Sib-pair Command: eval

Class	Global
Name	eval
Arguments	[Scheme expression]

Accesses the Scheme read-eval-print-loop. If called without arguments, presents the Scheme prompt "%%", otherwise evaluates the rest of the line as if it were a Scheme expression. Sib-pair macro variables and functions are stored within the Scheme environment, and so can be read and written to.

For fuller documentation of other Scheme commands, see the Scheme standard: Standard Revised^5 Report on the Algorithmic Language Scheme (R5RS). The Sib-pair Scheme interpreter is fairly minimal - it implements characters as single-character strings, and lacks vectors. The types of numbers are long integers and double precision reals. Basic macro functionality (define-macro) is also provided. Aside from this, most R5RS examples work without problems (the interpreter is a port of Minischeme/Tinyscheme to Fortran 95). Interfaces to two graphic libraries are also implemented (see below).

Scheme keywords:

<	Numerically less than
<=	Numerically less than or equal
=	Numerically equal
>	Numerically greater than
>=	Numerically greater than or equal to
-	Integer subtraction
/	Integer division
*	Integer multiplication
+	Integer addition
abs	Absolute value
and	Logical and
append	Append to end of list
apply	Apply function to list
apropos	List matching functions
assoc	Find matching pair in an "alist" (list of paired values) using equal?
assq	Find matching pair in an "alist" using eq?
assv	Find matching pair in an "alist" using eqv?
atom?	Is a simple number or string?
begin	Start a block
boolean?	Is a boolean?
car	First element of pair or list
cdr	Remainder of pair or list
caar	First element of first element of pair or list
cadr	Und so weiter
cdar
cddr
caaar
cdddr
caadr
cadar
caddr
cdaar
cdadr
cddar
call/cc
call-with-current-continuation
case	Conditional branching
char<?	Is char lexicographically less?
char>?	Is char lexicographically greater?
char<=?	Is char lexicographically less than or equal?
char>=?	Is char lexicographically greater than or equal?
char-alphabetic?	Is char alphabetic?
char-ci<?	Is case-insensitive char lexicographically less?
char-ci>?	Is case-insensitive char lexicographically greater?
char-ci<=?	Is case-insensitive char lexicographically less than or equal?
char-ci>=?	Is case-insensitive char lexicographically greater than or equal?
char-numeric?	Is char a digit?
char-whitespace?	Is char a tab, space, CR, NL, HR?
char->integer	Return ASCII code
char-downcase	Return lower case
char-upcase	Return upper case
closure?	Is a closure
cond	Conditional branching
cons	Create a Lisp pair of elements
cons-stream
current-second	Return seconds since epoch
define	Define a variable or function
delay
display	Print a variable or function
do	Looping construct
else
eq?
equal?
eqv?
error	Print an error message
eval	Evaluate a SEXPR (Scheme expression)
even?	Test if even
exact->inexact	Cast to real
exit	Exit Sib-pair completely
expt	Integer exponentiation
force
for-each	Like map, but used for side-effects only
format	Print formatted data
gc	Force a garbage collection
gcd	Greatest common divisor
gensym	Create a new unique symbol
get-closure-code
help	Minimal information about Scheme
if	Conditional branching
inexact->exact	Cast to integer
integer?	Is an integer
integer->char	Return character for given ASCII code
lambda	Function
lcm	Least common multiple
length	Gives length of a list
let	Declare a local variable
let*
letrec
list	Create a list
list?	Test if a list?
list-ref	Gives Nth element of a list
list-tail	Drops the first k elements of a list
ls	List Sib-pair variables
macro
make-list	Create a list of given length
make-string	Create a string of given length
map	Apply a function to each element of a list in turn
max	Maximum of arguments
member	Test if present in a list
memq	Test if present in a list using equal?
memv	Test if present in a list using eqv?
min	Minimum of arguments
modulo	Give modulo
negative?	Test if negative integer
newline	Print a newline
new-segment
not	Logical negation
null?	Test if a null
number?	Test if an integer number
number->string	Convert from number to string
odd?	Test if odd
or	Logical or
pair?	Test if a Lisp pair
positive?	Test if a positive integer
print-width
procedure?	Is a function?
quasiquote	Allow some of quoted expression to evaluate
quit	Leave the Scheme interpreter
quote	Quoted expression left unevaluated
quotient	Integer division
random	A random integer from U(1, N)
read
read-line	Read one line of input from standard input or file
remainder	Remainder
reverse	Reverse ordering of a list
run	Run a Sib-pair command
set!	Set the contents of an existing variable
set-car!	Set contents of first element of pair or list
set-cdr!	Set contents of rest of pair or list
sqrt	Integer square root
string?	Is argument a string?
string=?	Are strings equal?
substring?	Is string 1 a substring of string 2?
string<?	Is string lexicographically less?
string>?	Is string lexicographically greater?
string<=?	Is string lexicographically less than or equal?
string>=?	Is string lexicographically greater than or equal?
string-append	Concatenate strings
string-length	Length of argument string
string-ref	Get kth character from string
string-set!	Set the value of a substring
string-split	Split a string into a list of words
string->number	Convert from a string to a number
string->symbol	Convert from a string to a symbol
substring	Get the value of a substring
symbol?	Is a symbol?
symbol->string	Convert from a symbol to a string
system	Passes commands to the operating system
unquote
unquote-splicing
write
zero?	Test if equal to zero

