[R] How to delete designated sequences in alignment (DNAbin object)

This is a simple question but could not find any specific help information: I have a DNAbin object created with read.dna() of ape and would like to remove several sequences of "conflicting taxa". How can I do it using a vector with the lables of the taxa to remove? Thanks in advance

Re: [R] multicore and mclapply problem in calculation server

e, the systems gets quickly overflowed. So the solution is to split length(linH) into blocks equal to the number of cpus and the message to end-users is "be careful with parallel processing functions in R". Cheers Juan Antonio Balbuena El 19/12/2013 22:03, p_connolly escribió:

[R] multicore and mclapply problem in calculation server

Hello I am using package multicore for parallel computing in a Altix UltraViolet 1000 server with 64 CPUs and 960 GB of RAM memory. Access is managed by means of a SGE queue system. This is the first time I am using parallel computing and my experience with supercomputers is quite l

[R] Same code - error in one PC but not in other

Hello I am running exactly the same code on two different computers. In PC1 of the the code is working fine, whereas in PC2 I get this error Error in HP.LUT[, 1] : incorrect number of dimensions HP.LUT is an object within a function computed as HP.LUT <- which(HP ==1, arr.in=TRUE

Re: [R] transform dataframe with look-up table

t (pun intentional): End <- merge(merge(Start, transformer, by.x="Right", by.y="input", all.x=TRUE), transformer, by.x="Left", by.y="input", all.x=TRUE) Best wishes Juan Antonio El 25/07/2013 18:02, Brian Diggs escribió: On 7/25/20

[R] transform dataframe with look-up table

output for [5, ] should be NA NA. Thank you very much for your time. Juan Antonio Balbuena -- Dr. Juan A. Balbuena Marine Zoology Unit Cavanilles Institute of Biodiversity and Evolutionary Biology University of Valencia [1]http://www.uv.es/~balbuena P.O. Box 22085 [2

[R] use row and col names of a matrix to create colnames of a new one.

Hello I would appreciate any help with the following: Given a matrix with col and row names, such as > matrix1 <- matrix(rnorm(16),4) > rownames(matrix1) <- LETTERS(1:4) > colnames(matrix1) <- letters[1:4] > matrix1 a bc d A 1.6845882 -0.27809792 -0.87479

[R] procrustes (vegan) plot of residual differences

+/- SD. Thank you very much for your attention. Juan Antonio Balbuena -- Dr. Juan A. Balbuena Marine Zoology Unit Cavanilles Institute of Biodiversity and Evolutionary Biology University of Valencia [1]http://www.uv.es/~balbuena P.O. Box 22085 [2]http://www.uv.es/ca

[R] Error in ifelse(append, "a", "w") : , (list) object cannot be coerced to type 'logical'

Hello I will appreciate your help with the following. Running a script in R 2.14.1 under windows vista I get the following error message: Error in ifelse(append, "a", "w") : (list) object cannot be coerced to type 'logical' However, the very same script runs perfectly well

[R] Discarding a matrix based on the rowSums value

Hello I would appreciate your help on the followig. I want to generate random binary matrices but I need to discard those with all-1 rows. That is, for a 10x10 matrix with five 1's [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [1,]000000000 1 [2

[R] permutation within rows of a matrix

Hello This is probably a basic question but I am quite new to R. I need to permute elements within rows of a binary matrix, such as [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [1,]000010000 0 [2,]001100011