevel)
ModuleNone

Notes
 An improved correction for multiple testing
 Moskvina V, Schmidt KM (2008) Genet Epidemiol 32: 567-573






moskld




Name of routine: moskld 

Source lines: 68260 - 68285

Type subroutine

Call moskld(maxhap, loc1, loc2, loc, locpos, loctyp,  allele_buffer1, dataset, r)
ModuleNone

Notes
 wrapper for twold






stand




Name of routine: stand 

Source lines: 68290 - 68349

Type subroutine

Call stand(trait, dataset, typ)
ModuleNone

Notes
 Standardization of quantitative trait overall or *within* family
 as required by the approach of Commenge






lifetab




Name of routine: lifetab 

Source lines: 68352 - 68734

Type subroutine

Call lifetab(date1, date2, censor, covar, covtyp,  width1, width2, typ, dataset, plevel) 
ModuleNone

Notes






prodlim




Name of routine: prodlim 

Source lines: 68742 - 68872

Type subroutine

Call prodlim(trait, censor, dataset, typ, plevel)
ModuleNone

Notes
 Kaplan-Meier estimator of survival function and the Nelson-Aalen
 estimator of cumulative hazard.
 The Nelson-Aalen estimator is used to produce residuals, if requested.
 These are the deviance residuals of Therneau et al Biometrika 1990:
 equivalent to a variance-stabilized transformed martingale residual.






dorank




Name of routine: dorank 

Source lines: 68880 - 68953

Type subroutine

Call dorank(trget, trait, typ, dataset)
ModuleNone

Notes
 Rank trait values
 1=rank all
 2=within family rank
 3=Blom score all
 4=within family Blom score






wrsim




Name of routine: wrsim 

Source lines: 68958 - 69054

Type subroutine

Call wrsim(typ, mark, gene, allele_buffer, allele_buffer2, dataset, plevel)
ModuleNone

Notes
 Simulate a single marker, either unconditionally, or
 consistent with ibd sharing at a given locus






wrsimq




Name of routine: wrsimq 

Source lines: 69060 - 69171

Type subroutine

Call wrsimq(typ, trait, loctyp, prevalence, h2,  gene, allele_buffer, allele_buffer2, dataset, plevel)
ModuleNone

Notes
 Simulate a quantitative trait of given heritability,
 either unconditionally, or
 consistent with complete linkage to a given locus






wrsimqtl




Name of routine: wrsimqtl 

Source lines: 69176 - 69401

Type subroutine

Call wrsimqtl(trait, gene, smlfreq, smlpen, h2, dataset, plevel)
ModuleNone

Notes
 Simulate QTL genotypes conditional on binary trait values, heritability and 
 marginal QTL penetrances by rejection sampling 






permdata




Name of routine: permdata 

Source lines: 69405 - 69427

Type subroutine

Call permdata(trait, dataset)
ModuleNone

Notes
 Permute trait values within pedigrees






dateconv




Name of routine: dateconv 

Source lines: 69431 - 69488

Type subroutine

Call dateconv(locnam, trait, dataset, typ)
ModuleNone

Notes
 Convert to/from Julian etc






combine




Name of routine: combine 

Source lines: 69492 - 69518

Type subroutine

Call combine(crit, recto, nf, recfro, allele_buffer)
ModuleNone

Notes
 identify rare alleles at a marker locus and list for combination






swapalleles




Name of routine: swapalleles 

Source lines: 69522 - 69564

Type subroutine

Call swapalleles(loc, gene, allele_buffer, dataset)
ModuleNone

Notes
 swap diallelic marker alleles eg 1->2 2->1






ntcode




Name of routine: ntcode 

Source lines: 69568 - 69610

Type subroutine

Call ntcode(typ, gene, dataset)
ModuleNone

Notes
 recode SNP alleles to/from numerical coding A<->1 C<->2 G<->3 T<->4






flip




Name of routine: flip 

Source lines: 69614 - 69643

Type subroutine

Call flip(loc, gene, dataset)
ModuleNone

Notes
 flip alleles to complement eg other strand A<->T G<->C






atgc




Name of routine: atgc 

Source lines: 69647 - 69655

Type function

Call atgc(g)
ModuleNone

Notes
 complement nucleotide






nttonum




Name of routine: nttonum 

Source lines: 69659 - 69672

Type function

Call nttonum(g)
ModuleNone

Notes
 number code nucleotide






numtont




Name of routine: numtont 

Source lines: 69676 - 69684

Type function

Call numtont(g)
ModuleNone

Notes
 number code nucleotide






renumb




Name of routine: renumb 

Source lines: 69688 - 69741

Type subroutine

Call renumb(loc, gene, typ, allele_buffer, dataset)
ModuleNone

Notes
 renumber alleles to consecutive integers






recode




Name of routine: recode 

Source lines: 69746 - 69894

Type subroutine

Call recode(loc, gene, loctyp, nto, recto, nf, recfro, dataset, plevel) 
ModuleNone

Notes
 recode alleles or values for particular locus --
 replace all "from" values with "to" values






recast




Name of routine: recast 

Source lines: 69898 - 69955

Type subroutine

Call recast(typ, trait, dataset)
ModuleNone

Notes
 Recast aff or cat to qua or qua to aff or cat






snpenc




Name of routine: snpenc 

Source lines: 69959 - 70012

Type subroutine

Call snpenc(gene, trait, typ, dataset)
ModuleNone

Notes
 Dummy encode a SNP 1=add 2=dom 3=rec 






wribs




Name of routine: wribs 

Source lines: 70016 - 70156

Type subroutine

Call wribs(trait, gt, thresh, nloci, loc, loctyp, locpos,  dataset, plevel)
ModuleNone

Notes
 Multipoint IBS sharing for all pairs






ibspca




Name of routine: ibspca 

Source lines: 70160 - 70362

Type subroutine

Call ibspca(typ, nloci, loc, loctyp, locpos,  ncomps, loadvars, dataset, plevel)
ModuleNone

Notes
 Principal components or classical MDS analysis of multipoint IBS sharing






wribd




Name of routine: wribd 

Source lines: 70366 - 70536

Type subroutine

Call wribd(nmark, mark, loc, loctyp, locpos, dataset, burnin, iter, typ, plevel)
ModuleNone

Notes
 Monte-Carlo approach to estimating IBD sharing at a marker






markeribd




Name of routine: markeribd 

Source lines: 70540 - 70734

Type subroutine

Call markeribd(gene, iter, burnin, allele_buffer,  ped, dataset, ibdcount, ibdvar, plevel)
ModuleNone

Notes
 Monte-Carlo approach to estimating IBD sharing at a marker for a pedigree






dokin




Name of routine: dokin 

Source lines: 70738 - 70932

Type subroutine

Call dokin(typ, dataset, trait)
ModuleNone

Notes
 Write kinship coefficients






kinship




Name of routine: kinship 

Source lines: 70936 - 70982

Type subroutine

Call kinship(ped, dataset, kin)
ModuleNone

Notes
 Calculate kinship coefficient






frater




Name of routine: frater 

Source lines: 70986 - 71014

Type subroutine

Call frater(ped, dataset, kin, dom)
ModuleNone

Notes
 Calculate coefficient of fraternity






delta7




Name of routine: delta7 

Source lines: 71019 - 71054

Type function

Call delta7(peri, perj, ped, dataset, kin)
ModuleNone

Notes
 Coefficient of fraternity for one pair of relatives
 peri and perj are relative to start of current pedigree






doinbred




Name of routine: doinbred 

Source lines: 71059 - 71202

Type subroutine

Call doinbred(iter, dataset, trait, plevel)
ModuleNone

Notes
 Write MC estimates of inbreeding coefficients (and list of nodal ancestors)
 Also marks inbred individuals using dataset%untyped






invkin




Name of routine: invkin 

Source lines: 71207 - 71256

Type subroutine

Call invkin(ped, dataset, ainv)
ModuleNone

Notes

 A~ = (T~)' D~ T~






segerr




Name of routine: segerr 

Source lines: 71261 - 71299

Type subroutine

Call segerr(ped, dataset, rsd)
ModuleNone

Notes
 Calculate standard deviation of segregation error
 (used for gametic model breeding value calculation)






casekin




Name of routine: casekin 

Source lines: 71303 - 71474

Type subroutine

Call casekin(locnam, trait, gt, thresh, dataset, statval, plevel)
ModuleNone

Notes
 Give kinships among affecteds






ancest




Name of routine: ancest 

Source lines: 71479 - 71615

Type subroutine

Call ancest(locnam, trait, gt, thresh, dataset, plevel)
ModuleNone

Notes
 Find the ancestor(s) shared by the maximum number of affecteds
 Also calculate inbreeding among all cases within each family






wrdesc




Name of routine: wrdesc 

Source lines: 71619 - 71634

Type subroutine

Call wrdesc(pedigree, cid, sx, ndesc, ntot)
ModuleNone

Notes
 write person and number of descendants






mksegmod




Name of routine: mksegmod 

Source lines: 71638 - 72052

Type subroutine

Call mksegmod(narg, words, trait, gt, thresh, offset, censor,  nvar, varlist, nloci, loc, lochash, loctyp,  priran, nqtl, linkf, modtyp, shap)
ModuleNone

Notes
 Parse a mixed model






preseg




Name of routine: preseg 

Source lines: 72056 - 72112

Type subroutine

Call preseg(nvar, fixed, loc, loctyp, gene, allele_buffer, covariates)
ModuleNone

Notes
 Names and preliminary estimates for fixed effects part of mixed model






segsim




Name of routine: segsim 

Source lines: 72119 - 73148

Type subroutine

Call segsim(linkf, modtyp, shap, trait, gt, thresh, offset, censor,  nvar, fixed, gene, genemod, allele_buffer, loc, loctyp, locpos, burnin, iter, nbatch, nsamples, tune, nchain, nqtl, dataset, mlik, mpar, priran, mcalg, plevel)
ModuleNone

Notes
 Mixed model MCMC: simulate genotypes at 1..N unlinked QTLs
                            Gaussian breeding values
                            family intercepts
                            regression coefficients for fixed effects






genfreq




Name of routine: genfreq 

Source lines: 73152 - 73163

Type subroutine

Call genfreq(pall, qtl_buffer)
ModuleNone

Notes
 QTL genotypic log frequencies






oneprop




Name of routine: oneprop 

Source lines: 73168 - 73304

Type subroutine

Call oneprop(it, typ, mcalg, linkf, modtyp, nchain, nqtl, nfix, ncol, totobs, nprops, ncomp, tune, yvar, qtl_buffer, prop_buffer,  nfam, families, dataset,  empmu, empvar, lik, newlik, plevel)
ModuleNone

Notes
 One iteration of the sampler: either parameters or random effects
 Give "empirical" estimates of random effects variances






mhprop




Name of routine: mhprop 

Source lines: 73309 - 73395

Type subroutine

Call mhprop(iprop, linkf, modtyp, nchain, nqtl, nfix, ncol,  tune, yvar, qtl_buffer, nfam, families, dataset,  lik, newlik, plevel)
ModuleNone

Notes

 Metropolis sampler for global parameters






slprop




Name of routine: slprop 

Source lines: 73400 - 73528

Type subroutine

Call slprop(iprop, linkf, modtyp, nchain, nqtl, nfix, ncol,  qtl_buffer, nfam, families, dataset, lik, newlik, plevel)
ModuleNone

Notes
 end-of-mhprop

 Slice sampler for global parameters






parprop




Name of routine: parprop 

Source lines: 73534 - 73560

Type subroutine

Call parprop(typ, tune, yvar, oobounds)
ModuleNone

Notes
 end-of-slprop

 Make a proposal for one QTL model parameter for Metropolis sampler
 oobounds!=0 when proposal is illegal






parbounds




Name of routine: parbounds 

Source lines: 73566 - 73587

Type subroutine

Call parbounds(typ, oobounds)
ModuleNone

Notes
 end-of-parprop

 Check Metropolis proposal
 oobounds!=0 when proposal is illegal






qtlmod




Name of routine: qtlmod 

Source lines: 73601 - 73688

Type subroutine

Call qtlmod(linkf, modtyp, nqtl, qtl_buffer)
ModuleNone

Notes
 end-of-parbounds

 QTL allelic deviations, allele and genotype frequencies
 For identity link models, use  
   pA, mu, totvar, a2, d2, h2, c2 to calculate all other parameters
 For other GLMs, use
   VA etc
 model pars 1=P(all) 2=a 3=d 4=AA 5=AB 6=BB
            7=mu 8=totvar 9=VA 10=VD 11=VG 12=VC 13=VS 14=VE
            15=sdG 16=sdC 17=sdS 18=sdE
            19=a2 20=d2 21=h2 22=c2 23=s2 24=e2
            25..MAXPAR=Betas






