Re: [R] Difference between loops and vectorization

2010-12-01 Thread Dieter Menne
Santosh Srinivas wrote: > > A fundamental question ...I'm trying to understand the differences between > loop and vectorization ... I understand that it should be a natural choice > to use apply / adply when it is needed to perform the > same function across all rows of a data frame. Any pointer

Re: [R] Minor warning about seq

2010-12-01 Thread Dieter Menne
Prof. John C Nash wrote: > > I spent more time than I should have debugging a script because I wanted >x<-seq(0,100)*0.1 > > but typed >x<-seq(O:100)*0.1 > > seq(0:100) yields 1 to 101, > Which leads us to another rule: never use a variable called "O". I remember this was a no-no eve

Re: [R] pca analysis: extract rotated scores?

2010-12-01 Thread Mark Difford
Hi Liviu, >> However, I'm still confused on how to compute the scores when rotations >> (such as 'varimax' or other methods in GPArotation) are applied. PCA does an orthogonal rotation of the coordinate system (axes) and further rotation is not usually done (in contrast to factor analysis). Nei

Re: [R] non-linear fourth-order differential equations

2010-12-01 Thread Thomas Petzoldt
Hi Yanika, more information about deSolve (books, papers, tutorials) can be found on the deSolve homepage: http://desolve.r-forge.r-project.org and, of course, in the package documentations. If you need further help from the list, please provide a short reproducible example. Thomas Petzold

[R] Reordering entries in package manual PDF's

2010-12-01 Thread Aleksi Kallio
Hello, I have create my own R package and written the documentation in Rd format for each of the functions plus the package itself. However now the functions appear in a random order in the generated PDF and the package documentation is placed in between the functions, when I would like it t

[R] Graph in R with edge weights

2010-12-01 Thread arturs . onzuls
Can you please show code example, how to draw graph with some nodes and edges, but with weights. I only found here http://www.bioconductor.org/packages/release/bioc/vignettes/Rgraphviz/inst/doc/Rgraphviz.pdf- Using edge weights for labels, but... Here an example: > library("graph"); library(Rgrap

Re: [R] Error bars in lattice barchart with groups

2010-12-01 Thread Dieter Menne
Henning Wildhagen wrote: > > > i want to plot gene regulation data in a lattice barchart. To illustrate > the problem i encounter, the following code uses the "barley"dataset: > > > #No, i tried to add error bars using the following code: > .. > As Deepayan noted in # http://markmail.

[R] missing values

2010-12-01 Thread Iasonas Lamprianou
Dear all, i have spent a lot of time trying to solve this problem, but I am sure that there must be a simple solution. So, as a last resort, I am coming back to you again. I have a dataset with some (almost random) values in many variables. Lets say that the dataset represents the scores of stu

Re: [R] Save R2HTML as an object instead of file

2010-12-01 Thread Joel
Or is there any kind of File buffer that dossent save a file on the harddrive? coz this gives me the thing I want but it still saves the file on the HD > .HTML.file=(temp<-file("era.html","w+")) > HTML("NANALALA") > HTML(diag(3)) Then I can just use readLines(temp) to get the result but as

Re: [R] Save R2HTML as an object instead of file

2010-12-01 Thread Gregoire Pau
Hi Joel, The function hwrite() of the package hwriter does that. > library(hwriter) > hwrite(iris[1:10,]) See examples at http://www.embl.de/~gpau/hwriter/ Cheers, Greg --- Gregoire Pau EMBL Research Officer http://www.embl.de/~gpau/ On 01/12/10 08:53, Joel wrote: Hi Is it possible to inst

[R] .Internal(download())

2010-12-01 Thread Koray Kaya
Hello, I tried to use GEOQuery package of BioC. It does not download GSE. I investigated problem, understood that the problem was about internal function "download". Reccomendations about it mostly suggest switching any proxy off in R. I did, and nothing changed. I use Ubuntu Lucid 64 bit Tha

Re: [R] Problem in reading Excel spreadsheets

2010-12-01 Thread Ivan Calandra
Hi, I don't know much about RODBC, but the package xlsReadWrite works pretty well for me for reading and writing xls files (and it doesn't need Perl or anything else to run). Ivan Le 12/1/2010 08:56, Stephen Liu a écrit : Hi folks, Win 7 64bit R 2.12.0 32bit Problem in reading Excel sprea

Re: [R] How to draw a rect() behind a hist() ?

