[R] filled.contour colorbar without black color separators?
Dear list members,
I have been using filled.contour in order to plot EEG data. For the colors, I
used a conventional ramp from blue to red (blue - green - yellow - red), and
100 color levels to make the plot looking smooth:
(...) color.palette = colorRampPalette(c('blue','green', 'yellow','red'),
space='rgb'), nlevels = 100 (...)
My problem ist that filled.contour draws a black bar as a separation between
each color of the color bar (color key) so that color bar becomes essentially
black if I use many color levels. Is there a way to turn of this behavior? Any
advice would be greatly appreciated,
Gregor
--
Dr. rer. nat. Gregor Volberg gregor.volb...@psychologie.uni-regensburg.de (
mailto:gregor.volb...@psychologie.uni-regensburg.de )
University of Regensburg
Institute for Experimental Psychology
93040 Regensburg, Germany
Tel: +49 941 943 3862
Fax: +49 941 943 3233
http://www.psychologie.uni-regensburg.de/Greenlee/team/volberg/volberg.html
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Re: [R] Generate variable with Bivariate Normal Distribution
You could e.g. use the package mvtnorm (not horribly fast, but handy): (assuming that rho is the correlation) library(mvtnorm) m - c(mean1, mean2) #mean vector cov - rho*sqrt(variance1*variance2) sig - matrix(c(variance1, cov, cov, variance2), nrow=2) #covariance matrix rmvnorm(100, mean=m, sigma=sig) alternatively, you can transform manually via sigma^(1/2) (faster). This is covered in almost any (multivariate) statistics book. Gregor On Wed, 20 Oct 2010 12:29:53 +0700 สถาบันวิจัยและพัฒนา มหาวิทยาลัยราชภัฏอุบลราชธานี ird_u...@hotmail.com wrote: Dear All I want to generate variable with Bivariate Normal Distribution by use mean1 = a, variance1 = b, mean2 = c, variance2 = d, rho = e. How I can do this. Many Thanks. IRD [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] fast rowCumsums wanted for calculating the cdf
Dear all,
Maybe the easiest solution: Is there anything that speaks against generalizing
cumsum from base to cope with matrices (as is done in matlab)? E.g.:
cumsum(Matrix, 1)
equivalent to
apply(Matrix, 1, cumsum)
The main advantage could be optimized code if the Matrix is extreme nonsquare
(e.g. 100,000x10), but the summation is done over the short side (in this case
10).
apply would practically yield a loop over 100,000 elements, and vectorization
w.r.t.
the long side (loop over 10 elements) provides considerable efficiency gains.
Many regards,
Gregor
On Tue, 12 Oct 2010 10:24:53 +0200
Gregor mailingl...@gmx.at wrote:
Dear all,
I am struggling with a (currently) cost-intensive problem: calculating the
(non-normalized) cumulative distribution function, given the (non-normalized)
probabilities. something like:
probs - t(matrix(rep(1:100),nrow=10)) # matrix with row-wise probabilites
F - t(apply(probs, 1, cumsum)) #SLOOOW!
One (already faster, but for sure not ideal) solution - thanks to Henrik
Bengtsson:
F - matrix(0, nrow=nrow(probs), ncol=ncol(probs));
F[,1] - probs[,1,drop=TRUE];
for (cc in 2:ncol(F)) {
F[,cc] - F[,cc-1,drop=TRUE] + probs[,cc,drop=TRUE];
}
In my case, probs is a (30,000 x 10) matrix, and i need to iterate this step
around
200,000 times, so speed is crucial. I currently can make sure to have no NAs,
but
in order to extend matrixStats, this could be a nontrivial issue.
Any ideas for speeding up this - probably routine - task?
Thanks in advance,
Gregor
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R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] fast rowCumsums wanted for calculating the cdf
Dear all,
I am struggling with a (currently) cost-intensive problem: calculating the
(non-normalized) cumulative distribution function, given the (non-normalized)
probabilities. something like:
probs - t(matrix(rep(1:100),nrow=10)) # matrix with row-wise probabilites
F - t(apply(probs, 1, cumsum)) #SLOOOW!
One (already faster, but for sure not ideal) solution - thanks to Henrik
Bengtsson:
F - matrix(0, nrow=nrow(probs), ncol=ncol(probs));
F[,1] - probs[,1,drop=TRUE];
for (cc in 2:ncol(F)) {
F[,cc] - F[,cc-1,drop=TRUE] + probs[,cc,drop=TRUE];
}
In my case, probs is a (30,000 x 10) matrix, and i need to iterate this step
around
200,000 times, so speed is crucial. I currently can make sure to have no NAs,
but in
order to extend matrixStats, this could be a nontrivial issue.
Any ideas for speeding up this - probably routine - task?
Thanks in advance,
Gregor
__
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and provide commented, minimal, self-contained, reproducible code.
