Re: [R] Why Rscript behaves strangely with file name starting with 'size'?

2010-07-07 Thread Allan Engelhardt
It looks like a bug in R, not Rscript: what Rscript does is effectively R --file=size.R and you can easily test that echo 'print("Hello world")'> size.R R --file=size.R give you the error while cp size.R asize.R R --file=asize.R works as expected. None of which helps you directly, but p

Re: [R] how to define a function in R

2010-07-07 Thread Joshua Wiley
Hi Jason, I did not have time to actually test this code so there may be typos and some of it may not work as I thought. I would create a copy of your data in a test directory and experiment with that until you are confident you have everything working how you want . As a side note, since you ar

Re: [R] how to process this in R

2010-07-07 Thread Rainer M Krug
Hi On Wed, Jul 7, 2010 at 7:49 PM, jd6688 wrote: > > Here are what i am going to accomplish: > > I have 400 files named as xxx.txt. the content of the file looks like the > following: > >namecount > > 1. aaa 100 > 2. bbb2000 > 3. ccc300 > 4. ddd 3000 > > > more th

Re: [R] Boxplots over a Scatterplot

2010-07-07 Thread Peter Ehlers
On 2010-07-07 18:24, fsch wrote: I managed to solve the problem myself using: q=sort(unique(foram$stage[which(foram$length>0)])) boxplot(foram$logl~foram$stage, data=foram, outline=F, at=q, axes=TRUE, add=TRUE, col="gray82", medlwd=1) points(foram$stage,foram$logl, cex=.1) However, for fut

[R] random sample from arrays

2010-07-07 Thread Assa Yeroslaviz
Hello R users, I'm trying to extract random samples from a big array I have. I have a data frame of over 40k lines and would like to produce around 50 random sample of around 200 lines each from this array. this is the matrix ID xxx_1c xxx__2c xxx__3c xxx__4c xxx__5T xxx__6T xxx__7T xx

Re: [R] xyplot: key inside the plot region / lme: confidence bands for predicted

2010-07-07 Thread Kingsford Jones
On Wed, Jul 7, 2010 at 8:59 AM, Michael Friendly wrote: > No one replied to my second question: how to get standard errors or > confidence intervals for the > estimated fixed effects from lme().    AFAICS, intervals() only gives CIs > for coefficients. Assuming you mean 'predictions based on the

[R] Why Rscript behaves strangely with file name starting with 'size'?

2010-07-07 Thread thmsfuller...@gmail.com
Hello All, It seems weird to me that Rscript does the following thing and enters the R prompt mode. If I change the file name to something that doesn't start with 'size', then Rscript runs normally. Does anybody know what is going on? $ Rscript size.R WARNING: '--file=size.R' value is invalid: ig

Re: [R] LatticeExtra Parallel

2010-07-07 Thread John Antonakakis
The R Clinic is a fantastic website with many examples. There are some examples under the graphics section. http://biostat.mc.vanderbilt.edu/wiki/Main/RClinic > Date: Tue, 6 Jul 2010 23:29:33 -0400 > From: bjlwilkin...@gmail.com > To: deepayan.sar...@gmail.com > CC: r-help@r-project.o

Re: [R] LatticeExtra Parallel

2010-07-07 Thread Deepayan Sarkar
On Tue, Jul 6, 2010 at 8:29 PM, Ben Wilkinson wrote: > Thanks - that helps put the data on the same scale but it doesn't actually > add the scale as it still shows min and max on the axis. The scale maps from (min, max) -> (0, 1). You can compute and specify tick positions and labels accordingly.

Re: [R] Boxplots over a Scatterplot

2010-07-07 Thread Michael Friendly
Try scatterplot() in the car package. It draws boxplots for X & Y in the margins, auto scaled to the axes fsch wrote: Hello- I'm new to R, coding and stats. (Oh no.) Anyway, I have about 12000 data points in a data.frame (dealing with dimensions and geological stage information for fossil p

Re: [R] How do I test against a simple null that two regressions coefficients are equal?

2010-07-07 Thread markleeds
wow chuck. you really know how to dig up the archives. I don't know if it's exactly relevant for what the OP is asking but i did use the ( or atleast a )Â paper by hotelling and it was titled "the selection of variates for use in prediction with some comments on the general problem of

Re: [R] forcing a zero level in contr.sum

2010-07-07 Thread Gabor Grothendieck
On Wed, Jul 7, 2010 at 10:55 PM, Charles C. Berry wrote: > > > contr.mysum <- function (n, contrasts = TRUE, sparse = FALSE, > base=length(levels)) > { The memisc package has a contr.sum function with a base= argument. __ R-help@r-project.org mailing l

Re: [R] Vector Assignment -- Why won't it let me do it?

2010-07-07 Thread David Winsemius
On Jul 7, 2010, at 8:39 PM, Adam Berrones wrote: I have looked absolutely everywhere but I cannot figure out why my Mac will not let me create simple data vectors. blah Error: object 'blah' not found blah <- c(1, 2, 3) Error in c(1, 2, 3) : 'file' must be a character string or connecti

Re: [R] SAM program and R mirror - which port to open?

2010-07-07 Thread RICHARD M. HEIBERGER
Assuming you are on Windows, you can probably do this within R, without involving the IT department. ?setInternet2 for the details and discussion. Enter the line setInternet2(use = TRUE) before doing the install.packages() On Wed, Jul 7, 2010 at 7:55 PM, Katie Ashton wrote: > To whom this m

Re: [R] How do I test against a simple null that two regressions coefficients are equal?

2010-07-07 Thread Charles C. Berry
On Wed, 7 Jul 2010, chen jia wrote: Hi there, I run two regressions: y = a1 + b1 * x + e1 y = a2 + b2 * z + e2 I want to test against the null hypothesis: b1 = b2. How do I design the test? You are testing a non-nested hypothesis, which requires special handling. The classical test is du

Re: [R] forcing a zero level in contr.sum

2010-07-07 Thread Berwin A Turlach
G'day Stephen, On Wed, 7 Jul 2010 16:41:18 -0400 "Bond, Stephen" wrote: > Please, do not post if you do not know the answer. People will see > this has answers and skip. > > I tried with > mat1=contrasts(fixw$snconv) > mat1=mat1[,-2] > summary(frm2sum <- glm(resp.frm ~ > C(snconv,contr=mat1)+m

Re: [R] Vector Assignment -- Why won't it let me do it?

2010-07-07 Thread RICHARD M. HEIBERGER
> > > > blah > Error: object 'blah' not found > > blah <- c(1, 2, 3) > Error in c(1, 2, 3) : 'file' must be a character string or connection > > It used to work, and 6 months later I'm back on R, and now it will not > work. > > Most likely, you inadvertently masked the base function c with your own

Re: [R] ifelse statement

2010-07-07 Thread karena
that makes sense. thank you, guys! -- View this message in context: http://r.789695.n4.nabble.com/ifelse-statement-tp2281576p2281706.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.c

Re: [R] Boxplots over a Scatterplot

2010-07-07 Thread fsch
I managed to solve the problem myself using: q=sort(unique(foram$stage[which(foram$length>0)])) boxplot(foram$logl~foram$stage, data=foram, outline=F, at=q, axes=TRUE, add=TRUE, col="gray82", medlwd=1) points(foram$stage,foram$logl, cex=.1) However, for future reference since this was my fir

[R] SAM program and R mirror - which port to open?

2010-07-07 Thread Katie Ashton
To whom this may concern, I am having issues installing a program called "SAM" (Statistical Analysis of Microarrays) which is an excel add in and requires the use of R. Due to the firewall at my hospital, R cannot connect to a mirror and therefore cannot install necessary files for the complete

[R] Vector Assignment -- Why won't it let me do it?

2010-07-07 Thread Adam Berrones
I have looked absolutely everywhere but I cannot figure out why my Mac will not let me create simple data vectors. > blah Error: object 'blah' not found > blah <- c(1, 2, 3) Error in c(1, 2, 3) : 'file' must be a character string or connection It used to work, and 6 months later I'm back on R, a

[R] glmnet - choosing the number of features

2010-07-07 Thread Brian Tsai
Hi, I am trying to use the glmnet package to do some simple feature selection. However, I would ideally like to be able to specify the number of features to return (the glmnet package, as far as I can tell, only allows specification of a regularization parameter, lambda, that in turn returns a m

Re: [R] forcing a zero level in contr.sum

2010-07-07 Thread Charles C. Berry
If I surmise correctly, you want something like contr.sum but with the option to select the level with the row of '-1' and no column. Here '3' is that level: contr.sum(3) [,1] [,2] 110 201 3 -1 -1 relevel() and contr.sum() generally will not do what you want witho

Re: [R] meaning of warning messages after spss-import

2010-07-07 Thread David Winsemius
I have not seen that particular subtype documented in the archives, but others (subtpes 16 and 17 if I remember correctly) were due to difficulties in extracting value labels from the incompletely documented spss file structure. Have you examined the resulting data object with str()? -

Re: [R] way to get t-values from glm.fit output?

2010-07-07 Thread Seth
Sorry to bother everyone. Soon after posting my question I found out what summary.glm() will do to a glm.fit object. Gotta love having your learning curve exposed in public :) Seth -- View this message in context: http://r.789695.n4.nabble.com/way-to-get-t-values-from-glm-fit-output-tp2281737p

Re: [R] way to get t-values from glm.fit output?

2010-07-07 Thread David Winsemius
On Jul 7, 2010, at 9:48 PM, Seth wrote: Hi, I am working with a function that makes use of glm.fit. Without modifying the somewhat long code too much, I would like to have t-values returned for the predictor variables used in the fitting process. Is there a relatively straightforward

[R] way to get t-values from glm.fit output?

2010-07-07 Thread Seth
Hi, I am working with a function that makes use of glm.fit. Without modifying the somewhat long code too much, I would like to have t-values returned for the predictor variables used in the fitting process. Is there a relatively straightforward way to do this? Thanks, Seth Myers -- View this

Re: [R] Inverting a scale(X)

2010-07-07 Thread Godfrey van der Linden
On 2010-07-03, at 17:43 , Peter Ehlers wrote: > > On 2010-07-03 0:05, Godfrey van der Linden wrote: >> G'day, All. >> >> I have been trying to trackdown a problem in my R analysis script. I perform >> a scale() operation on a matrix then do further work. >> >> Is there any way of inverting th

[R] Using nlm or optim

2010-07-07 Thread Anita Narwani
Hello, I am trying to use nlm to estimate the parameters that minimize the following function: Predict<-function(M,c,z){ + v = c*M^z + return(v) + } M is a variable and c and z are parameters to be estimated. I then write the negative loglikelihood function assuming normal errors: nll<-function

Re: [R] ifelse statement

2010-07-07 Thread Godfrey van der Linden
On 2010-07-08, at 10:33 , Duncan Murdoch wrote: > On 07/07/2010 7:32 PM, Gabor Grothendieck wrote: >> On Wed, Jul 7, 2010 at 7:22 PM, Duncan Murdoch >> wrote: >> >>> On 07/07/2010 5:58 PM, karena wrote: >>> Hi, I am a newbie of R, and playing with the "ifelse" statement. I

Re: [R] ifelse statement

2010-07-07 Thread Duncan Murdoch
On 07/07/2010 7:32 PM, Gabor Grothendieck wrote: On Wed, Jul 7, 2010 at 7:22 PM, Duncan Murdoch wrote: On 07/07/2010 5:58 PM, karena wrote: Hi, I am a newbie of R, and playing with the "ifelse" statement. I have the following codes: ## first, for(i in 1:3) { for(j in 2:4) { cor.temp

[R] help compiling add-on package

2010-07-07 Thread Timothy W. Hilton
Hello r-help, I am having trouble installing the add-on package gstat. I suspect (but I'm not sure) that the trouble may be that it runs all the checks for gcc, then uses Intel's compiler to actually compile. I have not been able to successfully force it to use gcc to test that theory. R CMD IN

Re: [R] Boxplots over a Scatterplot

2010-07-07 Thread Peter Ehlers
Would it really be so hard to provide commented, minimal, self-contained, _reproducible_ code ? -Peter Ehlers On 2010-07-07 15:16, fsch wrote: Hello- I'm new to R, coding and stats. (Oh no.) Anyway, I have about 12000 data points in a data.frame (dealing with dimensions and geological s

Re: [R] quantiles on rows of a matrix

2010-07-07 Thread Peter Ehlers
On 2010-07-07 16:52, Jim Bouldin wrote: I'm trying to obtain the mean of the middle 95% of the values from each row of a matrix (that is, the highest and lowest 2.5% of values in each row are removed before calculating the mean). I am having all sorts of problems with this; for example the com

Re: [R] How to quick check two rows are the same?

2010-07-07 Thread Erik Iverson
Yi wrote: Hi, folks, Suppose the data is as follows: ### x=1:10 y=2:11 z=3:12 data1=data.frame(x,y) data2=data.frame(x,z) ## In real case, how to check data1$x and data2$x are the same or not? I am using for-loop to do this. Is there a quicker way? all(data1$x == data2$x) or i

Re: [R] ifelse statement

2010-07-07 Thread Gabor Grothendieck
On Wed, Jul 7, 2010 at 7:22 PM, Duncan Murdoch wrote: > On 07/07/2010 5:58 PM, karena wrote: >> >> Hi, I am a newbie of R, and playing with the "ifelse" statement. >> >> I have the following codes: >> ## first, >> >> for(i in 1:3) { >> for(j in 2:4) { >> cor.temp <- cor(iris.allnum[,i], iris.allnu

Re: [R] quantiles on rows of a matrix

2010-07-07 Thread David Winsemius
On Jul 7, 2010, at 6:52 PM, Jim Bouldin wrote: I'm trying to obtain the mean of the middle 95% of the values from each row of a matrix (that is, the highest and lowest 2.5% of values in each row are removed before calculating the mean). A winsorized.mean? I am having all sorts of p

[R] How to quick check two rows are the same?

2010-07-07 Thread Yi
Hi, folks, Suppose the data is as follows: ### x=1:10 y=2:11 z=3:12 data1=data.frame(x,y) data2=data.frame(x,z) ## In real case, how to check data1$x and data2$x are the same or not? I am using for-loop to do this. Is there a quicker way? Thanks! Yi [[alternative HTML ver

Re: [R] ifelse statement

2010-07-07 Thread Duncan Murdoch
On 07/07/2010 5:58 PM, karena wrote: Hi, I am a newbie of R, and playing with the "ifelse" statement. I have the following codes: ## first, for(i in 1:3) { for(j in 2:4) { cor.temp <- cor(iris.allnum[,i], iris.allnum[,j]) if(i==1 & j==2) corr.iris <- cor.temp else corr.iris <- c(corr.iris, cor.

Re: [R] What does `_data` mean in transform()?

2010-07-07 Thread David Winsemius
On Jul 7, 2010, at 6:32 PM, thmsfuller...@gmail.com wrote: Hi All, I meant to take the min row by row. But the result is apparently not what I want. Changing min to pmin solve the problem. df=data.frame(X=1:10, Y=1:10) transform(df, Z=min(X,10-Y)) X Y Z 1 1 1 0 2 2 2 0 3 3 3 0

[R] start value in nlminb

2010-07-07 Thread Carrie Li
Hi, all I am doing a optimization problem using nlminb. It seems to me that the result is kind of sensitive to the starting value. (It happened that the resulting parameter doesn't change from the starting value.) Any suggestions on giving the starting value ? or any other function that can do opt

Re: [R] quantiles on rows of a matrix

2010-07-07 Thread Bill.Venables
apply(matrix1, 1, quantile, probs = c(0.05, 0.9), na.rm = TRUE) may be what you are looking for. -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Jim Bouldin Sent: Thursday, 8 July 2010 8:52 AM To: R help Subject: [R] quantiles on

[R] quantiles on rows of a matrix

2010-07-07 Thread Jim Bouldin
I'm trying to obtain the mean of the middle 95% of the values from each row of a matrix (that is, the highest and lowest 2.5% of values in each row are removed before calculating the mean). I am having all sorts of problems with this; for example the command: apply(matrix1,1,function(x) quantil

[R] What does `_data` mean in transform()?

2010-07-07 Thread thmsfuller...@gmail.com
Hi All, I meant to take the min row by row. But the result is apparently not what I want. Changing min to pmin solve the problem. > df=data.frame(X=1:10, Y=1:10) > transform(df, Z=min(X,10-Y)) X Y Z 1 1 1 0 2 2 2 0 3 3 3 0 4 4 4 0 5 5 5 0 6 6 6 0 7 7 7 0 8 8 8 0 9 9

Re: [R] LondonR July Meeting

2010-07-07 Thread raghu
Hello Sarah I am unable to register for this event as the link you had supplied goes nowhere. Any other method of registering pls? Thx Raghu On Wed, Jul 7, 2010 at 8:08 PM, Sarah Lewis-2 [via R] < ml-node+2281370-1994523266-309...@n4.nabble.com > wrote: > I am pleased to announce to agenda for

[R] How do I test against a simple null that two regressions coefficients are equal?

2010-07-07 Thread chen jia
Hi there, I run two regressions: y = a1 + b1 * x + e1 y = a2 + b2 * z + e2 I want to test against the null hypothesis: b1 = b2. How do I design the test? I think I can add two equations together and divide both sides by 2: y = 0.5*(a1+a2) + 0.5*b1 * x + 0.5*b2 * z + e3, where e3 = 0.5*(e1 + e2

Re: [R] how to calculate summary statistics for each factor

2010-07-07 Thread karena
yeah, both work. Thank you, guys... -- View this message in context: http://r.789695.n4.nabble.com/how-to-calculate-summary-statistics-for-each-factor-tp2279777p2281532.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.

Re: [R] problems with write.table, involving loops & paste statement

2010-07-07 Thread CocaCola
Thank you! That was the appropriate adjustment - it's working as I need it to! =) -CC -- View this message in context: http://r.789695.n4.nabble.com/problems-with-write-table-involving-loops-paste-statement-tp2281410p2281572.html Sent from the R help mailing list archive at Nabble.com. ___

[R] Boxplots over a Scatterplot

2010-07-07 Thread fsch
Hello- I'm new to R, coding and stats. (Oh no.) Anyway, I have about 12000 data points in a data.frame (dealing with dimensions and geological stage information for fossil protists) and have plotted them in a basic scatter plot. I also added a boxplot to overlay these points. Each worked fine i

[R] ifelse statement

2010-07-07 Thread karena
Hi, I am a newbie of R, and playing with the "ifelse" statement. I have the following codes: ## first, for(i in 1:3) { for(j in 2:4) { cor.temp <- cor(iris.allnum[,i], iris.allnum[,j]) if(i==1 & j==2) corr.iris <- cor.temp else corr.iris <- c(corr.iris, cor.temp) } } this code is working fine.

[R] meaning of warning messages after spss-import

2010-07-07 Thread Katharina Manderscheid
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 I have imported a spss-data set with the read.spss command and received the following warning messages. Does this mean that something did not work correctly? What am I to make out of these messages? Thanks for your help, Katharina Warning messages:

Re: [R] How do I unsubscribe from the mailing list?

2010-07-07 Thread David Winsemius
On Jul 7, 2010, at 6:05 PM, addi wei wrote: Hello, I have tried multiple times to unsubscribe from the general mailing list to no avail. I only wish to receive emails when someone posts a response in my thread. How do I do this? I suspect many people send a copy of their response to the O

[R] How do I unsubscribe from the mailing list?

2010-07-07 Thread addi wei
Hello, I have tried multiple times to unsubscribe from the general mailing list to no avail. I only wish to receive emails when someone posts a response in my thread. How do I do this? Thanks. -- - Addi __ R-help@r-project.org mailing list https:/

Re: [R] when all I have is a contingency table....

2010-07-07 Thread Derek Ogle
A.Z., You could recreate the data (I assumed that the values are discrete integers and not a bin for a continuous variable) ... value <- 1:6 count <- c(10,8,12,9,14,7) d <- rep(value,count) table(d) ... and then do what you want with the data in the d vector ... summary(d) hist(d) > On 07-J

Re: [R] forcing a zero level in contr.sum

2010-07-07 Thread David Winsemius
Please do not post with ambiguous questions lacking sufficient R code and data to represent the problem. On Jul 7, 2010, at 4:41 PM, Bond, Stephen wrote: Please, do not post if you do not know the answer. People will see this has answers and skip. More likely people will see that it has in

Re: [R] when all I have is a contingency table....

2010-07-07 Thread Joris Meys
See Teds answer for histogram (I'd go with barplot). For most statistical procedures there is a weighted version (e.g. weighted.mean() for the mean). Your counts are valid weights for most procedures. Cheers Joris On Wed, Jul 7, 2010 at 10:39 PM, Andrei Zorine wrote: > Hello, > I just need a hi

Re: [R] when all I have is a contingency table....

2010-07-07 Thread Ted Harding
On 07-Jul-10 20:39:32, Andrei Zorine wrote: > Hello, > I just need a hint here: > Suppose I have no raw data, but only a frequency table I have, and I > want to run basic statistical procedures with it, like histogram, > descriptive statistics, etc. How do I do this with R? > For example, how do I

Re: [R] Visualization of coefficients

2010-07-07 Thread Achim Zeileis
On Wed, 7 Jul 2010, Michael Friendly wrote: Tal Galili wrote: Hello David, Thanks to your posting I started looking at the function in the arm package. It appears this function is quite mature, and offers (for example) the ability to easily overlap coefficients from several models. I update

Re: [R] problems with write.table, involving loops & paste statement

2010-07-07 Thread Joris Meys
To be correct, everything is written to all folders according to my testing. There is absolutely no need whatsoever to use l_ply. And in any case, take as much as possible outside the loop, like the library statement and the max.col. Following is _a_ solution, not the most optimal, but as close a

[R] meaning of warning messages after spss-import

2010-07-07 Thread Katharina Manderscheid
I have imported a spss-data set with the read.spss command and received the following warning messages. Does this mean that something did not work correctly? What am I to make out of these messages? Thanks for your help, Katharina Warning messages: 1: In read.spss("/Daten/ESS4DE.spss/ESS4DE.sav"

Re: [R] lattice xyplot with bty="l"

2010-07-07 Thread László Sándor
Thank you, this has been really helpful, I think I have managed to produce the desired effect. However, I am having trouble with generating and passing subscripts from the main xyplot call to panel.superpose. My code resembles the examples (e.g. pp 71-73) in your 2008 book --- though I cannot refe

Re: [R] xyplot of function only shows diagonal plots

2010-07-07 Thread Deepayan Sarkar
On Wed, Jul 7, 2010 at 12:17 PM, DrHatch wrote: > I expected this script to show nine panels, each with a plot of the > function. > But when I run it, only the diagonal panels have content. > Executing > print(trel_1) shows what I expected in the upper left corner. > I am using R ver. 2.11.0 and l

[R] when all I have is a contingency table....

2010-07-07 Thread Andrei Zorine
Hello, I just need a hint here: Suppose I have no raw data, but only a frequency table I have, and I want to run basic statistical procedures with it, like histogram, descriptive statistics, etc. How do I do this with R? For example, how do I plot a histogram for this table for a sample of size 60?

Re: [R] forcing a zero level in contr.sum

2010-07-07 Thread Bond, Stephen
Please, do not post if you do not know the answer. People will see this has answers and skip. I tried with mat1=contrasts(fixw$snconv) mat1=mat1[,-2] summary(frm2sum <- glm(resp.frm ~ C(snconv,contr=mat1)+mprime+mshape,data=fixw,family="quasibinomial")) the unwanted level is still there. Unbel

Re: [R] Boxplots from data.frame

2010-07-07 Thread Brian Diggs
On 7/7/2010 1:11 PM, Ian Bentley wrote: Hi all, I'm trying to use ggplot to make a boxplot of some data, but I can't seem to figure out how to make it use the data I'm giving it. The data is in a data.frame so that it has two columns: meltl value L1 1234 1 1234 1 1235 1 ... 1255 1 2335

Re: [R] xyplot: filtering out empty plots

2010-07-07 Thread Deepayan Sarkar
On Tue, Jul 6, 2010 at 2:47 AM, Coen van Hasselt wrote: > Hello, > > I would like to know how I can filter out empty plots in xyplot, when > stratifying on some variables. > > Example: > > I have a dataset in which I plot CONC ~ TIME, stratified for patient > ID(1,2,..,100), FORM(1,2) and BOOST (1

[R] R2 function from PLS to use a model on test data

2010-07-07 Thread Addi Wei
Hello, I am having some trouble using a model I created from plsr (of train) to analyze each invididual R^2 of the 10 components against the test data. For example: mice1 <- plsr(response ~factors, ncomp=10 data=MiceTrain) R2(mice1)##this provides the correct R2 for the Train data for 1

Re: [R] lattice xyplot with bty="l"

2010-07-07 Thread Deepayan Sarkar
2010/7/5 László Sándor : > Hi all, > > Back in 2007, Deepayan and Patrick had an exchange about how to modify > axes for lattice plots (pasted below). I need something similar, but I > also need to produce ticks on the axes. Deepayan quickly coded up > substitute gridlines because they needed to ma

Re: [R] Boxplots from data.frame

2010-07-07 Thread Sarah Goslee
What about this: > testdata <- cbind.data.frame(value = runif(100), L1 = rep(1:10, each=10)) > head(testdata) value L1 1 0.3370902 1 2 0.6766098 1 3 0.2433171 1 4 0.8848674 1 5 0.5253600 1 6 0.4067238 1 > tail(testdata) value L1 95 0.8149121 10 96 0.5186669 10 97 0.1080695 1

Re: [R] forcing a zero level in contr.sum

2010-07-07 Thread David Winsemius
On Jul 7, 2010, at 4:04 PM, Bond, Stephen wrote: Clarifying my question: options(contrasts = c("contr.sum", "contr.poly")) contrasts() [,1] [,2] [,3] [,4] [,5] 0110000 0301000 0500100 0600010 07000

[R] Boxplots from data.frame

2010-07-07 Thread Ian Bentley
Hi all, I'm trying to use ggplot to make a boxplot of some data, but I can't seem to figure out how to make it use the data I'm giving it. The data is in a data.frame so that it has two columns: >meltl value L1 1234 1 1234 1 1235 1 ... 1255 1 2335 2 3444 2 ... 10001 50 12311 50 ... The fi

Re: [R] how to define a function in R

2010-07-07 Thread Stephan Kolassa
Hi, I recommend that you look at the following help pages and experiment a little (maybe create a toy directory with only three or four files with a few lines each): ?files ?dir ?grep ?strsplit Good luck! Stephan jd6688 schrieb: Here are what i am going to accomplish: I have 400 files na

Re: [R] forcing a zero level in contr.sum

2010-07-07 Thread Bond, Stephen
Clarifying my question: options(contrasts = c("contr.sum", "contr.poly")) > contrasts(fixw$snconv) [,1] [,2] [,3] [,4] [,5] 0110000 0301000 0500100 0600010 0700001 09 -1 -1 -1 -1 -1 I

Re: [R] how to define a function in R

2010-07-07 Thread jd6688
Here are what i am going to accomplish: I have 400 files named as xxx.txt. the content of the file looks like the following: namecount 1. aaa 100 2. bbb2000 3. ccc300 4. ddd 3000 more that 1000 rows in each files. these are the areas i need help: 1. how can i on

Re: [R] Producing residual plots by time for lme object

2010-07-07 Thread Deepayan Sarkar
On Fri, Jul 2, 2010 at 11:40 AM, Gregory Gentlemen wrote: > Fellow R-users, > > I have a longitudinal data set with missing values in it. I would like to > produce a residual plot for each time using panel.xyplot function but I get > an error message. Here's a simple example, > > library(nlme) >

Re: [R] how to define a function in R

2010-07-07 Thread jd6688
Hi Joshua: Here are what i am going to accomplish: I have 400 files named as xxx.txt. the content of the file looks like the following: namecount 1. aaa 100 2. bbb2000 3. ccc300 4. ddd 3000 more that 1000 rows in each files. these are the areas i need help: 1.

