similar to: Sweave in PNG: driver online

Dear all, It is my understanding that using 'importFrom' in the NAMESPACE of a package allows to avoid conflicts between different packages defining objects with identical names. However, I can still see conflicts while loading the package using 'library'. Here is a toy example, with a package 'foo' importing 'as.igraph' from the igraph package, and 'nj'

Dear all, I have a package implementing a shiny app, putting the R code of the app (server.R and ui.R) in inst/... and then having a simple function merely starting the app with something along the lines of: runApp(system.file("inst/...")) However, the app itself uses functions from packages which are not used elsewhere in the code. What is the best way to declare these dependencies

Dear R developers, I am having a slightly weird issue with a S4 method defined in my package adegenet 1.2-4, with R 2.11.0. As far as I know, the problem is new, and the code implementing the method has not changed for more than a year and worked well so far. The problem is the following. I define, in the package, a method "[" for the S4 class 'genind'. The method's

Hello, Here is a late answer, but an answer nonetheless to the question I asked almost one year ago on this list: > On Wed, 29 Mar 2006, Thibaut Jombart wrote: >> Hello list, <http://tolstoy.newcastle.edu.au/R/help/06/03/24318.html#24322qlink1> />> / />> does anyone know if Monmonier algorithm is available in R? I've checked / />> several spatial

Hello list, Here is a problem I had. I write this to the list in case the solution I found would be useful to anyone else. I had to Sweave document including pixmap pictures, which are very heavy when converted into pdf pictures. In practice, this eventually led to very heavy pdf, sometimes impossible to read. So the first solution I found was to save pictures in png, when too heavy in pdf :

Hello list, despite I already posted a mail on this topic on R help, I guess this place may be more appropriate. I'll make it shorter this time. Sorry for posting twice. I found that using pixmap pictures in a Sweave document was sometimes almost impossible, due to the huge size of the pdf pictures produced. The first solution I found was to save pictures in png, when too heavy in pdf.

Dear list, here is a problem I met when trying to use a method for an S4 object, without loading the package in which the method was defined. I do not know if this is a bug, or a mistake of mine. Normally, I think the package in which the appropriate method is defined is loaded automatically when calling the method. The problem is that if the package is indeed loaded automatically, the

Hello list, does anyone know if Monmonier algorithm is available in R? I've checked several spatial libraries, but I didn't find anything related to it. However, there is a huge documentation and I may have missed it. Before coding it, I'd like to be sure it doesn't already exist. Cheers, Thibaut Jombart. -- ###################################### Thibaut JOMBART CNRS UMR

Dear R community, I'm working with PCA and CCA methods, and I have a theoretical question. Why is it necesary to have more temporal values than variables when the CCA O PCA are going to be used? Could you advise to me some any paper about it? Thanks in advance, [[alternative HTML version deleted]]

I am receiving the above error ( full r session output below) the script runs OK in windows. and "genotypes" and "ploidy" are both correct arguments any suggestions would be most welcome Nevil Amos MERG/ACB Monash University School of Biological Sciences > library(Geneland) Loading required package: RandomFields Loading required package: fields Loading required

Dear list, I may have found a bug in model.frame.default (called by the lm function). The problem arises in my R dev version but not in my R 2.4.0. Here is my config : > version _ platform x86_64-unknown-linux-gnu arch x86_64

Dear R user, I am using Sweave to write my reports with R code. Unlucly my code take a lot of time to run, and I don't want to run it multiple time, if possible, as I am still developping the tools. It seems that a sweave run does not save the enviroment at the end of the process, is there a way to avoid to lunch multiple time the same commands? maybe it could be possible to store chunck of

Hello, I'm trying to insert R source code (functions) in an appendix of a latex document. I guess the easiest way to do so is to use the package Sweaved (file : Sweaved.sty) provided with the latest R version. Latex succeeds in loading the package, but my problem comes from the use of this very package. I tried to use the 'Schunk' environment, but '#' characters generate

I do the these passages: library(Geneland) set.seed(1) data <- simdata(nindiv=200, coord.lim=c(0,1,0,1) , number.nuclei=5 , allele.numbers=rep(10,20), IBD=FALSE, npop=2, give.tess.grid=FALSE) geno <- data$genotypes coord <- t(data$coord.indiv) path.mcmc <-

Dear R-help, I would like to include the documentation of an R function in an *.rnw document processed by Sweave. Because I'm sharing my *.rnw files with colleagues under Linux and Windows (I'm on Mac OS X), I would like a pure R solution. The naive approach doesn't work, because Sweaving this *.rnw file: -------- tmp.rnw -------- \documentclass{article} \begin{document}

I get tables with millions of rows. For plotting to a screen-size jpg, obviously just about 1000 points are enough. Instead of feeding plot() the original millions of rows, I'd rather shrink the original dataframe, using some kind of the following interpolation: -- split dataframe into chunks of N rows each, e.g. 1000 rows each -- compute average for each column -- issue one new row

Hi, I am trying to calculate Moran's I test for the residuals for a regression equation, but I have trouble converting my coordinates into nb format. I have used the dnearneigh() funtion now with an arbitrarily high upper distance to make it include all plots. However, when I do the lm.morantest() I get a Moran's I value which is the same as the expected value and a P-value of 1. I

Hi, I am a new student to R and I was hoping someone could help me with the error message I keep getting when I try to use the nb2listw() function. I have 45 sites and I want to get an autocorrelation value for sites within 1000m of each other. coords<-cbind(EAST,NORTH) coords<-as.matrix(coords) nb1000<-dnearneigh(coords,0,1000,longlat=TRUE) then when I try to run the

Dear all, (Mac OS X 10.4.11, R 2.6.0) I have a quantitative dataset with a lot of Na?s in it. So many, that it is not possible to delete all rows with NA?s and also not possible, to delete all variables with NA?s. Is there a function for a principal component analysis, that can deal with so many NA?s. Thanks in advance Birgit Birgit Lemcke Institut f?r Systematische Botanik

Hi everyone, I have a matrix that contains 1000 replicates of a sample of a list of values. I want to group each row (row=replicate) into my defined bin ranges and then calculate the mean and stdev for each of the bin ranges (so I will have 1000 rows but ncol=number of bin ranges). I don't know how to group rows in a matrix matrix according to another vector (which is what I think I need to