Re: [R] long output in R
Not answering your question, But if you where to ask this regarding plots, the answer would be to use: par(ask = T) Best, Tal Contact Details:--- Contact me: tal.gal...@gmail.com | 972-52-7275845 Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) | www.r-statistics.com (English) -- On Thu, Apr 22, 2010 at 1:01 AM, Mingfeng Lin mingfeng@gmail.comwrote: Hello all: Is there a way to set up R such that, when you have a very long output from a command, it will pause when it has displayed one-screen of information and ask me to press a button to continue displaying? I happen to have one such command and the information I need is at the top of the output - and it's just nowhere to be seen. (If you are familiar with Stata, I'm looking for something equivalent to the -set more on- option there. Thanks a lot! Mingfeng __ 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.
[R] time difference
Hi, Does anyone know how to take a time difference when the format of the time is as 13:22:23.586? I am trying to take the difference of time between stock transactions and need to keep the three decimal places for seconds. I have tried *diff(strptime(x, %H:%M:%S.000))*, but apperantly that doesn't work. Carol Gao [[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] Assigning week numbers
On Wed, Apr 21, 2010 at 6:50 PM, Michael Hosack mhosa...@hotmail.com wrote:
I provided a minimized version of my dataframe at the bottom of this message
containing the results of David's code in variable ('wkoffset') and Jeff
Hallman's code in ('WEEK'). Jeff's code produced the correct results (thank
you Jeff) though I have been unable to understand it. David, as you can see
your code begins week 2 for year 2011 on a Wednesday, rather than on a
Saturday, as it should. Your adjustment seems not to correct the problem, but
I concede I may be using it incorrectly. If you are obtaining the correct
results please let me know what I am doing wrong.
Thanks,
Mike
Hello again,
Just for fun, I implemented the gist of your original code in R. It's
much longer and not as elegant as the other solutions, but perhaps
someone can learn something from it.
Regards,
Gustaf
Daterange-range(SCHEDULE3$DATE.)
Daterange[1]-paste(as.numeric(
substr(as.character(Daterange[1]),1,4))-1,
-05-01,sep=)
Daterange[2]-paste(as.numeric(
substr(as.character(Daterange[2]),1,4))+1,
-05-01,sep=)
alldates-seq(from=Daterange[1],to=Daterange[2],by=1)
My.locale-Sys.getlocale(LC_TIME)
Sys.setlocale(LC_TIME,English_USA.1252)
Week-1
allweeks-vector(length=length(alldates))
for(i in seq_along(alldates)){
if(weekdays(alldates[i])==Saturday){
Week-Week+1
}
if(substr(as.character(alldates[i]),6,10)==05-01){
Week-1
}
allweeks[i]-Week
}
SCHEDULE3$Week-allweeks[match(SCHEDULE3$DATE.,alldates)]
Sys.setlocale(LC_TIME,My.locale)
--
Gustaf Rydevik, M.Sci.
tel: +46(0)703 051 451
address:Essingetorget 40,112 66 Stockholm, SE
skype:gustaf_rydevik
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] long output in R
There are at least two functions that may be of interest to you in this regard: 'head' (there is also 'tail') 'page' On 21/04/2010 23:01, Mingfeng Lin wrote: Hello all: Is there a way to set up R such that, when you have a very long output from a command, it will pause when it has displayed one-screen of information and ask me to press a button to continue displaying? I happen to have one such command and the information I need is at the top of the output - and it's just nowhere to be seen. (If you are familiar with Stata, I'm looking for something equivalent to the -set more on- option there. Thanks a lot! Mingfeng __ 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. -- Patrick Burns pbu...@pburns.seanet.com http://www.burns-stat.com (home of 'Some hints for the R beginner' and 'The R Inferno') __ 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 crashing oddly
A similar problem was mentioned before: https://stat.ethz.ch/pipermail/r-sig-mixed-models/2008q3/001425.html There appears to be a bug in the C code leading to memory corruption. Best, -- Wolfgang Viechtbauerhttp://www.wvbauer.com/ Department of Methodology and StatisticsTel: +31 (0)43 388-2277 School for Public Health and Primary Care Office Location: Maastricht University, P.O. Box 616 Room B2.01 (second floor) 6200 MD Maastricht, The Netherlands Debyeplein 1 (Randwyck) Original Message From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Michael Steven Rooney Sent: Wednesday, April 21, 2010 17:41 To: r-help@r-project.org Subject: [R] R crashing oddly Hi, I am working with the package nlme, and I tried creating a new correlation class (which, according to the help pages, is possible if you write a few new method functions). Anyways, I think I am 99% of the way there, but I have a recurring problem with R crashing on seemingly innocuous statements (I have set debug() on nearly every function, so I can see where it is failing). For instance, sometime the code fails on the simple statement: object[[i]] Two things are odd about this: 1. It's not the first time I call object[[i]] 2. If I run save() on the object just before the crash, open the object in a new workspace and run object[[i]], then no crash or error occurs. [[ is not the only function that has been giving me grief. Certain C routines that get called multiple time have displayed very similar behavior (ie. they work fine several times before they crash, and if the object is exported just before the crash and the routine is called in a new workspace there is no error). The behavior kind of reminds me of the craziness that occur with an uninitialized pointer (thinking back to coding in C in college). The other thing that points me in that direction is that Windows returns an error code ending ...5, which I believe indicates a segmentation fault. I was also wondering whether there might be some rogue global variable, but I have no idea what. I have struggling with this for a week. Does anyone have any insights on what might be wrong or what I might try? Thanks so much, Mike [[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] Huge data sets and RAM problems
