[R] means and error bars on xyplot for binary data

2011-06-28 Thread Louis Plough
Hi, I have binary (0,1) data for a trait as my response variable, and a dependent variable, genotype, with three classes (AA, AB, BB). I would like to plot this data so that across the three genoytpes, even though the points are all either 0 or 1, i want them to stack up or be seen using 'jitter'.

[R] Odp: data.frame: How to get the classes of all components and how to remove their factor structure?

2011-06-28 Thread Petr PIKAL
Hi > Dear expeRts, > > I have two questions concerning data frames: > (1) How can I apply the class function to each component in a data.frame? > As you can see below, applying class to each column is not the right > approach; applying it to each component seems bulky. > (2) After transforming

[R] Odp: data.frame: How to get the classes of all components and how to remove their factor structure?

2011-06-28 Thread Petr PIKAL
> > Dear expeRts, > > I have two questions concerning data frames: > (1) How can I apply the class function to each component in a data.frame? > As you can see below, applying class to each column is not the right > approach; applying it to each component seems bulky. > (2) After transforming

Re: [R] testInstalledPackages

2011-06-28 Thread Uwe Ligges
On 27.06.2011 23:56, Cody Hamilton wrote: Dear group, When running the installation test: testInstalledPackages("both",outDir='c:/Test') I got the following message: Running ‘testci.R’ comparing ‘testci.Rout’ to ‘testci.Rout.save’ ... files differ in number of lines: and then? Please n

Re: [R] R-GUI shutdown

2011-06-28 Thread Uwe Ligges
On 27.06.2011 23:54, xin123620 wrote: Dear R Users, I was using R to import several years traffic data, but every time after data successfully imported (no error or warning) when I tried to save this workplace or tackle these data, R GUI would automatically shut down. Would you have any ideas

Re: [R] testInstalledPackages

2011-06-28 Thread Duncan Murdoch
On 27/06/2011 5:56 PM, Cody Hamilton wrote: Dear group, When running the installation test: testInstalledPackages("both",outDir='c:/Test') I got the following message: Running ‘testci.R’ comparing ‘testci.Rout’ to ‘testci.Rout.save’ ... files differ in number of lines: Please note the test d

Re: [R] Odp: data.frame: How to get the classes of all components and how to remove their factor structure?

2011-06-28 Thread Marius Hofert
Dear Petr, thanks for your posts, they perfectly answered my questions. Cheers, Marius On 2011-06-28, at 09:49 , Petr PIKAL wrote: >> >> Dear expeRts, >> >> I have two questions concerning data frames: >> (1) How can I apply the class function to each component in a > data.frame? >> As yo

[R] time series question

2011-06-28 Thread Albert-Jan Roskam
Hi, I have a long data file with time data that change to wide format using reshape. The data contain Values and Factors. Some values are missing but can be obtained by multiplying value of year T-1 with Factor of year T. Sometimes, multiple succesive years have no values, so the calculated v

[R] lattice multiple y-scale possible?

2011-06-28 Thread Steve Corsi
Hi I am attempting to use the lattice bwplot function to generate boxplots of numerous parameters (1-panel/parameter) by site (x-axis). The parameters have quite different ranges of values, so it would be best to have a separate y-axis range for each panel. Below is a basic example of what I a

[R] Running R from windows command prompt

2011-06-28 Thread siddharth arun
1. I have a R program in a file say "functions.R". I load the "functions.R" file the R using source("function.R") and then call functionsf1(), f2() etc. which are declared and defined within "function.R" file. I also need to load a couple of R libraries using library() before I can use f1(), f2()

Re: [R] Running R from windows command prompt

2011-06-28 Thread Uwe Ligges
On 28.06.2011 11:54, siddharth arun wrote: 1. I have a R program in a file say "functions.R". I load the "functions.R" file the R using source("function.R") and then call functionsf1(), f2() etc. which are declared and defined within "function.R" file. I also need to load a couple of R librar

[R] help required for GO Annotation problem

2011-06-28 Thread suman pal
Hello, I basically want to use R-help, and post some problems which I am facing. The Ref is a well known Genome Biology paper "Bioconductor: open software development for computational biology and bioinformatics" by Robert C Gentleman et al., 2004. Generating Heatmaps till Fig2 is working so I t

Re: [R] gam confidence interval (package mgcv)

2011-06-28 Thread Simon Wood
not sure if I'm missing something here, but since you are using a log link, isn't the ratio you are looking for given by the `treatmentB' parameter in the summary (independent of X) > summary(gfit) [snip] Parametric coefficients: Estimate Std. Error t value Pr(>|t|) (Intercept) 1.

