Re: [R] User's function

Lisa - I think this is what you're looking for: myfunction = function(...)do.call(cbind,list(...)) - Phil Spector Statistical Computing Facility Department of Statistics

Re: [R] Apparent different in symbol scaling between xyplot and grid.points

Thanks Baptiste, I think you nailed it. baptiste auguie wrote: Hi, I think the size mismatch occurs because of a different default for the fontsize (and grid.points has a size of 1 character by default). Compare the following two examples, # default grid.newpage() pushViewport(viewport(x=unit

[R] Distribution fitting with binned data

Hello I need to fit a distribution to a histogram data set. I have read Ricci's guide to distribution fitting, and am ready to begin experimenting with the techniques it mentions, but I am uncertain how to get my data in the format he uses. My problem is that my data is binned. So for

Re: [R] Arules - Association Rules

Michael, thanks a lot, it works! Now I have to study the dataset to mining some interesting rules. Just one more question, I saw ways to find rules that contains some itens. But, Is there a method to find rules that doesn't have a item? Thanks again! You were very helpfull!!! 2009/12/4 Michael

Re: [R] Distribution fitting with binned data

On Dec 4, 2009, at 2:04 PM, Bradley W. Settlemyer wrote: Hello I need to fit a distribution to a histogram data set. I have read Ricci's guide to distribution fitting, and am ready to begin experimenting with the techniques it mentions, but I am uncertain how to get my data in the form

Re: [R] User's function

Exactly, that's waht I want. Thank you very much! Lisa Phil Spector wrote: > > Lisa - > I think this is what you're looking for: > > myfunction = function(...)do.call(cbind,list(...)) > > > - Phil Spector >St

Re: [R] Naming conventions for R?

This is historical and compatibility. The story as I heard it is that on the computer where the original S language was developed had a key that produced a left pointing arrow and that was used as the assignment operator (later <- was added as an alternative for other computer systems). When k

Re: [R] Multiple grouping on the X axis.

The boxplot function has an 'at' argument that you can use to specify where to plot the boxes, could you just use this to group the boxplots? Or the lattice package can put each group into its own panel to show the grouping. Hope this helps, -- Gregory (Greg) L. Snow Ph.D. Statistical Data Ce

Re: [R] grep() exclude certain patterns?

On Fri, Dec 4, 2009 at 11:54 AM, Duncan Murdoch wrote: > On 04/12/2009 12:52 PM, Peng Yu wrote: >> >> The external grep program has an option -v to select non-matching >> lines. I'm wondering if how to exclude certain patterns in grep() in >> R? >> > > ?grep I don't see which argument to use. __

[R] no html help upon upgrading to 2.10

I just upgraded from 2.8.1 to 2.10 on Windows Vista. BIG MISTAKE apparently because now when I type: > help(functionname) or ?functionname I get only a small text window giving some very basic info on the topic, e.g.: base-package package:baseR Documentation The

Re: [R] latex.table for table with character and numeric columns

Gerrit Draisma wrote: > > Hallo, > I have a dataset with one or two columns with character data > and the rest with numeric data. > Using latex.table from the quantreg package produced a table, > but I cannot set the decimals. > For instance: > --- > > x<-data.frame(Name=c("Jan","Piet","Jan"),

[R] categorical vs numerical

What ways are there to plot categorical vs numerical data in R. I have two columns: one with categorical data in 5 categories a,b,c,d,e, and a numerical column with integers between 1 and 100. I have used a boxplot with a,b,c,d,e on the x-axis and an increasing numerical scale on the y-axis. T

Re: [R] grep() exclude certain patterns?

use !grepl On Fri, Dec 4, 2009 at 2:43 PM, Peng Yu wrote: > On Fri, Dec 4, 2009 at 11:54 AM, Duncan Murdoch > wrote: > > On 04/12/2009 12:52 PM, Peng Yu wrote: > >> > >> The external grep program has an option -v to select non-matching > >> lines. I'm wondering if how to exclude certain pattern

[R] How to duplicate each row in a data.frame?