Dear all, Thank you very much for your replies and help. I will try to work with your suggestions and come back to you if I need something more. Kind regards, Stella Pachidi On Thu, Apr 22, 2010 at 5:30 AM, kMan kchambe...@gmail.com wrote: You set records to NULL perhaps (delete, shift up). Perhaps your system is susceptible to butterflies on the other side of the world. Your code may have 'worked' on a small section of data, but the data used did not include all of the cases needed to fully test your code. So... test your code! scan(), used with 'nlines', 'skip', 'sep', and 'what' will cut your read time by at least half while taking less RAM memory to do it, do most of your post processing, and give you something to better test your code. Or, don't use 'nlines' and lose your time/memory benefits over read.table(). 'skip' will get you right to the point before where things failed. That would be an interesting small segment of data to test with. wordpad can read your file (and then some). Eventually. Sincerely, KeithC. -Original Message- From: Stella Pachidi [mailto:stella.pach...@gmail.com] Sent: Monday, April 19, 2010 2:07 PM To: r-h...@stat.math.ethz.ch Subject: [R] Huge data sets and RAM problems Dear all, This is the first time I am sending mail to the mailing list, so I hope I do not make a mistake... The last months I have been working on my MSc thesis project on performing data mining techniques on user logs of a software-as-a-service application. The main problem I am experiencing is how to process the huge amount of data. More specifically: I am using R 2.10.1 in a laptop with Windows 7 - 32bit system, 2GB RAM and CPU Intel Core Duo 2GHz. The user logs data come from a query Crystal report (.rpt file) which I transform with some Java code into a tab separated file. Although with a small subset of my data everything manages to run, when I increase the data set I get several problems: The first problem is with the use of read.delim(). When I try to read a big amount of data (over 2.400.000 rows and 18 attributes at each row) it doesn't seem to transform all table into a data frame. In particular, the data frame returned has 1.220.987 rows. Furthermore, as one of the data attributes is DataTime, when I try to split this column into two columns (one with Data and one with the Time), the returned result is quite strange, as the two new columns appear to have more rows than the data frame: applicLog.dat - read.delim(file.txt) #Process the syscreated column (Date time -- Date + time) copyDate - applicLog.dat[[ï..syscreated]] copyDate - as.character(copyDate) splitDate - strsplit(copyDate, ) splitDate - unlist(splitDate) splitDateIndex - c(1:length(splitDate)) sysCreatedDate - splitDate[splitDateIndex %% 2 == 1] sysCreatedTime - splitDate[splitDateIndex %% 2 == 0] sysCreatedDate - strptime(sysCreatedDate, format=%Y-%m-%d) op - options(digits.secs = 3) sysCreatedTime - strptime(sysCreatedTime, format =%H:%M:%OS) applicLog.dat[[ï..syscreated]] - NULL applicLog.dat - cbind (sysCreatedDate,sysCreatedTime,applicLog.dat) Then I get the error: Error in data.frame(..., check.names = FALSE) : arguments imply differing number of rows: 1221063, 1221062, 1220987 Finally, another problem I have is when I perform association mining on the data set using the package arules: I turn the data frame into transactions table and then run the apriori algorithm. When I put too low support in order to manage to find the rules I need, the vector of rules becomes too big and I get problems with the memory such as: Error: cannot allocate vector of size 923.1 Mb In addition: Warning messages: 1: In items(x) : Reached total allocation of 153Mb: see help(memory.size) Could you please help me with how I could allocate more RAM? Or, do you think there is a way to process the data by loading them into a document instead of loading all into RAM? Do you know how I could manage to read all my data set? I would really appreciate your help. Kind regards, Stella Pachidi PS: Do you know any text editor that can read huge .txt files? -- Stella Pachidi Master in Business Informatics student Utrecht University -- Stella Pachidi Master in Business Informatics student Utrecht University email: s.pach...@students.uu.nl tel: +31644478898 __ 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] time difference
?strptime
Read the documentation and you will find reference to %OSn
x - strptime('13:45:34.123', format=%H:%M:%OS)
x
[1] 2010-04-22 13:45:34
format(x, format=%H:%M:%OS3)
[1] 13:45:34.123
On Thu, Apr 22, 2010 at 2:58 AM, Carol Gao carol.g...@gmail.com wrote:
Hi,
Does anyone know how to take a time difference when the format of the time
is as 13:22:23.586? I am trying to take the difference of time between
stock
transactions and need to keep the three decimal places for seconds. I have
tried *diff(strptime(x, %H:%M:%S.000))*, but apperantly that doesn't work.
Carol Gao
[[alternative HTML version deleted]]
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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.
--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem that you are trying to solve?
[[alternative HTML version deleted]]
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[R] time series' year not recognized
I am working with time series and I have encountered a problem with R not recognizing a series properly. I can do the tests and fitting, but when I want to decompose the series I got a message: d-decompose(data) Error in decompose(dane) : time series has no or less than 2 periods Maybe I have made a mistake in defining the TS? However, when I input time(data), R correctly recognizes which value corresponds to which year. I give the code for data formating below: library(urca) data(npext) x-npext[c(year,unemploy)] #Nelson Plosser extended data set x-c(na.omit(npext$unemploy)) #getting rid of NA's for initial years from the data set data-ts(x, start=1890, frequency=1) Thanks. [[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] Convert character string to top levels + NAN
Dear all, I have several character strings with a high number of different levels. unique(x) gives me values in the range of 100-200. This creates problems as I would like to use them as predictors in a coxph model. I therefore would like to convert each of these strings to a new string (x_new). x_new should be equal to x for the top n categories (i.e. the top n levels with the highest occurrence) and NAN elsewhere. For example, for n=3 x_new would have three levels: The three most common levels of x + NAN. Is there some convenient way of doing this? Thanks in advance, Michael Michael Haenlein Associate Professor of Marketing ESCP Europe Paris, France [[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] R 2.11.0 is released