2010-12-01 Thread Ivan Calandra
Hi, For your second question, take a look at ?clip. The example explains really well what you can do and how. HTH, Ivan Le 12/1/2010 04:42, Peter Ehlers a écrit : On 2010-11-30 17:27, Jason Edgecombe wrote: Hi, I have the following code: hist(gps$heartpercent, breaks=5) rect(90, par("usr")

Re: [R] Error bars in lattice barchart with groups

2010-12-01 Thread Dieter Menne
This is an interesting discussion on barchart (without error bars) http://www.decisionsciencenews.com/2010/08/11/which-chart-is-better/ Dieter -- View this message in context: http://r.789695.n4.nabble.com/Error-bars-in-lattice-barchart-with-groups-tp3065864p3066860.html Sent from the R help

Re: [R] missing values

2010-12-01 Thread Ivan Calandra
Hi, (a) sum() and mean() have a na.rm argument that should be set to TRUE. (b) let's try with an example: x <- c(1:5, NA, NA, 6:10, NA) x[is.na(x)] <- 0 ## replace NAs by 0 HTH, Ivan Le 12/1/2010 10:00, Iasonas Lamprianou a écrit : Dear all, i have spent a lot of time trying to solve this p

Re: [R] Problem in reading Excel spreadsheets

2010-12-01 Thread Stephen Liu
Hi Ivan, Thanks for your advice. I have problem running xlsReadWrite on 64 bit Win7. > library(xlsReadWrite) xlsReadWrite version (cran shlib) Copyright (C) 2010 Hans-Peter Suter, Treetron, Switzerland. !! Your installation contains the cran placeholder shlib (dll/so). Please get the regular sh

Re: [R] missing values

2010-12-01 Thread Michael Bedward
And just to add to Ivan's comment, if you are using the rowSums or colSums functions with a matrix or data.frame they also have the na.rm argument. Michael On 1 December 2010 20:16, Ivan Calandra wrote: > Hi, > > (a) sum() and mean() have a na.rm argument that should be set to TRUE. > > (b) let'

Re: [R] How to draw a rect() behind a hist() ?

2010-12-01 Thread Jim Lemon
On 12/01/2010 12:27 PM, Jason Edgecombe wrote: Hi, I have the following code: hist(gps$heartpercent, breaks=5) rect(90, par("usr")[3], 100, par("usr")[4], col = "red") How do I get the rectangle to appear behind the histogram. Barring that, how can I make certain bars of the histogram to be a

[R] how to remove grid lines from coplot graphs

2010-12-01 Thread Seth Roberts
coplot() usually puts grid lines in the panels it makes. To see examples, example(coplot). How can I remove those grid lines? Seth Roberts [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/l

Re: [R] missing values

2010-12-01 Thread Iasonas Lamprianou
thank you, I'll have a go and let you know if i have problems Dr. Iasonas Lamprianou Assistant Professor (Educational Research and Evaluation) Department of Education Sciences European University-Cyprus P.O. Box 22006 1516 Nicosia Cyprus Tel.: +357-22-713178 Fax: +357-22-590539 Honorary R

Re: [R] Save R2HTML as an object instead of file

2010-12-01 Thread Eric Lecoutre
Hi Joel, You can use: obj=diag(3) txt=capture.output(HTML(obj,file="")) Then you may manipulate elements, paste with collapse argument, replace parts with gsub and so on. HTH, Eric 2010/12/1 Joel > > Hi > > Is it possible to instead of getting the HTML code written to a file, get > it > s

[R] .Internal(download())

2010-12-01 Thread Koray Kaya
Hello, I tried to use GEOQuery package of BioC. It does not download GSE. I investigated problem, understood that the problem was about internal function "download". Reccomendations about it mostly suggest switching any proxy off in R. I did, and nothing changed. I use Ubuntu Lucid 64 bit Thank

[R] problems formulating arguments to lme()

2010-12-01 Thread Robert Kinley
this is a clearer (I hope) version of an earlier post - My problem is formulating the random = argument to give estimates of all 9 random components for this kind of setup where there are (I think) 9 variance/covariance components ... Study.1Study.2 ... Stud

Re: [R] Adding text to a multiplot (via mfrow)

2010-12-01 Thread smj_115
Hi Peter Many thanks. I will have a go with that and see if I have any joy. Your advice is much appreciated. Sam -- View this message in context: http://r.789695.n4.nabble.com/Adding-text-to-a-multiplot-via-mfrow-tp3065850p3067003.html Sent from the R help mailing list archive at Nabble.com.