I want to duplicate each line in 'df' 3 times. But I'm confused why 'z' is a 6 by 4 matrix. Could somebody let me know what the correct way is to duplicate each row of a data.frame? df=expand.grid(x1=c('a','b'),x2=c('u','v')) n=3 z=apply(df,1 ,function(x){ result=do.call(rbind,rep(list(x

Re: [R] How to duplicate each row in a data.frame?

df[rep(1:nrow(df),each=3),] - Phil Spector Statistical Computing Facility Department of Statistics UC Berkeley

Re: [R] How to duplicate each row in a data.frame?

I *think* this is from from 'StatsRUs' - how about as.data.frame(lapply(df,function(x)rep(x,n))) hth, david freedman pengyu.ut wrote: > > I want to duplicate each line in 'df' 3 times. But I'm confused why > 'z' is a 6 by 4 matrix. Could somebody let me know what the correct > way is to dupli

Re: [R] grep() exclude certain patterns?

The invert argument seems a likely candidate, you could also do perl=TRUE and use negations within the pattern (but that is probably overkill for your original question). Could you explain to us the process that you use to search for answers to your questions before posting? You have been ask

Re: [R] How to duplicate each row in a data.frame?

Phil Spector's solution is the best way to get your triplicating job done. As for why the result of your apply call is a 6 by 4 matrix, read the help file for apply where it talks about how it 'simplifies' the result. For FUN's that do not return a scalar the simplification algorithm may be surpr

Re: [R] no html help upon upgrading to 2.10

?help (see argument help_type) ?options This has been asked before. My understanding is that there was a licensing issue with Microsoft's compiled html help; so what you need to do is specify options(help_type = "html") in your startup process. There are a variety of ways to do so, explained

[R] logical masking of a matrix converts it to a vector

One problem I've been having is the special case in which only one row/column remains and the variable gets converted into a vector when entries are removed by logical masking. This is a problem because subsequent code may rely on matrix operations (apply, colsums, dim, etc) For example: > a <- ma

Re: [R] logical masking of a matrix converts it to a vector

On Dec 4, 2009, at 3:52 PM, Austin Huang wrote: One problem I've been having is the special case in which only one row/column remains and the variable gets converted into a vector when entries are removed by logical masking. This is a problem because subsequent code may rely on matrix operati

Re: [R] logical masking of a matrix converts it to a vector

> One problem I've been having is the special case in which only one > row/column remains and the variable gets converted into a vector when > entries are removed by logical masking. This is a problem because > subsequent > code may rely on matrix operations (apply, colsums, dim, etc) For example:

Re: [R] logical masking of a matrix converts it to a vector

b <- a[rmask,,drop=FALSE] - Phil Spector Statistical Computing Facility Department of Statistics UC Berkeley

Re: [R] logical masking of a matrix converts it to a vector

Check out `drop' ?drop a <- matrix(c(1, 2, 3, 4), nrow = 2) rmask <- c(TRUE, FALSE) b <- a[rmask, , drop=FALSE] colSums(b) This will maintain the matrix structure. Ravi. --- Ravi Varadhan, Ph.D. Assistant Pro

Re: [R] logical masking of a matrix converts it to a vector

Hi Austin, What version of R are you using? It works for me for R 2.10.0 Patched on Win XP Pro: R> a <- matrix(c(1, 2, 3, 4), nrow = 2) R> a # [1] 1 3 # [2] 2 4 R> rmask <- c(TRUE, FALSE) R> a[rmask,] # [1] 1 3 HTH, Jorge On Fri, Dec 4, 2009 at 3:52 PM, Austin Huang <> wrote: > One problem I'

Re: [R] grep() exclude certain patterns?

