[R] boxplot colors
Hello everyone, I am trying to color two boxplots on the same graph two different colors. I have tried the following boxplot(5,1:19,5,20:39,col=c(red,blue)) but all I get are two blue boxes. Any help would be appreciated Paul [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Re move row.names column in dataframe
Hello, aa-c(1,1,2,2,3,3,4,4,5,5,6,6) bb-c(56,56,33,33,53,53,20,20,63,63,9,9) cc-data.frame(aa,bb) uniquedf - unique(cc) View(uniquedf) Why does the column row.names appear in the new dataframe and how do I get rid of it. uniquedf$row.names - NULL does not seem to work. For what I'm doing this is a useless column and can cause confusion and/or problems for subsequent merging/filtering etc. Thanks. -- View this message in context: http://www.nabble.com/Remove-row.names-column-in-dataframe-tp18050179p18050179.html Sent from the R help mailing list archive at Nabble.com. __ 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] passing arguments to a function problem
Dear R-users,
is there some way how to pass various colnames to the following code for
sorting data.frames?
mydf.ordered-with(mydf, mydf[order(colname1,colname2, colnameX, decreasing
= TRUE), ])
I was trying something like
Afunction-function (mydf,colnames,decreasing=T){
mydf.ordered-with(mydf, mydf[order(colnames, decreasing = decreasing),
])
}
but it didnt work
please help
thank you
Jiri Voller
[[alternative HTML version deleted]]
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Adding columns of Aggregates to existing dataframe
Thanks. ave() is the exact function I was after. tonyxv wrote: Hello, I have a dataframe ID1 ID2 A1B3 A1B4 A1B3 A1B3 A2B1 A2B1 A2B4 A3B2 A3B2 A5B1 A5B1 A5B6 A5B4 A6B2 I want to add extra columns to the dataframe CountID1 and CountID2 which is the actual count of values such as A1 etc ie ID1 ID2CountID1CountID2 A1B3 4 3 A1B4 4 4 A1B3 4 3 A1B3 4 3 A2B1 3 4 A2B1 3 4 A2B4 3 3 A3B2 2 3 A3B2 2 3 A5B1 4 4 A5B1 4 4 A5B6 4 1 A5B4 4 4 A6B2 1 3 I know this can be done by first creating temporary aggregate dataframes then merging with the original. Is there an easier way if i want to calculate many aggregates without having to merge many temp tables. Thanks. -- View this message in context: http://www.nabble.com/Adding-columns-of-Aggregates-to-existing-dataframe-tp18039838p18050190.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Re move row.names column in dataframe
- There is no column in the data frame called row.names. It only looks that way when you use the viewer. - All data frames must have row and column names. This is not negotiable. Also, the row.names will not interfere with any merging operation because they are not a column of the data frame: they are the row names. Bill Venables CSIRO Laboratories mailto:[EMAIL PROTECTED] http://www.cmis.csiro.au/bill.venables/ -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of tonyxv Sent: Sunday, 22 June 2008 11:15 AM To: r-help@r-project.org Subject: [R] Re move row.names column in dataframe Hello, aa-c(1,1,2,2,3,3,4,4,5,5,6,6) bb-c(56,56,33,33,53,53,20,20,63,63,9,9) cc-data.frame(aa,bb) uniquedf - unique(cc) View(uniquedf) Why does the column row.names appear in the new dataframe and how do I get rid of it. uniquedf$row.names - NULL does not seem to work. For what I'm doing this is a useless column and can cause confusion and/or problems for subsequent merging/filtering etc. Thanks. -- View this message in context: http://www.nabble.com/Remove-row.names-column-in-dataframe-tp18050179p18 050179.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] boxplot colors
You are drawing four box plots, not two. Two of them are just the number 5. The two box plots that are only 5 don't have a box, so you can't see that they're red. Try this: boxplot(1:19,20:39,col=c(red,blue)) Paul Adams-8 wrote: Hello everyone, I am trying to color two boxplots on the same graph two different colors. I have tried the following boxplot(5,1:19,5,20:39,col=c(red,blue)) but all I get are two blue boxes. Any help would be appreciated Paul [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- View this message in context: http://www.nabble.com/boxplot-colors-tp18051541p18052038.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R vs. Bugs
Your request is too vague for us to be very helpful. However OpenBUGS runs without very frequent crashes only on some ix86 Linux machines -- and what those are is unclear and Uwe Ligges and I (working on BRugs) have been unable to find one recently. There are dozens of Bayesian MCMC packages on CRAN (look at its Bayesian task view). Most are less general and faster than BUGS. There is no 'AMCMC package in R'. There is at least one third-party effort of that name, not on CRAN and explicitly claiming The R function amcmc() will tend to run rather _slowly_, (his emphasis) so perhaps that is not the one you mean. On Sun, 22 Jun 2008, Peter Muhlberg wrote: A naive question from a non-statistician: I'm looking into running a Bayesian analysis of a model with high dimensionality. It's not a standard model (the likelihood requires a lot of code to implement), 'code' in what language? Note that MCMC does *not* require the likelihood to be calculated, and its renaissance in statistics ca 30 years ago was for models for which the likelihood is not even known completely. and I'm using a Linux machine. Was wondering if someone has any thoughts on what the advantages of OpenBugs are as opposed to just R (or should I be thinking WinBUGS under Wine?)? The AMCMC package in R promises to run MCMC's very rapidly. Have read that OpenBugs as a project was 'stalling' in 2007. Peter -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ 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] I can't see plots
Hi, I use RSPerl on Ubuntu and Apache2 web server. It is my first experience with R language :-) I have the next code embedded into a Perl CGI: use R; use RReferences; my @x; R::initR(--silent,--no-save); R::library(RSPerl); @x = R::call(rnorm, 10); R::call(plot, [EMAIL PROTECTED]); The CGI works but no plot is shown. Apache2 web server log [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] No HTML package list update in 2.7.0?
Hi all, As I was uploading a couple of little fixes to prettyR, I remembered that there was a question I wanted to ask. I remember the package list being updated whenever I installed a new package (at least on Linux, oh yes, Fedora Core 9 now), but not on Windows (I just used to unzip the packages and manually update the package list). Since I have upgraded to 2.7.0, the HTML package list isn't updated. I couldn't find anything about this in the install stuff for the new features (what is a tangled vignette anyway?). Is this just something that has slipped beneath the legendary radar of the team? Am I really the first to notice this? Jim __ 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] I can't see plots
Hi, I am using RSPerl package on Ubuntu and Apache2 web server. It is my first experience with R language :-) I have the next code embedded into a Perl CGI: use R; use RReferences; my @x; R::initR(--silent,--no-save); R::library(RSPerl); @x = R::call(rnorm, 10); R::call(plot, [EMAIL PROTECTED]); The CGI works but no plot is shown. Apache2 web server log says: [Sun Jun 22 12:01:41 2008] [error] [client 127.0.0.1] Error in pdf() : unable to start device pdf, referer: http://localhost/html/proveta.html [Sun Jun 22 12:01:41 2008] [error] [client 127.0.0.1] In addition: Warning message:, referer: http://localhost/html/proveta.html [Sun Jun 22 12:01:41 2008] [error] [client 127.0.0.1] In pdf() : cannot open 'pdf' file argument 'Rplots.pdf', referer: http://localhost/html/proveta.html [Sun Jun 22 12:01:41 2008] [error] [client 127.0.0.1] Caught error in R::call(), referer: http://localhost/html/proveta.html However, if I use R directly plots are correctly shown. Can anybody help me? Thanks! Josep Lluís Figueras (from Barcelona) [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] passing arguments to a function problem
See orderBy in the doBy package.
On Sat, Jun 21, 2008 at 7:58 PM, Jiří Voller [EMAIL PROTECTED] wrote:
Dear R-users,
is there some way how to pass various colnames to the following code for
sorting data.frames?
mydf.ordered-with(mydf, mydf[order(colname1,colname2, colnameX, decreasing
= TRUE), ])
I was trying something like
Afunction-function (mydf,colnames,decreasing=T){
mydf.ordered-with(mydf, mydf[order(colnames, decreasing = decreasing),
])
}
but it didnt work
please help
thank you
Jiri Voller
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] No HTML package list update in 2.7.0?