Re: [R] Weired problem when passing arguments using ...?

2010-07-07 Thread Henrique Dallazuanna
Try write.table instead. On Wed, Jul 7, 2010 at 1:56 PM, thmsfuller...@gmail.com < thmsfuller...@gmail.com> wrote: > Hello All, > > I'm trying to pass the argument col.names to write.csv using '...'. > But I got the following warnings. Maybe it is very simple. But I'm not > sure what I am wrong.

Re: [R] forcing a zero level in contr.sum

2010-07-07 Thread David Winsemius
On Jul 7, 2010, at 3:13 PM, Bond, Stephen wrote: I need to use contr.sum and observe that some levels are not statistically different from the overall mean of zero. What is the proper way of forcing the zero estimate? It seems the column corresponding to that level should become a column of

Re: [R] Weired problem when passing arguments using ...?

2010-07-07 Thread David Winsemius
On Jul 7, 2010, at 12:56 PM, thmsfuller...@gmail.com wrote: Hello All, I'm trying to pass the argument col.names to write.csv using '...'. But I got the following warnings. Maybe it is very simple. But I'm not sure what I am wrong. Could you please help point to me what the problem is? #

[R] problems with write.table, involving loops & paste statement

2010-07-07 Thread CC
Hi! I want to write portions of my data (3573 columns at a time) to twenty folders I have available titled "A_1" to "A_20" such that the first 3573 columns will go to folder A_1, next 3573 to folder A_2 and so on. This code below ensures that the data is written into all 20 folders, but only the

Re: [R] how to process this in R

2010-07-07 Thread Sarah Goslee
Hi, You might want to check out ?system ?read.table and ?subset and also ?sub and maybe ?strsplit Reading one of the good intro to R documents out there would also help you get started with this fairly straightforward task Beyond that, you did a good job of explaining your problem, but this is o

Re: [R] Weired problem when passing arguments using ...?

2010-07-07 Thread Charles C. Berry
On Wed, 7 Jul 2010, thmsfuller...@gmail.com wrote: Hello All, I'm trying to pass the argument col.names to write.csv using '...'. But I got the following warnings. Maybe it is very simple. But I'm not sure what I am wrong. Could you please help point to me what the problem is? Its not a _prob

Re: [R] use sliding window to count substrings found in large string

2010-07-07 Thread David Winsemius
On Jul 7, 2010, at 1:26 PM, Gabor Grothendieck wrote: On Wed, Jul 7, 2010 at 1:25 PM, Gabor Grothendieck wrote: On Wed, Jul 7, 2010 at 1:15 PM, Immanuel wrote: Hey, big help, thanks! One little question remains, if I create more then one string and table ... - # gener

Re: [R] plotmath vector problem; full program enclosed

2010-07-07 Thread Allan Engelhardt
On 07/07/10 18:52, Paul Johnson wrote: > [...] > 1: > axis(1, line=6, at=mu+dividers*sigma, > labels=as.expression(c(b1,b2,b3,b4,b5), padj=-1)) > > > 2: > axis(1, line=9, at=mu+dividers*sigma, > labels=c(as.expression(b1),b2,b3,b4,b5), padj=-1) > > This second one shouldn't work, I think.

Re: [R] Batch files process and String parsing

2010-07-07 Thread Nikhil Kaza
?list.files In particular look at pattern argument. ?file.rename ?lapply ?read.table ?"[" Nikhil Kaza Asst. Professor, City and Regional Planning University of North Carolina nikhil.l...@gmail.com On Jul 7, 2010, at 1:11 PM, jd6688 wrote: Here are what i am going to accomplish: I have 400

[R] xyplot of function only shows diagonal plots

2010-07-07 Thread DrHatch
I expected this script to show nine panels, each with a plot of the function. But when I run it, only the diagonal panels have content. Executing > print(trel_1) shows what I expected in the upper left corner. I am using R ver. 2.11.0 and lattice ver. 0.18-8 on Windows XP under Eclipse and StatE

[R] forcing a zero level in contr.sum

2010-07-07 Thread Bond, Stephen
I need to use contr.sum and observe that some levels are not statistically different from the overall mean of zero. What is the proper way of forcing the zero estimate? It seems the column corresponding to that level should become a column of zeros. Is there a way to achieve that without me const

