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/