See https://bugzilla.redhat.com/show_bug.cgi?id=442727 Right now I seem to be using /usr/share/doc/R-2.7.0/html to get the list (on finzi.psych.upenn.edu) On 06/22/08 20:43, Jim Lemon wrote: Hi all, As I was uploading a couple of little fixes to prettyR, I remembered that there was a question I wanted to ask. I remember the package list being updated whenever I installed a new package (at least on Linux, oh yes, Fedora Core 9 now), but not on Windows (I just used to unzip the packages and manually update the package list). Since I have upgraded to 2.7.0, the HTML package list isn't updated. I couldn't find anything about this in the install stuff for the new features (what is a tangled vignette anyway?). Is this just something that has slipped beneath the legendary radar of the team? Am I really the first to notice this? Jim -- Jonathan Baron, Professor of Psychology, University of Pennsylvania Home page: http://www.sas.upenn.edu/~baron __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Coloring Stripchart Points, or Better, Lattice Equivalent
Below is a revised set of code that demonstrates my question a little more clearly, I hope. When plotting all the data (5th panel), col sym don't seem to be passed correctly, as the (random) first value for col sym are used for all points (run the code, then run it again, you'll see how the 5th panel changes depending upon col sym for the first data point). The 5th panel should ideally be the sum of the 4 panels above, keeping col sym intact. Also, I would rather have this in lattice or ggplot2, if anyone sees how to convert it. Thanks once again, several of you have made very useful suggestions off list. Bryan samples - 100 # must be even index - round(runif(samples, 1, 100)) # set up data resp - rbinom(samples, 1, 0.5) yr - rep(c(2005, 2006), samples/2) all - data.frame(index, resp, yr) all$sym - ifelse(all$resp == 1, 1, 3) all$col - ifelse(all$yr == 2005, red, blue) all$count - rep(1, length(all$index)) all - all[order(all$index, all$yr, all$resp),] # for easier inspection row.names(all) - c(1:samples) # for easier inspection one - all[(all$yr == 2005 all$resp == 0),] # First 2005/0 at top two - all[(all$yr == 2005 all$resp == 1),] # Then 2005/1 three - all[(all$yr == 2006 all$resp == 0),] # Now 2006/0 four - all[(all$yr == 2006 all$resp == 1),] # Finally 2006/1 par(mfrow = c(5, 1)) par(plt = c(0.1, 0.9, 0.25, 0.75)) stripchart(one$index, method = stack, ylim = c(0,10), xlim = c(1,100), col = one$col, pch = one$sym) mtext(2005/0, side = 3) stripchart(two$index, method = stack, ylim = c(0,10), xlim = c(1,100), col = two$col, pch = two$sym) mtext(2005/1, side = 3) stripchart(three$index, method = stack, ylim = c(0,10), xlim = c(1,100), col = three$col, pch = three$sym) mtext(2006/0, side = 3) stripchart(four$index, method = stack, ylim = c(0,10), xlim = c(1,100), col = four$col, pch = four$sym) mtext(2006/1, side = 3) stripchart(all$index, method = stack, ylim = c(0,10), xlim = c(1,100), col = all$col, pch = all$sym) mtext(col sym always taken from 1st data point when all data is plotted!, side = 3) __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] I can't see plots
Josep Lluís Figueras wrote: Hi, I am using RSPerl package on Ubuntu and Apache2 web server. It is my first experience with R language :-) I have the next code embedded into a Perl CGI: use R; use RReferences; my @x; R::initR(--silent,--no-save); R::library(RSPerl); @x = R::call(rnorm, 10); R::call(plot, [EMAIL PROTECTED]); The CGI works but no plot is shown. Apache2 web server log says: [Sun Jun 22 12:01:41 2008] [error] [client 127.0.0.1] Error in pdf() : unable to start device pdf, referer: http://localhost/html/proveta.html [Sun Jun 22 12:01:41 2008] [error] [client 127.0.0.1] In addition: Warning message:, referer: http://localhost/html/proveta.html [Sun Jun 22 12:01:41 2008] [error] [client 127.0.0.1] In pdf() : cannot open 'pdf' file argument 'Rplots.pdf', referer: http://localhost/html/proveta.html [Sun Jun 22 12:01:41 2008] [error] [client 127.0.0.1] Caught error in R::call(), referer: http://localhost/html/proveta.html However, if I use R directly plots are correctly shown. Because you aren't running R interactively, it's trying to open a pdf device. This is failing (file permissions maybe?). You should probably specify exactly what device to open, and if it's something that writes a file, where to write it. Duncan Murdoch Can anybody help me? Thanks! Josep Lluís Figueras (from Barcelona) [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] I can't see plots
Hi there, try to open a graphic device with x11(), may be. cheers, miltinho On 6/22/08, Josep Lluís Figueras [EMAIL PROTECTED] wrote: Hi, I am using RSPerl package on Ubuntu and Apache2 web server. It is my first experience with R language :-) I have the next code embedded into a Perl CGI: use R; use RReferences; my @x; R::initR(--silent,--no-save); R::library(RSPerl); @x = R::call(rnorm, 10); R::call(plot, [EMAIL PROTECTED]); The CGI works but no plot is shown. Apache2 web server log says: [Sun Jun 22 12:01:41 2008] [error] [client 127.0.0.1] Error in pdf() : unable to start device pdf, referer: http://localhost/html/proveta.html [Sun Jun 22 12:01:41 2008] [error] [client 127.0.0.1] In addition: Warning message:, referer: http://localhost/html/proveta.html [Sun Jun 22 12:01:41 2008] [error] [client 127.0.0.1] In pdf() : cannot open 'pdf' file argument 'Rplots.pdf', referer: http://localhost/html/proveta.html [Sun Jun 22 12:01:41 2008] [error] [client 127.0.0.1] Caught error in R::call(), referer: http://localhost/html/proveta.html However, if I use R directly plots are correctly shown. Can anybody help me? Thanks! Josep Lluís Figueras (from Barcelona) [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] I can't see plots
Maybe this help you http://www.rforge.net/Cairo/index.html http://www.rosuda.org/R/GDD/ daniel cegielka -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of milton ruser Sent: Sunday, June 22, 2008 5:56 PM To: Josep Lluís Figueras Cc: r-help@r-project.org Subject: Re: [R] I can't see plots Hi there, try to open a graphic device with x11(), may be. cheers, miltinho On 6/22/08, Josep Llums Figueras [EMAIL PROTECTED] wrote: Hi, I am using RSPerl package on Ubuntu and Apache2 web server. It is my first experience with R language :-) I have the next code embedded into a Perl CGI: use R; use RReferences; my @x; R::initR(--silent,--no-save); R::library(RSPerl); @x = R::call(rnorm, 10); R::call(plot, [EMAIL PROTECTED]); The CGI works but no plot is shown. Apache2 web server log says: [Sun Jun 22 12:01:41 2008] [error] [client 127.0.0.1] Error in pdf() : unable to start device pdf, referer: http://localhost/html/proveta.html [Sun Jun 22 12:01:41 2008] [error] [client 127.0.0.1] In addition: Warning message:, referer: http://localhost/html/proveta.html [Sun Jun 22 12:01:41 2008] [error] [client 127.0.0.1] In pdf() : cannot open 'pdf' file argument 'Rplots.pdf', referer: http://localhost/html/proveta.html [Sun Jun 22 12:01:41 2008] [error] [client 127.0.0.1] Caught error in R::call(), referer: http://localhost/html/proveta.html However, if I use R directly plots are correctly shown. Can anybody help me? Thanks! Josep Llums Figueras (from Barcelona) [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Coloring Stripchart Points, or Better, Lattice Equivalent
Try this: library(lattice) all$resp - as.factor(all$resp) stripplot(~ index | resp * yr, all, col = all$col, pch = all$sym, layout = c(1, 4)) On Sun, Jun 22, 2008 at 10:43 AM, Bryan Hanson [EMAIL PROTECTED] wrote: Below is a revised set of code that demonstrates my question a little more clearly, I hope. When plotting all the data (5th panel), col sym don't seem to be passed correctly, as the (random) first value for col sym are used for all points (run the code, then run it again, you'll see how the 5th panel changes depending upon col sym for the first data point). The 5th panel should ideally be the sum of the 4 panels above, keeping col sym intact. Also, I would rather have this in lattice or ggplot2, if anyone sees how to convert it. Thanks once again, several of you have made very useful suggestions off list. Bryan samples - 100 # must be even index - round(runif(samples, 1, 100)) # set up data resp - rbinom(samples, 1, 0.5) yr - rep(c(2005, 2006), samples/2) all - data.frame(index, resp, yr) all$sym - ifelse(all$resp == 1, 1, 3) all$col - ifelse(all$yr == 2005, red, blue) all$count - rep(1, length(all$index)) all - all[order(all$index, all$yr, all$resp),] # for easier inspection row.names(all) - c(1:samples) # for easier inspection one - all[(all$yr == 2005 all$resp == 0),] # First 2005/0 at top two - all[(all$yr == 2005 all$resp == 1),] # Then 2005/1 three - all[(all$yr == 2006 all$resp == 0),] # Now 2006/0 four - all[(all$yr == 2006 all$resp == 1),] # Finally 2006/1 par(mfrow = c(5, 1)) par(plt = c(0.1, 0.9, 0.25, 0.75)) stripchart(one$index, method = stack, ylim = c(0,10), xlim = c(1,100), col = one$col, pch = one$sym) mtext(2005/0, side = 3) stripchart(two$index, method = stack, ylim = c(0,10), xlim = c(1,100), col = two$col, pch = two$sym) mtext(2005/1, side = 3) stripchart(three$index, method = stack, ylim = c(0,10), xlim = c(1,100), col = three$col, pch = three$sym) mtext(2006/0, side = 3) stripchart(four$index, method = stack, ylim = c(0,10), xlim = c(1,100), col = four$col, pch = four$sym) mtext(2006/1, side = 3) stripchart(all$index, method = stack, ylim = c(0,10), xlim = c(1,100), col = all$col, pch = all$sym) mtext(col sym always taken from 1st data point when all data is plotted!, side = 3) __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R vs. Bugs