I've rolled up R-2.11.0.tar.gz a short while ago. This is a development release which contains a number of new features. Also, a number of mostly minor bugs have been fixed. See the full list of changes below. NOTE: The build platform has been changed for this release. Please watch out extra carefully for anomalies. You can get it from http://cran.r-project.org/src/base/R-2/R-2.11.0.tar.gz or wait for it to be mirrored at a CRAN site nearer to you. Binaries for various platforms will appear in due course. For the R Core Team Peter Dalgaard These are the md5sums for the freshly created files, in case you wish to check that they are uncorrupted: MD5 (AUTHORS) = ac9746b4845ae81f51cfc99262f5 MD5 (COPYING) = eb723b61539feef013de476e68b5c50a MD5 (COPYING.LIB) = a6f89e2100d9b6cdffcea4f398e37343 MD5 (FAQ) = 5b653442bedab476a4eff7468192fb5f MD5 (INSTALL) = 70447ae7f2c35233d3065b004aa4f331 MD5 (NEWS) = 59017734fb8474f98f994c7a5a27f9fb MD5 (ONEWS) = a8c985af5ad5e9c7e0a9f502d07baeb4 MD5 (OONEWS) = 4f004de59e24a52d0f500063b4603bcb MD5 (R-latest.tar.gz) = c6c1e866299f533617750889c729bfb3 MD5 (README) = 433182754c05c2cf7a04ad0da474a1d0 MD5 (RESOURCES) = 020479f381d5f9038dcb18708997f5da MD5 (THANKS) = f2ccf22f3e20ebaa86f8ee5cc6b0f655 MD5 (R-2/R-2.11.0.tar.gz) = c6c1e866299f533617750889c729bfb3 This is the relevant part of the NEWS file: CHANGES IN R VERSION 2.11.0 SIGNIFICANT USER-VISIBLE CHANGES o Packages must have been installed under R = 2.10.0, as the current help system is the only one now supported. o A port to 64-bit Windows is now available as well as binary package repositiories: see the 'R Administration and Installation Manual'. o Argument matching for primitive functions is now done in the same way as for interpreted functions except for the deliberate exceptions call switch .C .Fortran .Call .External all of which use positional matching for their first argument, and also some internal-use-only primitives. o The default device for command-line R at the console on Mac OS X is now quartz() and not X11(). NEW FEATURES o The 'open' modes for connections are now interpreted more consistently. open = r is now equivalent to open = rt for all connections. The default open = now means rt for all connections except the compressed file connections gzfile(), bzfile() and xzfile() for which it means rb. o R CMD INSTALL now uses the internal untar() in package utils: this ensures that all platforms can install bzip2- and xz-compressed tarballs. In case this causes problems (as it has on some Windows file systems when run from Cygwin tools) it can be overridden by the environment variable R_INSTALL_TAR: setting this to a modern external tar program will speed up unpacking of large (tens of Mb or more) tarballs. o help(try.all.packages = TRUE) is much faster (although the time taken by the OS to find all the packages the first time it is used can dominate the time). o R CMD check has a new option '--timings' to record per-example timings in file pkg.Rcheck/pkg-Ex.timings. o The TRE library has been updated to version 0.8.0 (minor bugfixes). o grep[l], [g]sub and [g]regexpr now work in bytes in an 8-bit locales if there is no marked UTF-8 input string: this will be somewhat faster, and for [g]sub() give the result in the native encoding rather than in UTF-8 (which returns to the behaviour prior to R 2.10.0). o A new argument 'skipCalls' has been added to browser() so that it can report the original context when called by other debugging functions. o More validity checking of UTF-8 and MBCS strings is done by agrep() and the regular-expression matching functions. o The undocumented restriction on gregexpr() to length(text) 0 has been removed. o Package tcltk now sends strings to Tcl in UTF-8: this means that strings with a marked UTF-8 encoding are supported in non-UTF-8 locales. o The graphics engine now supports rendering of raster (bitmap) images, though not all graphics devices can provide (full) support. Packages providing graphics devices (e.g., Cairo, RSvgDevice, cairoDevice) will need to be reinstalled. There is also support in the graphics engine for capturing raster images from graphics devices (again not supported on all graphics devices). o R CMD check now also checks if the package and namespace can be unloaded: this provides a check of the .Last.lib() and .onUnload() hook functions (unless --install=fake). o prop.table(x) now accepts a one-dimensional table for x. o A new function vapply() has been
Re: [R] time difference
Carol Gao carol.gaox at gmail.com writes: Hi, Does anyone know how to take a time difference when the format of the time is as 13:22:23.586? I am trying to take the difference of time between stock transactions and need to keep the three decimal places for seconds. I have tried *diff(strptime(x, %H:%M:%S.000))*, but apperantly that doesn't work. Carol Gao [[alternative HTML version deleted]] I found this: http://tolstoy.newcastle.edu.au/R/e6/help/09/05/15738.html It seems to me that this is partly an options issue. Maybe this is something to work with: options(digits.secs=3) strptime(x, %H:%M:%S%OS) __ 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] overlaying a levelplot on a map plot
Thanks for the suggestions Unfortunately contour won't in this case as it expects the x,y values to be in an ascending sequence. -- View this message in context: http://r.789695.n4.nabble.com/overlaying-a-levelplot-on-a-map-plot-tp2019419p2020292.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] R2.11.0 - rasterImage() and barplot fill-patterns
Hello Peter, Thank you, and the R core team, for the new release. I see that in R 2.11.0 there is now support for rendering of raster (bitmap) images through rasterImage(). I am wondering - can this be used to create a texture/fill-pattern for hist()/barplot() ? (A request made several times throughout the years on the mailing list. For example: http://osdir.com/ml/lang.r.general/2005-07/msg00799.html ) (I am also sending this e-mail to the maintainers of lattice, ggplot2 and gplots in the hope for more perspectives) With much respect, Tal Contact Details:--- Contact me: tal.gal...