chkbin




Name of routine: chkbin 

Source lines: 73692 - 73710

Type subroutine

Call chkbin(nqtl, oobounds)
ModuleNone

Notes
 check bounds on linear binomial model terms






triprop




Name of routine: triprop 

Source lines: 73715 - 73726

Type subroutine

Call triprop(tune, p)
ModuleNone

Notes
 end-of-chkbin

 Circularized triangular random proportion






linfun




Name of routine: linfun 

Source lines: 73732 - 73756

Type subroutine

Call linfun(linkf, y, thresh)
ModuleNone

Notes
 end-of-triprop

 link function for binary data
 linkf=1 identity 2 logit 3 probit 4 MFT 5=Log






dens




Name of routine: dens 

Source lines: 73761 - 73799

Type function

Call dens(x, mu, sd, shap, cens, modtyp)
ModuleNone

Notes
 end-of-linfun

 Poisson or Binomial or Gaussian log density for FPM






pedlik




Name of routine: pedlik 

Source lines: 73805 - 73843

Type subroutine

Call pedlik(linkf, modtyp, nchain, nqtl, nfix, ncol,  qtl_buffer, nfam, families, dataset, lik, oobounds, plevel)
ModuleNone

Notes
 end-of-dens

 Calculate likelihood under FPM for entire sample of pedigrees
 over all chains (replicates)






seglik




Name of routine: seglik 

Source lines: 73848 - 73900

Type subroutine

Call seglik(linkf, modtyp, ichain, nqtl, nfix, qtl_buffer, family, dataset, plevel)
ModuleNone

Notes
 end-of-pedlik

 Calculate likelihood under FPM for one pedigree (one chain/replicate)






oneseg




Name of routine: oneseg 

Source lines: 73906 - 74137

Type subroutine

Call oneseg(it, linkf, modtyp, ichain, nqtl, nfix, qtl_buffer, prop_buffer, family, dataset, mcalg, plevel)
ModuleNone

Notes
 end-of-seglik

 Update (gene-dropping) genotypes at one of N unlinked QTLs
 or Gaussian polygenotype or familial random intercept






oneslice




Name of routine: oneslice 

Source lines: 74141 - 74278

Type subroutine

Call oneslice(ieff, linkf, modtyp, shap, ichain, nqtl, nfix,  qtl_buffer, family, dataset, plevel)
ModuleNone

Notes
 Slice sampler updating Gaussian polygenotype






sliceprop




Name of routine: sliceprop 

Source lines: 74283 - 74308

Type subroutine

Call sliceprop(ieff, idx, mztwin_proposal, twinlist, ichain, prop, family)
ModuleNone

Notes
 end-of-oneslice

 copy proposal to appropriate location






idxlik




Name of routine: idxlik 

Source lines: 74314 - 74361

Type subroutine

Call idxlik(linkf, modtyp, shap, ichain, nqtl, nfix,  qtl_buffer, family, dataset, lik, gtplik)
ModuleNone

Notes
 end-of-sliceprop

 Gaussian polygenotype likelihood contribution of individual idx (and
 affected relatives)






seglf




Name of routine: seglf 

Source lines: 74365 - 74443

Type subroutine

Call seglf(typ, idx, ichain, linkf, modtyp, shap, nqtl, nfix,  qtl_buffer, family, dataset, yp, lik, gtplik)
ModuleNone

Notes
 Likelihood contribution of a founder






seglnf




Name of routine: seglnf 

Source lines: 74447 - 74514

Type subroutine

Call seglnf(typ, idx, ichain, curmo, linkf, modtyp, shap, nqtl, nfix,  qtl_buffer, family, dataset, yp, lik, gtplik)
ModuleNone

Notes
 Likelihood contribution of a nonfounder






isimped




Name of routine: isimped 

Source lines: 74519 - 74602

Type subroutine

Call isimped(ped, dataset, qtl_buffer, set)
ModuleNone

Notes
  Resimulate (gene-dropping) genotypes at a single autosomal locus
  in descendants of randomly selected index






simpol




Name of routine: simpol 

Source lines: 74606 - 74688

Type subroutine

Call simpol(vsd, ichain, family)
ModuleNone

Notes
 Propose updated additive polygenic values in a pedigree






simmat




Name of routine: simmat 

Source lines: 74693 - 74726

Type subroutine

Call simmat(vstep, ichain, family)
ModuleNone

Notes
 end-of-simpol

 Propose updated sibship/maternal effects in a pedigree






empval




Name of routine: empval 

Source lines: 74732 - 74831

Type subroutine

Call empval(linkf, modtyp, nchain, nqtl, nfix, nfam, families, totobs, empmu, empvar)
ModuleNone

Notes
 end-of-simmat

 Get empirical estimates of random effects
 Tote up empirical statistics for random effects: VG, VC, VS, VE






initvc




Name of routine: initvc 

Source lines: 74836 - 74903

Type subroutine

Call initvc(nchain, nfam, families)
ModuleNone

Notes
 end-of-empval

 Initialize additive genetic and/or maternal random effects






set2hap




Name of routine: set2hap 

Source lines: 74909 - 74936

Type subroutine

Call set2hap(ichain, iqtl, num, set, hset, typ)
ModuleNone

Notes
 end-of-initvc

 Copy or swap genotypes from set to hset
 1=set->hset; 2=hset->set; 3=swap






fpmpred




Name of routine: fpmpred 

Source lines: 74941 - 74977

Type subroutine

Call fpmpred(typ, idx, ichain, linkf, nqtl, nfix,  family, yp, ypf)
ModuleNone

Notes
 end-of-set2hap

 FPM Linear predictor






updateblups




Name of routine: updateblups 

Source lines: 74981 - 75043

Type subroutine

Call updateblups(whichblup, nvals, nchain, nfam, families)
ModuleNone

Notes
 Accumulate BLUP for additive genetic effects






dobatch




Name of routine: dobatch 

Source lines: 75047 - 75076

Type subroutine

Call dobatch(nbatch, nvar, batch, batchse)
ModuleNone

Notes
 Produce batch estimates of Monte-Carlo error variance






wronep




Name of routine: wronep 

Source lines: 75080 - 75113

Type subroutine

Call wronep(idx, it, ichain, yp, iqtl, nqtl, ieff, lik, family, dataset)
ModuleNone

Notes
 Print oneseg's proposed genotypes for one individual






wrfpm




Name of routine: wrfpm 

Source lines: 75118 - 75208

Type subroutine

Call wrfpm(it, linkf, modtyp, ichain, nqtl, nfix, family, dataset)
ModuleNone

Notes
 end-of-wronep

 Print simulated genotypes from FPM iteration






wlscor




Name of routine: wlscor 

Source lines: 75212 - 75254

Type subroutine

Call wlscor(cor, npairs)
ModuleNone

Notes
 WLS analysis of familial correlations






domft




Name of routine: domft 

Source lines: 75258 - 75411

Type subroutine

Call domft(trait, prevalence, logrid, higrid, gridstep,  dataset, mlik, mpar, iter, plevel)
ModuleNone

Notes
 MFT






sibqtl




Name of routine: sibqtl 

Source lines: 75415 - 75682

Type subroutine

Call sibqtl(tranam, trait, locnam, gene, allele_buffer, dataset, pval, plevel, toler)
ModuleNone

Notes
 Variance components analysis






varcom




Name of routine: varcom 

Source lines: 75690 - 76344

Type subroutine

Call varcom(modtyp, nterms, terms, loc, loctyp, locpos,  gene, genemod, allele_buffer, nmark, mark, dataset, mlik, mpar, pval, plevel, burnin, iter, typ,  approx, toler)
ModuleNone

Notes
 Variance components analysis
 modtyp 1=MVN 2=MFT
 typ 1=CE 2=AE 3=ACE 4=ADE
     5=AQE (6 if ibd matrix in script)
     7=CQE






mvnlik




Name of routine: mvnlik 

Source lines: 76348 - 76402

Type function

Call mvnlik(npar, parest)
ModuleNone

Notes
 MVN model loglikelihood






mftlik




Name of routine: mftlik 

Source lines: 76406 - 76462

Type function

Call mftlik(npar, parest)
ModuleNone

Notes
 MFT model loglikelihood






vcprofile




Name of routine: vcprofile 

Source lines: 76466 - 76496

Type subroutine

Call vcprofile(whichpar, vc_nfix, npar, parest, modlik, lo95, up95)
ModuleNone

Notes
 Function to give profile likelihood for given parameter of MVN model






brent_proflik




Name of routine: brent_proflik 

Source lines: 76500 - 76518

Type function

Call brent_proflik(x)
ModuleNone

Notes
 Function to give profile likelihood for A in AE model






vcov




Name of routine: vcov 

Source lines: 76522 - 76567

Type subroutine

Call vcov(va, vq, ve, vcvmat)
ModuleNone

Notes
 GLS model VCOV for fixed effects part of MVN mixed model






thinibd




Name of routine: thinibd 

Source lines: 76571 - 76602

Type subroutine

Call thinibd(ped, dataset, nobs, ibd1, ibd2)
ModuleNone

Notes
 Drop covariance matrix entries for unused records






syminv




Name of routine: syminv 

Source lines: 76606 - 76647

Type subroutine

Call syminv(a, n, c, logdet, info)
ModuleNone

Notes
 Call to LINPACK routines to invert packed lower triangular symmetric matrix






gibinv




Name of routine: gibinv 

Source lines: 77028 - 77080

Type subroutine

Call gibinv(cov, n, invcov, logdet, iter)
ModuleNone

Notes
 D. A. Harville. Use of the Gibbs sampler to invert large, possibly
 sparse, positive definite matrices. Linear Algebra and its
 Applications, 289:203

 Proposal of Harville is Gibbs sampler using just (3)
 1.  Set arbitrary starting values for z, z*
     for instance z_i=0, z*_i=i
 2.  Sample Phi as a vector containing independent draws according
     with definition (5) and (6):
       (5) E(Phi)=0 (6) E(Phi[k]*Phi[l])=I*delta(k,l)
 3.  Update z, z* by using equations (3)
       (3) z_i[k] = Phi_i[k]/sqrt(c_ii) -
                    Sum(z_j[k] c_ij, j=1,i-1)/c_ii -
                    Sum(z_j[k-1] c_ij, j=i+1,n)/c_ii
 4.  p = p + 1
 5.  Go to step 2 until abs(z'z*) < tol
 6.  Sample Phi as a vector containing independent draws according
     with definition (5) and (6)
 7.  Update z using equation (3)
 8.  Accumulate Cov(z) in s
 9.  Go to step 6 to compute the next round of iteration (B - p times)
 10. Set the final estimate: Inv(C) =  s/(B - p)






oneinv




Name of routine: oneinv 

Source lines: 77084 - 77107

Type subroutine

Call oneinv(n, nn, cov, z)
ModuleNone

Notes
 One iteration of update of z






brent




Name of routine: brent 

Source lines: 77134 - 77231

Type function

Call brent(ax, bx, f, tol)
ModuleNone

Notes
  
 Brent's one-dimensional minimizer
  
 The method used is a combination of golden section search and
 successive parabolic interpolation.  Convergence is never much
 slower than that for a Fibonacci search.  If F has a continuous
 second derivative which is positive at the minimum (which is not
 at AX or BX), then convergence is superlinear, and usually of the
 order of about 1.324....
  
 INPUT PARAMETERS
  
  AX    (real)  left endpoint of initial interval
  BX    (real) right endpoint of initial interval
  F     Real function of the form REAL FUNCTION F(X) which evaluates
          F(X)  for any  X in the interval  (AX,BX)
        Must be declared EXTERNAL in calling routine.
  TOL   (real) desired length of the interval of uncertainty of the
        final result ( .ge. 0.0)
  
 OUTPUT PARAMETERS
  
 FMIN   abcissa approximating the minimizer of F
 AX     lower bound for minimizer
 BX     upper bound for minimizer
  





globhom




Name of routine: globhom 

Source lines: 77235 - 77400

Type subroutine

Call globhom(dataset, plevel)
ModuleNone

Notes
 Calculate observed and expected homozygosity for all individuals






globhom_onelocus




Name of routine: globhom_onelocus 

Source lines: 77404 - 77431

Type subroutine

Call globhom_onelocus(gene, loctyp, dataset, exphom)
ModuleNone

Notes
 Homozygosity contribution for ith locus






mulhom




Name of routine: mulhom 

Source lines: 77436 - 77747

Type subroutine

Call mulhom(trait, gt, thresh, xlinkd, iter, mincnt,  nloci, loc, loctyp, locpos, map, dataset, plevel)
ModuleNone