I've done some looking around in R and elsewhere to answer my question on the value of R vs. Bugs for MCMC. So, for anyone who is curious, here's what I think I've found: Bugs compiles its code, which should make it much faster than a pure R program. Packages such as AMCMC run MCMC in R, potentially with a user-defined C function for the density--which should make it comparable in speed to Bugs. The packages MCMCpack (MCMCmetrop1R function) and mcmc seem designed to run w/ a density function written in R. MCMCpack does have functions that use precompiled C code from the Scythe library (which looks nice), but I see no simple way to add a C density function. AMCMC and Bugs seem to use adaptive MCMC, but the other R packages don't appear to do so, which may mean another performance reduction. I see no way to insert my own proposal density in the R functions. JAG, a Java-based version of BUGS, apparently allows users to create their own samplers, which might be a way to insert a different proposal density. Details about how to install a sampler are not given in the manual, which, incidentally, is nevertheless much better than the Bugs manual. Also, the proposal density I'd want would probably treat different variables differently, so I may need Metropolis within Gibbs, not standard Gibbs sampling. Can't get a clear picture of what JAG's algorithm(s) are--the manual doesn't mention Metropolis. WinBugs and OpenBugs can't be made to run easily on Linux. It looks like WinBugs running under WINE might be the simplest viable configuration, though I don't know how well or quickly it runs under WINE or how much memory WINE ends up consuming. Given all this, it may be easiest for my purposes to try to tweak the AMCMC code to allow a different proposal density. Maybe. Peter __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Coloring Stripchart Points, or Better, Lattice Equivalent
Thanks Gabor, I'm getting closer. Is there a way to spread out resp values vertically for a given value of index? In base graphics, stripchart does this with method = stack. But in lattice, stack = TRUE does something rather different, and I don't see a combination of lattice arguments that does it like base graphics. Thanks, Bryan On 6/22/08 12:48 PM, Gabor Grothendieck [EMAIL PROTECTED] wrote: Actually I am not sure if my prior answer was correct. I think its ok with one panel but you might have to use a panel function is there are several. With one panel it seems ok: stripplot(~ index, all, col = all$col, pch = all$sym) On Sun, Jun 22, 2008 at 12:28 PM, Gabor Grothendieck [EMAIL PROTECTED] wrote: Try this: library(lattice) all$resp - as.factor(all$resp) stripplot(~ index | resp * yr, all, col = all$col, pch = all$sym, layout = c(1, 4)) On Sun, Jun 22, 2008 at 10:43 AM, Bryan Hanson [EMAIL PROTECTED] wrote: Below is a revised set of code that demonstrates my question a little more clearly, I hope. When plotting all the data (5th panel), col sym don't seem to be passed correctly, as the (random) first value for col sym are used for all points (run the code, then run it again, you'll see how the 5th panel changes depending upon col sym for the first data point). The 5th panel should ideally be the sum of the 4 panels above, keeping col sym intact. Also, I would rather have this in lattice or ggplot2, if anyone sees how to convert it. Thanks once again, several of you have made very useful suggestions off list. Bryan samples - 100 # must be even index - round(runif(samples, 1, 100)) # set up data resp - rbinom(samples, 1, 0.5) yr - rep(c(2005, 2006), samples/2) all - data.frame(index, resp, yr) all$sym - ifelse(all$resp == 1, 1, 3) all$col - ifelse(all$yr == 2005, red, blue) all$count - rep(1, length(all$index)) all - all[order(all$index, all$yr, all$resp),] # for easier inspection row.names(all) - c(1:samples) # for easier inspection one - all[(all$yr == 2005 all$resp == 0),] # First 2005/0 at top two - all[(all$yr == 2005 all$resp == 1),] # Then 2005/1 three - all[(all$yr == 2006 all$resp == 0),] # Now 2006/0 four - all[(all$yr == 2006 all$resp == 1),] # Finally 2006/1 par(mfrow = c(5, 1)) par(plt = c(0.1, 0.9, 0.25, 0.75)) stripchart(one$index, method = stack, ylim = c(0,10), xlim = c(1,100), col = one$col, pch = one$sym) mtext(2005/0, side = 3) stripchart(two$index, method = stack, ylim = c(0,10), xlim = c(1,100), col = two$col, pch = two$sym) mtext(2005/1, side = 3) stripchart(three$index, method = stack, ylim = c(0,10), xlim = c(1,100), col = three$col, pch = three$sym) mtext(2006/0, side = 3) stripchart(four$index, method = stack, ylim = c(0,10), xlim = c(1,100), col = four$col, pch = four$sym) mtext(2006/1, side = 3) stripchart(all$index, method = stack, ylim = c(0,10), xlim = c(1,100), col = all$col, pch = all$sym) mtext(col sym always taken from 1st data point when all data is plotted!, side = 3) __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Redefining the for loop
Hi,
I have the following problem:
I want to redefine the for loop (or define a similar statement) to change its
behavior under some circumstances. So, I would like sthg. like
For = function ( var, vec, statement ) {
if ( ... ) {
/* my implementation of for */
}
else {
/* call R's for loop */
}
}
I tried to manipulate the elements of the list one gets by
e = quote( for ( i in (1:10) ) print(*) )
That means, storing the variable in e[[2]] (my trials didn't work), and the
statement in e[[4]], but I failed.
How can one do this in R? It would be best, if I could redefine for directly,
so that one can use the same syntax, i.e., with the statement after the
function call.
Can somebody help me?
Thanks!
{
--
Jetzt dabei sein: http://www.shortview.de/[EMAIL PROTECTED]
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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[R] readLines problem in iteration
Hi there
My script at each iteration produces a .dat file which I save in a directory
with write.table. Then I need to read each line of this file and create a
directory for each line and put elements of that row in that directory. I do it
with the following script which I have inserted somewhere between my outer
iteration loop, it works fine for the first iteration, but the problem is that
it does nothing at next iterations. How can I solve this problem, is there
anything wrong with my code?
Thanks in advance for your help.
write.table(X, file = model.dat, append = FALSE, sep = , eol = \n,
na = NA, dec = ., row.names = FALSE, col.names = FALSE, qmethod =
c(escape, double))
mother-getwd()
count - 0;
con- file(model.dat, open=r)
while (length(line) 0) {
line-readLines(con,n=1)
count - count +1
cat(read row no, count, ,\n, sep=);
print(line)
foldername - paste(Iteration,c, ant, count)
dir.create (foldername)
setwd(foldername)
write.table(line, file = params.in, append = FALSE, sep = , eol = \n,
na = NA, dec = ., row.names = FALSE, col.names = FALSE, qmethod =
c(escape, double))
#system(run_misf_calc.py)
setwd(mother)
}
close(con)
[[alternative HTML version deleted]]
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Coloring Stripchart Points, or Better, Lattice Equivalent
I tried it with a simple example to make it easier to check the result and it does seem we need a panel function, pnl: library(lattice) DF - data.frame(x = 1:5, col = c(1:4, 1), g = c(1, 1, 2, 2, 2), pch = c(1:3, 2:1)) pnl - function(x, y, subscripts, col, pch, ...) panel.stripplot(x, y, col = col[subscripts], pch = pch[subscripts], ...) stripplot(~ x | g, DF, col = DF$col, pch = DF$pch, panel = pnl) Using the same panel function, pnl, we can spread out resp into two different panels like this: all$resp - as.factor(all$resp) # as before stripplot(~ index | resp, all, col = all$col, pch = all$sym, panel = pnl, layout = 1:2) On Sun, Jun 22, 2008 at 1:09 PM, Bryan Hanson [EMAIL PROTECTED] wrote: Thanks Gabor, I'm getting closer. Is there a way to spread out resp values vertically for a given value of index? In base graphics, stripchart does this with method = stack. But in lattice, stack = TRUE does something rather different, and I don't see a combination of lattice arguments that does it like base graphics. Thanks, Bryan On 6/22/08 12:48 PM, Gabor Grothendieck [EMAIL PROTECTED] wrote: Actually I am not sure if my prior answer was correct. I think its ok with one panel but you might have to use a panel function is there are several. With one panel it seems ok: stripplot(~ index, all, col = all$col, pch = all$sym) On Sun, Jun 22, 2008 at 12:28 PM, Gabor Grothendieck [EMAIL PROTECTED] wrote: Try this: library(lattice) all$resp - as.factor(all$resp) stripplot(~ index | resp * yr, all, col = all$col, pch = all$sym, layout = c(1, 4)) On Sun, Jun 22, 2008 at 10:43 AM, Bryan Hanson [EMAIL PROTECTED] wrote: Below is a revised set of code that demonstrates my question a little more clearly, I hope. When plotting all the data (5th panel), col sym don't seem to be passed correctly, as the (random) first value for col sym are used for all points (run the code, then run it again, you'll see how the 5th panel changes depending upon col sym for the first data point). The 5th panel should ideally be the sum of the 4 panels above, keeping col sym intact. Also, I would rather have this in lattice or ggplot2, if anyone sees how to convert it. Thanks once again, several of you have made very useful suggestions off list. Bryan samples - 100 # must be even index - round(runif(samples, 1, 100)) # set up data resp - rbinom(samples, 1, 0.5) yr - rep(c(2005, 2006), samples/2) all - data.frame(index, resp, yr) all$sym - ifelse(all$resp == 1, 1, 3) all$col - ifelse(all$yr == 2005, red, blue) all$count - rep(1, length(all$index)) all - all[order(all$index, all$yr, all$resp),] # for easier inspection row.names(all) - c(1:samples) # for easier inspection one - all[(all$yr == 2005 all$resp == 0),] # First 2005/0 at top two - all[(all$yr == 2005 all$resp == 1),] # Then 2005/1 three - all[(all$yr == 2006 all$resp == 0),] # Now 2006/0 four - all[(all$yr == 2006 all$resp == 1),] # Finally 2006/1 par(mfrow = c(5, 1)) par(plt = c(0.1, 0.9, 0.25, 0.75)) stripchart(one$index, method = stack, ylim = c(0,10), xlim = c(1,100), col = one$col, pch = one$sym) mtext(2005/0, side = 3) stripchart(two$index, method = stack, ylim = c(0,10), xlim = c(1,100), col = two$col, pch = two$sym) mtext(2005/1, side = 3) stripchart(three$index, method = stack, ylim = c(0,10), xlim = c(1,100), col = three$col, pch = three$sym) mtext(2006/0, side = 3) stripchart(four$index, method = stack, ylim = c(0,10), xlim = c(1,100), col = four$col, pch = four$sym) mtext(2006/1, side = 3) stripchart(all$index, method = stack, ylim = c(0,10), xlim = c(1,100), col = all$col, pch = all$sym) mtext(col sym always taken from 1st data point when all data is plotted!, side = 3) __ 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] two newbie questions
# I've tried to make this easy to paste into R, though it's probably
so simple you won't need to.