Re: [R] Problem in reading Excel spreadsheets

2010-12-01 Thread Ivan Calandra
Hi again, There are also other packages to read and write xls files, including gdata (read), dataframe2xls and writeXLS (write), which depend on Perl or Python if I'm not mistaken. I have no idea whether they work on Windows 64 bits. Visit Crantastic http://crantastic.org/ Ivan Le 12/1/2010

Re: [R] Difficulty loading packages into R version 2.12.0

2010-12-01 Thread Uwe Ligges
Run update.packages(checkBuilt=TRUE) to get package binaries that were compield for your version of R. Uwe Ligges On 24.11.2010 04:24, john moran wrote: Apologies for my previous effort in HTML which apparently was scrubbed Dear R-users I wonder if I could get advice on the above proble

Re: [R] ggplot2 histograms

2010-12-01 Thread Small Sandy (NHS Greater Glasgow & Clyde)
Thanks Thierry Using the position_dodge positioning option ought to work but there is something wrong with the scaling when the binwidth is not = 1. You can begin to see this with the example I sent: If you do ggplot(data=dafr, aes(x = d1, fill=d2)) + geom_histogram(binwidth = 1, position = pos

[R] mailing list subscription

2010-12-01 Thread dondom
[[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,

Re: [R] Pass an operator to function

2010-12-01 Thread Duncan Murdoch
On 30/11/2010 9:54 PM, randomcz wrote: Hi guys, How to pass an operator to a function. For example, test<- function(a, ">", b) { return(a>b) #the operator is passed as an argument } Thanks, It's much simpler than the other suggestions. Just pass the operator, and treat it as a fun

Re: [R] .Internal(download())

2010-12-01 Thread Duncan Murdoch
On 01/12/2010 5:12 AM, Koray Kaya wrote: Hello, I tried to use GEOQuery package of BioC. It does not download GSE. I investigated problem, understood that the problem was about internal function "download". Reccomendations about it mostly suggest switching any proxy off in R. I did, and nothing

[R] Lattice dotplots

2010-12-01 Thread barbara . chaves
Dear, I have a dataset with 4 subjects (see ID in example), and 4 treatment (see TRT in example) which are tested on 2 locations and in 3 blocs. By using Lattice dotplot, I made a graph that shows the raw data per location and per bloc. In that graph, I would like to have a reference line per

Re: [R] reference text variables as column name to plot [SOLVED]

2010-12-01 Thread Graves, Gregory
The following works nicely. Thank you. plot(z, sf[[s]], type="l") #where the dataframe name in my case is "sf" Sorry - I meant to say there were 24 rows in each column, so z=1:24 Gregory A. Graves, Lead Scientist Everglades REstoration COoordination and VERification (RECOVER) Restoration Scie

Re: [R] Problem in reading Excel spreadsheets

2010-12-01 Thread Gabor Grothendieck
On Wed, Dec 1, 2010 at 2:56 AM, Stephen Liu wrote: > Hi folks, > > Win 7 64bit > R 2.12.0 32bit > > Problem in reading Excel spreadsheets > There are quite a few alternatives for reading Excel spreadsheets. They are listed here: http://rwiki.sciviews.org/doku.php?id=tips:data-io:ms_windows --

Re: [R] Where is gdata?

2010-12-01 Thread Gabor Grothendieck
On Sun, Nov 28, 2010 at 6:44 AM, Stephen Liu wrote: > Hi folks, > > Win 7 64 bit > R 32 bit > >> install.packages("gregmisc") > Installing package(s) into > ‘C:\Users\satimiswin764\Documents/R/win-library/2.12’ > (as ‘lib’ is unspecified) > --- Please select a CRAN mirror for use in this session

Re: [R] Welcome to the "R-help" mailing list

2010-12-01 Thread Ista Zahn
Hi Bill, Please keep the R list copied. I don't think you've given enough information to pin down your problem. This works: dat <- read.table(textConnection("dates returns 2000-1-4 -0.038344718 2000-1-50.00195 2000-1-60.000955702 2000-1-70.027090384 2000-1-100.011189966 2

Re: [R] pca analysis: extract rotated scores?

2010-12-01 Thread He Zhang
Hi, I am also doing PCA. Is the following right for extracting the scores? library(psych) pca<-principal(data,nfactors=,rotate="varimax",scores=T) pca$loadings pca$score Best regards, He On Tue, Nov 30, 2010 at 10:22 AM, Liviu Andronic wrote: > Dear all > I'm unable to find an example of extra

Re: [R] cluster analysis: predefined clusters

2010-12-01 Thread deriK2000
Peter Langfelder wrote: > > On Fri, Nov 26, 2010 at 6:55 AM, Derik Burgert wrote: >> Dear list, >> >> running a hierachical cluster analysis I want to define a number of >> objects that build a cluster already. In other words: I want to force >> some of the cases to be in the same cluster from

Re: [R] ggplot2 histograms

2010-12-01 Thread Ista Zahn
Hi Sandy, I don't have an answer to your question, but wanted to share another possibility: ggplot(data=dafr, aes(x = d1, fill=d2)) + geom_histogram(binwidth = 1, position = position_identity(), alpha=.5) Best, Ista On Wed, Dec 1, 2010 at 6:09 AM, Small Sandy (NHS Greater Glasgow & Clyde) wrote