[R] ggplot2 multiple group barchart
hi there.. i got a problem with ggplot2. here my example: library (ggplot2) v1 - c(1,2,3,3,4) v2 - c(4,3,1,1,9) v3 - c(3,5,7,2,9) gender - c(m,f,m,f,f) d.data - data.frame (v1, v2, v3, gender) d.data x - names (d.data[1:3]) y - mean (d.data[1:3]) pl - ggplot (data=d.data, aes (x=x,y=y)) pl - pl + geom_bar() pl - pl + coord_flip() pl - pl + geom_text (aes(label=round(y,1)),vjust=0.5, hjust=4,colour=white, size=7) pl this gives me a nice barchart to compare the means of my variables v1,v2 and v3. my question: how do i have to proceed if i want this barchart splittet by the variable gender. so i get two small bars for v1, one for female and one for male, two bars for v2 etc. i need them all in one chart. fill=gender, position=dodge do not work... any ideas? thanks a lot greg __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Function for Estimating Fractional Multinomial Logit Model?
I need to estimate a model that predicts the proportional split of travel among the vehicles of a household based on vehicle characteristics such as age, fuel economy, and travel cost per mile. The model estimation dataset has a record for each household vehicle with information about the vehicle, the household, and the proportion of the total household vehicle travel using that vehicle. I have not been able to figure out how use multinomial logit estimation functions in R to predict proportions rather than categorical probabilities. I have found from searching the web that there is a Stata function, FMLOGIT, that will do what I want. Does anyone know how this can be done in R? All of my model estimation scripts for the large model I'm building are in R and I would like to keep it that way to create a nice replicable set of scripts and data to document the model. Thanks much. Brian Gregor Senior Transportation Analyst Oregon Department of Transportation Transportation Planning Analysis Unit 555 13th Street NE Salem, OR 97301 503-986-4120 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] transforming character categories
Dear R users, apologies for this quite simple question. I've tried serverall approaches, however, could not generate the desired result. I have a large data frame, which has several cathegories encoded as character strings, for example. Name, income, gender, ... ... from 1000$ to 2000$ ... ... from 2000$ to 3000$ ... ... more than 3000$... ... from 1000$ to 2000$ ... ... from 1000$ to 2000$ ... How can I transform this column into numeric values for the categories, for example in somethins like this: ... 1000 ... ... 2000 ... ... 3000 ... ... 1000 ... ... 1000 ... __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] transforming character categories
Thanks Gabor, but in my case not every value ist actually encoded within the character string. Vor example, I have an answer category, which is more than one Mio. $. (not in the column income...). I have the feeling, that there must be an another, straightforward way or function for transformation of levels / categories, but I just cannot make it work. - greg Try this. It matches the first numeric string on each line applying as.numeric to it and then using c to simplify the resulting list to a numeric vector. x - c(from 1000$ to 2000$, from 2000$ to 3000$, more than 3000$, + from 1000$ to 2000$, from 1000$ to 2000$) library(gsubfn) strapply(x, ([0-9]+).*, as.numeric, simplify = c) [1] 1000 2000 3000 1000 1000 See the gsubfn home page for more: http://gsubfn.googlecode.com On Sun, Jun 28, 2009 at 4:25 AM, Gregor Povhgregorp...@yahoo.de wrote: Dear R users, apologies for this quite simple question. I've tried serverall approaches, however, could not generate the desired result. I have a large data frame, which has several cathegories encoded as character strings, for example. Name, income, gender, ... ... from 1000$ to 2000$ ... ... from 2000$ to 3000$ ... ... more than 3000$... ... from 1000$ to 2000$ ... ... from 1000$ to 2000$ ... How can I transform this column into numeric values for the categories, for example in somethins like this: ... 1000 ... ... 2000 ... ... 3000 ... ... 1000 ... ... 1000 ... __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] graphically representing frequency of words in a speech?
The only thing that I found for R is by Gregor Gorjanc, but the
information seems to be dated:
http://www.bfro.uni-lj.si/MR/ggorjan/software/R/index.html#tagCloud
Hi,
Yes, I have tried to create a tag cloud plot in R, but I abandoned the project
due to other things. The main obstacle was that in R we need to take
care of the fontsizes and placement of words, while this is very easy with
say browsers, who do all the renderind. I tracked the last version of the R file
which is pasted bellow. I must say that I do not remember the status of the
code so use it as you wish. If anyone wishes to take this project further,
please
do so!
