similar to: Cannot convert from phylo to hclust , error!!???

Hello Folks, I have 5 columns for thousands of tree records that record whether that tree was alive or dead. I want to recode the columns such that the cell reads "found" when a live tree is first observed, "alive" for when a tree is found alive and is not just found, and "mort" when it was previously alive but is now dead. Given the following: > tree_live

If visit_guest() fails, then it returns a null pointer; later on, free_tree() is called unconditionally on the variables, thus dereferencing null pointers. Thus guard the free_tree() invocations. --- diff/diff.c | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/diff/diff.c b/diff/diff.c index 5851a1c9c..1f1ab6933 100644 --- a/diff/diff.c +++ b/diff/diff.c @@ -389,8

Hi All, There is something I don't quite understand about R memory management. I have the following function function (AdGroupId) { print(memory.size()) channel <- odbcConnect("RDsn", uid = "xxxx", case = "tolower", pwd = "xxxxxx") Tree1 <- sqlQuery(channel, "exec SelectAdgroups 111120,0", as.is = c(FALSE, FALSE,

Hello, I've been trying to figure out how to access the individual elements from an object of class phylo. I am reading in 201 trees created by paup as below. > read.nexus("A_30knj_200t.txt", tree.names= NULL) -> anj30 > anj30[1] $tree1 $edge [,1] [,2] [1,] "-1" "-2" [2,] "-2" "-3" [3,] "-3" "1"

Dear All, I get some problems using the 'phylo' and dissimilarity functions in R. I converted an output from 'hclust' into an order of phylo so as to be able to use the 'consensus' function on it. Each time I submit the consensus codes, my computer hangs. When I tried to see what the contents of the object converted into order phylo is, I get the message

I am beginning to work with the 'ape' package in R, and have run into some trouble. I generated a UPGMA tree based on DNA sequence distance in Paup* and read it into R, where it became an object of class "phylo". However, I need it to be classified as a "dendrogram" for my purposes (to use it to order the layout of a heatmap). I get an error using as.hclust.phylo

[markdown format] I'm glad to introduce you the new package aVirtualTwins. This package is an adaptation of VirtualTwins method of subgroup identification from [Foster, J. C., Taylor, J. M.G. and Ruberg, S. J. (2011)](http://onlinelibrary.wiley.com/doi/10.1002/sim.4322/abstract). ### Explanation Virtual Twins has been created to find subgroup of patients in a random clinical trial with

[markdown format] I'm glad to introduce you the new package aVirtualTwins. This package is an adaptation of VirtualTwins method of subgroup identification from [Foster, J. C., Taylor, J. M.G. and Ruberg, S. J. (2011)](http://onlinelibrary.wiley.com/doi/10.1002/sim.4322/abstract). ### Explanation Virtual Twins has been created to find subgroup of patients in a random clinical trial with

Hello all, I'm now working with hclust objects and was hoping to perform some basic editing on them like: - Joining = the merging of two hclust objects (so they will share one root) - Splicing = So to cut/extract a branch out of an hclust object - that by itself will be an hclust object. I noticed I could extract one element of an hclust object by turning it into a dendrogram,

Dear all, I'm trying to use phylo.pca function from phytools for the first time. I'm using an ultrametric tree with 167 tips and all branch lengths transformed to 1. I lunched the pPCA like this: pPCA<-phyl.pca(tree,data,method = "lambda") For some reason it takes for ever and never reaches the end of the process. I tried with method="BM" and the process runs

Hi all, I am a phylogenetic student, I'm running SH test to examine free (tree1) and constrained (tree2) trees using R phangorn package. The outputs are like the following and i'm confused how should i interpret them!!!   Trees      ln L           Diff ln L    p-value [1,]     1 -1422.921   0.00000  0.4952 [2,]     2 -1457.282  34.36085  0.0201 Why it gives us two p values? Would you

I've been comparing variables among objects (taxa) related by known trees, using phylogentically independent contrasts in the ape package, and want to move on to more complex models e.g. by using gls with appropriate correlation terms. My trees contain lots of (hard) polytomies and information about ancestors, which I've been including- creating fully dichotomous trees by using zero branch

This is a call for comments, regarding what you do expect when copying multible source tree roots leading to the same directory root, using rsync. This problem may be discussed now, because in versions before rsync-2.5.6, the algorithm for removing the so called "duplicated files" was broken. That's why we expect nobody used it anyway in earlier versions - but who knows.. Example:

Hello, R-users,   I have a datafile with 37313 records and each record has 5 different measurements on the same variables. The format looks like this: treeID, VIG0, VIG1, VIG2, VIG3, VIG4 I was trying to convert the one row record to 5 rows record with format like this (treeID, MEASUREMENT, VIGOR). My code like this:   treeMeas<-matrix(data=0,nrow=(length(tree1$indivTree)*5), ncol=3)

Hello, I have a question about margins when plotting an unrooted tree (type="unrooted") with the 'ape' package ver. 1.7. When I plot an unrooted tree with: no.margin=TRUE it seems that the margins are still there. It appears to be only when type="unrooted". I'm plotting multiple plots using layout() and would like to be able to get rid of the margins or if

An embedded and charset-unspecified text was scrubbed... Name: not available URL: <https://stat.ethz.ch/pipermail/r-help/attachments/20091125/62ecd9aa/attachment-0001.pl>

Hi, I'm very much enjoying using the ape package to produce phylogenetic trees with colored branches (using edge.color). Is it also possible to specify that some branches should be drawn as dotted lines? That would be really useful. I've tried messing around with edge.width, but that doesn't seem to help me get dotted lines. thanks, Janet Young

Dear R-help subscribers, I have a quite stupid question about using lapply. I have the following function: create.gradient <- function(i){ colorgrad01<-color.scale(seq(0,1,by=0.01), extremes=c("red","blue")) tree1$edge[i,1] -> x tree1$edge[i,2] -> y print(x) print(y) all2[x] -> z all2[y] -> z2 round(z, digits = 2) -> z round(z2, digits = 2) -> z2

Hi, Use `check.names=FALSE` head(dd,2) #? Phylo.Tree Genesis.Tree #1????????? 1??????????? 2 #2????????? 2??????????? 3 ?dd <- data.frame("Phylo Tree"= c(1:10), "Genesis Tree"= c(2:11),check.names=FALSE) head(dd,2) #? Phylo Tree Genesis Tree #1????????? 1??????????? 2 #2????????? 2??????????? 3 write.csv(dd,"Crish.csv",row.names=FALSE) ?yy<-

Hi, I'm doing hierarchical clustering, and want to export my dendrogram to a tree-viewing/editing software. I can do this by converting the data to Newick format (hc2Newick in ctc package), but I can't get branch lengths to show in the resulting phylogram. I figured it might help to convert my hclust object into a phylo object (as.phylo in ape package), but the following lines give me