Re: [R] Running R from windows command prompt

2011-06-28 Thread siddharth arun
Thanks for your help. I tried the way you mentioned for my first question. But I am not getting any results. Can you please explain in detail the process through which I can run a R code from windows command prompt. 2011/6/28 Uwe Ligges > > > On 28.06.2011 11:54, siddharth arun wrote: > >> 1. I

[R] problem with corrgram function

2011-06-28 Thread Niels Janssen
Dear list, I have a problem with the "corrgram" function. It does not seem to "color" large negative correlations, while the same correlation, if positive, provides no problems. Is this a bug? require(corrgram) a = seq(1,100) b = -jitter(seq(1,100), 80)

Re: [R] lattice multiple y-scale possible?

2011-06-28 Thread Dennis Murphy
Hi: bwplot(dat~site|parameter,data=mydat, layout=c(1,5), cex=2, xlab="Site Name", ylab="", labels=levels(mydat$site), scales=list(tick.number=list(4), rot = c(0, 90), y = list(relation = 'free'))) Does that work? Dennis On Mon, Jun 27, 2011 at 10:4

[R] Regarding accuracy function in library forecast

2011-06-28 Thread siddharth arun
I want to find the error in the forecasting values. I used the function accuracy() under forecast library. But, I didn't understand how it is calculating the errors? Can anybody help? -- Siddharth Arun, 4th Year Undergraduate student Industrial Engineering and Management, IIT Kharagpur

Re: [R] Creating a Polar Plot with expanding points as radius increases

2011-06-28 Thread Jim Lemon
On 06/28/2011 08:35 AM, Patrick Jemison wrote: I'd like to create a polar plot similar to those created by the polarFreq function in the openair package. However, this package seems to be specific to wind speed and direction, and requires a "ws" (wind speed) and a "wd" (wind direction) column.

Re: [R] Kernel Density Estimation at manually specified points

2011-06-28 Thread Stephen Ellison
May be a kludge, but it might be simpler to write your own density function for a few specified points. For example my.density <- function(x, bw = 'nrd0', at) { x<-na.omit(x) # #Borrowed from density.default for compatibility if (is.character(bw)) { if (leng

Re: [R] Running R from windows command prompt

2011-06-28 Thread Mike Marchywka
> To: lig...@statistik.tu-dortmund.de > CC: r-help@r-project.org > Subject: Re: [R] Running R from windows command prompt > > Thanks for your help. > > I tried the way you mentioned for my first question. But I am not getting > any results. > Can you please explain in detail the process throu

Re: [R] Running R from windows command prompt

2011-06-28 Thread Uwe Ligges
On 28.06.2011 13:56, Mike Marchywka wrote: To: lig...@statistik.tu-dortmund.de CC: r-help@r-project.org Subject: Re: [R] Running R from windows command prompt Thanks for your help. I tried the way you mentioned for my first question. But I am not getting any results. Can you please expla

[R] Date format issue.

2011-06-28 Thread Ashim Kapoor
Dear R helpers, I have 2 questions : - 1. My excel sheet has a column with dates like 01/03/1980 which is formatted as 03/80 when I read this into R it reads as Mar-80. How can I read it in the source format ? 2. > v<-c("Mar-80") > as.Date(v,format="%b-%y") [1] NA > Could someone please tell m

Re: [R] Date format issue.

2011-06-28 Thread jim holtman
You get the NA since it is indeterminate as to the date; paste on a 1 for the day" > v<-c("Mar-80") > as.Date(paste(v, '1'),format="%b-%y %d") [1] "1980-03-01" On Tue, Jun 28, 2011 at 8:04 AM, Ashim Kapoor wrote: > Dear R helpers, > > I have 2 questions : - > > 1. My excel sheet has a column wi

Re: [R] Date format issue.