Re: [R] how to remove grid lines from coplot graphs

2010-12-01 Thread Peter Ehlers
On 2010-12-01 01:51, Seth Roberts wrote: coplot() usually puts grid lines in the panels it makes. To see examples, example(coplot). How can I remove those grid lines? > > Seth Roberts > That's hard-coded in coplot. But you can easily make a modified copy of coplot. Here are the steps: 1. make

[R] Plot a matrix recursively

2010-12-01 Thread alcesgabbo
Hi, I have the following matrix (named m): key sensor_date Laser_1 Laser_2 Laser_3 2010-09-30T15:00:12+020063 1 2010-10-31T15:05:07+0100

[R] parametric estimators for species richness in R

2010-12-01 Thread yangwenjing
Dear everyone, I am doing some work about species richness estimation. Nonparametric estimation (such as Chao1, Jacknife1) can be done just using function "specpool()" and "estimateR()" in package "vegan". The problem is that I can not found any functions for parametric estimation (such as MMMe

Re: [R] Troubles using postscript(family = "ComputerModern")

2010-12-01 Thread Martin Maechler
> David Winsemius > on Mon, 29 Nov 2010 09:46:08 -0500 writes: > On Nov 29, 2010, at 9:00 AM, pilchat wrote: >> Hi guys, >> >> to make it easier, here is a simple case with the same issues. I use >> the short function below to make the attached PS file. >>

[R] anova error

2010-12-01 Thread Jean . Coursol
Just for fun This small program gives negative Sum of Sq in anova (with R versions 2.9.2 and 2.10.0) (linux 32 kernel 2.6.29.6-smp slackware 13.0) : y = c(3.6, 5.0, 5.0, 4.6, 4.5, 4.3, 4.5, 5.1, 4.5, 4.3) trans = as.factor(c("NT","NT","NT","NT","NT","T","T","T","T","T")) lc = lm(y ~ trans) l1

[R] Searching for packages for normalizing Metabolomic data

2010-12-01 Thread nqueralt
Hi everybody, I am a beginner in the steps of pre-processing and data analysis of non-targeted metabolomic profiling experiments. Anyone knows if there exists some tool for normalizing this type of data (raw data or XCMS matrix data) in R repositories? Many thanks in advance. Best r

Re: [R] Plot a matrix recursively

2010-12-01 Thread Gerrit Eichner
Take a look at ?matplot HTH, Gerrit On Wed, 1 Dec 2010, alcesgabbo wrote: Hi, I have the following matrix (named m): key sensor_date Laser_1 Laser_2 Laser_3 2010-09-30T15:00:12+02006

Re: [R] Plot a matrix recursively

2010-12-01 Thread Roland Rau
On 12/01/2010 02:43 PM, alcesgabbo wrote: I plot the first column with the following function: plot(m[,1],type="o", xaxt="n",ylim=c(min(m[,1:length(colnames(m))])-1, max(m[,1:length(colnames(m))])+1)) for the other columns I use there functions: lines(m[,2],type=\"o\") lines(m[,3],type=\"o\")

Re: [R] Lattice dotplots

2010-12-01 Thread Peter Ehlers
On 2010-12-01 04:02, barbara.cha...@bayer.com wrote: Dear, I have a dataset with 4 subjects (see ID in example), and 4 treatment (see TRT in example) which are tested on 2 locations and in 3 blocs. By using Lattice dotplot, I made a graph that shows the raw data per location and per bloc. In tha

Re: [R] anova error

2010-12-01 Thread Peter Ehlers
It might be a good idea not to use an outdated version of R. I don't see your "problem" in R 2.12.0. Peter Ehlers On 2010-12-01 05:44, jean.cour...@math.u-psud.fr wrote: Just for fun This small program gives negative Sum of Sq in anova (with R versions 2.9.2 and 2.10.0) (linux 32 kernel 2.6.29

Re: [R] pca analysis: extract rotated scores?

2010-12-01 Thread Mark Difford
Hi He Zhang, >> Is the following right for extracting the scores? >> ... >> pca$loadings >> pca$score Yes. But you should be aware that the function principal() in package psych is standardizing your data internally, which you might not want. That is, the analysis is being based on the correla

Re: [R] Lattice dotplots

2010-12-01 Thread Dieter Menne
barbara.chaves wrote: > > > I have a dataset with 4 subjects (see ID in example), and 4 treatment (see > TRT in example) which are tested on 2 locations and in 3 blocs. By using > Lattice dotplot, I made a graph that shows the raw data per location and > per bloc. In that graph, I would like

Re: [R] Searching for packages for normalizing Metabolomic data

2010-12-01 Thread Martin Morgan
On 12/01/2010 05:57 AM, nquer...@clinic.ub.es wrote: > Hi everybody, > > > > I am a beginner in the steps of pre-processing and data analysis of > non-targeted metabolomic profiling experiments. > Anyone knows if there exists some tool for normalizing this type of data (raw > data or XCMS

Re: [R] Where is gdata?

