Nevil Amos
2010-May-20 09:34 UTC
[R] Geneland error on unix: Error in MCMC(........ :, unused argument(s) (ploidy = 2, genotypes = geno)
I am receiving the above error ( full r session output below) the
script runs OK in windows. and "genotypes" and "ploidy" are
both
correct arguments
any suggestions would be most welcome
Nevil Amos
MERG/ACB
Monash University School of Biological Sciences
> library(Geneland)
Loading required package: RandomFields
Loading required package: fields
Loading required package: spam
Package 'spam' is loaded. Spam version 0.21-0 (2010-03-13).
Type demo( spam) for some demos, help( Spam) for an overview
of this package.
Help for individual functions is optained by adding the
suffix '.spam' to the function name, e.g. 'help(chol.spam)'.
Attaching package: 'spam'
The following object(s) are masked from 'package:base':
backsolve, forwardsolve, norm
Try help(fields) for an overview of this library
fields web: http://www.image.ucar.edu/Software/Fields
Loading required package: mapproj
Loading required package: maps
Loading required package: snow
Loading required package: tcltk
Loading Tcl/Tk interface ... done
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
o Geneland is loaded o
o o
o * Please * o
o o
o Register on o
o http://www2.imm.dtu.dk/~gigu/Geneland/register.php o
o o
o See manual on o
o http://www2.imm.dtu.dk/~gigu/Geneland/#Manual o
o o
o Type citation("Geneland") for a quick citation guide o
o o
o See http://www2.imm.dtu.dk/~gigu/Geneland/# o
o for additional references o
o o
o This is Geneland-3.2.1 o
o o
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Warning message:
In fun(...) : no DISPLAY variable so Tk is not available
> DIRLIST<-c("Adult_ALL
NO_ANW/")#,"Adult_Or_ANW/","Adult_Females/","Adult_Males/")
> for(d in DIRLIST){
+ theWd<- paste("/nfs/monash/home/namos/Rwork/",d,sep="")
+ setwd(theWd)
+ SPP.CODES
<-"EYR"#c("BT","EYR","FH","SPP","STP")
+ for (sp in SPP.CODES){
+ path.sp<- paste(theWd,sp,"/",sep="")
+ dir.create(path.sp)
+ GENO.TABLE<-paste(theWd,sp,"geno",sep="")
+ XY.TABLE<-paste(theWd,sp,"xy",sep="")
+ MINPOP=1
+ MAXPOP=25
+ INITPOP=1
+ NITS=500000
+ THIN=NITS/1000
+ nrun <- 10
+ burnin <- 200
+ geno<-noquote(read.table(GENO.TABLE))
+ coord<-read.table(XY.TABLE)
+
+ ## Loop for multiple runs
+
+ for(irun in 1:nrun)
+ {
+ ## define path to MCMC directory
+
+ path.mcmc <- paste(path.sp,irun,"/",sep="")
+ dir.create(path.mcmc)
+ MCMC(coordinates=coord, ploidy=2, genotypes=geno, varnpop=T,
npopmax=MAXPOP, npopinit=MINPOP, spatial=T, freq.model="Correlated",
nit=NITS, thinning=500, rate.max=nrow(geno), delta.coord=100,
path.mcmc=path.mcmc)
+ ## MCMC postprocessing
+ PostProcessChain(coordinates=coord,path.mcmc=path.mcmc,genotypes=geno,
nxdom=50,nydom=50,burnin=burnin)
+ }
+ ## Computing average posterior probability
+
+ lpd <- rep(NA,nrun)
+ for(irun in 1:nrun)
+ {
+ path.lpd <-
paste(path.mcmc,"log.posterior.density.txt",sep="")