2011-06-28 Thread Ashim Kapoor
You get the NA since it is indeterminate as to the date; paste on a 1 > for the day" > Alright Jim, Many thanks. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE d

[R] Using Match in a lookup table

2011-06-28 Thread Michael Pearmain
Hi All, I'm having a few problems using match and a lookup table, previous Googling show numerous solutions to matching a lookup table to a dataset, My situation is slightly different as i have multiple lookup tables, (that i cannot merge - for integrity reasons) that i wish to match against my da

[R] coxph() - unexpected result using Crawley's seedlings data (The R Book)

2011-06-28 Thread Jacob Brogren
Hi, I ran the example on pp. 799-800 from Machael Crawley's "The R Book" using package survival v. 2.36-5, R 2.13.0 and RStudio 0.94.83. The model is a Cox's Proportional Hazards model. The result was quite different compared to the R Book. I have compared my code to the code in the book but ca

[R] chull increase number of points

2011-06-28 Thread pete
Dear R-help, I am using the chull function to create a convex hull of a series of about 20,000 data points. A pain is temporary, glory is forever! Powered by Linux. www.linux.org Scanned for viruses using ClamAV. www.clamav.net. [[alternative HTM

[R] Error in library (nls)

2011-06-28 Thread matotope
Hi everybody, I'm not very experienced with R software. I have used it several times for some of the population genetics analyses. I have problem with executing one of the script. The script is created by another software called Gimlet and it is aimed to calculate rarefaction curve in R software. H

[R] connecting R and PostgreSQL

2011-06-28 Thread Aya74656
Dear R-helpers, I'm an absolute beginner using both R and PostgreSQL, but now I have to work with both programs. I need to connect R and my Postgres-database, but every attempt so far has failed (I tried using the RpgSQL package as well as RdbiPgSQL, the first, following this manual (http://co

Re: [R] Error in library (nls)

2011-06-28 Thread Ben Bolker
matotope gmail.com> writes: > > Hi everybody, > I'm not very experienced with R software. I have used it several times for > some of the population genetics analyses. I have problem with executing one > of the script. The script is created by another software called Gimlet and > it is aimed to c

Re: [R] chull increase number of points

2011-06-28 Thread Ben Bolker
pete nevill.uk.net> writes: > I am using the chull function to create a convex > hull of a series of about 20,000 data points. And your question is ... ? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do re

Re: [R] Date format issue.

2011-06-28 Thread David Winsemius
On Jun 28, 2011, at 8:04 AM, Ashim Kapoor wrote: Dear R helpers, I have 2 questions : - 1. My excel sheet has a column with dates like 01/03/1980 which is formatted as 03/80 when I read this into R it reads as Mar-80. You should be able to change that from the format menu in Excel. If

Re: [R] coxph() - unexpected result using Crawley's seedlings data (The R Book)

2011-06-28 Thread David Winsemius
On Jun 28, 2011, at 6:51 AM, Jacob Brogren wrote: Hi, I ran the example on pp. 799-800 from Machael Crawley's "The R Book" using package survival v. 2.36-5, R 2.13.0 and RStudio 0.94.83. The model is a Cox's Proportional Hazards model. The result was quite different compared to the R Boo

[R] A masked function is a masked function by any other name

2011-06-28 Thread Juan Carlos Borrás
Dear all, It looks like I do not grasp the concept of masked functions enough as to solve this trivial problem. The code that replicates the problem (a source code tree that realizes a R package actually) is under github so one can call it clone it easily from the command line (though more experien

Re: [R] Using Match in a lookup table

2011-06-28 Thread David Winsemius
On Jun 28, 2011, at 6:18 AM, Michael Pearmain wrote: Hi All, I'm having a few problems using match and a lookup table, previous Googling show numerous solutions to matching a lookup table to a dataset, My situation is slightly different as i have multiple lookup tables, (that i cannot mer

Re: [R] A masked function is a masked function by any other name

2011-06-28 Thread Duncan Murdoch
On 28/06/2011 9:38 AM, Juan Carlos Borrás wrote: Dear all, It looks like I do not grasp the concept of masked functions enough as to solve this trivial problem. The code that replicates the problem (a source code tree that realizes a R package actually) is under github so one can call it clone it

Re: [R] Error in library (nls)

2011-06-28 Thread David Winsemius
On Jun 28, 2011, at 8:09 AM, matotope wrote: Hi everybody, I'm not very experienced with R software. I have used it several times for some of the population genetics analyses. I have problem with executing one of the script. The script is created by another software called Gimlet and it

Re: [R] coxph() - unexpected result using Crawley's seedlings data (The R Book)

2011-06-28 Thread Robert A LaBudde
Did you create the 'status' variable the way indicated on p. 797? Frequently with Surv() it pays to use syntax such as Surv(death, status==1) to make a clear logical statement of what is an event (status==1) vs. censored. PS. Next time include head(seedlings) and str(seedlings) to make clear

Re: [R] connecting R and PostgreSQL

2011-06-28 Thread Gabor Grothendieck
On Tue, Jun 28, 2011 at 8:15 AM, wrote: > Dear R-helpers, > > I'm an absolute beginner using both R and PostgreSQL, but now I have to work > with both programs. I need to connect R and my Postgres-database, but every > attempt so far has failed (I tried using the RpgSQL package as well as > Rd