2010-12-01 Thread Gavin Simpson
On Wed, 2010-12-01 at 07:32 -0500, Gabor Grothendieck wrote: > On Sun, Nov 28, 2010 at 6:44 AM, Stephen Liu wrote: > > In the end it appears that there was no problem in accessing the gdata > package or any of its components and that the poster's problem stemmed > from issuing this series of com

Re: [R] ggplot2 histograms

2010-12-01 Thread Hadley Wickham
> However if you do: > ggplot(data=dafr, aes(x = d1, fill=d2)) + geom_histogram(binwidth = 1, > position = position_dodge(width=0.99)) > > The position of first bin which goes from 0-2 appears to start at about 0.2 > (I accept that there is some "white space" to the left of this) while the > pos

[R] attempted merge() returns: cannot coerce type 'closure' to vector of type 'any'

2010-12-01 Thread Karl Brand
Hi Dimtris and esteemed useRs, I don't understand why i get this error message when attempting to use merge() - > temp <- merge(x, y[,17, drop=FALSE], by=rownames, sort=FALSE) Error in as.vector(x, mode) : cannot coerce type 'closure' to vector of type 'any' It should work because: > all(r

Re: [R] Plot a matrix recursively

2010-12-01 Thread alcesgabbo
thanks! very useful -- View this message in context: http://r.789695.n4.nabble.com/Plot-a-matrix-recursively-tp3067283p3067443.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mail

Re: [R] anova error

2010-12-01 Thread Ben Bolker
Peter Ehlers ucalgary.ca> writes: > > It might be a good idea not to use an outdated version of R. > I don't see your "problem" in R 2.12.0. > > Peter Ehlers > > On 2010-12-01 05:44, Jean.Coursol math.u-psud.fr wrote: > > Just for fun > > > > This small program gives negative Sum of Sq in a

[R] New package Rd2roxygen: Convert Rd to roxygen documentation

2010-12-01 Thread Yihui Xie
Hi, A new package Rd2roxygen has been released on CRAN: http://cran.r-project.org/package=Rd2roxygen (source package available; binaries to come) This package can be useful for developers who used to document their functions in the raw Rd files but want to switch to roxygen now using inline roxyg

[R] log-normal Centile

2010-12-01 Thread Robert Quinn
I am having problems trying to get R to graph data input that is log-normal on the horizontal (x) axis. The data is log (base 10), and I am more interested in viewing the tails of the distribution. The closest I can get with this is log on the vertical (y) axis and linear on the horizontal axis.

Re: [R] Simple question on eval

2010-12-01 Thread Lamke
Thank you so much Joshua. That's exactly what I am looking for. What I wanted to do is to pass a parameter to a function and I have to run the functions 30 times. Instead of typing them all out, I created a long string of "f(a);f(b);f(c) ..." using paste() and use eval and parse to evaluative t

Re: [R] Simple question on eval

2010-12-01 Thread Ivan Calandra
Isn't it what do.call() does? Ivan Le 12/1/2010 16:39, Lamke a écrit : Thank you so much Joshua. That's exactly what I am looking for. What I wanted to do is to pass a parameter to a function and I have to run the functions 30 times. Instead of typing them all out, I created a long string of

[R] Wiener-Granger Causality Test in R

2010-12-01 Thread CALEF ALEJANDRO RODRIGUEZ CUEVAS
Hello dudes. I'm developing VAR analysis based on suggestions made by Horváth in its paper Canonical Correlation Analysis and Wiener-Granger Causality Tests. That's the reason I'm looking for if there's any R package to develop Wiener - Granger Causality Test. Thanks a lot for your unvaluable he

Re: [R] anova error

2010-12-01 Thread David Winsemius
On Dec 1, 2010, at 9:18 AM, Peter Ehlers wrote: It might be a good idea not to use an outdated version of R. I don't see your "problem" in R 2.12.0. Furthermore isn't it a bit to be asking why the sign on a number that is effectively zero happens to be negative? I would think that FAQ 7

[R] sem package: optimization did not converge

2010-12-01 Thread Maike Luhmann
In specifying a CFA model using the sem package, I got the following warning message: In sem.default(ram = ram, S = S, N = N, param.names = pars, var.names = vars, : Could not compute QR decomposition of Hessian. Optimization probably did not converge. This is the complete input (incl

