search for: phylo

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" [4,] "...

Hello, The following code does'nt work for me. The last command reports an error. I have created a consensus tree using the consensus comand from phylo but cannot manipulate the phylo object afterwards to create a dendogram , by transforming the phylo object into a hclust object and then into a dendogram ?? Thanks for any help library(ade4) library(cluster) library(stats) library(ape) data<-read.table(file="in.matrix",header=FALS...

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.c...

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 ord...

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 because the tree is not ultrametric. Is there no way to convert a non-ultrametric tree of class "phylo" into a "de...

...ect - 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, but that doesn't enable me to turn it back into an hclust object. Are there any functions that can aid with this? Maybe through the ape package and the phylo objects? Thanks, Tal ----------------Contact Details:------------------------------------------------------- Contact me: Tal.Galili@gmail.com | 972-52-7275845 Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) | www.r-statistics.com (English) -------------------------------...

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 this "Error in UseMethod("as.phylo") : no applicable method for 'as.phylo' applied to an object of class "character": data = read...

...g, which is not nearly the detail that goes into this function. I am wondering how to begin cracking this function open (and others) so I can learn more about it and perhaps code my own corClass one day. Thanks. > corBrownian function (value = 1, phy, form = ~1) { if (!inherits(phy, "phylo")) stop("object \"phy\" is not of class \"phylo\"") attr(value, "formula") <- form attr(value, "fixed") <- TRUE attr(value, "tree") <- phy class(value) <- c("corBrownian", "corPhyl&qu...

Hi, I was recently splitting some massive phylo class objects with extract.clade() and noticed what appears to be a bug in how tip labels are copied from the full tree to the pruned tree. This possible bug was also mentioned here: http://www.mail-archive.com/r-sig-phylo at r-project.org/msg00537.html An example: library(ape) set.seed(5) x &...

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 pro...

Dear list, I am trying to plot a radial dendrogram using the ape package, which requires my data to be of class 'phylo'. Currently I have my dendrogram stored as an object of class 'dendrogram' which was produced from an outside bit of C code, but was made into an object of class 'igraph.eigenc' and converted to a dendrogram using 'as.dendrogram()' from the igraph package. I would like t...

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

...Samba 3.0.) Invalid combination of parameters for service Public. Level II oplocks can only be set if oplocks are also set. Invalid combination of parameters for service homes. Level II oplocks can only be set if oplocks are also set. Server role: ROLE_DOMAIN_PDC 2. pings - OK 3. smbclient -L PHYLO Everything looks OK, including information for server, workgroup and master. 4. nmblookup -B PHYLO __SAMBA__ - looks OK added interface ip=155.101.106.50 bcast=155.101.106.255 nmask=255.255.255.0 querying __SAMBA__ on 155.101.106.50 Got a positive name query response from 155.101.106.50 ( 155....

Hi, Using Ape, I have constructed an object of class "phylo", using the method 'nj' (lets call the object 'tree_ja'). I also have a given subset of 'tree_ja' in a vector (lets call the vector 'subspecies'). What I want to do, is construct a nj tree - plot(tree_ja) - but have the species in vector 'subspecies'...

I saw an example online of taking hclust dendrogram and plotting it using ggplot2 and thought I would give it a try to see what it would look like. I get an error when trying to use ggplot; Error: ggplot2 doesn't know how to deal with data of class phylo. Regular plot works fine but I can't get ggplot2 to work. see code below.... rows=100 columns=100 #create matrix all=matrix(nrow=rows, ncol=columns) #initialize first column all[,1]=rbinom(rows,1,.5) #set probability probv=.9 for (j in 2:columns) { for (i in 1:rows) { #...

...=========== Nicholas J. Matzke Ph.D. Candidate, Graduate Student Researcher Huelsenbeck Lab Center for Theoretical Evolutionary Genomics 4151 VLSB (Valley Life Sciences Building) Department of Integrative Biology University of California, Berkeley Graduate Student Instructor, IB200B Principles of Phylogenetics: Ecology and Evolution http://ib.berkeley.edu/courses/ib200b/ http://phylo.wikidot.com/ Lab websites: http://ib.berkeley.edu/people/lab_detail.php?lab=54 http://fisher.berkeley.edu/cteg/hlab.html Dept. personal page: http://ib.berkeley.edu/people/students/person_detail.php?person=370 Lab...

...9 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable to trigger the bug: plot(0:1,0:1) text(0.5,0.5,"abc",srt=3D-1e-9) this doesn't happen for positive, small srt, or for negative srt with magnitude greater than about 1e-8 (the example in plot.phylo in the ape package triggers it, with a srt value of -3e-15). plot(0:1,0:1) for (i in 1:10) { cat(i,"\n") text(0.5,0.5,"hello",srt=3D(-10^-i)) } I have traced this a fair ways into the C code -- I think it happens somewhere in clipText -- but I'm not sure. Sorry not...

Dear all, The version 1.0 of ape (analysis of phylogenetics and evolution) is now on CRAN. The jump from version 0.2-1 to 1.0 is explained by the fact that the initial objectives of the project have been completed. The relevant part of the Changes file is shown below. All comments, suggestions, or bug reports are welcome. Emmanuel Paradis...

dear group members, I am looking for a function that assess the stability of cluster. The result of hclust function is an hclust object which can be plot as a dendrogram. However to have confidence in the tree topology usualy bootstap is applied. I understand that I can apply bootstarp on the original data and then run hclust(dist() ) as much as I resampled but how to comapre the topologies the I

...fail.default(list(Phenology = c(NA_integer_, NA_integer_, : missing values in object" I'm having trouble navigating around this error message, and any suggestions would be appreciated. Thanks! Rose -- View this message in context: http://r.789695.n4.nabble.com/Model-Selection-with-Phylogenetic-Independent-Contrasts-tp3814652p3814652.html Sent from the R help mailing list archive at Nabble.com.