gg
### tagCloud.R
###
### What: Tag cloud plot functions
### Time-stamp: 2006-09-10 02:53:29 ggorjan
###
tagCloud - function(x, n=100, decreasing=TRUE,
threshold=NULL, fontsize=c(12, 36),
align=TRUE, expandRow=TRUE,
justRow=bottom, title,
textGpar=gpar(col=navy),
rectGpar=gpar(col=white),
titleGpar=gpar(), viewGpar=gpar(),
mar=c(1, 1, 1, 1))
{
UseMethod(tagCloud)
}
tagCloud.default - function(x, n=100, decreasing=TRUE,
threshold=NULL, fontsize=c(12, 36),
align=TRUE, expandRow=TRUE,
justRow=bottom, title,
textGpar=gpar(col=navy),
rectGpar=gpar(col=white),
titleGpar=gpar(), viewGpar=gpar(),
mar=c(1, 1, 1, 1))
{
if(!is.null(dim(x))) stop('x' must be a vector)
tagCloud.table(table(x), n=n, decreasing=decreasing, fontsize=fontsize,
threshold=threshold, align=align, expandRow=expandRow,
justRow=justRow, title=title, textGpar=textGpar,
rectGpar=rectGpar, titleGpar=titleGpar, viewGpar=viewGpar,
mar=mar)
}
tagCloud.table - function(x, n=100, decreasing=TRUE,
threshold=NULL, fontsize=c(12, 36),
align=TRUE, expandRow=TRUE,
justRow=bottom, title,
textGpar=gpar(col=navy),
rectGpar=gpar(col=white),
titleGpar=gpar(), viewGpar=gpar(),
mar=c(1, 1, 1, 1))
{
## --- Check ---
if(length(dim(x)) != 1)
stop('x' must be one dimensional table)
## --- Threshold ---
if(!is.null(threshold)) x - x[x = threshold]
## --- Number of units ---
N - length(x)## length of table
if(is.null(n)) { ## if n=NULL, plot all units
n - N
} else {
if(n N) n - N## if n is to big, decrease it
if(n 1) n - round(N * n) ## if n is percentage of units
}
fontsizeLength - length(fontsize)
if(fontsizeLength != 2)
stop('fontsize' must be of length two)
## --- Sort and subset ---
if(n N) { ## only if we want to plot subset of units
tmp - sort(x, decreasing=decreasing)
x - x[names(x) %in% names(tmp[1:n])]
}
## --- Get relative freq ---
x - prop.table(x)
## --- Fontsize ---
fontsizeDiff - diff(fontsize)
xDiff - max(x) - min(x)
if(xDiff != 0) {
off - ifelse(fontsizeDiff 0, min(x), max(x))
fontsize - (x - off) / xDiff * fontsizeDiff + min(fontsize)
} else { ## all units have the same frequency
fontsize - rep(min(fontsize), times=n)
}
## --- Viewport and rectangle ---
grid.newpage()
width - unit(1, npc)
height - unit(1, npc)
vp - viewport(y=unit(mar[1], lines), x=unit(mar[2], lines), ,
width=width - unit(mar[2] + mar[4], lines),
height=height - unit(mar[1] + mar[3], lines),
just=c(left, bottom), gp=viewGpar, name=main)
pushViewport(vp)
if(!missing(title))
grid.text(title, y=height, gp=titleGpar, name=title)
grid.rect(gp=rectGpar, name=cloud)
## --- Grobs ---
tag - vector(mode=list, length=4)
names(tag) - c(fontsize, grob, width, height)
tag[[1]] - tag[[2]] - tag[[3]] - tag[[4]] - vector(mode=list, length=n)
for(i in 1:n) {
tag$fontsize[[i]] - fontsize[i]
tag$grob[[i]] - textGrob(names(x[i]), gp=gpar(fontsize=fontsize[i]))
tag$width[[i]] - convertWidth(grobWidth(tag$grob[[i]]), unitTo=npc,
valueOnly=TRUE)
tag$height[[i]] - convertHeight(grobHeight(tag$grob[[i]]), unitTo=npc,
valueOnly=TRUE)
}
## --- Split lines ---
row - colWidth - vector(length=n)
row[1] - 1
colWidth[1] - 0
lineWidth - tag$width[[1]]
j - 1
gapWidth - convertWidth(stringWidth( ), unitTo=npc, valueOnly=TRUE)
maxWidth - convertWidth(width, unitTo=npc, valueOnly=TRUE)
for(i in 2:length(tag
[R] Using spdep example data and R code : bbox should never contain infinite values
Hi, I am facing with a problem when running a code against the sample data from spdep. I am getting SpatialPoints object : bbox should never contain infinite values In additionl Warning Messages: 1. In min(x): no non-missing arguments to min; returning Inf 2. In max(x): no non-missing arg... The code I am trying to execute: sidgams-opgamdata=as(nc, data.frame), radius=30, step=10, alpha=.002) gampoints-SpatialPoints(sidsgam[,c(x,y)]*1000, CRS(+proj=utm +zone=18 +datum=WGS84)) The input dataset is a modified polygon (in WGS datum) of North Carolina that comes with spdep, but using some other additional fields for calculation. I would be very happy to receive a suggestion on corecting this. Thanks! Dejan [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] density plot probabilities
hello ! I have question concerning *kernel density plots*: how to plot density vs. the probability of a vector, when that vector is very short (5-10 values)? I tried: plot(density(x)) or hist(x,probability=T,border=white) lines(density(x)) for small length of vectors, the ylab is not 0ylab1 but fro example from 0 to 3. thats confusing for a density... why is that? thanks for your time. cheers, gregor __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] correction for density plot question
sorry! I ment to plot the probability vs. the values of course. not the probability vs. the density... cheers,gregor __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] R and Xcode Editor
Hi From the R for OS X FAQ page: (http://cran.r-project.org/bin/macosx/RMacOSX-FAQ.html ) 4.4.6 Editor (internal and external): Using AppleScript it is easy to implement Command-E and Command-Return like functionality. How? Regards, Gregor. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] logistic regression - exp(estimates)?