Re: [R] About the covariant

2011-06-28 Thread David Winsemius
On Jun 28, 2011, at 12:57 AM, Lao Meng wrote: Thanks David for your reply. You said "a single slope and intercept are estimated for each variable".Actually I can only get one intercept no matter how many Sorry. You are right. You get individual slopes (and differences for factors) referen

Re: [R] Creating a Polar Plot with expanding points as radius increases

2011-06-28 Thread Patrick Jemison
Hi Jim, That sounds pretty great! I am happy to have contributed a stimulus for action to be taken in further developing the tools. I'll keep an eye out for your update. Thanks, Patrick On Tue, Jun 28, 2011 at 6:29 AM, Jim Lemon wrote: > On 06/28/2011 08:35 AM, Patrick Jemison wrote: >> >> I'

Re: [R] help required for GO Annotation problem

2011-06-28 Thread David Winsemius
On Jun 28, 2011, at 5:34 AM, suman pal wrote: Hello, I basically want to use R-help, and post some problems which I am facing. The Ref is a well known Genome Biology paper "Bioconductor: open software development for computational biology and bioinformatics" by Robert C Gentleman et al.,

Re: [R] Using Match in a lookup table

2011-06-28 Thread David Winsemius
On Jun 28, 2011, at 10:29 AM, Michael Pearmain wrote: > Thanks for the idea David, > My problem comes from having (say) upto 10 different match files, so > nested ifelse whilst would work doesn't seem and elegant solution, Well, you cannot mix text and numeric modes in a vector as you appea

[R] chull increase number of points

2011-06-28 Thread pete
Dear R-help, I am using the chull function to create a convex hull of a series of about 20,000 data points. A [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do

Re: [R] lattice multiple y-scale possible?

2011-06-28 Thread Steven R Corsi
Dennis Adding in y = list(relation = 'free') to the scales argument worked very well. Thanks! Steve === Steven R. CorsiPhone: (608) 821-3835 Research Hydrologist email: srco...@usgs.gov U.S. Geological Survey Wisconsin Water Science Cente

Re: [R] Error in library (nls)

2011-06-28 Thread matotope
Hi Ben, thanks for your advise. I put the comment in front of the line with nls. Now the message doesn't appear but the script won't produce the result files which I need (the result files are empty). When executing the script, R asks for number of iterations and after that it states "Read 20 item

Re: [R] Using Match in a lookup table

2011-06-28 Thread Michael Pearmain
Thanks for the idea David, My problem comes from having (say) upto 10 different match files, so nested ifelse whilst would work doesn't seem and elegant solution, However if needs must.. Mike On 28 June 2011 14:39, David Winsemius wrote: > > On Jun 28, 2011, at 6:18 AM, Michael Pearmain wrote:

Re: [R] Error in library (nls)

2011-06-28 Thread matotope
Hi, I installed the 2.8.0 version and it seems to be working fine now. Thanks for the help guys! matotope -- View this message in context: http://r.789695.n4.nabble.com/Error-in-library-nls-tp3630143p3630552.html Sent from the R help mailing list archive at Nabble.com. __

[R] problem with rJava : same as message from wwreith on Mon, 27 Jun 2011

2011-06-28 Thread Olivier ETERRADOSSI
Hi R-listers, I run R version 2.13.0, on a i386-pc-mingw32/i386 platform under Windows XP. I perform daily update of my installed packages. I've got the most recent Java for this platform installed, as I am told by the JavaUpdater when checking. (and I've read the posting guide, so that I'm no

Re: [R] coxph() - unexpected result using Crawley's seedlings data (The R Book)

2011-06-28 Thread Jacob Brogren
Hi, sorry about that; here is the full output - data set, structure, model and result. Cheers Jacob > seedlings cohort death gapsize status 1 September 7 0.5889 1 2 September 3 0.6869 1 3 September12 0.1397 1 4 September 1 0.1921 1 5 September

Re: [R] help required for GO Annotation problem

2011-06-28 Thread James W. MacDonald
Hi Suman, On 6/28/2011 10:02 AM, David Winsemius wrote: On Jun 28, 2011, at 5:34 AM, suman pal wrote: Hello, I basically want to use R-help, and post some problems which I am facing. The Ref is a well known Genome Biology paper "Bioconductor: open software development for computational biolog

Re: [R] What does class "call" mean? How do I make class "formula" into a "call"?

