similar to: ctc package

Dear R helpers, I have a data set with 4 types (W, C, E & S). Now I have values for all types plus all possible combinations (the order is unimportant): W, C, WC, E, WE, CE, WCE, S, WS, CS, WCS, ES, WES, CES & WCES. Ideally I would like to represent everything in one graph and as concise as possible. Drawing 4 circles and depicting it as overlap just gives me 13 out of the 15

Hi R helpers... I am having troubles because of the discrepancy between the dendrogram plotted from hclust and what is wrote in the hc2Newick file. I've got a matrix C: > hc <- hclust(dist(C)) > plot(hc) with the: > write(hc2Newick(hc),file='test.newick') both things draw completely different "trees"... I have also tried with the raw distance matrix D and

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

Dear R-helpers and Klaus, I would like to know how to write out a tree file with bootstrap from phangorn package. That tree file could be in newick format or others. I am new for phylogenetic operation in R. Could you please give me any directions on that? Thanks in advance. Best wishes, Jian-Feng, ######## # as a example # I accomplished 1000 bootstrap simulation on a fit object (a maximum

Dear List members, I would like to test whether an observed occupancy of lakes in a landscape has occurred randomly (by chance) or not. How can I do that? The problem is that it concerns only a single species and I would like to use binary data only. At first I thought of generating null models and test the observed occupancy against the randomly generated one. However, this needs more than one

I am having trouble displaying a dendrogram of evolutionary relationships (a phylogram imported from the ape package) as the vertical component of a heatmap, but keeping the hierarchical clustering of the horizontal component. The relationships of the vertical component in the generated heatmap are not that of the dendrogram, although the ordering is. In more detail, I am attempting to generate

Greetings I have a bunch of NAs in a column of categorical variables designating the size classes (e.g., smallest to largest: 1,2,3,4) of cave crickets. I'd like to substitute "U" (for unknown) for the NAs. Can anyone give me an idea how to do this? Thanks in advance. Cheers Kurt *************************************************************** Kurt Lewis Helf, Ph.D. Ecologist

Hi, I am a beginner for R. I had use gplots to generate a heatmap as following: >heatmap.2(matrix, col=topo.colors(75), dendrogram="column", Rowv=FALSE, trace="none", key=TRUE, keysize=0.8, density.info="none", cexRow=0.2, cexCol=0.6) It work well. It generate heatmap whith rcolumn clustering dendrogram and I can export a very nice graph. But I don not know how

Hi, I have generated a skyline plot of a tree in newick format using "ape". How can I plot the error bars for this graph? I only have the the tree data. un<-"((((8.1:0, 20.1:0):0, 6.1:3):123, (((((35.1:0, (22.1:0, (43.1:1, 29.1:0):0):0):4, 25.1:6):0, ((42.1:0, 21.1:0):3, (39.1:0, 2.1:0):3):1):8, (3.1:0, 7.1:0):8):48, (((((15.1:0, 14.1:0):0, 11.1:0):0, 37.1:0):0,

Hi, I've been investigating the ape package for a while, and I was wondering if it is possible to: - display the names of the internal nodes (from a newick tree) - plot a pie-chart on top of each of the internal branches in a phylogram plot Thanks in advance, Cheers, Albert.

Greetings Though I have months in chronological order in my data table, the data were sampled every other month (i.e., February, April, June, August, October, December), every time I try to plot them (on the x-axis) they are plotted in alphabetical order. What am I missing? Cheers Kurt *************************************************************** Kurt Lewis Helf, Ph.D. Ecologist EEO

We''ve seen this question a lot lately, so I''ve just added it to the FAQ. It''s currently section 5.3. http://wiki.xensource.com/xenwiki/XenFaq#head-4f9c83e35d885a98c082f7e30bc25a11429e0c96 or http://tinyurl.com/3bdhbb It''s my first post to the Wiki, so please let me know if you''ve got any corrections, advice, screaming insults... please let me

Greetings Does anyone have any suggestions for reducing pdf file size, particularly pdfs containing photos, without sacrificing quality? Thanks for any tips in advance. Cheers Kurt *************************************************************** Kurt Lewis Helf, Ph.D. Ecologist EEO Counselor National Park Service Cumberland Piedmont Network P.O. Box 8 Mammoth Cave, KY 42259 Ph: 270-758-2163

Greetings Using the following command I've been trying to subset a dataframe of counts of an organism to compute the sizes of groups for use as a predictor: Hs.patches <- as.data.frame(with(Hs.long, table(Cave,Year,Month,Region,Plot,))) I am getting the following error message that I do not understand: ERROR: argument is missing, with no default Can anyone shed light on this

Hi all, I'm on Mac OS X 10.4... So I've got a small python script I need to run from R. However, to get the python script working, I need to have the shell that R calls get settings from my .bash_profile file, which apparently it doesn't currently (the shell R calls uses an older version of python, and also this older version of python can't see various python modules I have

Hello, I have some measurements that I am trying to fit a model to. I also have uncertainties for these measurements. Some of the measurements are not well detected, so I'd like to use a limit instead of the actual measurement. (I am always dealing with upper limits, i.e. left censored data.) I have successfully run survreg using the combination of well detected measurements and limits,

Greetings I want to remove numbers from a string of characters that identify sites so that I can merge two data frames. For example, a site in one frame is called "001a Frozen Niagara Entrance" whereas the same site in the other data frame is called "Frozen Niagara Entrance". It seems to me the easiest thing to do would be to remove the numbers from the first data

All Is there a script in R equivalent to the "if then" transforms one can perform in Systat? For example, I want to create a "Treatment" column coded either 1 or 2 for twelve field sites in a large data set. Ideally, I'd be able to tell R to code sites a-f as 1 and sites g-l as 2. Cheers Kurt *************************************************************** Kurt Lewis

My goal is simple: calcuate GC content of each sequence in a list of nucleotide sequences. I have figured out how to vectorize, but all my attempts at memoization failed. Can you show me how to properly memoize my function? There is a StackOverflow post on the subject of memoization, but it does not help me: http://stackoverflow.com/questions/7262485/options-for-caching-memoization-hashing-in-r

Hi all, I am having a problem indexing one of my mailboxes using the solr fts backend in dovecot 2.1.12 For many mailboxes it works just fine, but on one mailbox I currently always get a panic. solr setup: Java: icedtea 6.1.11.5 Solr: 3.6.2 running in tomcat 7.0.32 Command to reproduce error: doveadm index -u my at user badmailbox I already noticed that there have been some solr backend fixes