On Fri, Dec 4, 2009 at 2:35 PM, Greg Snow wrote: > The invert argument seems a likely candidate, you could also do perl=TRUE and > use negations within the pattern (but that is probably overkill for your > original question). I don't see 'invert' in the R version (2.7.1) that I use. Here is the

Re: [R] logical masking of a matrix converts it to a vector

On Dec 4, 2009, at 4:03 PM, Jorge Ivan Velez wrote: Hi Austin, What version of R are you using? It works for me for R 2.10.0 Patched on Win XP Pro: R> a <- matrix(c(1, 2, 3, 4), nrow = 2) R> a # [1] 1 3 # [2] 2 4 R> rmask <- c(TRUE, FALSE) R> a[rmask,] # [1] 1 3 Doesn't work on a Mac (ad

Re: [R] grep() exclude certain patterns?

On Fri, Dec 4, 2009 at 3:06 PM, Peng Yu wrote: > On Fri, Dec 4, 2009 at 2:35 PM, Greg Snow wrote: >> The invert argument seems a likely candidate, you could also do perl=TRUE >> and use negations within the pattern (but that is probably overkill for your >> original question). > > I don't see '

[R] pdf pagesize

Hi, when I create huge pdf files (width is 6meters) with R I cannot open them in Adobe Acrobat reader (I tried version 9 and some lower). I use pdf() of grDevices version 2.8.1 and CairoPDF from Cairo version 1.4-4. When I add the (perhaps since pdf version 1.7 pagesizes of more than 200in are poss

[R] [R-pkgs] New Package: pgfSweave

At long last pgfSweave has finally made its way to CRAN. The pgfSweave package is about speed and style of graphics. For speed, the package provides capabilities for “caching” graphics generated with Sweave on top of the caching funcitonality of cacheSweave. For style the pgfSweave package facilit

[R] simple reshape of a large data frame (reshape() runs out of memory)

Hello everyone, I'm having a problem performing reshape() on a large data frame. The operation is fairly trivial but it makes R run out of memory. The data frame has the following structure: ID DATE1 DATE2VALTYPE VALUE 'abcd1233' 2009-11-12

Re: [R] How to compute contrast where there are interaction terms in the linear model?

On Fri, Dec 4, 2009 at 12:18 PM, Charles C. Berry wrote: > On Fri, 4 Dec 2009, Peng Yu wrote: > >> On Tue, Dec 1, 2009 at 4:04 PM, Charles C. Berry >> wrote: >>> >>> On Tue, 1 Dec 2009, Peng Yu wrote: >>> Could somebody recommend some textbook how to compute contrast when there are inte

[R] RandomForest - getTree status code

What does a status value of -3 mean when I do a regression with RF and use the getTree function? left daughter right daughter split var split point status prediction 12 311 4.721000e+03 -3 15.8489576 24 5 5 6.500

Re: [R] Incorporating the results of White's HCCM into a linear regression:

On 2009.12.03 23:52:15, Yoseph Zuback wrote: > Hi Frank, > > I'm trying to repair heteroscedastic variables using the hccm. A > statistician in my department gave an incomplete solution that included: > > > OLS1$coefficients/(sqrt(hccm(OLS1))) > > Trying to solve my problem I get different resu

Re: [R] how to calculate covariance matrix in R? why cov doesn't work

Jorge, It really helps. I appreciate your help a lot! Chen On Fri, Dec 4, 2009 at 12:04 AM, Jorge Ivan Velez [via R] < ml-node+948281-1243760...@n4.nabble.com > wrote: > Try this: > > a <- c(9,3,5) > b<-c(3,4,1) > cbind(a, b) > # a b > # [1,] 9 3 > # [2,] 3 4 > # [3,] 5 1 > > cov(cbind(a,

Re: [R] how to seperate a matrix

Thanks a lot, Jorge. It works well! On Fri, Dec 4, 2009 at 12:00 AM, Jorge Ivan Velez [via R] < ml-node+948277-873392...@n4.nabble.com > wrote: > Hi aegea, > > Here is one: > > m <- structure(c(6, 5, 20, 7, 8, 25, 14, 8, 9, 10, 11, 12, 13, 14, > 1, 2, 3, 4, 5, 6, 7), .Dim = c(7L, 3L)) > > m1 <-

[R] tobit model fluid milk consumption

__ 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] Tobit model fluid milk consumption

Hi all, I fit a Tobit model to Fluid milk consumption (dependent variable) data using survreg. 1) The square root of the dependent variable was used to correct for heteroscedasticity since it provides the best fit. 2) The output before transformation of numeric variables in scores (by "Make.Z")

Re: [R] EM Mixture Models

Hello, I am not too sure if anyone tried this out. but I ma fitting a mixture model via the EM algorithmn. But then I tried using CAMAN package and I seem to get different results. Has anyone else had this problem? For example, I am fitting the Inness data from the text Medical Applications of Fini

Re: [R] (Grouped + Stacked) Barplot

Thanks Greg for your suggestion! On Thu, Dec 3, 2009 at 11:50 AM, Greg Snow wrote: > A bar graph including both stacked and grouped bars will put lots of pretty > colors on the page and probably be eyecatching, but is unlikely to be the > most effective way to convey the actual meaning of the da

[R] Help: barchart() {lattice}

Hi All, I'm trying par(mfrow(c(1,2))) with barchart(), but its not working. Can I display two or more barcharts on a same page using some other function? I'm using following code --- where barchart() part is taken from help manual. library(lattice) par(mfrow=c(1,2)) barchart(yield ~ variety | sit

[R] Installing RandomForest on SuSe Linux - warnings

I installed RF on Linux OpenSuSe 11.1 and while it did install and did run a model I had created on Windows correctly, it gave me a lot of "uninitialized" warnings. I don't know if these are significant and so am a little concerned even though my model ran. Any thoughts? Thanks R version 2

[R] Use of apply rather than a loop

Colleagues, R 2.9.0 on all platforms I have a dataset that contains three columns of interest: ID's, serial elapsed times, and a marker. Representative data: Subject TimeMarker 1 100.5 0 1 101 0 1

Re: [R] Error when running Conditional Logit Model

Dear Dr. Winsemius, Thank you very much for your reply. I have tried many possible combinations (even with the model of only 2 predictors) but it produces the same message. With more than 4000 observations, I think 14 predictors might not be too many. Although my dependent variable (Pin) is

Re: [R] Error when running Conditional Logit Model

On Dec 4, 2009, at 5:49 PM, Hien Nguyen wrote: Dear Dr. Winsemius, Thank you very much for your reply. I have tried many possible combinations (even with the model of only 2 predictors) but it produces the same message. With more than 4000 observations, I think 14 predictors might not be

Re: [R] Use of apply rather than a loop

Dennis Fisher wrote: > > Colleagues, > > R 2.9.0 on all platforms > > I have a dataset that contains three columns of interest: ID's, serial > elapsed times, and a marker. Representative data: > Subject TimeMarker > 1 100.5 0 > 1

Re: [R] Use of apply rather than a loop

You could try using merge: > d<-data.frame(Subject=rep(11:13,each=3),Time=101:109,Marker=c(0,1,0, 0,0,0, 0,0,1)) > d Subject Time Marker 1 11 101 0 2 11 102 1 3 11 103 0 4 12 104 0 5 12 105 0 6 12 106 0

Re: [R] Use of apply rather than a loop

Try this: transform(DF, Time = ave(1:nrow(DF), Subject, FUN = function(ix) if (any(Marker[ix] == 1)) Time - Time[Marker == 1] else Time)) On Fri, Dec 4, 2009 at 5:47 PM, Dennis Fisher wrote: > Colleagues, > > R 2.9.0 on all platforms > > I have a dataset that contains three columns of int

Re: [R] no html help upon upgrading to 2.10

On 04/12/2009 3:46 PM, Bert Gunter wrote: ?help (see argument help_type) ?options This has been asked before. My understanding is that there was a licensing issue with Microsoft's compiled html help; so what you need to do is specify There was nothing new there: CHM is discouraged (or at

Re: [R] grep() exclude certain patterns?

On Fri, 2009-12-04 at 15:18 -0600, Peng Yu wrote: > On Fri, Dec 4, 2009 at 3:06 PM, Peng Yu wrote: > > On Fri, Dec 4, 2009 at 2:35 PM, Greg Snow wrote: > >> The invert argument seems a likely candidate, you could also do perl=TRUE > >> and use negations within the pattern (but that is probably o

Re: [R] Use of apply rather than a loop

That should be: transform(DF, Time = ave(1:nrow(DF), Subject, FUN = function(ix) with(DF[ix,], if (any(Marker == 1)) Time - Time[Marker == 1] else Time))) On Fri, Dec 4, 2009 at 6:36 PM, Gabor Grothendieck wrote: > Try this: > > transform(DF, Time = ave(1:nrow(DF), Subject, FUN = function(ix

Re: [R] grep() exclude certain patterns?

Maybe, atleast for the most used functions, there should be a section in the .Rd file with name "for newbies"? Kjetil On Fri, Dec 4, 2009 at 6:18 PM, Peng Yu wrote: > On Fri, Dec 4, 2009 at 3:06 PM, Peng Yu wrote: >> On Fri, Dec 4, 2009 at 2:35 PM, Greg Snow wrote: >>> The invert argument seem

[R] [Ann] R brush for SyntaxHighlighter

Hello, I've written a brush for R for the SyntaxHighlighter JavaScript library. It allows you to display R code on a web page with the proper syntax highlighting. It's available here: http://demitri.com/code Comments and suggestions for improvement are welcome! Cheers, Demitri __

[R] expression and font type of bold

Dear R users, i would like to have expression on my plot written in bold italic font and use following: text(0.01,70,expression(bolditalic(r^2==0.67)),pos= 4) However, only the letter r appears bold and italic, but not the whole expression. How should i change it? Thank you for your help, Alla. _

Re: [R] Help R2WinBUGS

I try it again and it works. Thank you. TTsai wrote: > > Hello, > > I have problem running WinBUGS from R. > The following example works in WinBUGS but it does not work in R through > package R2WinBUGS. > Does anyone know what the problem is? > > x <- c(0.2, 1.1, 1, 2.2, 2.5, 2.9, 2.9, 3.6,

Re: [R] Help: barchart() {lattice}

Hello Xin, Take a look at the examples under ?print.trellis Using your original example, you could use: require(lattice) p1=barchart(yield ~ variety | site, data = barley, groups = year, layout = c(1,6), ylab = "Barley Yield (bushels/acre)", scales = list(x = list(abb

Re: [R] How to compute contrast where there are interaction terms in the linear model?

On Fri, 4 Dec 2009, Peng Yu wrote: On Fri, Dec 4, 2009 at 12:18 PM, Charles C. Berry wrote: On Fri, 4 Dec 2009, Peng Yu wrote: On Tue, Dec 1, 2009 at 4:04 PM, Charles C. Berry wrote: On Tue, 1 Dec 2009, Peng Yu wrote: Could somebody recommend some textbook how to compute contrast when t

Re: [R] grep() exclude certain patterns?

On Fri, 4 Dec 2009, Peng Yu wrote: On Fri, Dec 4, 2009 at 2:35 PM, Greg Snow wrote: The invert argument seems a likely candidate, you could also do perl=TRUE and use negations within the pattern (but that is probably overkill for your original question). I don't see 'invert' in the R versi

[R] paste adjacent elements matching string

Hi all, I would like to combine elements of a vector: vec <- c("astring", "b", "cstring", "d", "e") > vec [1] "astring" "b" "cstring" "d" "e" such that for every element that contains "string" at the end, it is combined with the next element, so that I get this: > res [1] "ast

Re: [R] grep() exclude certain patterns?