[R] Sequence for repeated numbers

2010-12-01 Thread Luana Marotta
Hello fellows, I would like to create a sequence for repeated numbers in a dataset. For example: ID <- c(1:20) grade <- c(4,4,4,5,5,7,7,7,7,8,8,8,9,9,9,9,9,10,10,10) Data: ID Grade 1 4 2 4 3 4 4 5 5 5 6 7 7 7 8 7 9 7 (...) I would like to create a variable "sequence": Data:

Re: [R] ggplot2 histograms

2010-12-01 Thread Small Sandy (NHS Greater Glasgow & Clyde)
Sorry this should have ben to the whole list: Hadley I think I've sorted it out in my head but for the record, and just to be sure... I guess what I was expecting was that the width parameter would be independent of binwidth. Thus a width parameter of 0.5 would always indicate an overlap of hal

[R] [R-lme] Extract estimated variances from output of lme?

2010-12-01 Thread Tingting Zhan
Hi all, I have the output of summary() of an lme object called "lme.exp1", for example # > summary(lme.exp1) Linear mixed-effects model fit by REML Data: DATA Log-restricted-likelihood: -430.8981 Fixed: fixed.exp1 Random effects: Formu

Re: [R] anova error

2010-12-01 Thread Douglas Bates
On Wed, Dec 1, 2010 at 9:02 AM, Ben Bolker wrote: > > > Peter Ehlers ucalgary.ca> writes: > >> >> It might be a good idea not to use an outdated version of R. >> I don't see your "problem" in R 2.12.0. >> >> Peter Ehlers >> >> On 2010-12-01 05:44, Jean.Coursol math.u-psud.fr wrote: >> > Just for

[R] Font family not found in Windows font database

2010-12-01 Thread Mark Ebbert
Dear R Gurus, I have a fairly simple problem, but I haven't been able to find the answer on 'the google' or in the r-help archives. I am generating plots on both Windows and OS X where I need to guarantee that the font used is Arial. In my plot command I specify 'fontfamily="Arial"'. The probl

[R] Question regarding legend look

2010-12-01 Thread Filoche
Hi everyone. I have a quick question regarding the look of my legend in my plot. As you can see in the next figure, I have 3 series. http://r.789695.n4.nabble.com/file/n3067466/legend.png However, I find rather difficult to differentiate the series 1 and 3 according to their line type (lty).

Re: [R] Simple question on eval

2010-12-01 Thread Joshua Wiley
Here are two options that might work for you given the little bit you've said: ## If its the same parameter all 30 times ## say, for example, base = 4.5 to log for(i in 1:30) { print(log(1:10, base = 4.5)) } ## if they are different parameters, you could try lapply(X = c(1.3, 3, 2.2, 4, 5), FUN

Re: [R] Sequence for repeated numbers

2010-12-01 Thread Jonathan P Daily
Try this: > ord <- order(grade) > ID <- Id[ord] > grade <- grade[ord] > sequence <- unlist(sapply(table(grade), FUN = function(x) 1:x), use.names = F) And as a general tip, it is much easier to work with related values like ID and grade if they are in a data frame. Such as: > dat <- data.frame

[R] Poisson GLM warning message

2010-12-01 Thread Anna Berthinussen
Hi, I receive the following warning message when I run a poisson GLM in R: "glm.fit: fitted rates numerically 0 occurred" The model summary is shown below. The variable 'Species' consists of counts of different species ranging from 0 to 4. I suspect this may have something to do with the warn

Re: [R] missing values

2010-12-01 Thread Doran, Harold
You can also explore the classical() function in the MiscPsycho package that does item analysis. > -Original Message- > From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On > Behalf Of Iasonas Lamprianou > Sent: Wednesday, December 01, 2010 4:52 AM > To: Michael Be

Re: [R] Sequence for repeated numbers

2010-12-01 Thread Jorge Ivan Velez
Hi Luana, Try this: ID <- 1:20 grade <- c(4, 4, 4, 5, 5, 7, 7, 7, 7, 8, 8, 8, 9, 9, 9, 9, 9, 10, 10, 10) d <- data.frame(ID, grade) d$Sequence <- do.call(c, sapply(rle(grade)$lengths, seq)) d HTH, Jorge On Wed, Dec 1, 2010 at 11:08 AM, Luana Marotta <> wrote: > Hello fellows, > > I would like

Re: [R] Sequence for repeated numbers

2010-12-01 Thread Phil Spector
Luana - It's probably not the most efficient way, but here's a solution that's not dependent on the grades being sorted: grade <- c(4,4,4,5,5,7,7,7,7,8,8,8,9,9,9,9,9,10,10,10) unlist(sapply(rle(grade)$lengths,function(x)seq(1,x))) [1] 1 2 3 1 2 1 2 3 4 1 2 3 1 2 3 4 5 1 2 3