# I have some data (there are many more variables, but this is a
reasonable approximation of it)
# here's a fabricated data frame that is similar in form to mine:
my.df - data.frame(replicate(10, round(rnorm(100, mean=3.5, sd=1
var.list - c(dv1, dv2, dv3, iv1, iv2, iv3, iv4, iv5,
intv1, intv2)
names(my.df) - var.list
# I have some are DVs:
dvs - c(dv1, dv2, dv3)
# some IVs:
ivs - c(iv1, iv2, iv3, iv4, iv5)
# and some binary interaction variables:
intvs - c(intv1, intv2)
library(car)
my.df[intvs] - lapply(my.df[intvs], function(x)
recode(x, recodes = lo:3.5=0; 3.5:hi=1; ,as.factor.result = FALSE))
# now I loop through a series of interactions using the vector numbers:
for(dv in 1:3) {
for(iv in 4:8) {
for (intv in 9:10) {
jpeg(paste(names(my.df[iv]), names(my.df[dv]), names(my.df[intv]),
.jpg, sep=_))
with(data.frame(my.df), {
my.fit - lm( my.df[[dv]] ~ my.df[[iv]] + my.df[[intv]] +
my.df[[iv]]:my.df[[intv]])
colors - ifelse (my.df[[intv]] == 1, black, grey)
plot(my.df[[iv]], my.df[[dv]], xlab=names(my.df[iv]),
ylab=names(my.df[dv]), col=colors, pch=.)
curve (cbind (1, 1, x, 1*x) %*% coef(my.fit), add=TRUE, col=black)
curve (cbind (1, 0, x, 0*x) %*% coef(my.fit), add=TRUE, col=gray)
})
dev.off()
}
}
}
# Question1: Works fine, but using the vector numbers feels kludgy --
especially if the variables in question aren't consecutive.
# Is there a more elegant way of doing this with my lists of variable
names? Something like this, for example:
for(dv in dvs) {
for(iv in ivs) {
for (intv in intvs) {
jpeg(paste(dv, iv, intv, .jpg, sep=_))
with(data.frame(my.df), {
my.fit - lm(my.df[dv] ~ my.df[iv] + my.df[intv] + my.df[iv]:my.df[intv])
colors - ifelse (my.df[[intv]] == 1, black, grey)
plot(my.df[iv], my.df[dv], xlab=iv, ylab=names(dv), col=colors, pch=.)
curve (cbind (1, 1, x, 1*x) %*% coef(my.fit), add=TRUE, col=black)
curve (cbind (1, 0, x, 0*x) %*% coef(my.fit), add=TRUE, col=gray)
})
dev.off()
}
}
}
# Clearly that's wrong -- why it's wrong is obscure to me, though!
Please educate me!
# Question2: Could this could be done by using apply rather than a loop?
# Or is looping better here bc there are several actions performed at
each iteration?
# I'm still trying to get my head around all the ways to ditch looping in R.
Donald Braman
http://www.law.gwu.edu/Faculty/profile.aspx?id=10123
http://research.yale.edu/culturalcognition
http://ssrn.com/author=286206
__
R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] two newbie questions
This does away with the 'for' loops and uses 'expand.grid' to create
the combinations. I think I got the right variables substituted:
my.df - data.frame(replicate(10, round(rnorm(100, mean=3.5, sd=1
var.list - c(dv1, dv2, dv3, iv1, iv2, iv3, iv4, iv5,
intv1, intv2)
names(my.df) - var.list
# I have some are DVs:
dvs - c(dv1, dv2, dv3)
# some IVs:
ivs - c(iv1, iv2, iv3, iv4, iv5)
# and some binary interaction variables:
intvs - c(intv1, intv2)
library(car)
my.df[intvs] - lapply(my.df[intvs], function(x)
recode(x, recodes = lo:3.5=0; 3.5:hi=1; ,as.factor.result = FALSE))
# now I loop through a series of interactions using the vector numbers:
# create a dataframe of values to check
xpnd - expand.grid(dvs, ivs, intvs) # create combinations
invisible(apply(xpnd, 1, function(.row) {
jpeg(paste(paste(.row, collapse=_),.jpg, sep=''))
my.fit - lm( my.df[[.row[1]]] ~ my.df[[.row[2]]] + my.df[[.row[3]]] +
my.df[[.row[2]]]:my.df[[.row[3]]])
colors - ifelse (my.df[[.row[3]]] == 1, black, grey)
plot(my.df[[.row[2]]], my.df[[.row[1]]], xlab=.row[2],
ylab=.row[1], col=colors, pch=.)
curve (cbind (1, 1, x, 1*x) %*% coef(my.fit), add=TRUE, col=black)
curve (cbind (1, 0, x, 0*x) %*% coef(my.fit), add=TRUE, col=gray)
dev.off()
}
))
On Sun, Jun 22, 2008 at 6:26 PM, Donald Braman [EMAIL PROTECTED] wrote:
# I've tried to make this easy to paste into R, though it's probably
so simple you won't need to.
# I have some data (there are many more variables, but this is a
reasonable approximation of it)
# here's a fabricated data frame that is similar in form to mine:
my.df - data.frame(replicate(10, round(rnorm(100, mean=3.5, sd=1
var.list - c(dv1, dv2, dv3, iv1, iv2, iv3, iv4, iv5,
intv1, intv2)
names(my.df) - var.list
# I have some are DVs:
dvs - c(dv1, dv2, dv3)
# some IVs:
ivs - c(iv1, iv2, iv3, iv4, iv5)
# and some binary interaction variables:
intvs - c(intv1, intv2)
library(car)
my.df[intvs] - lapply(my.df[intvs], function(x)
recode(x, recodes = lo:3.5=0; 3.5:hi=1; ,as.factor.result = FALSE))
# now I loop through a series of interactions using the vector numbers:
for(dv in 1:3) {
for(iv in 4:8) {
for (intv in 9:10) {
jpeg(paste(names(my.df[iv]), names(my.df[dv]), names(my.df[intv]),
.jpg, sep=_))
with(data.frame(my.df), {
my.fit - lm( my.df[[dv]] ~ my.df[[iv]] + my.df[[intv]] +
my.df[[iv]]:my.df[[intv]])
colors - ifelse (my.df[[intv]] == 1, black, grey)
plot(my.df[[iv]], my.df[[dv]], xlab=names(my.df[iv]),
ylab=names(my.df[dv]), col=colors, pch=.)
curve (cbind (1, 1, x, 1*x) %*% coef(my.fit), add=TRUE, col=black)
curve (cbind (1, 0, x, 0*x) %*% coef(my.fit), add=TRUE, col=gray)
})
dev.off()
}
}
}
# Question1: Works fine, but using the vector numbers feels kludgy --
especially if the variables in question aren't consecutive.
