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.nitschke at uniklinik-freiburg.de
URL: http://www.uniklinik-freiburg.de/fbi/people/kai-nitschke.html
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.nitschke at 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.nitschke at 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.nitschke at uniklinik-freiburg.de > URL: http://www.uniklinik-freiburg.de/fbi/people/kai-nitschke.html > > ______________________________________________ > R-devel at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel >-- Gabriel Becker, PhD Associate Scientist (Bioinformatics) Genentech Research [[alternative HTML version deleted]]
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 <gmbecker at 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.nitschke at 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.nitschke at 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.nitschke at uniklinik-freiburg.de >> URL: http://www.uniklinik-freiburg.de/fbi/people/kai-nitschke.html >> >> ______________________________________________ >> R-devel at r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-devel >> > > > > -- > Gabriel Becker, PhD > Associate Scientist (Bioinformatics) > Genentech Research >