@gmail.com | 972-52-7275845 Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) | www.r-statistics.com (English) -- On Thu, Apr 22, 2010 at 12:01 PM, Peter Dalgaard pd@cbs.dk wrote: I've rolled up R-2.11.0.tar.gz a short while ago. This is a development release which contains a number of new features. Also, a number of mostly minor bugs have been fixed. See the full list of changes below. NOTE: The build platform has been changed for this release. Please watch out extra carefully for anomalies. You can get it from http://cran.r-project.org/src/base/R-2/R-2.11.0.tar.gz or wait for it to be mirrored at a CRAN site nearer to you. Binaries for various platforms will appear in due course. For the R Core Team Peter Dalgaard These are the md5sums for the freshly created files, in case you wish to check that they are uncorrupted: MD5 (AUTHORS) = ac9746b4845ae81f51cfc99262f5 MD5 (COPYING) = eb723b61539feef013de476e68b5c50a MD5 (COPYING.LIB) = a6f89e2100d9b6cdffcea4f398e37343 MD5 (FAQ) = 5b653442bedab476a4eff7468192fb5f MD5 (INSTALL) = 70447ae7f2c35233d3065b004aa4f331 MD5 (NEWS) = 59017734fb8474f98f994c7a5a27f9fb MD5 (ONEWS) = a8c985af5ad5e9c7e0a9f502d07baeb4 MD5 (OONEWS) = 4f004de59e24a52d0f500063b4603bcb MD5 (R-latest.tar.gz) = c6c1e866299f533617750889c729bfb3 MD5 (README) = 433182754c05c2cf7a04ad0da474a1d0 MD5 (RESOURCES) = 020479f381d5f9038dcb18708997f5da MD5 (THANKS) = f2ccf22f3e20ebaa86f8ee5cc6b0f655 MD5 (R-2/R-2.11.0.tar.gz) = c6c1e866299f533617750889c729bfb3 This is the relevant part of the NEWS file: CHANGES IN R VERSION 2.11.0 SIGNIFICANT USER-VISIBLE CHANGES o Packages must have been installed under R = 2.10.0, as the current help system is the only one now supported. o A port to 64-bit Windows is now available as well as binary package repositiories: see the 'R Administration and Installation Manual'. o Argument matching for primitive functions is now done in the same way as for interpreted functions except for the deliberate exceptions call switch .C .Fortran .Call .External all of which use positional matching for their first argument, and also some internal-use-only primitives. o The default device for command-line R at the console on Mac OS X is now quartz() and not X11(). NEW FEATURES o The 'open' modes for connections are now interpreted more consistently. open = r is now equivalent to open = rt for all connections. The default open = now means rt for all connections except the compressed file connections gzfile(), bzfile() and xzfile() for which it means rb. o R CMD INSTALL now uses the internal untar() in package utils: this ensures that all platforms can install bzip2- and xz-compressed tarballs. In case this causes problems (as it has on some Windows file systems when run from Cygwin tools) it can be overridden by the environment variable R_INSTALL_TAR: setting this to a modern external tar program will speed up unpacking of large (tens of Mb or more) tarballs. o help(try.all.packages = TRUE) is much faster (although the time taken by the OS to find all the packages the first time it is used can dominate the time). o R CMD check has a new option '--timings' to record per-example timings in file pkg.Rcheck/pkg-Ex.timings. o The TRE library has been updated to version 0.8.0 (minor bugfixes). o grep[l], [g]sub and [g]regexpr now work in bytes in an 8-bit locales if there is no marked UTF-8 input string: this will be somewhat faster, and for [g]sub() give the result in the native encoding rather than in UTF-8 (which returns to the behaviour prior to R 2.10.0). o A new argument 'skipCalls' has been added to browser() so that it can report the original context when called by other debugging functions. o More validity checking of UTF-8 and MBCS strings is done by agrep() and the regular-expression matching functions.
[R] install or uncompress package build in one platform in another platform
Hi, Is an R package built under Unix (package.tar.gz) could be installed on other platforms like windows or Mac? The compressed tar file (.tar.gz) built under Unix doesn't seem to be uncompressed under windows (unzip under windows instead of gunzip). How to proceed? Look forward to your reply, Carol __ 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 with tapply selection
Hi, I try to create a data.frame from results of a tapply. I have this results from tapply: -- , , tapinom sp 1 1 2 3 4 5 6 7 8 9 10 1 NA NA NA NA NA NA NA NA NA NA 4 NA NA NA NA NA NA NA NA NA 4 5 NA NA NA NA NA NA NA NA NA NA 6 NA NA NA NA NA NA NA NA NA NA 7 NA NA NA NA NA NA NA NA NA NA , , wasm sp 2 1 2 3 4 5 6 7 8 9 10 1 1 NA NA NA NA NA NA NA NA NA 4 4 NA NA NA NA NA NA NA NA NA 5 NA NA NA NA NA NA NA NA NA NA 6 NA NA NA NA NA NA NA NA NA NA 7 7 NA 7 7 7 7 NA NA 7 7 I try to enter in tapply result to make a vector for each name, like this: tapinom sp 1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 4 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA The problem is how a access the tapply results? I try using names, but it have no names, I try using [] but without sucess. Thanks Ronaldo -- Prof. Ronaldo Reis Júnior | .''`. UNIMONTES/DBG/Lab. Ecologia Comportamental e Computacional | : :' : Campus Universitário Prof. Darcy Ribeiro, Vila Mauricéia | `. `'` CP: 126, CEP: 39401-089, Montes Claros - MG - Brasil | `- Fone: (38) 3229-8192 | ronaldo.r...@unimontes.br | http://www.ppgcb.unimontes.br/lecc | LinuxUser#: 205366 [[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] Convert character string to top levels + NAN
On Apr 22, 2010, at 5:16 AM, Michael Haenlein wrote: Dear all, I have several character strings with a high number of different levels. unique(x) gives me values in the range of 100-200. This creates problems as I would like to use them as predictors in a coxph model. I therefore would like to convert each of these strings to a new string (x_new). x_new should be equal to x for the top n categories (i.e. the top n levels with the highest occurrence) and NAN elsewhere. For example, for n=3 x_new would have three levels: The three most common levels of x + NAN. Is there some convenient way of doing this? x - sample(c(top, three, levels, 0ther, strings), 30, replace=TRUE, prob=c(.3,.3,.3,.1,.1)) y - c(top, three, levels) xnew - x xnew[ !xnew %in% y ] - NAN # not same as NaN table(xnew) # xnew levelsNAN threetop 5 5 9 11 -- David. Thanks in advance, Michael Michael Haenlein Associate Professor of Marketing ESCP Europe Paris, France [[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. David Winsemius, MD West Hartford, CT __ 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] Help with tapply selection
Try this: as.vector(tapply(...)) On Thu, Apr 22, 2010 at 9:47 AM, Ronaldo Reis Junior chrys...@gmail.comwrote: Hi, I try to create a data.frame from results of a tapply. I have this results from tapply: -- , , tapinom sp 1 1 2 3 4 5 6 7 8 9 10 1 NA NA NA NA NA NA NA NA NA NA 4 NA NA NA NA NA NA NA NA NA 4 5 NA NA NA NA NA NA NA NA NA NA 6 NA NA NA NA NA NA NA NA NA NA 7 NA NA NA NA NA NA NA NA NA NA , , wasm sp 2 1 2 3 4 5 6 7 8 9 10 1 1 NA NA NA NA NA NA NA NA NA 4 4 NA NA NA NA NA NA NA NA NA 5 NA NA NA NA NA NA NA NA NA NA 6 NA NA NA NA NA NA NA NA NA NA 7 7 NA 7 7 7 7 NA NA 7 7 I try to enter in tapply result to make a vector for each name, like this: tapinom sp 1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 4 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA The problem is how a access the tapply results? I try using names, but it have no names, I try using [] but without sucess. Thanks Ronaldo -- Prof. Ronaldo Reis Júnior | .''`. UNIMONTES/DBG/Lab. Ecologia Comportamental e Computacional | : :' : Campus Universitário Prof. Darcy Ribeiro, Vila Mauricéia | `. `'` CP: 126, CEP: 39401-089, Montes Claros - MG - Brasil | `- Fone: (38) 3229-8192 | ronaldo.r...@unimontes.br | http://www.ppgcb.unimontes.br/lecc | LinuxUser#: 205366 [[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. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O [[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] question on rpart
--- Begin included message I have attempted to email the author of this package without success, just wondering if anybody else has experienced this. I am having an using rpart on 4000 rows of data with 13 attributes. I can run the same test on 300 rows of the same data with no issue. When I run on 4000 rows, Rgui.exe runs consistently at 50% cpu and the UI hangs it will stay like this for at least 4-5hours if I let it run, and never exit or become responsive. here is the code I am using both on the 300 and 4000 size subset : train-read.csv(input.csv,header=T) y-train[,18] x-train[,3:17] library(rpart) fit-rpart(y~.,x) Is this a known limitation of rpart, am I doing something wrong? potential workarounds? - I don't remember seeing a message from you. If I accidentally deleted one along with the daily junk mail I apologize. I run rpart on larger problems than this without issue. I'd have to see the data; perchance you have found a never-before-seen infinite loop. Terry Therneau __ 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] install or uncompress package build in one platform in another platform
On Apr 22, 2010, at 8:09 AM, carol white wrote: Hi, Is an R package built under Unix (package.tar.gz) could be installed on other platforms like windows or Mac? The compressed tar file (.tar.gz) built under Unix doesn't seem to be uncompressed under windows (unzip under windows instead of gunzip). How to proceed? If it has only R code then on a Mac the Archive Utility.app would decompress a tar.gz file and give you a package folder that you could put into the appropriate location in your Library. If it has compiled code then no, forget it. There must be ways to ungzip and untar files in Windows. -- David Winsemius, MD West Hartford, CT __ 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] overlaying a levelplot on a map plot
On Apr 22, 2010, at 5:33 AM, Simon Goodman wrote: Thanks for the suggestions Unfortunately contour won't in this case as it expects the x,y values to be in an ascending sequence. ?order David Winsemius, MD West Hartford, CT __ 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] Compare two data frames
I wonder if there is a more efficient way to do this task. Suppose I have two
data frames, such as
d1 - data.frame(x = c(1,2,3), y = c(4,5,6), z = c(7,8,9))
d2 - d1[, c('y', 'x')]
The first dataframe d1 has more variables than d2 and the variable columns are
in a different order.
So, what I want to do is compare the two frames on the variables that are
common between the two. First I find the common variables between the two
dataframes
common_order - intersect(colnames(d1), colnames(d2))
Then, I have to put the variables in d2 in the same order as d1 as
d2 - d2[, common_order]
Then, I keep only the variables in common between d1 and d2 as
d1 - d1[, common_order]
Then, finally I can do the compare on the common variables now in the same
order.
all.equal(d1, d2)
None of this is horribly difficult, but it requires a couple of steps that I am
wondering might be eliminated.
Harold
sessionInfo()
R version 2.10.1 (2009-12-14)
i386-pc-mingw32
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] MiscPsycho_1.6 statmod_1.4.6
loaded via a namespace (and not attached):
[1] tools_2.10.1
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Re: [R] How to stamp my graphs with date and time
Jun, I created a function called pageNum that does exactly what you want for both 'base' and 'lattice' graphics. You can find it here: http://ryouready.wordpress.com/2009/02/17/r-good-practice-adding-footnotes-to-graphics/ Kevin On Wed, Apr 21, 2010 at 7:23 PM, Jun Shen jun.shen...@gmail.com wrote: David, Duncan, Thanks. I didn't realize the functions in graphic also work in lattice. I thought they didn't work with each other. Jun On Wed, Apr 21, 2010 at 6:51 PM, Duncan Murdoch murdoch.dun...@gmail.com wrote: On 21/04/2010 5:41 PM, Jun Shen wrote: Dear all, How do stamp my graphs with date and time somewhere like left corner of the graph (not the plotting area). I know date() and Sys.time(), but where to? Thanks. Use mtext() to put text onto a plot. For example, plot(1) mtext(Sys.time(), side=1, line=4, at=par(usr)[1]) (You will need to play with the side=, line= and at= specifications to get the location you want.) Duncan Murdoch [[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. -- Kevin Wright [[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] R2.11.0 - rasterImage() and barplot fill-patterns
Hi, This idea was also discussed when Paul Murrell first announced the grid.raster function to R-devel, http://tolstoy.newcastle.edu.au/R/e8/devel/09/12/0912.html My personal conclusion was that vector fill patterns are generally better in terms of resolution and speed. Of course the situation might be different if one wanted to use a fancy image pattern, or if there was a fast implementation of tiling patterns at the C level. I wrote a proof-of-concept here --- my main issue is that the resulting grob is not vectorized, http://gridextra.googlecode.com/svn/trunk/inst/comparisonPattern.r Best, baptiste On 22 April 2010 14:10, Tal Galili tal.gal...@gmail.com wrote: Hello Peter, Thank you, and the R core team, for the new release. I see that in R 2.11.0 there is now support for rendering of raster (bitmap) images through rasterImage(). I am wondering - can this be used to create a texture/fill-pattern for hist()/barplot() ? (A request made several times throughout the years on the mailing list. For example: http://osdir.com/ml/lang.r.general/2005-07/msg00799.html ) (I am also sending this e-mail to the maintainers of lattice, ggplot2 and gplots in the hope for more perspectives) With much respect, Tal Contact Details:--- Contact me: tal.gal...@gmail.com | 972-52-7275845 Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) | www.r-statistics.com (English) -- On Thu, Apr 22, 2010 at 12:01 PM, Peter Dalgaard pd@cbs.dk wrote: I've rolled up R-2.11.0.tar.gz a short while ago. This is a development release which contains a number of new features. Also, a number of mostly minor bugs have been fixed. See the full list of changes below. NOTE: The build platform has been changed for this release. Please watch out extra carefully for anomalies. You can get it from http://cran.r-project.org/src/base/R-2/R-2.11.0.tar.gz or wait for it to be mirrored at a CRAN site nearer to you. Binaries for various platforms will appear in due course. For the R Core Team Peter Dalgaard These are the md5sums for the freshly created files, in case you wish to check that they are uncorrupted: MD5 (AUTHORS) = ac9746b4845ae81f51cfc99262f5 MD5 (COPYING) = eb723b61539feef013de476e68b5c50a MD5 (COPYING.LIB) = a6f89e2100d9b6cdffcea4f398e37343 MD5 (FAQ) = 5b653442bedab476a4eff7468192fb5f MD5 (INSTALL) = 70447ae7f2c35233d3065b004aa4f331 MD5 (NEWS) = 59017734fb8474f98f994c7a5a27f9fb MD5 (ONEWS) = a8c985af5ad5e9c7e0a9f502d07baeb4 MD5 (OONEWS) = 4f004de59e24a52d0f500063b4603bcb MD5 (R-latest.tar.gz) = c6c1e866299f533617750889c729bfb3 MD5 (README) = 433182754c05c2cf7a04ad0da474a1d0 MD5 (RESOURCES) = 020479f381d5f9038dcb18708997f5da MD5 (THANKS) = f2ccf22f3e20ebaa86f8ee5cc6b0f655 MD5 (R-2/R-2.11.0.tar.gz) = c6c1e866299f533617750889c729bfb3 This is the relevant part of the NEWS file: CHANGES IN R VERSION 2.11.0 SIGNIFICANT USER-VISIBLE CHANGES o Packages must have been installed under R = 2.10.0, as the current help system is the only one now supported. o A port to 64-bit Windows is now available as well as binary package repositiories: see the 'R Administration and Installation Manual'. o Argument matching for primitive functions is now done in the same way as for interpreted functions except for the deliberate exceptions call switch .C .Fortran .Call .External all of which use positional matching for their first argument, and also some internal-use-only primitives. o The default device for command-line R at the console on Mac OS X is now quartz() and not X11(). NEW FEATURES o The 'open' modes for connections are now interpreted more consistently. open = r is now equivalent to open = rt for all connections. The default open = now means rt for all connections except the compressed file connections gzfile(), bzfile() and xzfile() for which it means rb. o R CMD INSTALL now uses the internal untar() in package utils: this ensures that all platforms can install bzip2- and xz-compressed tarballs. In case this causes problems (as it has on some Windows file systems when run from Cygwin tools) it can be overridden by the environment variable R_INSTALL_TAR: setting this to a modern external tar program will speed up unpacking of large (tens of Mb or more) tarballs. o help(try.all.packages = TRUE) is much faster (although the time taken by the OS to find all the packages the first time it is used can dominate the time). o R CMD check has a new option '--timings' to record per-example timings in file
Re: [R] Compare two data frames
On Apr 22, 2010, at 9:41 AM, Doran, Harold wrote:
I wonder if there is a more efficient way to do this task. Suppose I
have two data frames, such as
d1 - data.frame(x = c(1,2,3), y = c(4,5,6), z = c(7,8,9))
d2 - d1[, c('y', 'x')]
The first dataframe d1 has more variables than d2 and the variable
columns are in a different order. So, what I want to do is compare
the two frames on the variables that are common between the two.
First I find the common variables between the two dataframes
common_order - intersect(colnames(d1), colnames(d2))
Then, I have to put the variables in d2 in the same order as d1 as
d2 - d2[, common_order]
Then, I keep only the variables in common between d1 and d2 as
d1 - d1[, common_order]
Then, finally I can do the compare on the common variables now in
the same order.
all.equal(d1, d2)
None of this is horribly difficult, but it requires a couple of
steps that I am wondering might be eliminated.
What you are doing sounds a lot like the operations that merge()
implements in one function.
--
David.
Harold
David Winsemius, MD
West Hartford, CT
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Re: [R] install or uncompress package build in one platform in another platform
On 22.04.2010 15:34, David Winsemius wrote: On Apr 22, 2010, at 8:09 AM, carol white wrote: Hi, Is an R package built under Unix (package.tar.gz) could be installed on other platforms like windows or Mac? The compressed tar file (.tar.gz) built under Unix doesn't seem to be uncompressed under windows (unzip under windows instead of gunzip). How to proceed? If it has only R code then on a Mac the Archive Utility.app would decompress a tar.gz file and give you a package folder that you could put into the appropriate location in your Library. If it has compiled code then no, forget it. There must be ways to ungzip and untar files in Windows. For more details see the R Installation and Administration manual that tells you how to install source packages under Mac aas well as under Windows. Uwe Ligges __ 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] install or uncompress package build in one platform in another platform
On 22/04/2010 8:09 AM, carol white wrote: Hi, Is an R package built under Unix (package.tar.gz) could be installed on other platforms like windows or Mac? The compressed tar file (.tar.gz) built under Unix doesn't seem to be uncompressed under windows (unzip under windows instead of gunzip). How to proceed? Use either R CMD INSTALL foo.tar.gz at the cmd prompt, or from within R, install.packages(foo.tar.gz, repos=NULL, type=source). R knows how to do the decompression. If the package contains external code, this requires that you have the tools set up to compile it; see www.murdoch-sutherland.com/Rtools to get them for Windows. Most Windows users find it tricky to get the setup right at first, which is why we provide binaries for CRAN packages, and why Uwe provides the http://win-builder.r-project.org/ service. Simon Urbanek has a web page to provide the tools for the Mac. Duncan Murdoch __ 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] densCols: what are the computed densities and how to create a legend