The Sib-pair specific builtin commands that for example allowing access to locus data:

apropos <str>	lists commands containing that string.
help	Information about this Scheme implementation.
isatty? <fil>	test if interactive session.
file-exists? <fil>	test file.
file-list [<dir>]	list files in directory (Posix).
file-delete <fil>	delete file.
open-input-file <fil>	open a port.
close-input-port <port>	close a port.
read-line [<port>]	reads in next line from stdin or open file.
format <port> "{~[:num:][@][ASD~%]}" <args>...	formatted output.
regexp <expr> <str>	searches for regular expression in string.
string-split <str> [<sep>]	splits string on white space or optional char.
substring? <sub> <str>	returns start of substring in string.
system <cmd>	passes command to shell.
getenv <nam>	returns value of environment variable.
date	returns current date and time.
time	returns current time as number of seconds since epoch.
environment-bound? <name>	test if symbol bound to a variable

version	prints Sib-pair version.
run <cmd> ...	runs a Sib-pair command.
pass-command <cmd> ...	stores Sib-pair commands to the buffer for evaluation once you return to the usual Sib-pair prompt.

Sib-pair locus dataset accessors:

ls [<typ>]	creates a list of locus names (of given type "adhmqx"	.
nloci	returns total number of loci.
loc <index>	returns locus at that position in the locus list.
loc-set! <idx> <name>	set name of locus at that position in the locus list.
locord <loc>	returns position of a locus in the locus list.
locstat <loc>	returns last P-value for a locus.
locstat-init! <title>	initializes all locus P-values.
locstat-set! <loc> <value>	sets P-value for a locus.
locnotes <loc>	returns notes for a locus.
locnotes-set! <loc> <str>	rewrites notes for a locus.
loctyp <loc>	evaluates type of a locus ("adhmqx")	.
locrank <loc>	returns rank of locus test statistic.
map-position <loc>	returns map position for locus.
map-position-set! <loc> <pos>	sets map position for locus.
chromosome <loc>	returns locus chromosome.
chromosome-set! <loc> <chr>	sets locus chromosome.
stat-result ["pval|lik|npars|lrt|df|stat|var"]	returns result of last model.

Sib-pair phenotype dataset accessors:

nobs	number of pedigree records.
npeds	number of pedigrees.
nactpeds	number of active pedigrees
active-status	activity status of pedigrees
set-active-status! <idx> <lev>	set activity status of pedigree
active-pedigrees [<idx>...]	list of active pedigree names
pedigrees [<idx>...]	list of pedigree names.
pedigree-size [<idx>...]	size of ith pedigree.
pedigree-members [<idx>...]	list of indices of pedigree members
individual-name [<idx>...]	give ID for index.
set-pedigree-name! "<ped>" <newname>	Set pedigree ID string .
set-individual-name! <idx>|"<id>" |("<ped>" "<id>") <newname>	Set ID string for individual.
individual-idx [<id>|<idx>...]	give index for ID.
father [<idx>...]	father indices.
mother [<idx>...]	mother indices.
imztwin [<idx>...]	MZ twin pointer.
sex [<idx>...]	sex value for individual(s).
set-sex! [<idx>...] <sex>	set sex value for individual.
data <loc> [<idx>]	phenotype for individual(s).
set-data! <idx>|"<id>" |("<ped>" "<id>") <loc> <val>	Set phenotype for individual.
data-counts <loc> [<loc>]	tabulation of phenotype levels.
allele-freqs <loc>	tabulation of alleles.

