Re: [Rd] C_LogLin (stats/loglin)

[Kai Nitschke]

Hi Gabriel,

it actually works with: z <- .Call(stats:::C_LogLin, dtab, conf,  
table, start, nmar, eps, iter).

This helps me a great deal. I will inform myself further about SEXPs.

Thank you very much,
 Kai

Zitat von Gabriel Becker <gmbec...@ucdavis.edu>:

Kai,

Apologies for the double message, it didn't go to the list last time.

On Thu, Oct 22, 2015 at 9:59 AM, Kai Nitschke <
kai.nitsc...@uniklinik-freiburg.de> wrote:


“.Call” calls the C/C++ function “C_LogLin”. But when I am running it line
by line I get
the following error on line 23/24:
Error: object 'C_LogLin' not found

Hence, my questions:
1. Where does the original “loglin” function get the “C_LogLin” function
from (some libraries? where are they stored)?


The libraries are in the stats package, built from the c code found in the
/src  directory of the package's source code.


2. Why does it not work in the normal R command (line by) line but in the
implemented “loglin” function?


Notice that C_LogLin is not in quotes. That is actually an R object, not a
string, and it is one that is not exported by the stats package.
stats:::C_LogLin would probably work.


3. Is it possible to isolate the “C_LogLin” function so I can use it in
other scripts or programming languages e.g. Matlab?



A function called by the .Call interface is going to operate on R's
internal representation of R objects, called SEXPs, It won't work in other
languages without major reworking (I can't say how major without looking
for at the code to see if, e.g., it's just a wrapper that calls another c
function that might be amenable to that). Even then, you'd have to look at
if/how it deals with NAs, etc.

~G

On Thu, Oct 22, 2015 at 9:59 AM, Kai Nitschke <
kai.nitsc...@uniklinik-freiburg.de> wrote:

Hi everyone,

I have a question regarding a C function of the "stats" package in R.

I tried to understand the “loglin” basic function of the “stats” package
implemented in
R. The implemented function itself runs without any problem (perhaps see
sample). When I
ran it line by line it stopped at the lines 23-24 of the loglin-function;
(the following line):
z <- .Call(C_LogLin, dtab, conf, table, start, nmar, eps, iter)

“.Call” calls the C/C++ function “C_LogLin”. But when I am running it line
by line I get
the following error on line 23/24:
Error: object 'C_LogLin' not found

Hence, my questions:
1. Where does the original “loglin” function get the “C_LogLin” function
from (some libraries? where are they stored)?
2. Why does it not work in the normal R command (line by) line but in the
implemented “loglin” function?
3. Is it possible to isolate the “C_LogLin” function so I can use it in
other scripts or programming languages e.g. Matlab?

Thank you in advance for your help,
 Kai

--------------------------------------------
#Sample

# Example data
mytable = array(0,dim=c(3,4,5))
mytable[1,,1] = c(35,26,36,29); mytable[2,,1] = c(21,12,26,27);
mytable[3,,1] = c(9,26,23,38);
mytable[1,,2] = c(43,26,89,26); mytable[2,,2] = c(78,42,32,9);
mytable[3,,2] = c(34,39,42,51);
mytable[1,,3] = c(51,72,62,21); mytable[2,,3] = c(6,52,71,32);
mytable[3,,3] = c(35,36,48,21);
mytable[1,,4] = c(12,26,53,42); mytable[2,,4] = c(96,75,81,56);
mytable[3,,4] = c(32,65,75,63);
mytable[1,,5] = c(21,18,24,33); mytable[2,,5] = c(22,56,36,91);
mytable[3,,5] = c(32,65,63,14);

# Call of the original function works fine
loglin(mytable,list(c(1,2),c(1,3)))

# line by line does not work
table = mytable; margin = list(c(1,2),c(1,3)); start = rep(1,
length(table)); fit = FALSE; eps = 0.1;
iter = 20L; param = FALSE; print = TRUE;
rfit <- fit
dtab <- dim(table)
nvar <- length(dtab)
ncon <- length(margin)
conf <- matrix(0L, nrow = nvar, ncol = ncon)
nmar <- 0
varnames <- names(dimnames(table))
for (k in seq_along(margin)) {
        tmp <- margin[[k]]
        if (is.character(tmp)) {
            ## Rewrite margin names to numbers
            tmp <- match(tmp, varnames)
            margin[[k]] <- tmp
        }
        conf[seq_along(tmp), k] <- tmp
        nmar <- nmar + prod(dtab[tmp])
}
ntab <- length(table)
if (length(start) != ntab ) stop("'start' and 'table' must be same length")
z <- .Call(C_LogLin, dtab, conf, table, start, nmar, eps, iter)
...


--
Kai Nitschke, Dipl.-Psych.

Division of Functional Brain Imaging (FBI)
Dept. of Neurology, University of Freiburg

Breisacher Str. 64, 79095 Freiburg, Germany
Phone: +49 (0) 761 270 - 50410
Email: kai.nitsc...@uniklinik-freiburg.de
URL: http://www.uniklinik-freiburg.de/fbi/people/kai-nitschke.html

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--
Gabriel Becker, PhD
Associate Scientist (Bioinformatics)
Genentech Research


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