Re: [R] parametric estimators for species richness in R

2010-12-01 Thread Gavin Simpson
On Wed, 2010-12-01 at 21:23 +0800, yangwenjing wrote: > Dear everyone, > > I am doing some work about species richness estimation. Nonparametric > estimation (such as Chao1, Jacknife1) can be done just using function > "specpool()" and "estimateR()" in package "vegan". The problem is that > I can

Re: [R] Question regarding legend look

2010-12-01 Thread David Winsemius
On Dec 1, 2010, at 10:13 AM, Filoche wrote: Hi everyone. I have a quick question regarding the look of my legend in my plot. As you can see in the next figure, I have 3 series. http://r.789695.n4.nabble.com/file/n3067466/legend.png However, I find rather difficult to differentiate the s

Re: [R] Question regarding legend look

2010-12-01 Thread David Winsemius
On Dec 1, 2010, at 11:51 AM, David Winsemius wrote: On Dec 1, 2010, at 10:13 AM, Filoche wrote: Hi everyone. I have a quick question regarding the look of my legend in my plot. As you can see in the next figure, I have 3 series. http://r.789695.n4.nabble.com/file/n3067466/legend.png

[R] Beta values ca.jo

2010-12-01 Thread mliugonzal
Hello Anyone know how can I calculate the value of the beta parameter when I know the number of cointegrating relationships between two variables. I mean, I using the procedure: ca.jo I do the following: summary (ca.jo (UR [, c (2.52)], type = "trace" ECDET = "trend", K = 2, spec = "longrun"))

Re: [R] confidence interval for logistic joinpoint regression from package ljr

2010-12-01 Thread Vito Muggeo (UniPa)
dear M., I do not know how to get the SE for the joinpoint (or breakpoint) from your ljr fit. However you can find useful the segmented package which works for any GLM (including the logistic one) and it returns (approximate) StErr (and Conf Int) also for the joinpoint (breakpoint in the segme

Re: [R] Sequence for repeated numbers

2010-12-01 Thread Greg Snow
Try this: id <- 1:20 grade <- c(4,4,4,5,5,7,7,7,7,8,8,8,9,9,9,9,9,10,10,10) sequence <- ave( id, grade, FUN=seq ) # if grade is not sorted grade2 <- sample(grade) sequence2 <- ave( id, grade2, FUN=seq ) cbind( grade2, sequence2 ) -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermo

Re: [R] Poisson GLM warning message

2010-12-01 Thread Prof Brian Ripley
On Wed, 1 Dec 2010, Anna Berthinussen wrote: Hi, I receive the following warning message when I run a poisson GLM in R: "glm.fit: fitted rates numerically 0 occurred" The model summary is shown below. The variable 'Species' consists of counts of different species ranging from 0 to 4. I suspec

Re: [R] Question regarding legend look

2010-12-01 Thread Duncan Murdoch
On 01/12/2010 10:13 AM, Filoche wrote: Hi everyone. I have a quick question regarding the look of my legend in my plot. As you can see in the next figure, I have 3 series. http://r.789695.n4.nabble.com/file/n3067466/legend.png However, I find rather difficult to differentiate the series 1 and

[R] How to pass selection criteria in a function

2010-12-01 Thread CMcCarthy
Hi, Suppose I have the following data name score Abel    88 Baker  54 Charlie    77 stored a  table called myData. I want to write a function that will create a table which is a subset of myData containing those have a score > 75. I know I can do this with the following command:

Re: [R] How to pass selection criteria in a function

2010-12-01 Thread Charles C. Berry
On Wed, 1 Dec 2010, cmccar...@bmcc.cuny.edu wrote: Hi, Suppose I have the following data name score Abel??? 88 Baker? 54 Charlie??? 77 stored a? table called myData. I want to write a function that will create a table which is a subset of myData containing those have a score > 7

Re: [R] How to pass selection criteria in a function

2010-12-01 Thread Henrique Dallazuanna
Try this: newTable <- function(data, criteria) { do.call(subset, list(data, substitute(criteria))) } On Wed, Dec 1, 2010 at 3:56 PM, wrote: > Hi, > Suppose I have the following data > > name score > Abel88 > Baker 54 > Charlie77 > > stored a table called myData. > > >

Re: [R] Graph in R with edge weights

2010-12-01 Thread Ivan Alves
Hi Arthur, I was asking the same thing and came across the following (your need the "sna" library). http://students.washington.edu/mclarkso/documents/gplot%20Ver2.pdf Take a look at the edge.lwd and vertex.cex examples of the function gplot. You can use vectors for the different nodes. Kind r

Re: [R] How to pass selection criteria in a function

2010-12-01 Thread ChrisMath
Thank you all for your very fast replies. I tried Henrique's method (see one of the above posts) , and it works perfectly! Thanks again! -- View this message in context: http://r.789695.n4.nabble.com/How-to-pass-selection-criteria-in-a-function-tp3067765p3067829.html Sent from the R help mailin

