[R] install R package on Unix cluster

Hi R users, Working from a PC, I am trying to install the spatstat package on a Unix cluster. I created the following PBS file to send a job array: #!/bin/bash -ue #PBS -m ae #PBS -M my email #PBS -J 1-45 #PBS -A my username #PBS -N job name #PBS -l resources #PBS -l walltime cd $PBS_O_WORKDIR

Re: [R] string manipulation

thanks Lorenzo -Original Message- From: Steven Kennedy [mailto:stevenkennedy2...@gmail.com] Sent: Friday, 26 August 2011 11:31 AM To: Henrique Dallazuanna Cc: Lorenzo Cattarino; r-help@r-project.org Subject: Re: [R] string manipulation You can split your string, and then only take the f

[R] string manipulation

I R-users, I am trying to find the way to manipulate a character string to select a 4 digit number after some specific word/s. Example: mytext <- "I do not want the first number 1234, but the second number 5678" Is there any function that allows you to select a certain number of digits (in thi

[R] lapply, if statement and concatenating to a list

Hi R users I was wondering on how to use lapply & co when the applied function has a conditional statement and the output is a 'growing' object. See example below: list1 <- list('A','B','C') list2 <- c() myfun <- function(x,list2) { one_elem <- x cat('one_elem= ', one_elem, '\n') random <

[R] do not execute newline command

Hi R-users, To automate the creation of scripts, I converted the code (example below) into a character string and wrote the object to a file: Repeat <- " myvec <- c(1:12) cat('vector= ', myvec, '\n') " write (Repeat, 'yourpath/test.R') the problem is that one line of the code is a "cat" comman

[R] combining vectors into list

Hi R users I have these two vectors: Row <- sample(1:25, 10) Col <- sample(1:25, 10) Is there a way to combine them into a list, whose first component is a vector containing the first element of Row and the first element of Col, the second component is a vector containing the second e

[R] automatic coercion to character

Hi R users I am wondering how I can avoid automatic coercion of my numeric vector elements to character init <- c(age='N', R=as.numeric(0.5), S=as.numeric(0.8)) I have used as.numeric() but it does not seem to work Thank you Lorenzo [[alternative HTML version deleted]]

[R] get list index

value is 0.28): [[2]] [1] 0.28 0.45 0.59 0.69 0.80 0.87 0.95 0.94 0.98 and the position of course 2. I am looking for the index because I would like to subset the list afterwards (e.g. mylist[[2]]) and extract that element (i.e. the whole vector). Thanks for your help Lorenzo Lorenzo C

[R] convergence message & SE calculation when using optim( )

Hi R-users, I am trying to estimate function parameters using optim(). My count observations follows a Poisson like distribution. The problem is that I wanna express the lambda coefficient, in the passion likelihood function, as a linear function of other covariates (and thus of other coefficie

Re: [R] memory allocation problem

help anyway Lorenzo -Original Message- From: David Winsemius [mailto:dwinsem...@comcast.net] Sent: Wednesday, 3 November 2010 12:48 PM To: Lorenzo Cattarino Cc: r-help@r-project.org Subject: Re: [R] memory allocation problem Restart your computer. (Yeah, I know that what the help-desk always says.)

Re: [R] memory allocation problem

much appreciated Lorenzo -Original Message- From: Lorenzo Cattarino Sent: Wednesday, 3 November 2010 2:22 PM To: 'David Winsemius'; 'Peter Langfelder' Cc: r-help@r-project.org Subject: RE: [R] memory allocation problem Thanks for all your suggestions, This is what I

[R] memory allocation problem

ry.limit() or appended string in the target path), is that right? Thank you a lot Lorenzo From: Lorenzo Cattarino Sent: Wednesday, 3 November 2010 10:55 AM To: 'r-help@r-project.org' Subject: memory allocation problem I forgot to mention that I am using windows 7 (64-bit)

[R] memory allocation problem

Hi R users I am trying to run a non linear parameter optimization using the function optim() and I have problems regarding memory allocation. My data are in a dataframe with 9 columns. There are 656100 rows. >head(org_results) comb.id p H1 H2 Range Rep no.steps dist a

[R] memory allocation problem

I forgot to mention that I am using windows 7 (64-bit) and the R version 2.11.1 (64-bit) Thank you Lorenzo From: Lorenzo Cattarino Sent: Wednesday, 3 November 2010 10:52 AM To: r-help@r-project.org Subject: memory allocation problem Hi R users I am trying to run a non linear

[R] GAM function in mgcv package

Hi R-users I am trying to use the GAM function of the mgcv package. But I am having problem trying to specify the k parameter. Although I managed to run some models by giving to the parameter some (random) value, and it is explained by Wood (2006) that it does not seem to "really" affect th

[R] bind matrices by row

Hi R-users I have a series of matrices and I would like to bind them together by column using a loop (i.e. not writing cbind(matrix1, matrix2,matrix3)). The reason is because in my real data set I have a very large number of matrices. Example: matrix1 <- matrix (1:12,4,3) matrix2 <