hello. I have a question on the interpretation of a logistic model. is it helpful to exponentiate the coefficients (estimates)? I think I once read something about that, but I cannot remember where. if so, how would be the interpretation of the exp(estimate) ? would there be a change of the interpretation of the ANOVA table (or is the ANOVA table not really helpful at all?). thanks for your time. cheers, gregor rolshausen __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to compute p-Values
Andreas Klein wrote: Hello. How can I compute the Bootstrap p-Value for a one- and two sided test, when I have a bootstrap sample of a statistic of 1000 for example? My hypothesis are for example: 1. Two-Sided: H0: mean=0 vs. H1: mean!=0 2. One Sided: H0: mean=0 vs. H1: mean0 hi, do you want to test your original t.test against t.tests of bootstrapped samples from you data? if so, you can just write a function creating a vector with the statistics (t) of the single t.tests (in your case 1000 t.tests each with a bootstrapped sample of your original data - 1000 simulated t-values). you extract them by: tvalue=t.test(a~factor)$statistic then just calculate the proportion of t-values from you bootstrapped tests that are bigger than your original t-value. p=sum(simualted_tvalueoriginal_tvalue)/1000 (or did I get the question wrong?) cheers, gregor __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] curve fitting with given term
hello, I want to fit a curve to a simple x,y dataset - my problem is, that I want to fit it for the following term: n(1-e^x/y) - so I get the n constant for my data... can anyone help/comment on that? cheers, gregor __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] curve fitting with given term
ok. sorry for being blurry. I have x,y data, that probably fits a asymptotic curve (asymptote at N). now I want to fit a curve onto the data, that gives me the N. therefore I thought to fit an e-function, namely N(1-e^(y/x)) onto the data and get the N from the fitted curves' equation. in the course of this, I was looking for a R-function to fit a given function to data. (I believe there is some implementation in MatLab for this kind of question, anyhow, I wanted to look in R as well...) I am not an expert, so excuse my misuse of terms. I hope my problem graspable...? cheers, gregor Uwe Ligges wrote: gregor rolshausen wrote: hello, I want to fit a curve to a simple x,y dataset - my problem is, that I want to fit it for the following term: n(1-e^x/y) - so I get the n constant for my data... Not an R problem in the first place, but the question arises what n(1-e^x/y) means, its is just some scalar value so far. I am looking for some equation ... Uwe Ligges can anyone help/comment on that? cheers, gregor __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] PCA loadings differ vastly!
hi, I have two questions: #first (SPSS vs. R): I just compared the output of different PCA routines in R (pca, prcomp, princomp) with results from SPSS. the loadings of the variables differ vastly! in SPSS the variables load constantly higher than in R. I made sure that both progr. use the correlation matrix as basis. I found the same problem with rotated values (varimax rotation and rtex=T rotation). can anyone comment ? second: princomp(data, cor=T, rtex=T)$loadings vs. princomp(data, cor=T, rtex=F)$loadings gives me different loadings (expected because of rotation) with one dataset (11 variables) but returns the SAME values with another dataset (3 variables). comments ?? thanks for your time! cheers, gregor __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R2WinBUGS stopping execution
Richard.Cotton at hsl.gov.uk writes: I'm running OpenBUGS model via the R2WinBUGS package interface, under Windows. Is it possible to terminate running models, short of using the Windows Task Manager to forcibly exit the program? If you use OpenBUGS, then I guess you can not since R2WinBUGS just passes a call to BRugs and there is no way to stop that process or maybe it is - take a look in the list of processes. If you use WinBUGS, then you can safely kill it and R will not terminate. gg __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] WinBUGS posterior samples (via R2WinBUGS)?
Anny Huang annylhuang at gmail.com writes: I did some analysis using package R2WinBUGS to call WinBUGS. I set the iterations to 5 (fairly a large number, I think), but after the program was done, the effective posterior samples contained only 7 draws. I don't know why. This indicates that you have a mixing problem! I guess that you do not have enough information to retrieve the post. dist. of that parameter. You might try to reconsider your model or reparametrize it. gg __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] [Solved] Re: Sweave from Kile
Hi Matthieu! I am glad you solved your problem. Now I can compile direct from Kile! The only problem is that the command -ld only create the pdf, does not open it. Maybe are there other options from Script File of Gregor Gorjanc to compile with pdflatex (texi2dvi did not work) and open but I just made it from Kile: Settings-Configure Kile-Tools-Build-New Tool, configure it based on Archive for example, put the new command sweave and then add any command to open (viewpdf in my case). There are several arguments one can use with Sweave.sh. Try Sweave.sh --help and you will get the help informtion. Here is the relevant part about ways of compiling LaTeX and about direct opening with Acrobat Reader or similar applications. There are now the following ways of LaTeX processing: Command and path Script option Used tools - texi2dvi - PS -tp, --texi2dvi2ps texi2dvi and dvips - PS to PDF -tld, --texi2dvi2ps2pdf texi2dvi, dvips and ps2pdf - PDF -td, --texi2dvi2pdf texi2dvi with pdf option - latex - PS -lp, --latex2dvi2ps hardcoded set of 'latex and friends' and dvips - PS to PDF -lld, --latex2dvi2ps2pdf hardcoded set of 'latex and friends', dvips and ps2pdf - pdflatex - PDF -ld, --latex2pdf hardcoded set of 'pdflatex and friends' Open produced files (PDF or Postscript) via options bellow, which are one step further of options above and always imply them: -otp=gv, --opentexi2dvi2ps=gv -otld=acroread, --opentexi2dvi2ps2pdf=acroread -otd=acroread, --opentexi2dvi2pdf=acroread -olp=gv, --openlatex2dvi2ps=gv -olld=acroread, --openlatex2dvi2ps2pdf=acroread -old=acroread, --openlatex2pdf=acroread Files are opened with given application. Defaults are values taken from environmental variables PDFAPP and PSAPP. If these are not defined 'acroread' is taken for PDF and 'gv' for Postscript. Quotes are necessary in case of bad filenames. gg __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Sweave from Kile
Hi Matthieu, Does anybody have experience with Sweave run from Kile? I'm trying to make it run but have problems and don't know if the instructions are false or I do something wrong (my knowledge in bash and shell is too low to understand it)... ... It would help if you stated that you use mine Sweave.sh i.e. the one from http://cran.r-project.org/contrib/extra/scripts/Sweave.sh. I will assume you do. I will start with the second problem 2: If I run kile with sudo (sudo Kile), the problem disappears but a new one comes SweaveOnly output: * cd '/media/Partition_Commune/Mes documents/Ordi/LaTex/Sweave' * Sweave.sh −ld '\example1Leisch.Rnw' * Run Sweave and postprocess with LaTeX directly from command line −ld is not a supported file type! It should be one of: .lyx, .Rnw, .Snw., .nw or .tex Is the instructions false? Or do I do something wrong? Is there a single - or double - i.e. --. If I issue the following $ Sweave.sh --ld test.Rnw Run Sweave and postprocess with LaTeX directly from command line --ld is not a supported file type! It should be one of: .lyx, .Rnw, .Snw., .nw or .tex I get the same error. 1: finished with exit status 126 SweaveOnly output: * cd '/media/Partition_Commune/Mes documents/Ordi/LaTex/Sweave' * Sweave.sh −ld '\example1Leisch.Rnw' * /bin/bash: /usr/local/bin/Sweave.sh: Permission non accordée in english: permission not given It seems that chmod did not behave as you expected. First check file permissions with ls -l /usr/local/bin/Sweave.sh On my computer I get -rwxr-xr-x 1 root root 30K 2008-04-30 11:17 /usr/local/bin/Sweave.sh* Note that x is there three times i.e. anyone can run this script, the user, the group and others. Try with sudo chmod a+x /usr/local/bin/Sweave.sh and check the file permissions. gg __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Version 2.7.2 GUI acts awkward?
hi, I am running R 2.7.2 Windows - recently the GUI-windows (for example to change directory or read in R-scripts) do not open - well, they open, but close down directly afterwards. I can't select a directory or file ... I tried re-installing R - same problem again. does anybody have an idea? thanks gregor -- Gregor Rolshausen PhD Student; University of Freiburg, Germany e-mail: [EMAIL PROTECTED] tel. : ++49 761 2032559 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] ANOVA between within variance
dear Dr. Kubovy, I am sorry. but the Variance table is not exactly what I want. I want the partitioned VARIANCE for between and within the groups. the anova ()-table just gives me the SumSq and the mean Sq... I know how to run t.test and ANOVA! in the nlme-package there is the VarCorr function, which extracts the between and within variances, but only for nested ANOVAs. so my question was, if there is a function like that for not-nested ANOVAS ? sorry. maybe I should reformulate the question. cheers , gregor Am Sep 27, 2008 um 7:19 AM schrieb Michael Kubovy: Than all you need is to run a t-test, no? More generally (from ?lm): ctl - c(4.17,5.58,5.18,6.11,4.50,4.61,5.17,4.53,5.33,5.14) trt - c(4.81,4.17,4.41,3.59,5.87,3.83,6.03,4.89,4.32,4.69) group - gl(2,10,20, labels=c(Ctl,Trt)) weight - c(ctl, trt) anova(lm.D9 - lm(weight ~ group)) This gives you what you need: Analysis of Variance Table Response: weight Df Sum Sq Mean Sq F value Pr(F) group 1 0.690.691.42 0.25 Residuals 18 8.730.48 I am concerned that you have not spent enough time either studying stats or reading up on R. There are many good introductions to stats using R. _ Professor Michael Kubovy University of Virginia Department of Psychology USPS: P.O.Box 400400Charlottesville, VA 22904-4400 Parcels:Room 102Gilmer Hall McCormick RoadCharlottesville, VA 22903 Office:B011+1-434-982-4729 Lab:B019+1-434-982-4751 Fax:+1-434-982-4766 WWW:http://www.people.virginia.edu/~mk9y/ Gregor Rolshausen PhD Student Department of Evolutionary Ecology University of Freiburg im Breisgau; Hauptstrasse 1, 79108 Freiburg phone - +49.761.2559 email - [EMAIL PROTECTED] [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] ANOVA between within variance
hi, is there an option to calculate the 'within' 'between' group variances for a simple ANOVA (aov) model (2 groups, 1 trait, normally distr.) ? or do I have to calculate them from the Sum Sq ? thanks for your time and greetings, gregor -- Gregor Rolshausen PhD Student; University of Freiburg, Germany e-mail: [EMAIL PROTECTED] tel. : ++49 761 2032559 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Automatic placement of Legends