Notes
 Calculate observed and expected multipoint homozygosity
 Expected distribution simulated using given map






clcrun




Name of routine: clcrun 

Source lines: 77751 - 77795

Type subroutine

Call clcrun(ped, dataset, nmark, hset, runlen, totrunlen, averun)
ModuleNone

Notes
 calculate average maximum run length of homozygosity






simhap




Name of routine: simhap 

Source lines: 77799 - 77874

Type subroutine

Call simhap(nmark, recdist, alleles, ped, dataset, hset, plevel)
ModuleNone

Notes
 Drop haplotypes for all family members for given map






exclude




Name of routine: exclude 

Source lines: 77879 - 77905

Type subroutine

Call exclude(imp, nloci, loc, loctyp, locpos, dataset, inconsist, imputd, plevel)
ModuleNone

Notes
 Excluding genotypes from parental phenoset
 Straight Lange & Goradia AJHG 1987 40: 250-256






exclude_onelocus




Name of routine: exclude_onelocus 

Source lines: 77909 - 77981

Type subroutine

Call exclude_onelocus(imp, gene, loc, loctyp, dataset, inconsist, imputd, plevel)
ModuleNone

Notes
 Exclude at one locus






exclude_oneped




Name of routine: exclude_oneped 

Source lines: 77985 - 78283

Type subroutine

Call exclude_oneped(imp, reduce, locnam, gene, xlinkd, ped, dataset,  allele_buffer, set, gset, inconsist, imputd, plevel)
ModuleNone

Notes
 Do one pedigree at one locus






wrset




Name of routine: wrset 

Source lines: 78287 - 78317

Type subroutine

Call wrset(locnam, ped, dataset, set, gset)
ModuleNone

Notes
 write out phenoset






exc




Name of routine: exc 

Source lines: 78321 - 78455

Type subroutine

Call exc(locnam, xlinkd, gene, ped, dataset, set, gset,  inconsist, plevel)
ModuleNone

Notes
 perform exclusion for the pedigree regardless of imputation level






landg




Name of routine: landg 

Source lines: 78459 - 78577

Type subroutine

Call landg(xlinkd, currf, currm, sta, fin, sex, set, gset, change, incon)
ModuleNone

Notes
 2nd version of impute -- following Lange & Goradia, 1987






prune




Name of routine: prune 

Source lines: 78581 - 78605

Type subroutine

Call prune(idx, ngeno, gset, keep)
ModuleNone

Notes
 Remove unwanted genotypes from phenoset






swapg




Name of routine: swapg 

Source lines: 78609 - 78620

Type subroutine

Call swapg(idx, gset, j, k)
ModuleNone

Notes
 Swap two genotypes within a phenoset array






doblup




Name of routine: doblup 

Source lines: 78624 - 78697

Type subroutine

Call doblup(locnam, trait, h2, dataset, plevel)
ModuleNone

Notes
 Calculate BLUPs for VC model






blup




Name of routine: blup 

Source lines: 78701 - 78781

Type subroutine

Call blup(lam, trait, ped, dataset, ainv, bval, fmu)
ModuleNone

Notes
 Calculate BLUPs for current pedigree






hapassoc




Name of routine: hapassoc 

Source lines: 78790 - 79190

Type subroutine

Call hapassoc(nmark, markers, loc, loctyp, locpos, dataset, pval, plevel)
ModuleNone

Notes
 
 Association haplotype analysis for unphased data

 counts  ncells  ncat*(na1*(na1+1)/2)*(na2*(na2+1)/2)
 full    nfull   ncat*(nh1*(nh1+1)/2)*(nh2*(nh2+1)/2)
 scatter nfull*nobs
 model   nfull*(ncat + nh1 + nh2 + nh1*nh2 [ + ncat*nh1*nh2 ])






agl




Name of routine: agl 

Source lines: 79199 - 79229

Type subroutine

Call agl(nr, nc, design, sta, nalleles, nstrata)
ModuleNone

Notes
  
 Appropriate design matrix columns for allelic model
 a1 a2  gen
 2  0   1/1
 1  1   1/2
 1  1   2/1
 0  2   2/2
  





hap2gen




Name of routine: hap2gen 

Source lines: 79233 - 79284

Type subroutine

Call hap2gen(nrep, nmarkers, numals, scatter)
ModuleNone

Notes
 Phased genotype to unphased genotype mapping






nearloc




Name of routine: nearloc 

Source lines: 79302 - 79364

Type subroutine

Call nearloc(pos, thresh, maxcluster, nloci, loc, loctyp,  map, nmark, mark, plevel)
ModuleNone

Notes
 Convenience routine
 subroutine wrmat(nr, nc, mat)
   integer, intent(in) :: nr, nc
   double precision, dimension(nr*nc), intent(in) :: mat
   integer :: i, pos
   pos=0
   do i=1, nr
     write(*,*) i, ': ', mat(pos+1:pos+nc) 
     pos=pos+nc
   end do
 end subroutine wrmat

 The set of markers close to an index marker             A         B
 map distances are interpreted adjacently ie 10-5-15 = B unlinked 
                                                       C unlinked  10






dopeel




Name of routine: dopeel 

Source lines: 79393 - 79457

Type subroutine

Call dopeel(typ, gene, trait, maxiter, allele_buffer, dataset, plevel)
ModuleNone

Notes
 Iterative peeling in pedigrees -- Description from thesis of Schelling 2004

 1. for each pedigree member i to initialize anterior values to the population genotype
    frequency and posterior values to unity subsequently calculate its 
    penetrance values.
 2. Then, for each connector i
  a) for families in which i is an offspring, its anterior value ai (ui )
     is calculated non-recursively using (2.16) and the current values of
     the required quantities.
  b) for families in which i is a parent, its posterior value pij (ui )
     through each mate j is calculated non-recursively using (2.17) and the
     current values of the required quantities.
 Repeat 2 until values converge

 Additionally, anterior, posterior and penetrance values may be scaled
 to sum to unity over genotype as described in Wang et al. (1996) to
 avoid numerical underflow. The log scaling factors Kai , Kgi and Kpij
 for the anterior, posterior and penetrance values are also calculated
 using the current values of the required quantities. They denote the
 accumulative log of the scaling factors for the anterior, posterior
 and penetrance values for member i with its mother mi and father pi .

 In 2.16 and 2.17, S denotes set of mates, C denotes set of full-sibs

 typ=1 likelihood
 typ=2 GPE






itpeel




Name of routine: itpeel 

Source lines: 79461 - 79995

Type subroutine

Call itpeel(typ, ped, dataset, gene, allele_buffer, gfrq, transprob,  trait, maxiter, lik, ifail, plevel)
ModuleNone

Notes
 pth ped






filltrans




Name of routine: filltrans 

Source lines: 79999 - 80026

Type subroutine

Call filltrans(numal, ngeno, transprob)
ModuleNone

Notes
 Create table of transmission probabilities






postprod




Name of routine: postprod 

Source lines: 80030 - 80050

Type function

Call postprod(idx, geno, nmates, mates, postp)
ModuleNone

Notes
 Product of posterior values for all matings of ego






postprodex




Name of routine: postprodex 

Source lines: 80054 - 80078

Type function

Call postprodex(idx, except, geno, nmates, mates, postidx, postp)
ModuleNone

Notes
 Product of posterior values for all matings of ego save one






postscale




Name of routine: postscale 

Source lines: 80082 - 80096

Type function

Call postscale(idx, nmates, mates, pscale)
ModuleNone

Notes
 Sum of posterior value scaling factors for all matings of ego






postscalex




Name of routine: postscalex 

Source lines: 80100 - 80118

Type function

Call postscalex(idx, except, nmates, mates, postidx, pscale)
ModuleNone

Notes
 Sum of posterior value scaling factors for all matings of ego






nglist




Name of routine: nglist 

Source lines: 80122 - 80130

Type function

Call nglist(gtp,ngeno)
ModuleNone

Notes
 Length of list of genotypes






glist




Name of routine: glist 

Source lines: 80134 - 80142

Type function

Call glist(gtp, idx)
ModuleNone

Notes
 member of list of genotypes






itlik




Name of routine: itlik 

Source lines: 80146 - 80179

Type subroutine

Call itlik(trget, ngeno, gtp, nmates, mates, antp, postp, ascale, pscale, lik)
ModuleNone

Notes
 Likelihood from iterative peeling






dopeel2




Name of routine: dopeel2 

Source lines: 80185 - 80310

Type subroutine

Call dopeel2(typ, mark1, mark2, theta, maxiter,   allele_buffer1, allele_buffer2, dataset, plevel)
ModuleNone

Notes
 Two locus version
 typ=1 likelihood
 typ=2 grid






itpeel2




Name of routine: itpeel2 

Source lines: 80314 - 80916

Type subroutine

Call itpeel2(ped, dataset, mark1, mark2,  allele_buffer1, allele_buffer2, ngeno, phased, gfrq,  ngrid, grid, famlik, istat, maxiter, ifail, plevel)
ModuleNone

Notes
 Iterative peeling two codominant loci over grid of recombination fractions: pth ped






nglist2




Name of routine: nglist2 

Source lines: 80920 - 80925

Type function

Call nglist2(gtp)
ModuleNone

Notes
 Length of list of genotypes






glist2




Name of routine: glist2 

Source lines: 80929 - 80935

Type function

Call glist2(gtp, idx)
ModuleNone

Notes
 member of list of genotypes






transprob




Name of routine: transprob 

Source lines: 80939 - 80955

Type function

Call transprob(geno, fgeno, mgeno, ngeno, phased, prec, pnrec)
ModuleNone

Notes
 Parent-offspring triad






transmit




Name of routine: transmit 

Source lines: 80963 - 80976

Type function

Call transmit(p11, p12, p21, p22, c1, c2, prec, pnrec)
ModuleNone

Notes
 Transmission probabilities: two codominant loci, phased genotypes

 p11 | p12        c1
     |       =>
 p21 | p22        c2






itlik2




Name of routine: itlik2 

Source lines: 80980 - 81013

Type subroutine

Call itlik2(trget, gtp, nmates, mates, antp, postp, ascale, pscale, lik)
ModuleNone

Notes
 Likelihood from iterative peeling






fillphase




Name of routine: fillphase 

Source lines: 81017 - 81066

Type subroutine

Call fillphase(allele_buffer1, allele_buffer2, ngeno, phased, gfrq)
ModuleNone

Notes
 Phased genotype frequencies






doeigen




Name of routine: doeigen 

Source lines: 81068 - 81102

Type subroutine

Call doeigen(n)
ModuleNone



dcentre




Name of routine: dcentre 

Source lines: 81107 - 81131

Type subroutine

Call dcentre(n, nn, x)
ModuleNone

Notes
 double centre a distance matrix (lower triangular form)
 used for MDS






twinken




Name of routine: twinken 

Source lines: 81136 - 81296

Type subroutine

Call twinken(locnam, trait, cenloc, censor, mztwin, gt, thresh, dataset, plevel)
ModuleNone

Notes
 Oakes' Kendall tau for bivariate survival analysis 
 contrasting monozygotic twins v. other siblings.






eigen




Name of routine: eigen 

Source lines: 81300 - 81326

Type subroutine

Call eigen(typ, n, a, z)
ModuleNone

Notes
 Wrapper for EISPACK real symmetric matrix routines






rs




Name of routine: rs 

Source lines: 81333 - 81358

Type subroutine

Call rs(nm, n, a, w, matz, z, fv1, fv2, ierr)
ModuleNone

Notes
 This subroutine calls the recommended sequence of
 subroutines from the Eigensystem Subroutine Package (EISPACK)
 to find the eigenvalues and eigenvectors (if desired)
 of a real symmetric matrix.






tred1




Name of routine: tred1 

Source lines: 81367 - 81470

Type subroutine

Call tred1(nm, n, a, d, e, e2)
ModuleNone

Notes
 This EISPACK subroutine is a translation of the Algol procedure TRED1, 
 Num. Math. 11, 181-195(1968) by Martin, Reinsch, and Wilkinson.
 Handbook for Auto. Comp., Vol.II-Linear Algebra, 212-226(1971).
 This subroutine reduces a real symmetric matrix
 to a symmetric tridiagonal matrix using
 orthogonal similarity transformations.






tred2




Name of routine: tred2 

Source lines: 81479 - 81619

Type subroutine

Call tred2(nm, n, a, d, e, z)
ModuleNone

Notes
  
 This EISPACK subroutine is a translation of the Algol procedure TRED2, 
 Num. Math. 11, 181-195(1968) by Martin, Reinsch, and Wilkinson.
 Handbook for Auto. Comp., Vol.II-Linear Algebra, 212-226(1971).
 This subroutine reduces a real symmetric matrix to a
 symmetric tridiagonal matrix using and accumulating
 orthogonal similarity transformations.
  





tqlrat




Name of routine: tqlrat 

Source lines: 81627 - 81724

Type subroutine

Call tqlrat(n, d, e2, ierr)
ModuleNone

Notes
  
 This EISPACK subroutine is a translation of the Algol procedure TQLRAT, 
 Algorithm 464, Comm. ACM 16, 689(1973) By Reinsch.
  