2011-06-28 Thread Rita Carreira
Thank you Bert and Prof. Ripley for your feedback. I did read the language documentation and it was not entirely clear to me, but I'm one of those people that has to read and digest something before it clicks. However, I did realize that the issue with "call"and "formula" was not the real reas

Re: [R] problem with corrgram function

2011-06-28 Thread Eik Vettorazzi
yes it is. and a correlation of 0 isn't exactly white (#FF) either. have a look at the panel.pie function. the crucial part is ncol <- 14 pal <- col.corrgram(ncol) col.ind <- round(ncol * (corr + 1)/2) so an correlation near -1 maps to an index 0, which isn't a proper index in R.

Re: [R] coxph() - unexpected result using Crawley's seedlings data (The R Book)

2011-06-28 Thread Jacob Brogren
All, I rerun once again and managed to reproduce the results from the text book. Made no changes to the code. Could it be some problem with convergence? Anyhow, now it works! Cheers Jacob ps. I find "The R Book" very useful ds. 28 jun 2011 kl. 15.48 skrev Robert A LaBudde: > Did you create

Re: [R] Running R from windows command prompt

2011-06-28 Thread Arun Kumar Saha
Hi Siddharth, many experts already answered your query, however I would like to share how I run R in command prompt: 1. open command prompt 2. change working directory: cd C:\\R-2.13.0\bin\i386 (put the entire path here, however many people might find this step weird, you can have

Re: [R] A masked function is a masked function by any other name

2011-06-28 Thread Juan Carlos Borrás
Ops! Thank-you Duncan for clarifying the 2 vs. 3 colon difference and a couple of other things. Working like a charm now. Cheers, jcb! > If you are using ::: (three colons), then you may be looking into the > unexported functions in log4r.  The only normal way to see unexported > functions is to u

Re: [R] Running R from windows command prompt

2011-06-28 Thread Robert Baer
Subject: Re: [R] Running R from windows command prompt Hi Siddharth, many experts already answered your query, however I would like to share how I run R in command prompt: 1. open command prompt 2. change working directory: cd C:\\R-2.13.0\bin\i386 (put the entire path here, howe

[R] How do I output all the R-squares of an SUR? summary(fitSUR$eq[[1:4]])$r.squared does not work

2011-06-28 Thread StellathePug
Greetings R Users, I have a system of equations for which I would like to output all the R-squares. Assume there are four equations in my system, the only way I found to output all the R-squares is by calling them out one by one as this: summary(fitSUR$eq[[1]])$r.squared summary(fitSUR$eq[[2]])$r.

Re: [R] How do I output all the R-squares of an SUR? summary(fitSUR$eq[[1:4]])$r.squared does not work

2011-06-28 Thread Achim Zeileis
On Tue, 28 Jun 2011, StellathePug wrote: Greetings R Users, I have a system of equations for which I would like to output all the R-squares. Assume there are four equations in my system, the only way I found to output all the R-squares is by calling them out one by one as this: summary(fitSUR$e

[R] extracting data

2011-06-28 Thread Ana Kolar
Let's say I have an original data set which is called A and data extracted from this original data set, called B. Based on these A and B data set I would like to get data set C which includes all the remaining data from the data set A after we exclude data of the data set B. Any idea how to do

Re: [R] extracting data

2011-06-28 Thread Sarah Goslee
Hi Ana, On Tue, Jun 28, 2011 at 12:28 PM, Ana Kolar wrote: > Let's say I have an original data set which is called A and data extracted > from this original data set, called B. Based on these A and B data set I > would like to get data set C which includes all the remaining data from the > dat

Re: [R] extracting data

2011-06-28 Thread Ana Kolar
Hi Sarah, Thank you for your response. Here is a toy example: library(MatchIt) data(lalonde) A<-lalonde f<-treat ~ age + I(age^2) + educ + I(educ^2) + black + hispan +     married + nodegree + re74 + I(re74^2) + re75 + I(re75^2) m<-"nearest" m.out.base <- matchit(formula=f, data=A, method=m) B

Re: [R] cumulative incidence plot vs survival plot

2011-06-28 Thread array chip
Thank you Alan! Now I sort of understand what it means by competing risk! So in cuminc() function, the argument "fstatus" should be coded like: 0=censored, 1=event of interest, 2=event of competing risk. Then the function will calculate CI for each of the 2 types of events (event of interest an

Re: [R] Saved EPS does not match screen when using bquote(.(i))

