Dear Klaus, You were correct. This fixed the problem.
Many thanks, Mike On Fri, Jan 1, 2016 at 5:41 PM, Klaus Schliep <klaus.schl...@gmail.com> wrote: > Happy New Year, > it seems you have not properly installed the packages and you may want > also update R. > Cheers, Klaus > > On Fri, Jan 1, 2016 at 12:34 AM, Michael Pauers <mjpau...@gmail.com> > wrote: > >> Dear list, >> >> First, Happy New Year! >> >> Second, I will apologize in advance, as I am nothing more than a duffer >> with R, so I may ask several follow-up questions to this one. >> >> I have a set of 1000 trees that lack branch lengths. I have used >> previously used ape to calculate branch lengths on a single tree, but >> never >> on a multiphylo object. I did find and have tried the approach documented >> at this link: >> >> http://blog.phytools.org/2015/04/phylogenetic-regression-when-branch.html >> >> but I received a few error messages, including: >> >> > library(phytools) >> Error in gzfile(file, "rb") : cannot open the connection >> In addition: Warning messages: >> 1: package ‘phytools’ was built under R version 3.0.3 >> 2: In read.dcf(file.path(p, "DESCRIPTION"), c("Package", "Version")) : >> cannot open compressed file 'C:/Program >> Files/R/R-3.0.2/library/ape/DESCRIPTION', probable reason 'No such file or >> directory' >> 3: In gzfile(file, "rb") : >> cannot open compressed file '', probable reason 'No such file or >> directory' >> > library(phangorn) >> Error in gzfile(file, "rb") : cannot open the connection >> In addition: Warning messages: >> 1: package ‘phangorn’ was built under R version 3.0.3 >> 2: In read.dcf(file.path(p, "DESCRIPTION"), c("Package", "Version")) : >> cannot open compressed file 'C:/Program >> Files/R/R-3.0.2/library/ape/DESCRIPTION', probable reason 'No such file or >> directory' >> 3: In gzfile(file, "rb") : >> cannot open compressed file '', probable reason 'No such file or >> directory' >> >> and: >> >> > library(ape) >> > ## simulate 200 pure-birth trees: >> > trees<-ttrees<-pbtree(n=50,scale=1,nsim=200) >> Error: could not find function "pbtree" >> > ## ttrees contains the trees with their original branch lengths >> > ## we'll perform manipulations on trees >> > foo<-function(tree){ >> + obj<-fastBM(tree,nsim=2) >> + colnames(obj)<-c("x","y") >> + as.data.frame(obj) >> + } >> > xy<-lapply(ttrees,foo) >> Error in lapply(ttrees, foo) : object 'ttrees' not found >> > library(nlme) >> > fit.model<-function(tree,data){ >> + data$v<-diag(vcv.phylo(tree)) >> + fit<-gls(y~x,data=data,correlation=corBrownian(1,tree), >> + weights=varFixed(~v)) >> + setNames(c(coefficients(fit)[2],anova(fit)$"p-value"[2]), >> + c("beta","p-value")) >> + } >> > fit.true<-t(mapply(fit.model,trees,xy)) >> Error in mapply(fit.model, trees, xy) : object 'xy' not found >> > mean(fit.true[,1]) ## should be zero >> Error in mean(fit.true[, 1]) : object 'fit.true' not found >> > noogtree<-lapply(noogtree,compute.brlen) >> > class(noogtree)<-"multiPhylo" >> > fit.grafen<-t(mapply(fit.model,noogtree,xy)) >> Error in mapply(fit.model, noogtree, xy) : object 'xy' not found >> > utils:::menuInstallPkgs() >> Error in install.packages(NULL, .libPaths()[1L], dependencies = NA, type = >> type) : >> no packages were specified >> > fit.grafen<-t(mapply(fit.model,noogtree)) >> Error in data$v <- diag(vcv.phylo(tree)) : >> argument "data" is missing, with no default >> > fit.grafen<-t(mapply(fit.model,noogtree,xy)) >> Error in mapply(fit.model, noogtree, xy) : object 'xy' not found >> > mean(fit.grafen[,1]) >> Error in mean(fit.grafen[, 1]) : object 'fit.grafen' not found >> > foo<-function(tree){ >> + tree$edge.length<-rep(1,nrow(tree$edge)) >> + tree >> + } >> > trees<-lapply(ttrees,foo) >> Error in lapply(ttrees, foo) : object 'ttrees' not found >> > class(trees)<-"multiPhylo" >> > fit.equal<-t(mapply(fit.model,trees,xy)) >> Error in mapply(fit.model, trees, xy) : object 'xy' not found >> > mean(fit.equal[,1]) ## should be zero >> Error in mean(fit.equal[, 1]) : object 'fit.equal' not found >> >> Does anyone have any advice? Please let me know if I should provide more >> information. >> >> Thanks in advance, >> >> Mike Pauers >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> R-sig-phylo mailing list - R-sig-phylo@r-project.org >> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo >> Searchable archive at >> http://www.mail-archive.com/r-sig-phylo@r-project.org/ > > > > > -- > Klaus Schliep > Postdoctoral Fellow > Revell Lab, University of Massachusetts Boston > > [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
