search for: mytree

...identified a correlation between the corrupt trees and the working tree. It is the same code with the same data set. The only difference is that the training data is sampled randomly from the complete data set. The "copy-pasted" code below illustrates: > data <- load.data() > mytree <- run.tree(data) > mypred <- gen.predictions(mytree, data )...

Dear all, I don't understand the following behaviour: Running compar.gee (in library ape ) with and without the option 'data', it give me different results Example: .... Start R .... > load("eiber.RData") > ls() [1] "gee.na" "mydata" "mytree" > library(ape) > # runnig with the option data= mydata > compar.gee(alt ~ R, family="gaussian", data=mydata, phy=mytree) Loading required package: gee [1] "Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27" [1] "running glm to get initial regressi...

Dear all, I'm using the "ape" package in R and want to draw a phylogenetic tree with not only the tip labels but also some labels for the edges. e.g. Mark the edge AB as "m" in the tree ABC. Couldn't find a way to do that. Can someone help? Thanks, Hua

Dear All When drawing a classification tree with plot(mytree) text(mytree) the conditions are written just before the nodes branch. My question is: can one be certain that those conditions refer to the left-side branches? (The R documentation surprisingly lacks the information that I am asking for.) Thanks in advance, Paul

Hi all, I used rpart to fit a model, where the covariates in the model are categorical variables. Then I plotted the tree (mytree) and used the command "text" to add labels to the tree. In the nodes of the tree, the values of the covariates are represented with a, b or c. Is there a way to show the real value(s) of the variable in the nodes instead of a, b or c ? I found that the command "labels(mytree,minleng...

...ot;127"/><service name="netbios-ssn" method="probed" conf="10"/></port> </ports> <times srtt="647" rttvar="71" to="100000"/> </host>' I want to store this as a list of lists, so I do: mytree<-xmlTreeParse(mydoc) myroot<-xmlRoot(mytree) mylist<-xmlToList(myroot) Now my problem is that when I want to fetch the attributes of the services running of each port, the behavior is not consistent: > mylist[["ports"]][[1]][["service"]]$.attrs["name"]...

Hello I am trying to store output from a loop into an empty matrix. The current code I am using is: > M<-mat.or.vec(11,89) > for (j in list(3,91)) + {M[,(j-2)]<-pic(datain[,j], mytree)} datain is a matrix (11,91). I only want to use the pic() function on the columns 3:91. When I use this code output is stored into the 1st column of M and the 89th column of M but no other columns. Any help would be greatly appreciated Dean

Hello, Please let me know if this is a bug or a feature. I used to be able to do the following with 2.5.5. On a remote host I have /mytree and I mirrored at my local host as a regular user doing rsync -avz --delete kent@host:/mytree /. with 2.5.6 I get mkstemp .file.aFhK3N failed: Permission denied probably because rsync2.5.6 is attempting to create a temporary file on the root directory, which I don't have write permission. On...

...xcellent ape package (http://cran.r-project.org/src/contrib/Descriptions/ape.html) to import the evolutionary dendrograms. I have already manipulated the dendrogram to be ultrameric, with branches all the same length, to prevent an error, although I would prefer not to have to do so: library(ape) mytree <- read.tree(file = "ultra.newick", text = NULL, tree.names = NULL, skip = 0, comment.char = "#") #I then change them into a hclust: tree <- as.hclust(mytree) #and make this into a dendrogram dend <- as.dendrogram(tree) However, when I use this dendrogram as part of th...

Is there way on import or add to exclude directories? (Obvious candidate being log or tmp dirs.) I''m imagining something like this: $ svn import mytree file:///usr/local/svn/newrepos/some/project --exclude /tmp --exclude /log \ I have scoured "Version Control with Subversion" without luck but maybe I don''t understand some terminology somewhere... -- Posted via http://www.ruby-forum.com/. --~--~---------~--~----~------------...

I'm trying to create an app using TclTk and R Can someone please explain how I bind a click event to the tree widget (http://bioinf.wehi.edu.au/~wettenhall/RTclTkExamples/TreeWidget.html) Ideally I'd like to bind to particular elements in the tree but tkbind doesnt seem to work. thanks tom

I am using the function cutreeHybrid from the package dynamic Tree Cut and I need a list of the resulting clusters but I do not know how to get it. [[alternative HTML version deleted]]