+ lpd[irun] <- mean(scan(path.lpd)[-(1:burnin)])
+ }
+ ## Runs sorted by decreasing average posterior probability:
+ order(lpd,decreasing=TRUE)
+
+ #pdf("Number of pops.pdf",((210-10)/25.4),((297-10)/25.4))
+ #theWd<-getwd()
+ ##setwd(theWd)
+ #par(mfrow = c(5, 2),cex=0.25)
+ #for(irun in 1:nrun)
+ #
+ #{
+ #
+ ###Below is code form the Geneland Plotnpop function
+ # fileparam <- paste(path.mcmc, "parameters.txt", sep =
"")
+ # param <- as.matrix(read.table(fileparam))
+ # thinning <- as.numeric(param[param[, 1] == "thinning", 3])
+ # filenpop <- paste(path.mcmc, "populations.numbers.txt", sep
= "")
+ # npop <- scan(filenpop)
+ # sub <- -(1:burnin)
+ #
+ #plot((1:length(npop)) * thinning, npop, type = "l",ylab =
"Number of
classes", xlab = "Index of MCMC iteration Whole
chain",main=paste(path.mcmc,"\n","Run:", irun, sep =
" "), ylim = c(1,
max(npop)+ 0.5))
+ #hist(npop[sub], plot = TRUE, prob = TRUE, breaks = seq(0.5,max(npop)
+ 0.5, 1), xlab = paste("Nb. of pop. along the chain (after a burnin of
", burnin, "x", thinning, "i t.)", sep = ""),
main = "Number of
populations long the chain after burnin")
+ #
+ #
+ #}
+ #dev.off()
+ }
+ }
Error in MCMC(coordinates = coord, ploidy = 2, genotypes = geno, varnpop
= T, :
unused argument(s) (ploidy = 2, genotypes = geno)
Execution halted
Jombart, Thibaut
2010-May-20 09:48 UTC
[R] Geneland error on unix: Error in MCMC(........ :, unused argument(s) (ploidy = 2, genotypes = geno)
Hello,
you may want to contact directly the maintainer of Geneland for that kind of
issue. In any case, this post would be best suited for R-sig-genetics:
https://stat.ethz.ch/mailman/listinfo/r-sig-genetics
Best regards,
Thibaut
--
######################################
Dr Thibaut JOMBART
MRC Centre for Outbreak Analysis and Modelling
Department of Infectious Disease Epidemiology
Imperial College - Faculty of Medicine
St Mary?s Campus
Norfolk Place
London W2 1PG
United Kingdom
Tel. : 0044 (0)20 7594 3658
t.jombart at imperial.ac.uk
http://sites.google.com/site/thibautjombart/
http://adegenet.r-forge.r-project.org/
________________________________________
From: Nevil Amos [nevil.amos at gmail.com]
Sent: 20 May 2010 10:34
To: r-help at r-project.org; Jombart, Thibaut
Subject: Geneland error on unix: Error in MCMC(........ :, unused argument(s)
(ploidy = 2, genotypes = geno)
I am receiving the above error ( full r session output below) the
script runs OK in windows. and "genotypes" and "ploidy" are
both
correct arguments
any suggestions would be most welcome
Nevil Amos
MERG/ACB
Monash University School of Biological Sciences
> library(Geneland)
Loading required package: RandomFields
Loading required package: fields
Loading required package: spam
Package 'spam' is loaded. Spam version 0.21-0 (2010-03-13).
Type demo( spam) for some demos, help( Spam) for an overview
of this package.
Help for individual functions is optained by adding the
suffix '.spam' to the function name, e.g. 'help(chol.spam)'.