2011-06-28 Thread John Kruschke
Many thanks to Uwe Ligges, Peter Ehlers, and Dennis Murphy for suggesting work-arounds for this bug. Because the suggestions are work-arounds, rather than actually correcting the bug, I have opted simply to copy and paste the plotting commands a few times with the subscripts specified as constants

[R] how to print "<=" in plot title

2011-06-28 Thread array chip
Hi, how can I print "<=" (I mean the symbol of just one character) in the main title of a plot? for example: plot(1:10, main=paste("x <=", x)) where variable x is some number generated on the fly. Thanks John __ R-help@r-project.org mailing list ht

Re: [R] how to print "<=" in plot title

2011-06-28 Thread Bert Gunter
This is highly system dependent: what "character" do you intend to use for this 2 character representation? Hence, you need to follow the posting guide and give the "at a minimum" system info. ?sessionInfo -- Bert On Tue, Jun 28, 2011 at 10:25 AM, array chip wrote: > Hi, how can I print "<=" (I

Re: [R] extracting data

2011-06-28 Thread Peter Ehlers
On 2011-06-28 09:54, Ana Kolar wrote: Hi Sarah, Thank you for your response. Here is a toy example: library(MatchIt) data(lalonde) A<-lalonde f<-treat ~ age + I(age^2) + educ + I(educ^2) + black + hispan + married + nodegree + re74 + I(re74^2) + re75 + I(re75^2) m<-"nearest" m.out.base<-

Re: [R] cumulative incidence plot vs survival plot

2011-06-28 Thread array chip
Alan, Let's say that I code censoring as "0", recurrence as "1" for fstat and death/competing risk as "2". If a patient did not have recurrence and lost follow-up at 2 years in terms of recurrence monitoring, but he also died at 5 years. How should I code this patient? I think I still code this

Re: [R] how to print "<=" in plot title

2011-06-28 Thread array chip
Thanks Bert. here is info: R version 2.12.2 (2011-02-25) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C LC_TIME=English_United Stat

Re: [R] how to print "<=" in plot title

2011-06-28 Thread Peter Ehlers
On 2011-06-28 10:25, array chip wrote: Hi, how can I print "<=" (I mean the symbol of just one character) in the main title of a plot? for example: plot(1:10, main=paste("x<=", x)) where variable x is some number generated on the fly. x <- 2.718 plot(0, 0) title(bquote( x %<=% .(x) ))

Re: [R] how to print "<=" in plot title

2011-06-28 Thread array chip
Thank Peter! How do I make the title in bold font? John - Original Message From: Peter Ehlers To: array chip Cc: R Sent: Tue, June 28, 2011 10:52:07 AM Subject: Re: [R] how to print "<=" in plot title On 2011-06-28 10:25, array chip wrote: > Hi, how can I print "<=" (I mean the sym

Re: [R] testInstalledPackages

2011-06-28 Thread Cody Hamilton
Hello Duncan, testci.R is a test function for the survival package.  I compared the .Rout and .Rout.save files by eyeball (I'm on a Windows 7 machine, so I can't use the diff function). The only differences I found were in the file headers. This is the header from the .Rout file: R version 2

Re: [R] how to print "<=" in plot title

2011-06-28 Thread David Winsemius
On Jun 28, 2011, at 1:52 PM, Peter Ehlers wrote: On 2011-06-28 10:25, array chip wrote: Hi, how can I print "<=" (I mean the symbol of just one character) in the main title of a plot? for example: plot(1:10, main=paste("x<=", x)) where variable x is some number generated on the fly. x

Re: [R] how to print "<=" in plot title

2011-06-28 Thread Bert Gunter
For the record, I was wrong -- using plotmath's "less than or equal" does NOT require platform info. However, I was unsure if you meant that it was some kind of an arrow you wanted to render, a clear misinterpretation on my part. -- Bert On Tue, Jun 28, 2011 at 10:57 AM, array chip wrote: > Than

Re: [R] cumulative incidence plot vs survival plot

2011-06-28 Thread alanm (Alan Mitchell)
John, Since death precludes recurrence, censoring deaths would violate the KM estimator assumption that additional follow-up would eventually lead to an event. If your goal is to estimate the probability of recurrence, then you want CI with deaths as a competing risk. The cuminc function in the

Re: [R] Specify ID variable in daisy{cluster}

2011-06-28 Thread adlynch
Hi David - I wanted to thank you for your response! This was exactly what I needed. Sincerely, Alicia On Fri, Jun 17, 2011 at 3:33 PM, David L Carlson [via R] wrote: > You need to use hhid as the rownames for housing.cluster rather than > including it as a variable in the data.frame: > > housing