tolga.i.uzuner at jpmorgan.com writes: I am looking for a way to get legends placed automagically in an empty spot on a graph. Additional complication comes through my useage of multiple graphs on the same plot through mfrow. Take a look in Hmisc package. There is function for this task. Gregor __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Pros and Cons of R
Monica, here are some other Pros to consider about R: 1) IMHO, the most important reason for using R is that expressed by John Chambers as the aim of the S language: to turn ideas into software, quickly and faithfully. The broad capabilities of R facilitate the integration of data maintenance and cleaning, exploratory data analysis, model estimation, model implementation, model calibration, model application, and the reporting and display of model outputs. This has tremendous productivity advantages. For example, I was able to meet a tight timeline for developing a regional land use model because R allowed me to easily move through the steps of model development from data analysis to implementation. I even found that I could do some geographical operations that could not be done using our GIS software. In addition, all of the model outputs (including a very many maps) were produced with R. Once you learn how to use R in this way, you will find it takes less time to program the outputs in R than to produce them in GIS. R yields productivity advantages in smaller ways too. We've developed a number of small applications to solve GIS or other problems that could not be solved as easily using other tools. Moreover, once they have been solved using R, the solutions are easily automated or recycled in other contexts. 2) R facilitates documentation and replication. Previous to using R, we did our data analysis and implemented our models in a variety of platforms. For example, Access, Excel, SPSS and Stata were all previously used in household survey data processing and analysis. This was a documentation nightmare. All the steps can be done using R instead and documentation can be easily included in the scripts. If care is taken to use good naming conventions that emphasize readability, the scripts can be largely self documenting. This also facilitates group work. Since we started using R in our work, we have been able to greatly increase our modeling capabilities and output with no increase in staffing. Brian Gregor, P.E. Senior Transportation Analyst Oregon Department of Transportation Transportation Planning Analysis Unit 555 13th Street NE Salem, OR 97301 503-986-4120 Message: 22 Date: Thu, 22 May 2008 16:00:10 + From: Monica Pisica [EMAIL PROTECTED] Subject: [R] Pros and Cons of R To: r-help@r-project.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=Windows-1252 Hi, I am doing a very informal presentation for my office about R capabilities to deal with and analyze spatial data, display data and maps, and connections with GIS. I've used in my presentation info from the CRAN, the spatial Task view, and the more striking graphics examples from http://addictedtor.free.fr/graphiques/thumbs.php and NCEAS http://www.nceas.ucsb.edu/scicomp/GISSeminar/UseCases/MapProdWithRGraphi cs/OneMapProdWithRGraphics.html together with examples of my own work. I am finishing with pros and cons about R and I am wondering if you can come up with other examples, or comments. Here they are: Pros: - R is a programming environment well suited for statistical analysis. - R is open source and cross platforms (Windows, Mac, Linux). - Fortran, C (C++), and Python wrappers are in place. - Deals well with spatial data, has a robust graphical interface and has an active user group list / forum. - External packages for R are almost daily increasing, most of them based on published up-to-date books and peer-reviewed articles. - R related books ? quite a few ?. Cons: - R has a very steep learning curve. - There is no perfect ?beginner? book. - Experience with other programming languages is a plus / minus. - You can save scripts, but not *.exe. - It is updated several times a year (good) but there are no up-grades. - It seems that it is hard to install correctly under Linux. - Everything you want to do is a command line, minimal GUI. - Memory management problems (depends on your OS), especially when displaying big images at high resolution or working with huge matrices (hundreds of Mb). Also i am wondering if R works under 64 bit computers and if it takes advantage of it. Thanks, Monica __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Left censored responses in mixed effects models
Bert Gunter gunter.berton at gene.com writes: Dear R Fellow-Travellers: What is your recommended way of dealing with a left-censored response (non-detects) in (linear Gaussian) mixed effects models? Your description of the data calls for a tobit model http://en.wikipedia.org/wiki/Tobit_model I think you need to take a look in the survival package. Regards, Gregor __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] rbugs on linux and wine
Gregor Gorjanc wrote: Hi Alexander! You are mixing WinBUGS and OpenBUGS. R package Rbugs works with OpenBUGS, but the later does not work with Rbugs under Linux! Are you talking about rbugs or BRugs, Gregor? Ouch. Thank you Uwe! You are right, there are two R packages: rbugs and BRugs. Unfortunatelly, I do not have eany xperience with rbugs. Sorry. g __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] rbugs on linux and wine
Hi Alexander! You are mixing WinBUGS and OpenBUGS. R package Rbugs works with OpenBUGS, but the later does not work with Rbugs under Linux! Gregor __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] ipf function in R
Chandra,
While I can't advise on how to use the ipf function in the cat package,
I can offer the following function that we use here to balance rebalance
arrays with new marginal totals.