Hi Kate, the function does not directly return the calculated density values, however those can be recomputed through the internal function .smoothScatterCalcDensity This function is not exported from the grDevices name space, so you need to use the full qualifier: dat - cbind(rnorm(100), rnorm(100)) dc - densCols(dat) dd - grDevices:::.smoothScatterCalcDensity(dat, nbin=128) Densities are computed using a binning approach, and the grid of densities is available as the list item fhat. In order to map those to colors we need to find the absolute range of density values: dens - as.numeric(dd$fhat) dens - dens[dens0] range(dens) And now we can construct a mapping of values to colors: colLegend - data.frame(density=seq(min(dens), max(dens), len=10), color=I(colorRampPalette(blues9[-(1:3)])(10))) For plotting of a legend, you could try something like this: plot(NA, xlim=c(0,10), ylim=c(0,11), type=n, ann=FALSE, axes=FALSE) rect(0, 1:10, 1, 2:11, border=NA, col=colLegend$col) text(2, (1:10)+0.5, signif(colLegend$density, 2)) And to get everything in one plot, something like this: layout(matrix(rep(1:2, c(5,1)), nrow=1)) plot(dat, col=dc, pch=20) par(mar=c(5,0,5,0)) plot(NA, xlim=c(0,10), ylim=c(0,11), type=n, ann=FALSE, axes=FALSE) rect(0, 1:10, 1, 2:11, border=NA, col=colLegend$col) text(2, (1:10)+0.5, signif(colLegend$density, 2), adj=0) Please note that there might be some slight rounding errors here, since the colors for densCols are computed on a subset of bins (those in which the data points fall). The bandwidth smoothing results in non-zero density values for neighboring bins, and since we map our colors to the overall range of densities, we can end up being slightly off. If you want this to be 100% accurate, you have to figure out the densities for the filled bins only and map color space to that, in which case you essentially reproduce all that densCols is doing (type densCols in your R session to see the source code and copy paste what you need...) Hope that helps. Florian On Apr 20, 2010, at 4:08 PM, Kate Zinszer wrote: Hi Dr. Hahne, I saw that you were affiliated with this function so perhaps you have some insight in my problem that is stated below? Many thanks, Kate -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Kate Zinszer Sent: 19 avril 2010 15:21 To: r-help@R-project.org Subject: [R] densCols: what are the computed densities and how to create a legend Hi, I'm using the densCols function for a scatterplot and cannot figure out 1) how to extract the computed densities, and 2) how to create a legend based that represents the upper and lower ranges of the densities. For example: movers.den - densCols(move$x, move$y) table(movers.den) #08306B #083775 #083B7C #083D7E #3989C1 #3F8FC4 28 22 101 25 4 5 #4392C6 #65AAD3 #69ACD5 #6CAED6 #77B4D8 #98C6DF 14 684 3 9 plot(move, col=movers.den, pch=20,ylab=y coordinate movement (meters),xlab=x coordinate movement (meters)) abline(h=0, v=0, col = grey, lty=2) #legend?? Any help would be appreciated! Kate __ 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] Jonckheere-Terpstra test using coin package?
I am unfamiliar with how to use coin, but it looks like it should be doable - the vignette in coin.pdf does a Page test. The wikipedia page for Page's test explains how this is related to the Jonckheere-Terpstra test, which seems to suggest if it can do one it should be able to do the other. Add to that the fact that coin can do the unordered version of the J-T (which is just Kruskal-Wallis) and again, it seems like it should be able to do it. -- View this message in context: http://r.789695.n4.nabble.com/Jonckheere-Terpstra-test-using-coin-package-tp2019893p2020340.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 loop.
Thanks a lot for the help, but it’s not what I needed. -- View this message in context: http://r.789695.n4.nabble.com/R-loop-tp1979620p2020386.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] Amusing coincidence
...that this Danish movie would have an official release today: http://www.imdb.com/title/tt1434443/ http://filmz.dk/film/r/trailers/24836 -- Peter Dalgaard Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd@cbs.dk Priv: pda...@gmail.com -- Peter Dalgaard Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd@cbs.dk Priv: pda...@gmail.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] compare variables and take largest value?
On 22/04/2010 11:07 AM, Vlatka Matkovic Puljic wrote: Hi! I have v1, v2 and v3 (data in v. ranges 1 to 4) v1 [1] 1 1 1 1 NaN 1 1 4 1 1 3 v2 [1] 1 1 1 1 1 1 1 1 1 1 1 v3 [1] 1 1 1 1 1 1 1 1 1 1 1 I want R to compare entries in v1,v2,v3 and in v4 to put largest value (NA=0). For example. first line v4 would be 1, but last line v4 would be 3. What function should I use? pmax. Duncan Murdoch __ 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] cell-based high-throughput chemical compound screens package?
Hi I'm looking for a package to perform quality control, normalization and analysis of high throughput cell-base chemical screens. I know that the cellHTS2 package provides this for siRNA screens. Does anybody know if something like what I'm looking for exists? Thank you! Gabriele Zoppoli, MD Ph.D. Fellow, Experimental and Clinical Oncology and Hematology, University of Genova, Genova, Italy Guest Researcher, LMP, NCI, NIH, Bethesda MD Work: 301-451-8575 Mobile: 301-204-5642 Email: zoppo...@mail.nih.gov __ 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] compare variables and take largest value?
Thanx a lot! That's it! 2010/4/22 Duncan Murdoch murdoch.dun...@gmail.com On 22/04/2010 11:07 AM, Vlatka Matkovic Puljic wrote: Hi! I have v1, v2 and v3 (data in v. ranges 1 to 4) v1 [1] 1 1 1 1 NaN 1 1 4 1 1 3 v2 [1] 1 1 1 1 1 1 1 1 1 1 1 v3 [1] 1 1 1 1 1 1 1 1 1 1 1 I want R to compare entries in v1,v2,v3 and in v4 to put largest value (NA=0). For example. first line v4 would be 1, but last line v4 would be 3. What function should I use? pmax. Duncan Murdoch __ 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. -- ** Vlatka Matkovic Puljic 095/8618 171 [[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] Amusing coincidence
On Thu, Apr 22, 2010 at 3:27 PM, peter dalgaard pda...@gmail.com wrote: ...that this Danish movie would have an official release today: http://www.imdb.com/title/tt1434443/ Does it have music by this composer: http://www.imdb.com/name/nm1731203/ and stills photography by: http://www.imdb.com/name/nm2083657/ ? __ 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] using which to select range of values
Hi all, I would like to get the array index for a range of values, say 0 x 1.5. I'm wondering if there is an alternative for the following which I've done x0 - rnorm(100) x1 - ifelse(x0 0 x0 1.5,t,f) x2 - which(x1==t,arr.ind=TRUE) x0[x2] Thanks. -- Muhammad __ 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] compare variables and take largest value?