# Is there a more elegant way of doing this with my lists of variable
names? Something like this, for example:
for(dv in dvs) {
for(iv in ivs) {
for (intv in intvs) {
jpeg(paste(dv, iv, intv, .jpg, sep=_))
with(data.frame(my.df), {
my.fit - lm(my.df[dv] ~ my.df[iv] + my.df[intv] + my.df[iv]:my.df[intv])
colors - ifelse (my.df[[intv]] == 1, black, grey)
plot(my.df[iv], my.df[dv], xlab=iv, ylab=names(dv), col=colors, pch=.)
curve (cbind (1, 1, x, 1*x) %*% coef(my.fit), add=TRUE, col=black)
curve (cbind (1, 0, x, 0*x) %*% coef(my.fit), add=TRUE, col=gray)
})
dev.off()
}
}
}
# Clearly that's wrong -- why it's wrong is obscure to me, though!
Please educate me!
# Question2: Could this could be done by using apply rather than a loop?
# Or is looping better here bc there are several actions performed at
each iteration?
# I'm still trying to get my head around all the ways to ditch looping in R.
Donald Braman
http://www.law.gwu.edu/Faculty/profile.aspx?id=10123
http://research.yale.edu/culturalcognition
http://ssrn.com/author=286206
__
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.
--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem you are trying to solve?
__
R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] readLines problem in iteration
What is the value of 'line' on the first iteration? It appears to be
undefined. You probably want something like this:
while (TRUE){
line - readLines(con, n=1)
if (length(line) == 0) break
.your normal statements.
}
On Sun, Jun 22, 2008 at 3:29 PM, Yasin Hajizadeh
[EMAIL PROTECTED] wrote:
Hi there
My script at each iteration produces a .dat file which I save in a directory
with write.table. Then I need to read each line of this file and create a
directory for each line and put elements of that row in that directory. I do
it with the following script which I have inserted somewhere between my outer
iteration loop, it works fine for the first iteration, but the problem is
that it does nothing at next iterations. How can I solve this problem, is
there anything wrong with my code?
Thanks in advance for your help.
write.table(X, file = model.dat, append = FALSE, sep = , eol = \n,
na = NA, dec = ., row.names = FALSE, col.names = FALSE, qmethod =
c(escape, double))
mother-getwd()
count - 0;
con- file(model.dat, open=r)
while (length(line) 0) {
line-readLines(con,n=1)
count - count +1
cat(read row no, count, ,\n, sep=);
print(line)
foldername - paste(Iteration,c, ant, count)
dir.create (foldername)
setwd(foldername)
write.table(line, file = params.in, append = FALSE, sep = , eol = \n,
na = NA, dec = ., row.names = FALSE, col.names = FALSE, qmethod =
c(escape, double))
#system(run_misf_calc.py)
setwd(mother)
}
close(con)
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem you are trying to solve?
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] two newbie questions
Wow -- many thanks for the mind-*expanding* help! I'm really impressed by
R's ability to handle this so concisely It's going to take me a while to
get used to applying things to vectors, but the more I understand, the nicer
R looks.
On Sun, Jun 22, 2008 at 6:59 PM, jim holtman [EMAIL PROTECTED] wrote:
This does away with the 'for' loops and uses 'expand.grid' to create
the combinations. I think I got the right variables substituted:
my.df - data.frame(replicate(10, round(rnorm(100, mean=3.5, sd=1
var.list - c(dv1, dv2, dv3, iv1, iv2, iv3, iv4, iv5,
intv1, intv2)
names(my.df) - var.list
# I have some are DVs:
dvs - c(dv1, dv2, dv3)
# some IVs:
ivs - c(iv1, iv2, iv3, iv4, iv5)
# and some binary interaction variables:
intvs - c(intv1, intv2)
library(car)
my.df[intvs] - lapply(my.df[intvs], function(x)
recode(x, recodes = lo:3.5=0; 3.5:hi=1; ,as.factor.result = FALSE))
# now I loop through a series of interactions using the vector numbers:
# create a dataframe of values to check
xpnd - expand.grid(dvs, ivs, intvs) # create combinations
invisible(apply(xpnd, 1, function(.row) {
jpeg(paste(paste(.row, collapse=_),.jpg, sep=''))
my.fit - lm( my.df[[.row[1]]] ~ my.df[[.row[2]]] + my.df[[.row[3]]] +
my.df[[.row[2]]]:my.df[[.row[3]]])
colors - ifelse (my.df[[.row[3]]] == 1, black, grey)
plot(my.df[[.row[2]]], my.df[[.row[1]]], xlab=.row[2],
ylab=.row[1], col=colors, pch=.)
curve (cbind (1, 1, x, 1*x) %*% coef(my.fit), add=TRUE, col=black)
curve (cbind (1, 0, x, 0*x) %*% coef(my.fit), add=TRUE, col=gray)
dev.off()
}
))
On Sun, Jun 22, 2008 at 6:26 PM, Donald Braman [EMAIL PROTECTED]
wrote:
# I've tried to make this easy to paste into R, though it's probably
so simple you won't need to.
# I have some data (there are many more variables, but this is a
reasonable approximation of it)
# here's a fabricated data frame that is similar in form to mine:
my.df - data.frame(replicate(10, round(rnorm(100, mean=3.5, sd=1
var.list - c(dv1, dv2, dv3, iv1, iv2, iv3, iv4, iv5,
intv1, intv2)
names(my.df) - var.list
# I have some are DVs:
dvs - c(dv1, dv2, dv3)
# some IVs:
ivs - c(iv1, iv2, iv3, iv4, iv5)
# and some binary interaction variables:
intvs - c(intv1, intv2)
library(car)
my.df[intvs] - lapply(my.df[intvs], function(x)
recode(x, recodes = lo:3.5=0; 3.5:hi=1; ,as.factor.result = FALSE))
# now I loop through a series of interactions using the vector numbers:
for(dv in 1:3) {
for(iv in 4:8) {
for (intv in 9:10) {
jpeg(paste(names(my.df[iv]), names(my.df[dv]), names(my.df[intv]),
.jpg, sep=_))
with(data.frame(my.df), {
my.fit - lm( my.df[[dv]] ~ my.df[[iv]] + my.df[[intv]] +
my.df[[iv]]:my.df[[intv]])
colors - ifelse (my.df[[intv]] == 1, black, grey)
plot(my.df[[iv]], my.df[[dv]], xlab=names(my.df[iv]),
ylab=names(my.df[dv]), col=colors, pch=.)
curve (cbind (1, 1, x, 1*x) %*% coef(my.fit), add=TRUE, col=black)
curve (cbind (1, 0, x, 0*x) %*% coef(my.fit), add=TRUE, col=gray)
})
dev.off()
}
}
}
# Question1: Works fine, but using the vector numbers feels kludgy --
especially if the variables in question aren't consecutive.
# Is there a more elegant way of doing this with my lists of variable
names? Something like this, for example:
for(dv in dvs) {
for(iv in ivs) {
for (intv in intvs) {
jpeg(paste(dv, iv, intv, .jpg, sep=_))
with(data.frame(my.df), {
my.fit - lm(my.df[dv] ~ my.df[iv] + my.df[intv] +
my.df[iv]:my.df[intv])
colors - ifelse (my.df[[intv]] == 1, black, grey)
plot(my.df[iv], my.df[dv], xlab=iv, ylab=names(dv), col=colors,
pch=.)
curve (cbind (1, 1, x, 1*x) %*% coef(my.fit), add=TRUE, col=black)
curve (cbind (1, 0, x, 0*x) %*% coef(my.fit), add=TRUE, col=gray)
})
dev.off()
}
}
}
# Clearly that's wrong -- why it's wrong is obscure to me, though!
Please educate me!
# Question2: Could this could be done by using apply rather than a
loop?
# Or is looping better here bc there are several actions performed at
each iteration?
# I'm still trying to get my head around all the ways to ditch looping in
R.
Donald Braman
http://www.law.gwu.edu/Faculty/profile.aspx?id=10123
http://research.yale.edu/culturalcognition
http://ssrn.com/author=286206
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+1 513 646 9390
What is the problem you are trying to solve?
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[R] ggplot2-barplot
Hi all: I have been using ggplot2 graphics for quite some time now and I really like it. However, I haven't used barplots enough to understand the arquitecture behind it. Can someone show me how to make this simple barplot graph with ggplot2? I want PondName along the x axis and avgWt along the Y axis which represents the avgWt by each Pond. PondNameavgWt Pond01 21.5 Pond02 17.8 Pond03 17.8 Pond04 17.8 Pond05 16.375 Pond06 21.5 Pond07 21.5 Using sigmaplot or Excel is a simple task but I can't get it to work with ggplot2. I was trying: qplot(PondName,data=mydata,geom=bar) + geom_bar(fill=factor(PondName)) but I don't get the desired results. Thanks __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R vs. Bugs
Hey, good topic for a thread. I've wrestled with this over the years. I think there's some user confusion about what WinBUGS does. People who did not see BUGS before WinBUGS tend not to understand this in the same way... The unique / important contributions from WinBUGS are the collection of working examples and the Doodle code generator thing. All of the rest of it can be easily replaced by open source tools that exist or could easily exist. On Sun, Jun 22, 2008 at 11:34 AM, Peter Muhlberg [EMAIL PROTECTED] wrote: I've done some looking around in R and elsewhere to answer my question on the value of R vs. Bugs for MCMC. So, for anyone who is curious, here's what I think I've found: Bugs compiles its code, which should make it much faster than a pure R program. Packages such as AMCMC run MCMC in R, potentially with a user-defined C function for the density--which should make it comparable in speed to Bugs. The packages MCMCpack (MCMCmetrop1R function) and mcmc seem designed to run w/ a density function written in R. MCMCpack does have functions that use precompiled C code from the Scythe library (which looks nice), but I see no simple way to add a C density function. AMCMC and Bugs seem to use adaptive MCMC, but the other R packages don't appear to do so, which may mean another performance reduction. Think of performance as a combination of development time and run time. Andrew Martin's MCMCpack reduces development time by giving people some pre-packaged Gibbs sampling fitters for standard models, such as logistic regression. It still uses the same iterative sampling routines under the hood as most other MCMC approaches. The only difference there is that it has routines formatted in a way that will be familiar to R users. I do not believe a simulation model conducted in MCMCpack will take a different amount of run time than a well coded, custom version of the same that is prepared in WinBUGS or any other GIBBS sampler. The big difference is that MCMCpack offers routines for familiar models, and if one wants to thrown in some random parameter here or there, then MCMCpack won't be able to handle it. The U. Chicago professors provide the package bayesm which is roughly the same kind of thing. For pre-existing model types, an MCMC model can be conducted. Students ask Why learn BUGS when I can use MCMCpack (or bayesm)? Answer: no reason, unless you want to propose a model that is not already coded up by the package. I see no way to insert my own proposal density in the R functions. JAG, a Java-based version of BUGS, apparently allows users to create If you mean to refer to Martyn Plummer's project JAGS: http://www-ice.iarc.fr/~martyn/software/jags/ JAGS is Just Another Gibbs Sampler, and it is decidedly not written in Java. It is, rather, written in C++. JAGS is proposed as a more-or-less complete drop in replacement for BUGS, so the user can write up a BUGS style model and then hand it over to JAGS for processing, the same way we used BUGS before the WinBugs came along and tried to make it a pointy-clicky experience. JAGS has versions of the classic BUGS examples, and I think it is very well done. If you want to run a Gibbs Sampling exercise in Linux, I suggest you seriously consider using JAGS. You might use WinBUGS Doodle thingie to sketch out the code for your model, but then translate it to JAGS. (I put a bit of thought into packaging an RPM for Fedora users a few months ago, but ran into a few little packaging errors that put me off of it. Now I'm running Ubuntu and packaging for that is harder, at least for me...) I notice there are some R packages that are providing pre-packaged estimators for common models through JAGS. Check witness: bayescount Bayesian analysis of count distributions with JAGS bayesmixBayesian Mixture Models with JAGS It is disappointing/frustrating to me that the source code for WinBUGS/OpenBugs is kept in secret, because here's what I'd really like. 1. Make a version of Doodle for sketching out models. As far as I can see, Doodle is the only truly uniquely valuable component in Win/Open BUGS. It helps people get started by providing a code template. 2. Create an avenue for that Doodle code to travel to JAGS. rJAGS exists as an interface between R and jags. -- Paul E. Johnson Professor, Political Science 1541 Lilac Lane, Room 504 University of Kansas __ 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] Simulating Gaussian Mixture Models
Hi, Is there any package that I can use to simulate the Gaussian Mixture Model , which is a mixture modeling method that is widely used in statistical learning theory. I know there is a mclust, however, I think it is a little bit different from my problem. Thanks very much.. regards. -- Peng Jiang 江鹏 Ph.D. Candidate Antai College of Economics Management 安泰经济管理学院 Department of Mathematics 数学系 Shanghai Jiaotong University (Minhang Campus) 800 Dongchuan Road 200240 Shanghai P. R. China __ 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] problem in R for Linear mixed model~
Dear R users: I just got confused some R code used in linear mixed model~ example,two factors,A, B,C,A is fixed ,B,C are random,and B is nested in C,if I wannt to use linear mixed model,are the following code correct for each case? case1:want to know random effect of B, case1-lme(y~A*B*C,random=~B|C) where B|C stand for what?,mean B is nested in C? case2: how to wirte random effect of C? case2-lme(y~A*B*C,random=~C)? this doesnt work out,it seem it must have somehing like #|$ case3.omitting the random effect for B from case1 case3-update(case1,random=~1|C),so I just type 1,so the random effect of B will be removed from the model,there only left random effect of c ,the random effect I removed ,which include both random intercept and slope ,correct?? case4:omitting the random intercept case4-update(case1,random=B-1|C) this code I got from some paper,it said by inputing B-1|C,then the random intercept is removed,so,if I want to remove random slode,I input B-2|C,it doesnt work out. case5 :how to know the both random effect of B,and C,I dont know how to wirtie this in R . And I am a little confused of these R code,especially the #|# part,what deos this syntax really mean in LME package, Thank you for your time~ [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Simulating Gaussian Mixture Models
Take a look at mixtools. Tatiana On Jun 22, 2008, at 9:23 PM, Peng Jiang wrote: Hi, Is there any package that I can use to simulate the Gaussian Mixture Model , which is a mixture modeling method that is widely used in statistical learning theory. I know there is a mclust, however, I think it is a little bit different from my problem. Thanks very much.. regards. -- Peng Jiang 江鹏 Ph.D. Candidate Antai College of Economics Management 安泰经济管理学院 Department of Mathematics 数学系 Shanghai Jiaotong University (Minhang Campus) 800 Dongchuan Road 200240 Shanghai P. R. China __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Simulating Gaussian Mixture Models
Hi, Peng,
I had a piece of SAS code for 2-class gaussian mixture from my blog.
You might convert it to R code.
2-Class Gaussian Mixture Model in SAS
data d1;
do i = 1 to 100;
x = ranuni(1);
e = rannor(1);
y = 5 * x + e;
output;
end;
run;
data d2;
do i = 1 to 100;
x = ranuni(2);
e = rannor(2);
y = 15 + 10 * x - 5 * x ** 2 + e;
output;
end;
run;
data data;
set d1 d2;
run;
proc nlmixed data = data tech = quanew maxiter = 1000;
parms b10 = 0 b11 = 5 b12 = 0 b20 = 15 b21 = 10 b22 = -5
prior = 0.1 to 0.9 by 0.01 sigma = 1;
mu1 = b10 + b11 * x + b12 * x * x;
mu2 = b20 + b21 * x + b22 * x * x;
pi = constant('pi');
P1 = 1 / (((2 * pi) ** 0.5) * sigma) * exp(-0.5 * ((y - mu1) / sigma) ** 2);
P2 = 1 / (((2 * pi) ** 0.5) * sigma) * exp(-0.5 * ((y - mu2) / sigma) ** 2);
LH = P1 * prior + P2 * (1 - prior);
LL = log(LH);
model y ~ general(LL);
run;
/*
Parameter Estimates
Standard
Parameter Estimate ErrorDF t Value Pr |t| Alpha
b10 -0.17440.3450 200-0.510.61370.05
b11 5.34261.5040 200 3.550.00050.05
b12-0.064541.4334 200-0.050.96410.05
b20 15.36520.3099 20049.57.00010.05
b21 9.62971.4970 200 6.43.00010.05
b22 -5.47951.4776 200-3.710.00030.05
prior0.5000 0.03536 20014.14.00010.05
sigma1.0049 0.05025 20020.00.00010.05
*/
On 6/22/08, Peng Jiang [EMAIL PROTECTED] wrote:
Hi,
Is there any package that I can use to simulate the Gaussian Mixture Model
, which is a mixture modeling method that is widely used in statistical
learning theory.
I know there is a mclust, however, I think it is a little bit different
from my problem.
Thanks very much..
regards.