There are a number of builtin statistical functions (20100323 onwards), calling the appropriate Fortran routines.

pnorm <Z>	Gaussian upper tail probability
qnorm <p>	Gaussian quantile for given upper tail probability
pchisq <X2> <df> [<ncp>]	Central and non central chi-square upper tail probability
qchisq <p> <df>	Chi-square quantile for given upper tail probability
fp <F> <df1> <df2>	F upper tail probability
pgamma <X> <df>	Incomplete gamma integral
lgamma <X>	Log gamma
dbeta <X> <shape1> <shape2>	Density of Beta distribution.
bivnor <Z1> <Z2> <r>	Bivariate Gaussian upper tail probability
pmvnorm <p> <dir> <cor> ['genz]	Multivariate Gaussian tail probability
pchisqsum <X> <alpha>	Upper tail probability for distributions of quadratic forms in normal variables

And a few statistical data manipulation routines, that follow the XLispStat equivalents:

seq <sta> <fin> [<step>]	generate integer sequence.
sort <list>	Sort a list of numbers
order <list>	Indices of order of numbers in list
rank <list>	Rank of numbers in list
quantile <list> <p>	quantile(s) of list
sample-seq <N> <size> ['replace]	sample a sequence 1..N
sample <list> <size> ['replace]	sample a list
differences <list>	Lag-1 differences in list
which <list>	Indices of non-null elements of list
unique <list>	Indices of unique elements of list
duplicated <list>	Indices of repeat elements of list
intersect <list> <list>	Common elements of lists
setdiff <list> <list>	Elements unique to first list
union <list> <list>	Elements of both lists
list-select <list> <idx-list>	Sublist using indices
stats <list>	N, missing, mean, variance, min, max of list.
filter <test> <list>	filter contents of list

Sib-pair Scheme also now (2010-05-9) contains builtin functions to call the JAPI (java application programming interface) library (http://www.japi.de), which allows building GUIs etc. JAPI allows Fortran code to interface the Java AWT (Abstract Windowing Toolkit). The JAPI website details the commands.

j_start	Start JAPI listener
j_quit	Stop JAPI listener
j_frame	Create a frame
j_panel	Create a panel
j_borderpanel	Create a borderpanel
j_dialog	Create a dialogue
j_button	Create a button
j_radiobutton	Create a radiobutton
j_radiogroup	Create a radiogroup
j_checkbox	Create a checkbox
j_list	Create a list
j_add	Add an object to a container
j_setcolor	Set the foreground colour
j_setcolorbg	Set the background colour
j_setnamedcolorbg	Set the background colour
j_getselect	Return index of selected item
j_select	Select an item
j_deselect	Deselect an item
j_fileselect	A file dialog
j_filedialog	A file dialog
j_enable	Activate an object
j_disable	Deactivate an object
j_additem	Add an item to a list
j_seperator	Draw a separator
j_textfield	Create a textfield object
j_textarea	Create a textarea
j_setborderpos	Place an object using borderlayout
j_setrows	Set number of rows eg textarea
j_setcolumns	Set number of columns eg textarea
j_getrows	Get number of rows eg textarea
j_getcolumns	Get number of columns eg textarea
j_getlength	Get length in pixels of object
j_getselstart	Start of selected text
j_getselend	End of selected text
j_selecttext	Select text
j_gettext	Get text from label or list item
j_getseltext	Get selected text
j_getitem	Get a list item
j_label	Create a label
j_getcurpos	Get current cursor position
j_setcurpos	Set current cursor position
j_setfont	Set font
j_settext	Set text in object
j_inserttext	Insert text at position in eg textarea
j_replacetext	Replace text at position in eg textarea
j_delete	Delete text
j_dispose	Free resource
j_menubar	Create a menubar
j_menu	Create a menu
j_menuitem	Create an item for a menu
j_pack	Pack layout of frame or panel using layout manager
j_show	Make object visible
j_hide	Hide object
j_keylistener	Listen for key stroke if object active
j_getkeycode	Returns pressed key code
j_getkeychar	Returns pressed key ASCII code
j_mouselistener	Listen for mouse activation
j_getmousebutton	Return pressed mouse button
j_nextaction	Return next action of any object
j_getwidth	Get width of object (pixels)
j_getheight	Get height of object (pixels)
j_getpos	Get position of object (X.Y)
j_setpos	Set position of object (X,Y)
j_setsize	Get size of object (pixels)
j_setalign	Get layout alignment for object
j_setborderlayout	Layout manager
j_setgridlayout	Layout manager
j_setflowlayout	Layout manager