Re: [R] paste an unevaluated expression

;) Apply <- paste(object.result, section, sep=" <- ") Save <- format(substitute(save(result1, file='/home/uqlcatta/pbs/result1.RData'))) path <- '//atlas2/Research/Lorenzo Cattarino/PhD/myR/R_laboratory/' output <- paste(path, object.result, s

[R] paste an unevaluated expression

Hi R-users, I would like to create an expression without evaluating it. Then paste that expression to an object. Example: Result <- paste('Result', 1, sep="") paste(Result, substitute(apply(exp.des[1:10,], 1, one.row, parms=parameters)), sep="<-") However this pastes EACH element of th

[R] running R script on linux server

Hi R-users, I have a problem running my R code on a Linux cluster. What I did was write a .pbs file to instruct the cluster on what to do and how: #!/bin/sh #PBS -m ae #PBS -M uqlca...@uq.edu.au #PBS -A uq-CSER #PBS -N job1_lollo #PBS -l select=1:ncpus=1:NodeType=fast:mem=8GB #PBS

[R] accessing elements located after $ symbol

Hi R-users I am having troubles accessing elements after the $ symbol. Reproducible example: >test <- data.frame (first=1:10, second=11:20, third=21:30) >test$first #this works fine but when I try >interest <- "first" >test$interest # does not seem to work Could you tell me w

[R] name ONLY one column

Hi R-users I can not change the name of one column only of my matrix. my_matrix <- matrix (1:12,ncol=3) colnames(my_matrix)[1] <- 'myname' Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent thank you for your help Lorenzo [[alternat

Re: [R] extracting random effects from model formula

actually I need to extract the random effect from the formula, not the model any idea? From: Sacha Viquerat [mailto:sacha.v...@googlemail.com] Sent: Wed 22/09/2010 5:55 PM To: Lorenzo Cattarino Subject: Re: [R] extracting random effects from model formula Am

[R] extracting random effects from model formula

my example). Thanks Lorenzo From: Lorenzo Cattarino Sent: Wednesday, 22 September 2010 5:23 PM To: r-help@r-project.org Subject: extracting random effects from model formula Hi R-users I would like to extract the random effects ("1|SITE", "1+SPECIES|SITE" and &quo

[R] extracting random effects from model formula

Hi R-users I would like to extract the random effects ("1|SITE", "1+SPECIES|SITE" and "BA|SITE") from this model formula: Full_model <- formula (VAR ~ (1|SITE) + (1+SPECIES|SITE) + (BA|SITE) + HEIGHT + COND + NN_DIST) I tried: terms(Full_model) labels(terms(Full_model)) but I c

[R] sum of some matrix columns

Hi, I have the following matrix cc <- matrix (1:21, 3) cc[,3:4]<- 0 cc [,1] [,2] [,3] [,4] [,5] [,6] [,7] [1,]1400 13 16 19 [2,]2500 14 17 20 [3,]3600 15 18 21 and I would like to sum just the values in columns

[R] storing the results of an apply call

NA NA [14,] NA NA NA [15,] NA NA NA I would like to have just one column with the three groups of five values. Many thanks Lorenzo Lorenzo Cattarino PhD Candidate (Confirmed) Landscape Ecology and Conservation Group Centre for Spatial Environmental Research School

[R] modifying vector elements

""1.5.4x2" "1.5.4x3" "1.5.4x6" "1.5.5b" [49] "1.5.6a" "1.5.6b" "1.5.6x1" "1.5.6x2" "1.5.7a" "1.5.7b" [55] "1.5.7x1" "1.5.7x2" &q

Re: [R] applying quantile to a list using values of another object as probs

[mailto:jorgeivanve...@gmail.com] Sent: Tuesday, 18 May 2010 12:37 PM To: Lorenzo Cattarino Subject: Re: [R] applying quantile to a list using values of another object as probs Hi Lorenzo, How about this? lapply(1:length(mylist), function(i) quantile(mylist[[i]], probs = B[i,])) HTH, Jorge

Re: [R] applying quantile to a list using values of another object as probs

Hi Jim, Thanks for your reply. Your codes does work but I was hoping to find a way to use lapply and avoid the for loop. Lorenzo -Original Message- From: Jim Lemon [mailto:j...@bitwrit.com.au] Sent: Monday, 17 May 2010 8:27 PM To: Lorenzo Cattarino Cc: r-help@r-project.org Subject: Re

[R] applying quantile to a list using values of another object as probs

Hi r-users, I have a matrix B and a list of 3x3 matrices (mylist). I want to calculate the quantiles in the list using each of the value of B as probabilities. The codes I wrote are: B <- matrix (runif(12, 0, 1), 3, 4) mylist <- lapply(mylist, function(x) {matrix (rnorm(9), 3, 3)}) fo