similar to: Accessing the formals() of a non-exported method without :::?

Dear List, This may be related to this email thread initiated by Ben Bolker last month: https://stat.ethz.ch/pipermail/r-devel/2011-July/061630.html In answering this Question on StackOverflow http://stackoverflow.com/q/7195628/429846 I noticed that `methods()` was not listing some S3 methods for `plot()` provided by the mgcv package. At the time I wanted to check the development version of R as

>na.contiguous function (object, ...) UseMethod("na.contiguous") <environment: namespace:stats> this is what I get when I look for the source code for some functions- Is there a way to look at the source code? -- Let's not spend our time and resources thinking about things that are so little or so large that all they really do for us is puff us up and make us feel like

Dear List, I'm having considerable trouble setting up my environment (Linux, Fedora 16, Bash) to build and check packages under R Under Development (r61660). I'm doing this to better get a handle on difference in the output from running checks on examples in one of my packages. Note I compiled R Under Development myself The problem I am now having is whenever I try to build my analogue

Dear List, Further to my earlier email, I note that, for me at least, R CMD check is *not* reading R_LIBS from ~/.R/check.Renviron on R 2.15.2 patched (r61228) and R Under Development (r61660). The only way I can get R CMD check to look for packages in a user-supplied library is by explicitly exporting R_LIBS set to the relevant directory. R CMD build *does* read R_LIBS from ~/.R/build.Renviron

Dear List, Apologies for this off-topic post but it is R-related in the sense that I am trying to understand what R is telling me with the data to hand. ROC curves have recently been used to determine a dissimilarity threshold for identifying whether two samples are from the same "type" or not. Given the bashing that ROC curves get whenever anyone asks about them on this list (and

Dear List, A student in the Department where I work would like to produce a graphic similar to this one: http://image.guardian.co.uk/sys-files/Guardian/documents/2009/09/16/Public_spending_160909.pdf Does anyone know if the figure in the pdf can be generated in a specific software application for example? Any suggestions would be most gratefully received by the student concerned. Many thanks,

Hi, I was wondering whether a package that can perform dynamic linear models on times series data was available for R? Many Thanks, Gavin Simpson %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Gavin Simpson [T] +44 (0)20 7679 5522 ENSIS Research Fellow [F] +44 (0)20 7679 7565 ENSIS Ltd. & ECRC [E] gavin.simpson at

Dear List I am getting an error when checking my analogue package with R2.10.0-patched. The error comes when running a function within which I use the standard non-standard evaluation method. I've distilled the error and functions involved out into the following simple example to illustrate the error: ## Dummy data to illustrate formula method d <- data.frame(A = runif(10), B = runif(10),

Dear List, There seems to be an bug in compactPDF() or at least an inconsistency with the documented behaviour. The documentations states: Details: This by default makes use of ?qpdf?, available from <URL: http://qpdf.sourceforge.net/>, including a Windows binary. If ?gs_cmd? is non-empty, GhostScript is used. I don't have qpdf on my system so planned to use

Dear List, I need to add a subscript and a superscript to some of the ions in the labels on some plots. I have got to here but now I'm stuck: plot(1:10, xlab = expression(paste("nm SO"[4], " ", mu, "eq cm"^{-2}, " yr"^{-1}))) Which gives almost what I require. No matter what I tried, however, I could not get bot a sub script *and* a superscript

Hi I am having a particular problem with some glm models I am running. I have been adapting code from Bill Venables 'Programmers niche' in RNews Vol 2/2 to fit ca. 1000 glm models to a combination of species 0/1 data (as Y) and related physicochemical data (X), to automate the process of fitting this many models. I have successfully managed to fit all the models and have stored the

Dear list, given this formula: > fmla <- formula(y1 ~ spp1 + spp2 + spp3 + spp5) > fmla[[3]] spp1 + spp2 + spp3 + spp5 is this the intended behaviour of as.character: > as.character(fmla[[3]]) [1] "+" "spp1 + spp2 + spp3" "spp5" ? Where does the extra "+" come from? > as.character(fmla) [1] "~"

Dear List, In one of my packages I have an S3 method for the plot3d generic function from package rgl. I am trying to streamline my Depends entries but don't know how to have plot3d(foo) in the examples section for the plot3d method in my package, without rgl being in Depends. Note that I importFrom(rgl, plotd3d) and register my S3 method via S3Method() in the NAMESPACE. If rgl is not in

Dear r-Community, Step1: I would like to calculate a NMDS (package vegan, function metaMDS) with species data. Step2: Then I want to plot environmental variables over it, using function envfit. The Problem: One of these environmental variables is cos(EXPOSURE). But for flat releves there is no exposure. The value is missing and I can't call it 0 as 0 stands for east and west. Therefore I

Hello, If I want to see how, say, apply function is written, how would I be able to do that? Just typing "apply" at the prompt does not work. Thank you for help! Sergey

Dear list, I've just upgraded to Fedora Core 2 and seeing as there wasn't an rpm for this OS on CRAN yet I thought it was about time I had a go at compiling R myself. Having run into the X11 problem I switched to trying to install R-patched. I followed the instructions in the R Installation & Admin manual to download the sources of the Recommended packages and place the files in

Dear all I would like to show my audience that some variables are homogenous inside groups but different outside. I can use by with summary for all variables by(iris[,1:4], iris$Species, summary) what can be quite messy in case of more than few variables and about 8 groups or densityplot for one variable densityplot(~Petal.Length | Species, iris) I have two questions: 1. Is there

Dear List, I have a 47 species * 83 samples matrix containing percentage abundance data. I have two cluster analyses one of the samples and one of the species, and have ordered the rows and columns of the species by samples matrix according to these two cluster analyses. So far so good! Now what I want to do is create a plot with the species dendrogram at the top of the plot, the samples

Full_Name: Gavin Simpson Version: 2.5.0 OS: Linux (FC5) Submission from: (NULL) (128.40.33.76) Screeplots are a common plot-type used to interpret the results of various ordination methods and other techniques. A number of packages include ordination techniques not included in a standard R installation. screeplot() works for princomp and prcomp objects, but not for these other techniques as it

Hi I'm having a problem with model.frame, encapsulated in this example: y1 <- matrix(c(3,1,0,1,0,1,1,0,0,0,1,0,0,0,1,1,0,1,1,1), nrow = 5, byrow = TRUE) y1 <- as.data.frame(y1) rownames(y1) <- paste("site", 1:5, sep = "") colnames(y1) <- paste("spp", 1:4, sep = "") y1 model.frame(~ y1) Error in model.frame(formula, rownames,