search for: ericpante

Dear Listers, I emailed the list a few days ago about how to bootstrap a community matrix (species by sites) and get a consensus tree with node support. A friend pointed out that a similar question remained unanswered in 2004. I wish to re-word my question: is anyone aware of a package / method to obtain a majority-rule consensus tree from x distance matrices ? Is anyone using R to generate

Hello all, R just ''stopped working'' on my machine (ibook g4, os 10.3.9). between last time I used it and now, I did not do anything but check emails and browse the internet. when I try to start the GUI, it appears and disappears as rapidly. when I tried to run a session from the terminal, I got the following: mkdir: /tmp/Rtmp590-29493: Permission denied mkdir:

Dear R-listers, Is anyone familiar with a package that would perform bootstrapping on species/site matrices for clustering ? So far I have been using the vegan package to generate trees (Bray-Curtis index), but I would like to associate a certainty to each node (similarly to a phylogenetic tree). If no package exist, I would know how to generate bootstrapped matrices of distance, but how

Dear Listers, I am trying to match tables that DO NOT have the same length. The tables result from the function "table()" so they look like this: table 1 2 3 4 3 5 7 table 2 1 2 3 6 4 5 I need the following output: (NOTICE THE ZEROS) 1 2 3 4 table1 0 3 5 7 table2 6 4 5 0 Unfortunately, I was not successful using "match()". Previous postings explain how to do

Dear listers, a central problem in conservation biology is the selection of sites in reserve network design. many algorithms have been published, and I was wondering any have been implemented in R. I did not seen anything on CRAN or R-help, or on the web in general. Best regards, Eric Eric Pante ---------------------------------------------------------------- College of Charleston, Grice

Dear listers, I need to export a distance matrix in the following format : a 0.0 1.0 0.2 1.0 1.0 b 1.0 0.0 1.0 1.0 1.0 c 0.2 1.0 0.0 1.0 1.0 d 1.0 1.0 1.0 0.0 1.0 e 1.0 1.0 1.0 1.0 0.0 I tried write.matrix() from the MASS library, which gives: a b c d e 0.0 1.0 0.2 1.0 1.0 1.0 0.0 1.0 1.0 1.0 0.2 1.0 0.0 1.0 1.0 1.0 1.0 1.0 0.0 1.0 1.0 1.0 1.0 1.0 0.0 Does anyone know of an R trick to change

Hello Listers, I am trying to sample a vector to create a new one of sample length, witha sum equal to the sum of the initial vector: initial = 10, 30, 10 (sum=50) sample example = 5, 35, 10 (sum=50) or 25, 15, 10 (sum=50), etc ... My problem is to control the sum, so it stays constant. Any suggestions would be very helpful ! Thank you in advance, Eric

Dear listers, I am trying to assess variance components for a nested, mixed-effects model. I think I got an answer that make sense from R, but I have a warning message and I wanted to check that what I am looking at is actually what I need: my data are organized as transects within stations, stations within habitats, habitats within lagoons. lagoons: random, habitats: fixed the question is: