similar to: overplot() examples fail (package:gplots)

Dear R-helpers, I don't see a difference between the following two plots of effect objects, which I understand should be different. What am I missing? require(doBy) require(effects) data(budworm) m1 <- glm(ndead/20 ~ sex + log(dose), data=budworm, weight=ntotal, family=binomial) m1.eff <- all.effects(m1) plot(m1.eff, rescale.axis = FALSE, selection = 2, main = 'rescale =

Dear R-helpers, When I try > anova(txtE2.lme, txtE2.lme1) Model df AIC BIC logLik Test L.Ratio p-value txtE2.lme 1 10 8590 8638 -4285 txtE2.lme1 2 7 8591 8624 -4288 1 vs 2 6.79 0.0789 > latex(anova(txtE2.lme, txtE2.lme1)) Error: object "n.group" not found I don't even see n.group as one of the arguments of latex() I checked to see >

Hi Seth, The possibility of caching computations would be a great boon when one is iteratively refining a paper; so I'm most grateful for your work on this. Unfortunately I have a problem to report: ******************installing****************** > source("http://bioconductor.org/biocLite.R") > biocLite("weaver") Running getBioC version 0.1.8 with R version

I am having difficulty installing packages. For example, here I have tried to install "gplots" but to no avail. I have tried multiple mirrors and different packages (errbar) but after installation I seem to be unable to access any of the commands or help pages. I am a little concerned about the 'lib' missing message but this has been present for previous successful package

Hello, I am trying to use cluster.overplot from package plotrix and I get an error message when I add the "away" parameter: require(plotrix) distance <- read.table("distance.txt") cmd <- cmdscale(distance) cp <- cluster.overplot(cmd, away=2) Error in if (sum(overplots) > 1) { : missing value where TRUE/FALSE needed If I don't use "away",

Announcing gplots 2.5.0 --------------------------------- gplots provides additional plotting functions, including several enhanced versions of base R functions. Provided functions include: balloonplot, bandplot, barplot2, boxplot.n, colorpanel, heatmap.2, hist2d, lowess, ooplot, overplot, plot.lm2, plotCI, plotmeans, qqnorm.aov, residplot, rich.color, sinkplot, smartlegend, space,

Announcing gplots 2.5.0 --------------------------------- gplots provides additional plotting functions, including several enhanced versions of base R functions. Provided functions include: balloonplot, bandplot, barplot2, boxplot.n, colorpanel, heatmap.2, hist2d, lowess, ooplot, overplot, plot.lm2, plotCI, plotmeans, qqnorm.aov, residplot, rich.color, sinkplot, smartlegend, space,

Dear r-helpers, When I do an xYplot and display the result in a JavaGD() window, the font is sans-serif (presumably Helvetica). When I send the figure to a pdf, I get a serif font (presumably times). How do I insure that the font in the pdf is indeed the default sans serif? > sessionInfo() R version 2.4.1 (2006-12-18) i386-apple-darwin8.8.1 locale: C attached base packages: [1]

> (fm1 <- lmer2(Reaction ~ Days + (Days|Subject), sleepstudy)) Error in as.double(start) : Calloc could not allocate (888475968 of 4) memory ************************* > sessionInfo() R version 2.4.1 (2006-12-18) powerpc-apple-darwin8.8.0 locale: C attached base packages: [1] "grid" "datasets" "stats" "graphics" "grDevices"

The following code demonstrates an annoyance with plot.lm(): library(DAAGxtras) x11(width=3.75, height=4) nihills.lm <- lm(log(time) ~ log(dist) + log(climb), data = nihills) plot(nihills.lm, which=5) OR try the following xy <- data.frame(x=c(3,1:5), y=c(-2, 1:5)) plot(lm(y ~ x, data=xy), which=5) The "Cook's distance" text overplots the label for the point with the

Dear r-helpers, I downloaded http://popgen.unimaas.nl/~jlindsey/rcode/rmutil.tar (it was originally .tgz, but got unzipped by my browser). Can anyone give me detailed instructions on installing this and Lindsey's other packages on R version 2.4.0 (2006-10-03)---(powerpc- apple-darwin8.7.0, locale: C)? _____________________________ Professor Michael Kubovy University of Virginia

Hello I was wondering how I can achieve matlab style plotting in R, in the sense that matlab allows you to plot multiple sets of variables within the same x-y axes. plot in R does not seem to cater for this. I tried 'overplot' from the gplots package but this assumes different y axes for the variables. any suggestions would be very appreciated Maria [[alternative HTML version

Newbie trying to install wine in his Mac OSX, getting the old annoying message, home:~/Desktop/wine G3$ /Users/G3/Desktop/wine/tools/wineinstall WINE Installer v0.75 Running configure... configure: creating cache config.cache checking build system type... powerpc-apple-darwin8.7.0 checking host system type... powerpc-apple-darwin8.7.0 checking whether make sets $(MAKE)... no checking for gcc...

Hi, i have two files (file1.txt and file2.txt) which i would like to merge, based on certain criteria, i.e. it combines data based on matching geneID and exons. i have used the merge option, but it does not give me the desired outcome. merged.txt shows the result i would like. *File1. txt* ** AffyProbe ProbeType Flag GeneSymbol GeneID Exons Chrom Strand Affytart AffyEnd 1

Hi, i have two files (file1.txt and file2.txt) which i would like to merge, based on certain criteria, i.e. it combines data based on matching geneID and exons. i have used the merge option, but it does not give me the desired outcome. merged.txt shows the result i would like. *File1. txt* ** AffyProbe ProbeType Flag GeneSymbol GeneID Exons Chrom Strand Affytart AffyEnd 1

Dear r-helpers, I have been bitten by a cryptic comment in the help page for xYplot(). Here is some code from Madeline Bauer, one of the authors, which is essentailly the code on the help page for xYplot(): # This example uses the summarize function in Hmisc to # compute the median and outer quartiles. The outer quartiles are # displayed using "filled bands" set.seed(111) dfr

the following returns an error in an 'exists' call on my machine MyEnv <- new.env() setClass("Numeric", "numeric", where=MyEnv) franklin parlamis > version _ platform powerpc-apple-darwin8.7.0 arch powerpc os darwin8.7.0 system powerpc, darwin8.7.0 status beta major 2 minor 4.0 year

the code below has me confused: setClassUnion("index", c("numeric", "character", "logical")) extends("numeric") # i don't see the class union library(Matrix) extends("numeric") # now i see the class union i am aware that the "Matrix" package separately defines the "index" class union. is it the case that

i think these two code snippets exhibit a bug. they are identical but for the inclusion of an initial line in snippet [2] [1] setMethod("Math", signature(x = "numeric"), function(x) "Works") getGeneric("sqrt")(4) [2] getGeneric("sqrt")(4) setMethod("Math", signature(x = "numeric"), function(x) "Works")

Hi I used write() the other day to save some results. It seems that write() does not record the full precision of the objects being written: > write(pi,file="~/f",ncolumns=1) > pi.saved <- scan("~/f") Read 1 item > dput(pi) 3.14159265358979 > dput(pi.saved) 3.141593 > pi-pi.saved [1] -3.464102e-07 > This difficulty was particularly difficult to