[R] Batch files process and String parsing

2010-07-07 Thread jd6688
Here are what i am going to accomplish: I have 400 files named as xxx.txt. the content of the file looks like the following: namecount 1. aaa 100 2. bbb2000 3. ccc300 4. ddd 3000 more that 1000 rows in each files. these are the areas i need help: 1. how can i on

[R] how to process this in R

2010-07-07 Thread jd6688
Here are what i am going to accomplish: I have 400 files named as xxx.txt. the content of the file looks like the following: namecount 1. aaa 100 2. bbb2000 3. ccc300 4. ddd 3000 more that 1000 rows in each files. these are the areas i need help: 1. ho

[R] Weired problem when passing arguments using ...?

2010-07-07 Thread thmsfuller...@gmail.com
Hello All, I'm trying to pass the argument col.names to write.csv using '...'. But I got the following warnings. Maybe it is very simple. But I'm not sure what I am wrong. Could you please help point to me what the problem is? # fun=function(x, ...) { fr=parent.frame() tm

[R] LondonR July Meeting

2010-07-07 Thread Sarah Lewis
I am pleased to announce to agenda for next weeks LondonR meeting: LondonR meeting - 13th July 2010 Date:   Tuesday 13th July 2010 Time:    6pm - 9pm Venue:  The Shooting Star     125 - 129 Middlesex Street     E1 7JF     (N

Re: [R] plotmath vector problem; full program enclosed

2010-07-07 Thread Paul Johnson
On Wed, Jul 7, 2010 at 5:41 AM, Duncan Murdoch wrote: >>> >>> You want "as.expression(b1)", not "expression(b1)".  The latter means >>> "the >>> expression consisting of the symbol b1".  The former means "take the >>> object >>> stored in b1, and convert it to an expression.". >>> Thanks to

Re: [R] how to draw the legend about color from 3d picture

2010-07-07 Thread Sebastien Guyader
It may not help the original poster, but here's a solution based on what Greg said above: # Load plotrix library(plotrix) # Create a new layout to divide the graphics in 2, the first one (displaying the persp() graph) being 4 times larger than the second one (displying the legend) layout(matrix

[R] [R-pkgs] ggplot2 version 0.8.8

2010-07-07 Thread Hadley Wickham
ggplot2 ggplot2 is a plotting system for R, based on the grammar of graphics, which tries to take the good parts of base and lattice graphics and avoid bad parts. It takes care of many of the fiddly details that make plotting a hassle (l

Re: [R] export VTK from R : impossible to write data as float

2010-07-07 Thread yepri
So, the problem was that R exports only double sized floats (double), and Paraview requires single sized floats. The solution was just to write : writeBin(data,bfile_celldata,endian="swap",size=4) Special Thanks to Sebastian Gibb : http://www.mail-archive.com/r-help@r-project.org/msg100994.htm

[R] subscripts for panel.superpose in lattice

2010-07-07 Thread László Sándor
Hi, I am trying to superimpose (overlay) regression lines to scatter plots by groups with xyplot (dysfunctional code below). However, my call of panel.superpose breaks down because of the subscripts requirement. I tried to research the documentation and examples, but I cannot figure out how to mak

Re: [R] use sliding window to count substrings found in large string

2010-07-07 Thread Immanuel
Hey, saved my day. Now can watch the football semi-final thanks > Turn them into factors with the appropriate levels before counting > them with table: > > # generate an input string n long > set.seed(123) > n <- 300 > lets_1 <- paste(sample(letters[1:5], n, replace = TRUE), collapse = "") > lets_2

Re: [R] Data Labels in a barchart (Lattice or otherwise)

2010-07-07 Thread Greg Snow
> fortune(197) If anything, there should be a Law: Thou Shalt Not Even Think Of Producing A Graph That Looks Like Anything From A Spreadsheet. -- Ted Harding (in a discussion about producing graphics) R-help (August 2007) Also read the discussion started with: http://tolstoy.newcastle.ed

Re: [R] F# vs. R

2010-07-07 Thread Bernardo Rangel Tura
On Wed, 2010-07-07 at 17:31 +0200, Sergey Goriatchev wrote: > Hello, everyone > > F# is now public. Compiled code should run faster than R. > > Anyone has opinion on F# vs. R? Just curious > > Best, > S Sergey, F# is public, but is not open source. F# run in windows but run in AIX, linux, M

Re: [R] using objects from different workspaces

2010-07-07 Thread Greg Snow
Check out the high performance computing task view on CRAN. -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 > -Original Message- > From: r-help-boun...@r-project.org [mailto:r-help-boun...@r- > project.org] On Behalf Of M

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