--
Peng Jiang
江鹏
Ph.D. Candidate
Antai College of Economics Management
安泰经济管理学院
Department of Mathematics
数学系
Shanghai Jiaotong University (Minhang Campus)
800 Dongchuan Road
200240 Shanghai
P. R. China
__
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PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
===
WenSui Liu
Acquisition Risk, Chase
Email : [EMAIL PROTECTED]
Blog : statcompute.spaces.live.com
===
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[R] Getting only label column of a data frame
Hi, How can I extract the label only from a given data frame. Fore example from this data frame. print(dataf) V1 V2 V3 V4 V5 V6 V7 V8 V9 1114514.317.131.241.745.849.868.670.672.9 3545 10.215.620.923.231.431.736.248.451.9 8951 15.217.520.021.432.449.751.358.358.9 1109759.565.9 117.5 118.0 118.9 122.5 126.3 156.5 157.0 I want to get the label (first) column only: 11145 3545 8951 11097 Is there a quick way to achieve that? I tried this but fail: mylable - dataf[,1] Please advice. - Gundala Viswanath Jakarta - Indonesia __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Getting only label column of a data frame
Wait. The first column is really the rowname. So you want this: row.names(x) [1] 11145 3545 8951 11097 On Sun, Jun 22, 2008 at 10:16 PM, Gundala Viswanath [EMAIL PROTECTED] wrote: Hi, How can I extract the label only from a given data frame. Fore example from this data frame. print(dataf) V1 V2 V3 V4 V5 V6 V7 V8 V9 1114514.317.131.241.745.849.868.670.672.9 3545 10.215.620.923.231.431.736.248.451.9 8951 15.217.520.021.432.449.751.358.358.9 1109759.565.9 117.5 118.0 118.9 122.5 126.3 156.5 157.0 I want to get the label (first) column only: 11145 3545 8951 11097 Is there a quick way to achieve that? I tried this but fail: mylable - dataf[,1] Please advice. - Gundala Viswanath Jakarta - Indonesia __ 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. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem you are trying to solve? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] problem in R for Linear mixed model~
Hi, random=~1|B/C C is nested in B ##Example data=Oats regress=lme(yield~nitro*Variety,data=Oats,random=~1|Block/Variety) ##i.e. variety is nested in block summary(regress) ##End of example Best, Daniel - cuncta stricte discussurus - -Ursprüngliche Nachricht- Von: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Im Auftrag von Manli Yan Gesendet: Sunday, June 22, 2008 9:30 PM An: r-help@r-project.org Betreff: [R] problem in R for Linear mixed model~ Dear R users: I just got confused some R code used in linear mixed model~ example,two factors,A, B,C,A is fixed ,B,C are random,and B is nested in C,if I wannt to use linear mixed model,are the following code correct for each case? case1:want to know random effect of B, case1-lme(y~A*B*C,random=~B|C) where B|C stand for what?,mean B is nested in C? case2: how to wirte random effect of C? case2-lme(y~A*B*C,random=~C)? this doesnt work out,it seem it must have somehing like #|$ case3.omitting the random effect for B from case1 case3-update(case1,random=~1|C),so I just type 1,so the random effect of B will be removed from the model,there only left random effect of c ,the random effect I removed ,which include both random intercept and slope ,correct?? case4:omitting the random intercept case4-update(case1,random=B-1|C) this code I got from some paper,it said by inputing B-1|C,then the random intercept is removed,so,if I want to remove random slode,I input B-2|C,it doesnt work out. case5 :how to know the both random effect of B,and C,I dont know how to wirtie this in R . And I am a little confused of these R code,especially the #|# part,what deos this syntax really mean in LME package, Thank you for your time~ [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] One-to-one matching?
Hi folks, Can anyone suggest an efficient way to do matching without replacement, or one-to-one matching? pmatch() doesn't quite provide what I need... For example, lookupTable - c(a,b,c,d,e,f) matchSample - c(a,a,b,d) ##Normal match() behaviour: match(matchSample,lookupTable) [1] 1 1 2 4 My problem here is that both as in matchSample are matched to the same a in the lookup table. I need the elements of the lookup table to be excluded from the table as they are matched, so that no match can be found for the second a. Function pmatch() comes close to what I need: pmatch(matchSample,lookupTable) [1] 1 NA 2 4 Yep! However, pmatch() incorporates partial matching, which I definitely don't want: lookupTable - c(a,b,c,d,e,f) matchSample - c(a,a,b,d) pmatch(matchSample,lookupTable) [1] 1 6 2 4 ## i.e. the second a, matches f - I don't want this. Of course, when identical items ARE duplicated in both sample and lookup table, I need the matching to reflect this: lookupTable - c(a,a,c,d,e,f) matchSample - c(a,a,c,d) ##Normal match() behaviour match(matchSample,lookupTable) [1] 1 1 3 4 No good - pmatch() is better: lookupTable - c(a,a,c,d,e,f) matchSample - c(a,a,c,d) pmatch(matchSample,lookupTable) [1] 1 2 3 4 ...but we still have the partial matching issue... ##And of course, as per the usual behaviour of match(), sample elements missing from the lookup table should return NA: matchSample - c(a,frog,e,d) ; print(matchSample) match(matchSample,lookupTable) Is there a nifty way to get what I'm after without resorting to a for loop? (my code's already got too blasted many of those...) Thanks, Alec Zwart CMIS CSIRO [EMAIL PROTECTED] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] problem in R for Linear mixed model~
Hi: Thank you very much,and for your case if I wirte as regress=lme(yield~nitro*Variety,data=Oats,random=~Variety|Block) what this mean? Regards 2008/6/22 Daniel Malter [EMAIL PROTECTED]: Hi, random=~1|B/C C is nested in B ##Example data=Oats regress=lme(yield~nitro*Variety,data=Oats,random=~1|Block/Variety) ##i.e. variety is nested in block summary(regress) ##End of example Best, Daniel - cuncta stricte discussurus - -Ursprüngliche Nachricht- Von: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Im Auftrag von Manli Yan Gesendet: Sunday, June 22, 2008 9:30 PM An: r-help@r-project.org Betreff: [R] problem in R for Linear mixed model~ Dear R users: I just got confused some R code used in linear mixed model~ example,two factors,A, B,C,A is fixed ,B,C are random,and B is nested in C,if I wannt to use linear mixed model,are the following code correct for each case? case1:want to know random effect of B, case1-lme(y~A*B*C,random=~B|C) where B|C stand for what?,mean B is nested in C? case2: how to wirte random effect of C? case2-lme(y~A*B*C,random=~C)? this doesnt work out,it seem it must have somehing like #|$ case3.omitting the random effect for B from case1 case3-update(case1,random=~1|C),so I just type 1,so the random effect of B will be removed from the model,there only left random effect of c ,the random effect I removed ,which include both random intercept and slope ,correct?? case4:omitting the random intercept case4-update(case1,random=B-1|C) this code I got from some paper,it said by inputing B-1|C,then the random intercept is removed,so,if I want to remove random slode,I input B-2|C,it doesnt work out. case5 :how to know the both random effect of B,and C,I dont know how to wirtie this in R . And I am a little confused of these R code,especially the #|# part,what deos this syntax really mean in LME package, Thank you for your time~ [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.htmlhttp://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Columnwise Alternate Subsetting of a Data Frame
Hi, Given this data frame: print(repo.dat) V1 V2 V3 V4 V5 (can be more) 1 1007_s_at DDR1 2865.1 2901.3 1978.3 300.2 2 1053_at RFC2 103.681.6 108.0 101.3 I want to split them into two data frames yielding: V1 V2 V3 ... etc 1 1007_s_at DDR1 2865.11978.3 2 1053_at RFC2 103.6 108.0 (V2 and V3 is obtain from V2 and V4 of original repo.dat) and V1V2 V3 ...etc 1 1007_s_at DDR12901.3 300.2 2 1053_at RFC2 81.6101.3 (V2 and V3 is obtain from V3 and V5 of original repo.dat) In principle what we desire to do is to: 1. Given original data frame with V1, V2, V3, V4 2. Split the data frame into two based on V2,V4,V6 ... (even) and V3, V5, V7 ..(odd) in the original data frame 3. Meanwhile keep row names and V1 in two newly formed data frames. Is there a compact way to do it? - Gundala Viswanath Jakarta - Indonesia __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Simulating Gaussian Mixture Models
First, simulate a uniform r.v on [0,1] and then cast it to binary label according to your underlying mixing probability; Second, simulate a Gaussian r.v. in above selected component. Of course, you can vecterize the two steps to simply your code. X Peng Jiang 写道: Hi, Is there any package that I can use to simulate the Gaussian Mixture Model , which is a mixture modeling method that is widely used in statistical learning theory. I know there is a mclust, however, I think it is a little bit different from my problem. Thanks very much.. regards. -- Peng Jiang 江鹏 Ph.D. Candidate Antai College of Economics Management 安泰经济管理学院 Department of Mathematics 数学系 Shanghai Jiaotong University (Minhang Campus) 800 Dongchuan Road 200240 Shanghai P. R. China __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] One-to-one matching?
Try this. apseq() sorts the input and appends a
sequence number: 0, 1, ... to successive
occurrences of each value. Apply that to both
vectors transforms it into a problem that works
with ordinary match:
lookupTable - c(a, a,b,c,d,e,f)
matchSample - c(a, a,a,b,d)
# sort and append sequence no
apseq - function(x) {
+ x - sort(x)
+ s - cumsum(!duplicated(x))
+ paste(x, seq(s) - match(s, s))
+ }
match(apseq(matchSample), apseq(lookupTable))
[1] 1 2 NA 3 5
On Sun, Jun 22, 2008 at 10:57 PM, [EMAIL PROTECTED] wrote:
Hi folks,
Can anyone suggest an efficient way to do matching without
replacement, or one-to-one matching? pmatch() doesn't quite provide
what I need...
For example,
lookupTable - c(a,b,c,d,e,f)
matchSample - c(a,a,b,d)
##Normal match() behaviour:
match(matchSample,lookupTable)
[1] 1 1 2 4
My problem here is that both as in matchSample are matched to the same
a in the lookup table. I need the elements of the lookup table to be
excluded from the table as they are matched, so that no match can be
found for the second a.