On Fri, Dec 4, 2009 at 7:51 PM, Charles C. Berry wrote: > On Fri, 4 Dec 2009, Peng Yu wrote: > >> On Fri, Dec 4, 2009 at 2:35 PM, Greg Snow wrote: >>> >>> The invert argument seems a likely candidate, you could also do perl=TRUE >>> and use negations within the pattern (but that is probably overk

Re: [R] Error when running Conditional Logit Model

On Fri, 4 Dec 2009, David Winsemius wrote: On Dec 4, 2009, at 5:49 PM, Hien Nguyen wrote: Dear Dr. Winsemius, Thank you very much for your reply. I have tried many possible combinations (even with the model of only 2 predictors) but it produces the same message. With more than 4000 observ

Re: [R] paste adjacent elements matching string

On Dec 4, 2009, at 8:42 PM, Jill Hollenbach wrote: Hi all, I would like to combine elements of a vector: vec <- c("astring", "b", "cstring", "d", "e") vec [1] "astring" "b" "cstring" "d" "e" such that for every element that contains "string" at the end, it is combined with th

Re: [R] paste adjacent elements matching string

Try this which assumes that comma does not appear in any of the strings. You can substitute a different non-appearing character if a comma does appear in any of the strings: strsplit(gsub("string,", "string", paste(vec, collapse = ",")), ",")[[1]] It first runs all the strings together into a sin

Re: [R] Help: barchart() {lattice}

@ Francisco: Thanks, it worked. @ All: I'm able to change the colors of legend using following code: par.settings=simpleTheme(col=c(451,26,652)), key=list(space="right", cex=.96, text=list(c("A","B","C")), rectangles=list(size=1.7, border="white", col = c(451,26,652))) *Q. Using the foll

Re: [R] categorical vs numerical

If your group sizes are not too large, I would use jittered stripcharts. They're more informative than boxplots and much less subject to misinterpretation. One warning, I'm not fond of the default pch=0. -Peter Ehlers DispersionMap wrote: What ways are there to plot categorical vs numerical dat

Re: [R] Help: barchart() {lattice}

On Dec 4, 2009, at 10:17 PM, Xin Ge wrote: @ Francisco: Thanks, it worked. @ All: I'm able to change the colors of legend using following code: par.settings=simpleTheme(col=c(451,26,652)), key=list(space="right", cex=.96, text=list(c("A","B","C")), rectangles=list(size=1.7, border="white"

Re: [R] Help: barchart() {lattice}

Thanks David, it worked! On Fri, Dec 4, 2009 at 10:36 PM, David Winsemius wrote: > > On Dec 4, 2009, at 10:17 PM, Xin Ge wrote: > > @ Francisco: Thanks, it worked. >> >> >> @ All: I'm able to change the colors of legend using following code: >> >> par.settings=simpleTheme(col=c(451,26,652)), >>

Re: [R] grep() exclude certain patterns?

I am sure that you mentioned before that your are using 2.7.1, and possibly even why, but with the number of posts to this list each day and the number of different posters, I cannot keep track of what version everyone is using (well, I probably could, but I am unwilling to put in the time/effor

Re: [R] grep() exclude certain patterns?

> -Original Message- > From: r-help-boun...@r-project.org [mailto:r-help-boun...@r- > project.org] On Behalf Of Peng Yu > Sent: Friday, December 04, 2009 2:19 PM > To: r-h...@stat.math.ethz.ch > Subject: Re: [R] grep() exclude certain patterns? > [snip] > Here is another bad example. Se

Re: [R] adding bmp/jpg/gif to an existing plot

Hi, If you can first convert the image to ppm format, the pixmap package has an addlogo function that can do just what you want, x <- read.pnm(system.file("pictures/logo.ppm", package="pixmap")[1]) plot(1:10,1:10) addlogo(x, px=c(2, 4), py=c(6, 8), asp=1) One could probably get inspiration from

Re: [R] [Ann] R brush for SyntaxHighlighter

Hi, There is also the R package "highlight" [1,2] serving the same purpose but based on information from the R parser, not a static list. highlight can render in html, tex, and directly for the console (with the help of the xterm256 package [3]). Romain [1] http://cran.r-project.org/web/pa

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