#ipf.R
#Function to iteratively proportionally fit a multidimensional array
#IPF also known as Fratar method, Furness method, raking and two/three
dimensional balancing.
#This method of matrix balancing is multiplicative since the margin
factors (coefficients)
#are multiplied by the seed array to yield the balanced array.
#Ben Stabler, [EMAIL PROTECTED], 9.30.2003
#Brian Gregor, [EMAIL PROTECTED], 2002
#inputs:
#1) margins_ - a list of margin values with each component equal to a
margin
#Example: row margins of 210 and 300, column margins of 140 and 370
#and third dimension margins of 170 and 340.
#[[1]] [,1] [,2] [,3]
#210, 300
#[[2]]
#140, 370
#[[3]]
#170, 340
#2) seedAry - a multi-dimensional array used as the seed for the IPF
#3) iteration counter (default to 100)
#4) closure criteria (default to 0.001)
#For more info on IPF see:
#Beckmann, R., Baggerly, K. and McKay, M. (1996). Creating Synthetic
Baseline Populations.
# Transportation Research 30A(6), 415-435.
#Inro. (1996). Algorithms. EMME/2 User's Manual. Section 6.
#~~~
~~~
ipf - function(Margins_, seedAry, maxiter=100, closure=0.001) {
#Check to see if the sum of each margin is equal
MarginSums. - unlist(lapply(Margins_, sum))
if(any(MarginSums. != MarginSums.[1])) warning(sum of each margin
not equal)
#Replace margin values of zero with 0.001
Margins_ - lapply(Margins_, function(x) {
if(any(x == 0)) warning(zeros in marginsMtx replaced with
0.001)
x[x == 0] - 0.001
x
})
#Check to see if number of dimensions in seed array equals the
number of
#margins specified in the marginsMtx
numMargins - length(dim(seedAry))
if(length(Margins_) != numMargins) {
stop(number of margins in marginsMtx not equal to number of
margins in seedAry)
}
#Set initial values
resultAry - seedAry
iter - 0
marginChecks - rep(1, numMargins)
margins - seq(1, numMargins)
#Iteratively proportion margins until closure or iteration criteria
are met
while((any(marginChecks closure)) (iter maxiter)) {
for(margin in margins) {
marginTotal - apply(resultAry, margin, sum)
marginCoeff - Margins_[[margin]]/marginTotal
marginCoeff[is.infinite(marginCoeff)] - 0
resultAry - sweep(resultAry, margin, marginCoeff, *)
marginChecks[margin] - sum(abs(1 - marginCoeff))
}
iter - iter + 1
}
#If IPF stopped due to number of iterations then output info
if(iter == maxiter) cat(IPF stopped due to number of iterations\n)
#Return balanced array
resultAry
}
Brian Gregor, P.E.
Transportation Planning Analysis Unit
Oregon Department of Transportation
[EMAIL PROTECTED]
(503) 986-4120
Message: 143
Date: Wed, 05 Mar 2008 18:14:28 +1100
From: Chandra Shah [EMAIL PROTECTED]
Subject: [R] ipf function in R
To: r-help@r-project.org
Message-ID: [EMAIL PROTECTED]
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Hi
I have a 3 x 2 contingency table:
10 20
30 40
50 60
I want to update the frequencies to new marginal totals:
100 130
40 80 110
I want to use the ipf (iterative proportional fitting)
function which
is apparently in the cat package.
Can somebody please advice me how to input this data and
invoke ipf in R
to obtain an updated contingency table?
Thanks.
By the way I am quite new to R.
--
Dr Chandra Shah
Senior Research Fellow
Monash University-ACER Centre for the Economics of Education
and Training
Faculty of Education, Building 6,
Monash University
Victoria
Australia 3800
Tel. +61 3 9905 2787
Fax +61 3 9905 9184
www.education.monash.edu.au/centres/ceet
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Re: [R] R2WinBUGS sending variables as factors
James.Dell at csiro.au writes:
...
1) I can't seem to send variables classed as factors (Month), is there a
way do this?
You can not use factors per se in BUGS. You have to convert them to numeric
(integer) variables before.
2) Checking the Log in WinBUGS I can see that the model is Syntactically
correct, but Bugs is not able to recognise the the initial values for
each of the chains.
...
model
{
#Centre variables
mSeaW - mean(SeaW[])
s_dSeaW - sd(SeaW[])
#normalise Variables
nSeaWiFS - mSeaW/s_dSeaW
for(i in 1:N) {
log(lambda[i]) - delta0 + alpha1 * Month[i] + alpha2 * Lat[i] +
beta1 * (SeaW[i] - nSeaW)
I guess you want to use mSeaW here instead of nSeaW!
^ ^
# recalculate the original intercept term
Intercept - delta0 - beta1 * nSeaW
I guess you want to use nSeaWiFS here instead of nSeaW!
...
##And the Error Message from WinBUGS
model is syntactically correct
data(C:/Program Files/R/R-2.6.0/data.txt)
data loaded
compile(3)
made use of undefined node nSeaW
This warned you that the model is not OK!
