Hi,
This post might get you started:
http://romainfrancois.blog.free.fr/index.php?post/2009/03/07/What-functions-are-called-by-my-function
> tail( callees( nls ), 20 )
functions
names new.env nls.control nlsModel
8 1 2 2
nlsModel.plinear nls_port_fit nrow NROW
1 1 1 1
numeric parent.frame paste range
1 2 7 1
rep sapply sQuote stop
3 2 2 6
substitute switch tryCatch warning
3 2 1 5
Note that it gives you the special and builtins as well, so this like
"(", "[", "{" which you can filter out using something like this :
> funs <- callees( nls )
> funs[ grepl( "[.[:alpha:]]", names(funs) ) ]
functions
all.vars any as.character as.formula
2 3 3 2
as.integer as.list as.name assign
1 4 3 1
attr c .Call class
6 1 1 1
diff environment eval eval.parent
1 4 5 1
A bit more work would be required to filter out the ones you consider
"trivial", maybe this can help :
> sapply( names(funs), find )
$`<`
[1] "package:base"
$`<-`
[1] "package:base"
...
Too bad find only works with one object at once ... I have this
simplified version in package svTools :
# Similar to "find" but `what` can be a vector
# also, this one only searches in packages (position of the search path
# matching '^package:') and only gives one result per what
".find.multiple" <- function (what){
stopifnot(is.character(what))
sp <- grep( "^package:", search(), value = TRUE)
out <- rep( "" , length(what))
for (i in sp) {
ok <- what %in% ls(i, all.names = TRUE) & out == ""
out[ok] <- i
if (all(out!="")) break
}
names(out) <- what
sub("^package:", "", out)
}
> .find.multiple( names( funs ) )
< <- == >
"base" "base" "base" "base"
| || - :
"base" "base" "base" "base"
...
but this is probably not good enough since it ignores namespaces,
lexical scoping, ...
Another way is to use the -- about to be released -- "parser" package
(see highlight project on r-forge:
http://r-forge.r-project.org/projects/highlight/)
> require( parser )
> data <- attr( parser( "/tmp/nls.txt" ), "data" )
> data[ data$token.desc == "SYMBOL_FUNCTION_CALL", "text" ]
[1] "parent.frame" "nls.control" "c"
[4] "as.formula" "match.arg" "is.list"
[7] "is.environment" "stop" "match.call"
[10] "all.vars" "length" "all.vars"
...
but again this is only based on the parser and does not care about
namespaces or scoping
Anyway, hope this helps.
Romain
On 07/23/2009 08:28 AM, Andrej-Nikolai Spiess wrote:
Dear R-helpers,
does anyone know of some package/function that can build a network from
the functions that are implemented in a package,
i.e. visualize the cross-references from one function to another in the
same or some dependent package?
An example would be a function like 'nls' on top of the hierarchy and
then a network of nodes from the functions that are called within 'nls'
such as
'getInitial', 'nlsModel', 'nls_port_fit' etc. Important maybe also some
way to tweak such as not to include< trivial> functions such as
'as.formula'.
Many thanks in advance,
Andrej
_____________________________________
Dr. rer. nat. Andrej-Nikolai Spiess (Dipl. Biol.)
Department of Andrology
University Hospital Hamburg-Eppendorf
Martinistr. 52
20246 Hamburg
phone: +49-40-7410-51585
fax: +49-40-7410-51554
email: a.spi...@uke.de
--
Romain Francois
Independent R Consultant
+33(0) 6 28 91 30 30
http://romainfrancois.blog.free.fr
|- http://tr.im/tlNb : RGG#155, 156 and 157
|- http://tr.im/rw0p : useR! slides
`- http://tr.im/rw0b : RGG#154: demo of atomic functions
______________________________________________
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