 This subroutine finds the eigenvalues of a symmetric
 tridiagonal matrix by the rational QL method.






tql2




Name of routine: tql2 

Source lines: 81736 - 81878

Type subroutine

Call tql2(nm, n, d, e, z, ierr)
ModuleNone

Notes
  
 This EISPACK subroutine is a translation of the Algol procedure TQL2, 
 Num. Math. 11, 293-306(1968) by Bowdler, Martin, Reinsch, and Wilkinson.
 Handbook for Auto. Comp., Vol.II-Linear Algebra, 227-240(1971).
  
 This subroutine finds the eigenvalues and eigenvectors
 of a symmetric tridiagonal matrix by the ql method.
 The eigenvectors of a full symmetric matrix can also
 be found if  tred2  has been used to reduce this
 full matrix to tridiagonal form.






pythag




Name of routine: pythag 

Source lines: 81882 - 81903

Type function

Call pythag(a, b)
ModuleNone

Notes
  
 Finds dsqrt(A**2+B**2) without overflow or destructive underflow










Name of routine:  

Source lines: 81907 - 81921

Type function

Call epslon (x)
ModuleNone

Notes
 estimate unit roundoff in quantities of size x









Alphabetical list of routines








actlist
actped
addall
addcolon


addlet
addlist
addsexes
addtmpvar
addvar


agl
alias
aligntype
alldata
allinset


alogit
ancest
append
append
append_pair


append_string
appval
args
ascend
asstyp


atgc
aval
backchar
badloop
betacf


binirls
binop
binp
binreg
binz


bluefreq
blup
bonf
brent
brent_proflik


brent_tet
bsub
caar
cadaar
cadar


cadddr
caddr
cadr
calc_gtp_freqs
calclogrank


car
casekin
cat
ccpen
cdar


cddddr
cddr
cdr
ceqstr
check


chfind
chi2nc
chip
chisqd
chkbin


choose
chrnum
cisimped
ckibs
clcchi


clcibd
clcibs
clcmcn
clcpos
clcrun


clctdt
clean_AS164
clean_pairs
clean_props
clean_table


cleanup_alleles
cleanup_bank
cleanup_form
cleanup_hash
cleanup_loci


cleanup_mem
cleanup_peds
clearinput
close_port
clratom


clreg
clrmark
cntbad
cntclasses
cntibs


cntmark
cntprop
combine
compld
complete


compop
compsign
concat
concest
conchi


conlen
connect
conoff
cons
copy


copy_peds
copydata
copyfreq
corchi
corr


corrstd
corstring
cortest
countall
countargs


countfields
countmz
countships
couple
coutyp


covcor
covsrt
cpganova
cpibd
create_form


csimped
cubicld
cubiclik
dataset_uses
dataset_uses


dateconv
dattoset
davie
davstat
davwri


dcentre
decchr
decgtp
defpro
delfile


delta
delta7
dens
describe
dhwe2


dim_table
disjoin
display
dkbvrc
dksmrc


dkswap
dmatch
doanova
doapm
doasp


doassoc
dobatch
doblup
docomp
docount


docov
doeigen
dogen
dohash_id
dohash_ped_id


dohashids
dohist
dohomoz
dohrr
dohwe


doinbred
doito
dokin
domar
domatch_id


domatch_ped_id
domatch_string_id
domatch_string_ped_id
domft
domix


domqls
dopeel
dopeel2
dopenrose
doplot


dorank
doselect
dotdt
dpois
drop


dropt2
dryrun
dsort
dssp
duplicates


dweib
edit
eigen
emibskin
emllm


empval
encchr
encgtp
encode_geno1
encode_geno2


eow
eqv
error0
error1
escape


evalped
evdtailp
exc
exclude
exclude_onelocus


exclude_oneped
expand_alleles
expand_geno
expand_loci
expand_pairs


expand_pheno
expand_sgeno
expand_table
extpath
extprefix


extract_fa
extract_id
extract_imztwin
extract_iped
extract_mo


extract_ped
fact
famcor
famcovar
famerr


famimp
fammeans
famset
famsort
fchooser


fgz_close
fgz_open
fgz_read
fgz_rewind
fgz_write


filecols
fill2
fill_hash
filliben
fillin


fillin_mit
fillin_yha
fillphase
filltrans
filltri


find_hashtab
find_pair
findbracket
findend
findfile


findids
findlev
findlist
findloop
findmk


findml
findrank
findth
findwh
findword


fishzci
fishzse
fitbin
fitloglin
fixeff


flat_table
flip
flushinput
fonttype
foulik


found
fp
fpicker
fpicker
fpmpred


fprinter
frater
freq
fromplink
fsimped


ftdev
fval
gammad
gc
gc_mark


gencode
gencopy
gener
genfreq
genmatch


genof2
genof3
genof4
genoff
genot


gensym
get_geno
get_ivalue
get_listlen
get_namedgeno


get_snpallele1
get_snpallele2
get_string
get_strlen
get_substr


get_value
get_var
getbin
getcell
getchr


getfreq
getgeno
getint
getlabel
getlin


getnam
getrelval
getstrata
gettrait
getword


getyear
gibinv
givenc
gl
glist


glist2
glmscale
globhom
globhom_onelocus
grad


grrpen
handler
hap2gen
hapassoc
haploid_aov


haploid_ass
haploid_count
haploid_freq
haptogen
hashids


hashprint
head
help
hibd
hwe2


hwechi
hwep
ibeta
ibskin
ibskin_one


ibspca
idwidths
idxlik
iencgtp
inchap


inchar
incpo
incpos
incr
incr_table


inderr
indset
info
inht
inicov


init_globals
init_procs
init_scheme
init_scm
init_syntax


init_vars_global
initvc
insert_lochash
insert_pair
insert_table


insgen
insloc
inuclik
invkin
invmap


iquadmult
isactdip
isactive
isaff
isafun


isatom
isatwin
iscattrait
isclosure
iscomment


iscomp
iscompressed
iscontinuation
isdata
isenv


isfalse
isfloat
isgeno
isgzipped
ishaploid


isimped