Gregor
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Re: [R] Sweave and Scientific Workplace
Dietrich Trenkler Dietrich.Trenkler at uni-osnabrueck.de writes: Dear HelpeRs, a colleague of mine uses Scientific Workplace to write his LaTeX documents. I made his mouth water mentioning the advantages of using Sweave. Not using SW myself I wonder if anyone out there has gathered some experiences in using the combination of both. I can not say anything about SW, but LyX can do the same. I have a paper, that will probably appear in next issues of Rnews about using Sweave in LyX. Gregor __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Dealing with NA's in a data matrix
Henrique Dallazuanna wwwhsd at gmail.com writes: x[is.na(x)] - 0 On 05/12/2007, Amit Patel amitpatel_ak at yahoo.co.uk wrote: Hi I have a matrix with NA value that I would like to convert these to a value of 0. any suggestions also library(gdata) x - matrix(rnorm(16), nrow=4, ncol=4) x[1, 1] - NA NAToUnknown(x, unknown=0) Gregor __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Summary: Process multiple columns of data.frame
Thompson, David (MNR David.John.Thompson at ontario.ca writes:
Thank you Jim Holtman and Mark Leeds for your help.
Original question:
How do I do the following more concisely?
Bout[is.na(Bout$bd.n), 'bd.n'] - 0
Bout[is.na(Bout$ht.n), 'ht.n'] - 0
Bout[is.na(Bout$dbh.n), 'dbh.n'] - 0
. . .
Solution:
for (i in c('bd.n', 'ht.n', 'dbh.n')) Bout[is.na(Bout[[i]]), i] - 0
ABove solution is completely OK, but can be cumbersome. I wrote functions
NAToUnknown() and unknownToNA() with exactly the same problem in mind.
Take a look in gdata package. I also described the function in RNews
G. Gorjanc. Working with unknown values: the
gdata package. R News, 7(1):24–26, 2007.
http://CRAN.R-project.org/doc/Rnews/Rnews_2007-1.pdf.
For your example try the following:
library(gdata)
df.0 - as.data.frame( cbind(
c1=c(NA, NA, 10, NA, 15, 11, 12, 14, 14, 11),
c2=c(13, NA, 16, 16, NA, 12, 14, 19, 18, NA),
c3=c(NA, NA, 11, 19, 17, NA, 11, 16, 20, 13),
c4=c(20, NA, 15, 11, NA, 15, NA, 13, 14, 15),
c5=c(14, NA, 13, 16, 17, 17, 16, NA, 15, NA),
c6=c(NA, NA, 13, 11, NA, 16, 15, 12, NA, 20)) )
df.0
c1 c2 c3 c4 c5 c6
1 NA 13 NA 20 14 NA
2 NA NA NA NA NA NA
3 10 16 11 15 13 13
4 NA 16 19 11 16 11
5 15 NA 17 NA 17 NA
6 11 12 NA 15 17 16
7 12 14 11 NA 16 15
8 14 19 16 13 NA 12
9 14 18 20 14 15 NA
10 11 NA 13 15 NA 20
NAToUnknown(df.0, unknown=0)
c1 c2 c3 c4 c5 c6
1 0 13 0 20 14 0
2 0 0 0 0 0 0
3 10 16 11 15 13 13
4 0 16 19 11 16 11
5 15 0 17 0 17 0
6 11 12 0 15 17 16
7 12 14 11 0 16 15
8 14 19 16 13 0 12
9 14 18 20 14 15 0
10 11 0 13 15 0 20
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Re: [R] Confidence Intervals for Random Effect BLUP's
Rick Bilonick rab at nauticom.net writes: ... I think prediction interval is what is usually used. Regardless, I'm not sure how predict.lm will be of much help because I asked specifically about BLUP's for random effects and the last time I checked lm did not handle mixed effects models. Neither predict.lme and predict.lmer provide intervals. Here is the code that I included in my original e-mail. My simple question is, will this code correctly compute a prediction interval for each subjects random effect? In particular, will the code handle the bVar slot correctly? Some postings warned about inappropriate access to slots. Here is the code that I asked about in my original e-mail: Rick, I can not help you with your code as I am not familiar with slots in lmer outputs. Maybe lmer authors can help you - try on r-sig-mixed list. But you can check your results with running MCMC for the same model and you will get the whole posterior density of all your parameters that you put on prior with unknown variance i.e. random effects or sometimes also called BLUPs. There is a function in lme4 package that can do that! Gregor __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Meta-analysis mixed model
Diane Srivastava srivast at zoology.ubc.ca writes: I have a meta-analysis dataset which I would like to analyze as a mixed model, where the y-variable is a measure of effect size, the random effect is the study from which the effect size was extracted, and the fixed effect is a categorical explanatory variable. The complication is that we often have multiple estimates of effect size from a single study (e.g. the experiment was repeated in different years, or under different conditions). Being a meta-analysis, I need to weight the effect sizes by the inverse of the effect SE. Thus my dataset includes: study, effect size, SE, explanatory variables. Andrew Gelman shows in several places (his books, R2WinBUGS package) how to use data (your effect size estimates) from previous analyses. He has mean and variance of the estimate (the data) and models them. The key is that you will have to swicth to BUGS. It has very flexible model language! Regards, Gregor __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