Function pmatch() comes close to what I need:
pmatch(matchSample,lookupTable)
[1] 1 NA 2 4
Yep! However, pmatch() incorporates partial matching, which I
definitely don't want:
lookupTable - c(a,b,c,d,e,f)
matchSample - c(a,a,b,d)
pmatch(matchSample,lookupTable)
[1] 1 6 2 4
## i.e. the second a, matches f - I don't want this.
Of course, when identical items ARE duplicated in both sample and lookup
table, I need the matching to reflect this:
lookupTable - c(a,a,c,d,e,f)
matchSample - c(a,a,c,d)
##Normal match() behaviour
match(matchSample,lookupTable)
[1] 1 1 3 4
No good - pmatch() is better:
lookupTable - c(a,a,c,d,e,f)
matchSample - c(a,a,c,d)
pmatch(matchSample,lookupTable)
[1] 1 2 3 4
...but we still have the partial matching issue...
##And of course, as per the usual behaviour of match(), sample elements
missing from the lookup table should return NA:
matchSample - c(a,frog,e,d) ; print(matchSample)
match(matchSample,lookupTable)
Is there a nifty way to get what I'm after without resorting to a for
loop? (my code's already got too blasted many of those...)
Thanks,
Alec Zwart
CMIS CSIRO
[EMAIL PROTECTED]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] One-to-one matching?
How about x - lookupTable x[!(x %in% matchSample)] - NA pmatch(matchSample,x) Regards, Moshe. --- On Mon, 23/6/08, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote: From: [EMAIL PROTECTED] [EMAIL PROTECTED] Subject: [R] One-to-one matching? To: r-help@r-project.org Received: Monday, 23 June, 2008, 12:57 PM Hi folks, Can anyone suggest an efficient way to do matching without replacement, or one-to-one matching? pmatch() doesn't quite provide what I need... For example, lookupTable - c(a,b,c,d,e,f) matchSample - c(a,a,b,d) ##Normal match() behaviour: match(matchSample,lookupTable) [1] 1 1 2 4 My problem here is that both as in matchSample are matched to the same a in the lookup table. I need the elements of the lookup table to be excluded from the table as they are matched, so that no match can be found for the second a. Function pmatch() comes close to what I need: pmatch(matchSample,lookupTable) [1] 1 NA 2 4 Yep! However, pmatch() incorporates partial matching, which I definitely don't want: lookupTable - c(a,b,c,d,e,f) matchSample - c(a,a,b,d) pmatch(matchSample,lookupTable) [1] 1 6 2 4 ## i.e. the second a, matches f - I don't want this. Of course, when identical items ARE duplicated in both sample and lookup table, I need the matching to reflect this: lookupTable - c(a,a,c,d,e,f) matchSample - c(a,a,c,d) ##Normal match() behaviour match(matchSample,lookupTable) [1] 1 1 3 4 No good - pmatch() is better: lookupTable - c(a,a,c,d,e,f) matchSample - c(a,a,c,d) pmatch(matchSample,lookupTable) [1] 1 2 3 4 ...but we still have the partial matching issue... ##And of course, as per the usual behaviour of match(), sample elements missing from the lookup table should return NA: matchSample - c(a,frog,e,d) ; print(matchSample) match(matchSample,lookupTable) Is there a nifty way to get what I'm after without resorting to a for loop? (my code's already got too blasted many of those...) Thanks, Alec Zwart CMIS CSIRO [EMAIL PROTECTED] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] One-to-one matching?
Or use make.unique() in place of apseq()
On Sun, 22 Jun 2008, Gabor Grothendieck wrote:
Try this. apseq() sorts the input and appends a
sequence number: 0, 1, ... to successive
occurrences of each value. Apply that to both
vectors transforms it into a problem that works
with ordinary match:
lookupTable - c(a, a,b,c,d,e,f)
matchSample - c(a, a,a,b,d)
# sort and append sequence no
apseq - function(x) {
+ x - sort(x)
+ s - cumsum(!duplicated(x))
+ paste(x, seq(s) - match(s, s))
+ }
match(apseq(matchSample), apseq(lookupTable))
[1] 1 2 NA 3 5
On Sun, Jun 22, 2008 at 10:57 PM, [EMAIL PROTECTED] wrote:
Hi folks,
Can anyone suggest an efficient way to do matching without
replacement, or one-to-one matching? pmatch() doesn't quite provide
what I need...
For example,
lookupTable - c(a,b,c,d,e,f)
matchSample - c(a,a,b,d)
##Normal match() behaviour:
match(matchSample,lookupTable)
[1] 1 1 2 4
My problem here is that both as in matchSample are matched to the same
a in the lookup table. I need the elements of the lookup table to be
excluded from the table as they are matched, so that no match can be
found for the second a.
Function pmatch() comes close to what I need:
pmatch(matchSample,lookupTable)
[1] 1 NA 2 4
Yep! However, pmatch() incorporates partial matching, which I
definitely don't want:
lookupTable - c(a,b,c,d,e,f)
matchSample - c(a,a,b,d)
pmatch(matchSample,lookupTable)
[1] 1 6 2 4
## i.e. the second a, matches f - I don't want this.
Of course, when identical items ARE duplicated in both sample and lookup
table, I need the matching to reflect this:
lookupTable - c(a,a,c,d,e,f)
matchSample - c(a,a,c,d)
##Normal match() behaviour
match(matchSample,lookupTable)
[1] 1 1 3 4
No good - pmatch() is better:
lookupTable - c(a,a,c,d,e,f)
matchSample - c(a,a,c,d)
pmatch(matchSample,lookupTable)
[1] 1 2 3 4
...but we still have the partial matching issue...
##And of course, as per the usual behaviour of match(), sample elements
missing from the lookup table should return NA:
matchSample - c(a,frog,e,d) ; print(matchSample)
match(matchSample,lookupTable)
Is there a nifty way to get what I'm after without resorting to a for
loop? (my code's already got too blasted many of those...)
Thanks,
Alec Zwart
CMIS CSIRO
[EMAIL PROTECTED]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Charles C. Berry(858) 534-2098
Dept of Family/Preventive Medicine
E mailto:[EMAIL PROTECTED] UC San Diego
http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego 92093-0901
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Columnwise Alternate Subsetting of a Data Frame
You could do something like: k - dim(repo.dat)[2] odd - seq(from=1,to=k,by=2) even - seq(from=2,to=k,by=2) even-c(1,even) df1 - repo.dat[,odd) colnames(df1) - paste(V,odd,sep=) df2 - repo.dat[,even) colnames(df2) - paste(V,even,sep=) --- On Mon, 23/6/08, Gundala Viswanath [EMAIL PROTECTED] wrote: From: Gundala Viswanath [EMAIL PROTECTED] Subject: [R] Columnwise Alternate Subsetting of a Data Frame To: [EMAIL PROTECTED] Received: Monday, 23 June, 2008, 1:03 PM Hi, Given this data frame: print(repo.dat) V1 V2 V3 V4 V5 (can be more) 1 1007_s_at DDR1 2865.1 2901.3 1978.3 300.2 2 1053_at RFC2 103.681.6 108.0 101.3 I want to split them into two data frames yielding: V1 V2 V3 ... etc 1 1007_s_at DDR1 2865.11978.3 2 1053_at RFC2 103.6 108.0 (V2 and V3 is obtain from V2 and V4 of original repo.dat) and V1V2 V3 ...etc 1 1007_s_at DDR12901.3 300.2 2 1053_at RFC2 81.6101.3 (V2 and V3 is obtain from V3 and V5 of original repo.dat) In principle what we desire to do is to: 1. Given original data frame with V1, V2, V3, V4 2. Split the data frame into two based on V2,V4,V6 ... (even) and V3, V5, V7 ..(odd) in the original data frame 3. Meanwhile keep row names and V1 in two newly formed data frames. Is there a compact way to do it? - Gundala Viswanath Jakarta - Indonesia __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Columnwise Alternate Subsetting of a Data Frame
See ?split help.search() is (or should be) your friend. HTH, Chuck On Mon, 23 Jun 2008, Gundala Viswanath wrote: Hi, Given this data frame: print(repo.dat) V1 V2 V3 V4 V5 (can be more) 1 1007_s_at DDR1 2865.1 2901.3 1978.3 300.2 2 1053_at RFC2 103.681.6 108.0 101.3 I want to split them into two data frames yielding: V1 V2 V3 ... etc 1 1007_s_at DDR1 2865.11978.3 2 1053_at RFC2 103.6 108.0 (V2 and V3 is obtain from V2 and V4 of original repo.dat) and V1V2 V3 ...etc 1 1007_s_at DDR12901.3 300.2 2 1053_at RFC2 81.6101.3 (V2 and V3 is obtain from V3 and V5 of original repo.dat) In principle what we desire to do is to: 1. Given original data frame with V1, V2, V3, V4 2. Split the data frame into two based on V2,V4,V6 ... (even) and V3, V5, V7 ..(odd) in the original data frame 3. Meanwhile keep row names and V1 in two newly formed data frames. Is there a compact way to do it? - Gundala Viswanath Jakarta - Indonesia __ 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. Charles C. Berry(858) 534-2098 Dept of Family/Preventive Medicine E mailto:[EMAIL PROTECTED] UC San Diego http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego 92093-0901 __ 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.