Attaching package: 'spam'
The following object(s) are masked from 'package:base':
backsolve, forwardsolve, norm
Try help(fields) for an overview of this library
fields web: http://www.image.ucar.edu/Software/Fields
Loading required package: mapproj
Loading required package: maps
Loading required package: snow
Loading required package: tcltk
Loading Tcl/Tk interface ... done
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
o Geneland is loaded o
o o
o * Please * o
o o
o Register on o
o http://www2.imm.dtu.dk/~gigu/Geneland/register.php o
o o
o See manual on o
o http://www2.imm.dtu.dk/~gigu/Geneland/#Manual o
o o
o Type citation("Geneland") for a quick citation guide o
o o
o See http://www2.imm.dtu.dk/~gigu/Geneland/# o
o for additional references o
o o
o This is Geneland-3.2.1 o
o o
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Warning message:
In fun(...) : no DISPLAY variable so Tk is not available
> DIRLIST<-c("Adult_ALL
NO_ANW/")#,"Adult_Or_ANW/","Adult_Females/","Adult_Males/")
> for(d in DIRLIST){
+ theWd<- paste("/nfs/monash/home/namos/Rwork/",d,sep="")
+ setwd(theWd)
+ SPP.CODES
<-"EYR"#c("BT","EYR","FH","SPP","STP")
+ for (sp in SPP.CODES){
+ path.sp<- paste(theWd,sp,"/",sep="")
+ dir.create(path.sp)
+ GENO.TABLE<-paste(theWd,sp,"geno",sep="")
+ XY.TABLE<-paste(theWd,sp,"xy",sep="")
+ MINPOP=1
+ MAXPOP=25
+ INITPOP=1
+ NITS=500000
+ THIN=NITS/1000
+ nrun <- 10
+ burnin <- 200
+ geno<-noquote(read.table(GENO.TABLE))
+ coord<-read.table(XY.TABLE)
+
+ ## Loop for multiple runs
+
+ for(irun in 1:nrun)
+ {
+ ## define path to MCMC directory
+
+ path.mcmc <- paste(path.sp,irun,"/",sep="")
+ dir.create(path.mcmc)
+ MCMC(coordinates=coord, ploidy=2, genotypes=geno, varnpop=T,
npopmax=MAXPOP, npopinit=MINPOP, spatial=T, freq.model="Correlated",
nit=NITS, thinning=500, rate.max=nrow(geno), delta.coord=100,
path.mcmc=path.mcmc)
+ ## MCMC postprocessing
+ PostProcessChain(coordinates=coord,path.mcmc=path.mcmc,genotypes=geno,
nxdom=50,nydom=50,burnin=burnin)
+ }
+ ## Computing average posterior probability
+
+ lpd <- rep(NA,nrun)
+ for(irun in 1:nrun)
+ {
+ path.lpd <-
paste(path.mcmc,"log.posterior.density.txt",sep="")
+ lpd[irun] <- mean(scan(path.lpd)[-(1:burnin)])
+ }
+ ## Runs sorted by decreasing average posterior probability:
+ order(lpd,decreasing=TRUE)
+
+ #pdf("Number of pops.pdf",((210-10)/25.4),((297-10)/25.4))
+ #theWd<-getwd()
+ ##setwd(theWd)
+ #par(mfrow = c(5, 2),cex=0.25)
+ #for(irun in 1:nrun)
+ #
+ #{
+ #
+ ###Below is code form the Geneland Plotnpop function
+ # fileparam <- paste(path.mcmc, "parameters.txt", sep =
"")
+ # param <- as.matrix(read.table(fileparam))
+ # thinning <- as.numeric(param[param[, 1] == "thinning", 3])
+ # filenpop <- paste(path.mcmc, "populations.numbers.txt", sep
= "")
+ # npop <- scan(filenpop)
+ # sub <- -(1:burnin)
+ #
+ #plot((1:length(npop)) * thinning, npop, type = "l",ylab =
"Number of
classes", xlab = "Index of MCMC iteration Whole
chain",main=paste(path.mcmc,"\n","Run:", irun, sep =
" "), ylim = c(1,
max(npop)+ 0.5))
+ #hist(npop[sub], plot = TRUE, prob = TRUE, breaks = seq(0.5,max(npop)
+ 0.5, 1), xlab = paste("Nb. of pop. along the chain (after a burnin of
", burnin, "x", thinning, "i t.)", sep = ""),
main = "Number of
populations long the chain after burnin")
+ #
+ #
+ #}
+ #dev.off()
+ }
+ }
Error in MCMC(coordinates = coord, ploidy = 2, genotypes = geno, varnpop
= T, :
unused argument(s) (ploidy = 2, genotypes = geno)
Execution halted