Re: [R] Need help on nnet

2011-06-28 Thread arun
Hi Georg, I am new to R and I am curious if there is a simple way to do the feature selection you described: "feature selection is essentially an exhaustive approach which tries every possible subset of your predictors, trains a network and sees what the prediction error is. The subset which is b

[R] renaming multiple columns + interpolating temperature series

2011-06-28 Thread tomtomme
Greetings R Users, I´m new to R but at least managed to read in multiple files: filenames <- list.files(path=getwd()) numfiles <- length(filenames) for (all_temp in c(1:numfiles)) { filenames[all_temp] <- paste(filenames[all_temp],sep="") assign(gsub("[.]ASC$","temp",filenames[all_temp]),r

[R] Function unfold package RcmdrPlugin.survival

2011-06-28 Thread Rapha
Dear all, I am using the function ‘unfold’ from the ‘RcmdrPlugin.survival’ to convert my time-varying covariates dataset from wide to long. I managed to have it working for my data. However, the problem I have is that the observations after an event, won’t be dropped from the dataset. For example

Re: [R] How do I output all the R-squares of an SUR? summary(fitSUR$eq[[1:4]])$r.squared does not work

2011-06-28 Thread StellathePug
> sapply(fitSUR$eq, function(x) summary(x)$r.squared) > You can abbreviate that to: > sapply(summary(fitSUR)$eq, "[[", "r.squared") This is fantastic! Thanks so much. I had a hunch that it would be something related to the apply family but I am still not very good at using it. Thank you immensel

[R] R-Installation on Unix -- "Make: Don't know how to make #. Stop."

2011-06-28 Thread Zhou, Hong
Hi, all, ./configure was run successfully on my HP-UX ia64 server with exit=0, but when type make at prompt, get this error "Make: Don't know how to make #. Stop." Does anyone has any clues about this message? Thank you very much! #make Rmath.h is unchanged `libRblas.sl' is up to date. /app/R/

[R] Loop through each subject

2011-06-28 Thread Edward Patzelt
R help - I am attempting to write a script that has multiple subjects in 1 data file. Each subject has multiple rows with columns as variables. Here is my code, I am having problem executing it on each unique subject id (dat$Subject). getwd() setwd("/Users/edwardpatzelt/Desktop/Neuroimaging

Re: [R] how to print "<=" in plot title

2011-06-28 Thread array chip
Thank you David and Bert. x<-3plot(1:10) title(bquote( x <= .(x) )) would do what I want. But I also want the title printed in bold font. so I tried x<-3 plot(1:10) title(bquote(bold(x <= .(x)) )) But this did not print the "less than equal to" symbol and the number 3 (from variable x) in bol

[R] Axes labels, greek letters and spaces

2011-06-28 Thread Sam Albers
Hello all, I can't seem to figure how to use a greek character in expression() in plot() labels without adding a space. So for example below when plotting this out x<-1:10 plot(x,x^2, xlab=expression(Chlorophyll~italic(a)~mu~g~cm^-2)) the axis label read as μ g cm^-2 because I have space there

Re: [R] Loop through each subject

2011-06-28 Thread David Winsemius
On Jun 28, 2011, at 1:44 PM, Edward Patzelt wrote: R help - I am attempting to write a script that has multiple subjects in 1 data file. Each subject has multiple rows with columns as variables. Here is my code, I am having problem executing it on each unique subject id (dat $Subject).

Re: [R] chull increase number of points

2011-06-28 Thread Ben Bolker
nevill.uk.net> writes: > I am using the chull function to create a convex hull of a series of about > 20,000 data points. You already posted this statement (not a question). One more try? (You might as well read the posting guide while you're at it -- please refrain from sending your e-mai

Re: [R] how to print "<=" in plot title

2011-06-28 Thread David Winsemius
On Jun 28, 2011, at 2:19 PM, array chip wrote: Thank you David and Bert. x<-3plot(1:10) title(bquote( x <= .(x) )) would do what I want. But I also want the title printed in bold font. so I tried x<-3 plot(1:10) title(bquote(bold(x <= .(x)) )) But this did not print the "less than equal

Re: [R] Axes labels, greek letters and spaces

2011-06-28 Thread David Winsemius
The * operator can be used for a non-space separation. expression(Chlorophyll*italic(a)~mu*g~cm^-2) -- David. On Jun 28, 2011, at 2:21 PM, Sam Albers wrote: Hello all, I can't seem to figure how to use a greek character in expression() in plot() labels without adding a space. So for examp