Sib-pair Scheme (2010-11-29) also contains builtin functions to call the EGGX/ProCALL graphical library ( http://www.ir.isas.jaxa.jp/~cyamauch/eggx_procall/), which allows plotting and building simple GUIs etc under X Windows.

ggetdisplayinfo	Get X display info. Returns a list containing ndepth (8,16,24 bit), nrwidth (screen width), nrheight (screen height).
gopen	Open a window. Takes two optional arguments nxwidth (width of window in pixels) and nywidth (height of window in pixels). Returns the handle (integer window index) for the opened window.
gclose	Close the specified window. Takes one argument, the window handle.
gcloseall	Close all active windows. Takes no arguments.
newcoordinate	Set up new new coordinates system
newwindow	Change the coordinates system for a window. Takes five arguments: handle, x0, y0 (bottom left), x1, y1 (top right).
layer	Set drawing and display layers (0-7 per window). Takes three arguments: handle, index of display layer, index of drawing layer
copylayer	Copy one layer to another. Takes three arguments: handle, index of source layer, index of destination layer.
gsetbgcolor	Set background colour. Takes two arguments: handle, name of colour to set to (string).
gclr	Clear the specified window. Takes one argument: handle.
tclr	Clear the current terminal window
newpencolor	Change pen colour (0-14). Takes two arguments: handle, number (0-14) or colour name (black, white, red, green, blue cyan, magenta, yellow, dimgray, gray, darkred, darkgreen, darkblue, darkcyan, darkmagenta, darkyellow).
newcolor	Specify a new colour (X name). Takes two arguments: handle, name of colour to set to (string).
newrgbcolor	Specify a new colour (RGB values). Takes four arguments: handle, R, G, B.
newlinewidth	Specify line width. Takes two arguments: handle, line width.
newlinestyle	Specify line style. Takes two arguments: handle, line style (0=solid, 1=dotted).
pset	Draw a point. Takes three arguments: handle, xcoordinate, ycoordinate.
drawline	Draw a line. Takes five arguments: handle, x0, y0, x1, y1.
moveto	Move pen to point. Takes three arguments: handle, xcoordinate, ycoordinate.
lineto	Draw line from current pen location to point Takes three arguments: handle, xcoordinate, ycoordinate.
drawrect	Draw a rectangle. Takes five arguments: handle, x, y, width, height.
fillrect	Fill a rectangle. Takes five arguments: handle, x, y, width, height.
drawcirc	Draw a circle (ellipse). Takes five arguments: handle, x, y, xradius, yradius.
fillcirc	Fill a circle Takes five arguments: handle, x, y, xradius, yradius.
drawsym	Draw a symbol Takes three to five arguments: handle, x, y, optional type (1-10), optional size.
drawstr	Print a string on the window at specified position Takes four to five arguments: handle, x, y, string, optional size.
drawnum	Print a number on the window at specified position Takes four to six arguments: handle, x, y, string, optional size, optional number of digits.
gsetnonblock	Set event handling to be nonblocking
ggetch	Get a character from the keyboard if focus on window
ggetevent	Get a keyboard or mouse event for window
ggetxpress	Get a keyboard or mouse event for window

Example:

>> eval  
%% (define  (interval-list m n)
  (if (> m n)
      '()
      (cons m (interval-list (+ 1 m) n))))
(define (sieve l)
  (define (remove-multiples n l)
    (if (null? l)
        '()
        (if  (= (modulo (car l) n) 0)      ; division test
             (remove-multiples n (cdr l))
             (cons (car l)
                   (remove-multiples n (cdr l))))))
  (if (null? l)
      '()
      (cons (car l)
            (sieve (remove-multiples (car l) (cdr l))))))
(define (primes<= n)
  (sieve (interval-list 2 n)))
%% (primes<= 300)
(2 3 5 7 11 13 17 19 23 29 31 37 41 43 47 53 59 61 67 71 73 79 83 89 97 
101 103 107 109 113 127 131 137 139 149 151 157 163 167 173 179 181 191 
193 197 199 211 223 227 229 233 239 241 251 257 263 269 271 277 281 283 293)
%% (quit)
Leaving scheme!
>> eval (primes<= 30)
(2 3 5 7 11 13 17 19 23 29)
>> eval (define a "hello")
a
>> echo %a
hello
>> eval (define a '(10 9 8))
a
>>  echo %a[2]
 9