isinenv
isint
isinteger
isinuse


ismacro
ismark
ismarker
ismis
ismiss


ismzpair
isnumber
isop
isort
ispair


isport
isproc
ispromise
isqtrait
isreal


isstring
issymbol
issyntax
istrait
istrue


isvar
isvec
itlik
itlik2
ito


itpeel
itpeel2
ival
joinped
juststr


kinship
kwtest
landg
ld2
ldlist


ldp
ldtab
ldtest
legall
lfact


lifetab
linfun
list_var
listab
listchroms


listids
listloci
listpeds
ln
loadnam


loadset
loadvar
loccode
locfmt
logccs


logit
loglin
logrank
lorder
macloop


macsub
macvar
make_lochash
makeind
maketab


makewt
margen
marginal_table
markeribd
marseg


marshare
match
matchid
matrix_active
matrix_copy


matrix_copy_row
matrix_create
matrix_destroy
matrix_get_col
matrix_get_el


matrix_get_row
matrix_ncols
matrix_nrows
matrix_print
matrix_read


matrix_read_contents
matrix_read_row
matrix_read_unformatted
matrix_set_col
matrix_set_el


matrix_set_row
matrix_size
matrix_type
matrix_write
matrix_write_row


matrix_zero
mcfreq
mcgpe
mftlik
mhprop


missing
mixture
mk_atom
mk_closure
mk_const


mk_continuation
mk_number
mk_port
mk_proc
mk_real


mk_string
mk_symbol
mk_syntax
mkchoose
mkdummy


mksegmod
mktmpfil
moment
moskld
moskvina


msdsort
mulhom
mumson
mutage
mutate


mvbvu
mvndst
mvnlik
mvnlms
mzfind


mzgtp
mztest
nearloc
newlin
newloctyp


newlun
newstart
nextcmd
nextped
nextword


nglist
nglist2
non_alloc_rev
nonextped
ntcode


nttonum
nuchek
nucibd
nuclear
nuclik


nucseg
numtont
observed
ok_abbrev
onefam


oneinv
onelik
oneprop
oneseg
oneslice


onestripe
onetab
opchar
opcon
open_port


openlog
opexe0
opexe1
opexe10
opexe11


opexe12
opexe13
opexe14
opexe15
opexe2


opexe3
opexe4
opexe5
opexe6
opexe7


opexe8
opexe9
opsimple
order
ordvar


packer
padprint
pairlink
parbounds
parcon


parimp
parprop
parser
pearson
pedhead


pedibd
pedin
pedlik
pedout
pedsort


pedtab
permdata
permut
phist
pipe_close


pipe_open
pipe_read
pipe_rewind
pipe_write
popgen_homoz


popgen_init
popgen_summary
postmult
postmultm
postprod


postprodex
postscale
postscalex
pre_grapheps
precis


predmat
preseg
prexpr
prgtp
priallval


print_table
printatom
printmat
prirelval
processfam


procnum
proct
prodlim
propci
prrel


prune
prunep
pstring
pull
pythag


qqplot
qtdt
qtlmod
qtlpars
quadform


quadmult
quadxxm
quadxy
quadxy1
quadxym


quadxymv
ranall
randn
random
rankstat


rantri
rclrts
rcp
rcswp
rctdt


rctest
rctperm
rctsim
rctuse
rdfreq


rdlinloc
rdmerloc
rdplink
read_scheme_image
readbed


readbin
readcases
readgeno
readhapmap
readline


readmap
readnames
readpeds
readprobs
readstr


readstrexp
recast
reclen
recode
recrisk


regress
regwt
relations
remfam
remove


renumb
repl_scheme
replacedata
reverse
rewind_port


rs
rtheta
rvalue
s_retbool
s_return


s_save
same_loctyp
sample
save_scheme_image
scatter_grapheps


scheme_delim
sclean
search_table
sech
segerr


seglf
seglik
seglnf
segrat
segsim


seldel
selped
selstat
set2hap
set_caar


set_car
set_cdar
set_cdr
set_geno
set_hval


set_ivalue
set_string
set_substring
set_syntaxnum
set_type


set_value
setatom
setmark
setup_freq
setup_hash


setup_ibd
setup_loci
setup_mem
setup_mix
setup_pairs


setup_peds
setup_plink
setup_props
setup_stat
setup_table


setupmer
sextable
share
shell
shibd


shipcon
shipsiz
shorten
show_form
show_lochash


show_locus_allocation
show_one_carray
show_one_farray
show_one_iarray
show_ped_allocation


show_snp
showdata
showdups
shuffle
sibass


sibcor
sibloci
sibpair
sibqtl
sibvar


simchi
simdata
simhap
simhaploid
simibd


simil
simlogrank
simmat
simnuc
simpar


simped
simpev
simpol
skipspace
slash


sliceprop
slprop
snpenc
sort_table
sow


sow
srank
sshare
stamp
stand


start
startone
strattyp
streq
strfind


string_hash
sumcols_form
sumped
sumplot
sumstat


sumsym
sumucsc
survtab
swap
swapalleles


swapg
switch
syminv
symtest
syntaxnum


tab
tabgen
tabhap
tabid
tabmat


tabstat
tarone
tdtuse
test_port
testage


testhap
testpage
testsex
tetcor
thetaf


thincov
thinibd
thischr
tidydata
togreg


tojulian
token
tp
tql2
tqlrat


traceplot
trans
transmit
transprob
tred1


tred2
triprop
twidl
twincon
twincor


twinken
twobyk
twofrq
twohwe
twold


twopoi
typeof
typwords
unidens
uninf


uniqid
uniqnam
unop
unsel
unzipper


upchi
update
updateblups
useld
var


varcom
varlevels
varmet
vcov
vcprofile


vmerr
weishape
whall
whitehead
wlscor


wordpos
workpointers
wraff
wrall
wrans


wrarl
wrbeagle
wrbed
wrcri
wrcsv


wrdate
wrdesc
wrdot
wrfish
wrform


wrfpm
wrfreq
wrgen
wrgtp
wrhbd


wribd
wribs
wricas
wrid
wrind


wrinline
writebin
writeline
wrkout
wrlink


wrmap
wrmorg
wroddall
wronep
wrpap


wrpercent
wrpercentd
wrphe
wrprd
wrprop


wrpropci
wrset
wrsex
wrsim
wrsimq


wrsimqtl
wrsnp
wrsubped
wrtab
wrtrait


wrvert
xmeans
xsimped
xtab
xtrans


xy_grapheps
zero_table
zerop