Re: [R] Error in library (nls)

2011-06-28 Thread Ben Bolker
matotope gmail.com> writes: > I installed the 2.8.0 version and it seems to be working fine now. Hard to see from a brief glance at the code why it would not work in 2.13.0 as well, but glad you got the problem solved. If you will need to maintain and extend this code in the future it may be

Re: [R] cumulative incidence plot vs survival plot

2011-06-28 Thread alanm (Alan Mitchell)
>So in cuminc() function, the argument "fstatus" should be coded like: 0=censored, 1=event of interest, 2=event of competing risk. Then the function will calculate CI for each of the 2 types of events >(event of interest and event of competing risk), am I correct? Correct. >What about running regu

Re: [R] coxph() - unexpected result using Crawley's seedlings data (The R Book)

2011-06-28 Thread Ben Bolker
Jacob Brogren brogren.nu> writes: > > All, > > I rerun once again and managed to reproduce the results from the text book. > Made no changes to the code. Could > it be some problem with convergence? It is possible, but *extremely* unlikely, to get non-deterministic results from R (i.e. runn

Re: [R] how to print "<=" in plot title

2011-06-28 Thread array chip
David, I tried your suggestion, still not working: x<-3 plot(1:10) title(bquote(bold(x) <= bold(as.character(.(x)) ))) It prints x<=as.character(3) as title Thanks John - Original Message From: David Winsemius To: array chip Cc: Peter Ehlers ; R Sent: Tue, June 28, 2011 11:30:2

Re: [R] cumulative incidence plot vs survival plot

2011-06-28 Thread array chip
Thank you Alan again! Hope you could also share your thought on my another email about the coding of censoring before death.. Thanks again! John - Original Message From: alanm (Alan Mitchell) To: array chip ; David Winsemius Cc: r-help@r-project.org Sent: Tue, June 28, 2011 11:4

Re: [R] how to print "<=" in plot title

2011-06-28 Thread David Winsemius
On Jun 28, 2011, at 2:42 PM, array chip wrote: David, I tried your suggestion, still not working: x<-3 plot(1:10) title(bquote(bold(x) <= bold(as.character(.(x)) ))) It prints x<=as.character(3) as title Kids these days! No innovative spirit. Why in my day... they would be jumping with

Re: [R] Loop through each subject

2011-06-28 Thread Edward Patzelt
Huh, not sure I understand your feedback. There is only 1 file that is 1 large dataframe. I want to execute the commands on each subject in the dataframe and ouput their respective files with the subject # and file type appended (10_green.txt). How would I do this loop index? - Show quoted text

Re: [R] how to print "<=" in plot title

2011-06-28 Thread array chip
Thank you David for the obvious fix and sorry for my lacking innovative spirit, :-) Really, I know I haven't grasped the essence of plotting these math symbols in R. John - Original Message From: David Winsemius To: array chip Cc: Peter Ehlers ; R Sent: Tue, June 28, 2011 11:50:0

Re: [R] means and error bars on xyplot for binary data

2011-06-28 Thread Peter Ehlers
On 2011-06-28 00:12, Louis Plough wrote: Hi, I have binary (0,1) data for a trait as my response variable, and a dependent variable, genotype, with three classes (AA, AB, BB). I would like to plot this data so that across the three genoytpes, even though the points are all either 0 or 1, i want

Re: [R] how to print "<=" in plot title

2011-06-28 Thread David Winsemius
On Jun 28, 2011, at 2:52 PM, array chip wrote: Thank you David for the obvious fix and sorry for my lacking innovative spirit, :-) Really, I know I haven't grasped the essence of plotting these math symbols in R. A lot of people (including me) have had trouble understanding to to writ

Re: [R] R-Installation on Unix -- "Make: Don't know how to make #. Stop."

2011-06-28 Thread Ben Bolker
Zhou, Hong email.chop.edu> writes: > ./configure was run successfully on my HP-UX ia64 server with exit=0, > but when type make at prompt, get this > error "Make: Don't know how to make #. Stop." Does anyone has > any clues about this message? Thank you very much! > #make > Rmath.h is unchang

Re: [R] Loop through each subject

2011-06-28 Thread David Winsemius
On Jun 28, 2011, at 2:51 PM, Edward Patzelt wrote: Huh, not sure I understand your feedback. There is only 1 file that is 1 large dataframe. I want to execute the commands on each subject in the dataframe and ouput their respective files with the subject # and file type appended (10_gre

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