Re: [R] How to pass selection criteria in a function

2010-12-01 Thread David Winsemius
On Dec 1, 2010, at 1:12 PM, Charles C. Berry wrote: On Wed, 1 Dec 2010, cmccar...@bmcc.cuny.edu wrote: Hi, Suppose I have the following data name score Abel88 Baker 54 Charlie77 stored a table called myData. I want to write a function that will create a table which i

Re: [R] Question regarding legend look

2010-12-01 Thread Filoche
David Winsemius wrote: > > > ...BUT NOT SHOWN US CODE > OR SAMPLE DATA. > Hi and thank you for your help. For instance, here's my code: legend("topleft", inset = .05, title="Water masses", pch = c(22,25,21), lty = c(4,1,2), lwd = 1, c("North","Central","South"), horiz = F, pt.bg =c("gray

Re: [R] Question regarding legend look

2010-12-01 Thread Filoche
Thank you sir for your answer. I'll take a look at the original legend function and modify it for my own purpose. With regards, Phil -- View this message in context: http://r.789695.n4.nabble.com/Question-regarding-legend-look-tp3067466p3067894.html Sent from the R help mailing list archive at

[R] default arguments and '...' in a function

2010-12-01 Thread Antonio.Gasparrini
Dear R-users, I'm trying to work out a way to set default values for arguments in a function which includes the optional argument '...'. In practice, I have a 'plot' method for a function which specifies different types of plots. Every different plot should have different default arguments (fo

Re: [R] Font family not found in Windows font database

2010-12-01 Thread Paul Murrell
Hi On 2/12/2010 4:55 a.m., Mark Ebbert wrote: Dear R Gurus, I have a fairly simple problem, but I haven't been able to find the answer on 'the google' or in the r-help archives. I am generating plots on both Windows and OS X where I need to guarantee that the font used is Arial. In my plot com

Re: [R] Wiener-Granger Causality Test in R

2010-12-01 Thread Dennis Murphy
Hi: On Wed, Dec 1, 2010 at 7:49 AM, CALEF ALEJANDRO RODRIGUEZ CUEVAS < alejandro.rodriguez.cue...@gmail.com> wrote: > Hello dudes. > > I'm developing VAR analysis based on suggestions made by Horváth in its > paper Canonical Correlation Analysis and Wiener-Granger Causality Tests. > Poor Horvath

Re: [R] Minor warning about seq

2010-12-01 Thread Ray Brownrigg
I think both responses so far have missed the point, (assuming the O was a typo for zero). That is: > seq(0:1) [1] 1 2 when > seq(0,1) [1] 0 1 was intended. Ray Brownrigg On Wed, 01 Dec 2010, Ista Zahn wrote: > So you are warning us that you must type zero instead of the letter O > when we want

Re: [R] [R-lme] Extract estimated variances from output of lme?

2010-12-01 Thread Ben Bolker
Tingting Zhan jefferson.edu> writes: > > Hi all, > > I have the output of summary() of an lme object called "lme.exp1", for > example > > # > > summary(lme.exp1) > [snip] > for the common variance parameter sigma. But if I need the covariance >

[R] Extract specific rows from matrix

2010-12-01 Thread Ali S
I have a matrix with 3 years of data (2006, 2009, 2010). I am trying to split this matrix by year so that I have 3 separate matrices. My matrix looks like this:     Q16.1 Year Gender Grade1       3 2006      1     52       2 2006      0     53       3 2006      0     54       3 2006      0     5

[R] draw categorical histogram

2010-12-01 Thread phoebe kong
Hi, Can someone tell me how to draw a histogram for the following summary? Richard Minnie Albert Helen Joe Kingston 1233 56 6715 66 The summary tell that Richard has occurrence 12, Minnie has occurrence 33, and so on. I would like to view this summ

Re: [R] draw categorical histogram

2010-12-01 Thread Andrew Miles
Try: plot (myCatVariable) Andrew Miles Department of Sociology Duke University On Dec 1, 2010, at 2:51 PM, phoebe kong wrote: Hi, Can someone tell me how to draw a histogram for the following summary? Richard Minnie Albert Helen Joe Kingston 1233 56 6715

Re: [R] Extract specific rows from matrix

2010-12-01 Thread Jorge Ivan Velez
Hi Ali, Check ?split HTH, Jorge On Wed, Dec 1, 2010 at 2:50 PM, Ali S <> wrote: > I have a matrix with 3 years of data (2006, 2009, 2010). I am trying to > split this matrix by year so that I have 3 separate matrices. My matrix > looks like this: > Q16.1 Year Gender Grade1 3 2006

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