Only thing that when I put na.rm=FALSE, R is puting in v4 NA (as is largest) and I want to see NA as zero (0, smallest value) 2010/4/22 Vlatka Matkovic Puljic v.matkovic.pul...@gmail.com Thanx a lot! That's it! 2010/4/22 Duncan Murdoch murdoch.dun...@gmail.com On 22/04/2010 11:07 AM, Vlatka Matkovic Puljic wrote: Hi! I have v1, v2 and v3 (data in v. ranges 1 to 4) v1 [1] 1 1 1 1 NaN 1 1 4 1 1 3 v2 [1] 1 1 1 1 1 1 1 1 1 1 1 v3 [1] 1 1 1 1 1 1 1 1 1 1 1 I want R to compare entries in v1,v2,v3 and in v4 to put largest value (NA=0). For example. first line v4 would be 1, but last line v4 would be 3. What function should I use? pmax. Duncan Murdoch __ 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. -- ** Vlatka Matkovic Puljic 095/8618 171 -- ** Vlatka Matkovic Puljic 095/8618 171 [[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] Amusing coincidence
On 22-Apr-10 15:19:45, Barry Rowlingson wrote: On Thu, Apr 22, 2010 at 3:27 PM, peter dalgaard pda...@gmail.com wrote: ...that this Danish movie would have an official release today: http://www.imdb.com/title/tt1434443/ Does it have music by this composer: http://www.imdb.com/name/nm1731203/ and stills photography by: http://www.imdb.com/name/nm2083657/ ? Nah, it was all outsourced to http://www.imdb.com/name/nm0264036/ Ted. E-Mail: (Ted Harding) ted.hard...@manchester.ac.uk Fax-to-email: +44 (0)870 094 0861 Date: 22-Apr-10 Time: 16:34:19 -- XFMail -- __ 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] using which to select range of values
Hi, On Thu, Apr 22, 2010 at 11:21 AM, Muhammad Rahiz muhammad.ra...@ouce.ox.ac.uk wrote: Hi all, I would like to get the array index for a range of values, say 0 x 1.5. I'm wondering if there is an alternative for the following which I've done x0 - rnorm(100) x1 - ifelse(x0 0 x0 1.5,t,f) x2 - which(x1==t,arr.ind=TRUE) x0[x2] Two things: 1. Not that it really matters, but why are you using arr.ind=TRUE when x0 is just a normal vector? 2. Just skip the middle-man creation of x1: R x0 - rnorm(100) R x2 - which(x0 0 x0 1.5) R x0[x2] Why not just skip the middle man (x1)? -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact __ 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] using which to select range of values
On Apr 22, 2010, at 11:39 AM, Steve Lianoglou wrote: Hi, On Thu, Apr 22, 2010 at 11:21 AM, Muhammad Rahiz muhammad.ra...@ouce.ox.ac.uk wrote: Hi all, I would like to get the array index for a range of values, say 0 x 1.5. I'm wondering if there is an alternative for the following which I've done x0 - rnorm(100) x1 - ifelse(x0 0 x0 1.5,t,f) x2 - which(x1==t,arr.ind=TRUE) x0[x2] Two things: 1. Not that it really matters, but why are you using arr.ind=TRUE when x0 is just a normal vector? 2. Just skip the middle-man creation of x1: R x0 - rnorm(100) R x2 - which(x0 0 x0 1.5) R x0[x2] Why not just skip the middle man (x1)? Or just skip all the middle-men: x0[ which(x0 0 x0 1.5) ] And further simplification with logical indexing: x0[ x0 0 x0 1.5 ] -- David. -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact __ 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. David Winsemius, MD West Hartford, CT __ 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] using which to select range of values
On Apr 22, 2010, at 11:21 AM, Muhammad Rahiz wrote: Hi all, I would like to get the array index for a range of values, say 0 x 1.5. I'm wondering if there is an alternative for the following which I've done x0 - rnorm(100) x1 - ifelse(x0 0 x0 1.5,t,f) x2 - which(x1==t,arr.ind=TRUE) A further point. Since x1 was not an array, setting arr.ind=TRUE did nothing. That flag is designed to allow return of multiple dimensional results: arr - array(1:27, c(3,3,3) ) which(arr==9) [1] 9 which(arr==9, arr.ind=TRUE) dim1 dim2 dim3 [1,]331 x0[x2] Thanks. -- -- David Winsemius, MD West Hartford, CT __ 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] macro variable in R?
I need to create 10 matrices. say matrix 1-10.
matrix_1 is 1 by 1
matrix_2 is 2 by 2
matrix_3 is 3 by 3
.
.
.
matrix_10 is 10 by 10
I am just wondering if there are some functions in R that are similar to the
macro variables in SAS. so I can create these 10 matrices by doing:
for (i in 1: 10) {
matrix_$i - matrix(nrow=i, ncol=i)
}
rather thank creating these matrices one by one manually.
Anyone have any suggestions?
thanks,
karena
--
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[R] Multicolor main title in a plot or mtext
Dear R-users, the problem I'm facing today is to write a
multicolor main title in a plot.
I would like to have 3/4 colors to help people in the
audience to visually realize what is what in a 4x2 plot array
On top of each plot I would like to have two lines.
The 1st line will indicate what is plotted
The 2nd line will indicate a a reference
Graphically speaking I would like a result similar to this (simplified) one:
par(mfrow=c(2,4))
for(aux in 1:4){
plot(1,1)
mtext(1st treatm, cex=1, line=1.7, adj=0.1, col=1)
mtext(2nd treatm, cex=1, line=1.7, adj=0.5, col=2)
mtext(3rd treatm, cex=1, line=1.7, adj=0.9, col=3)
mtext(1st treatm, line=0.6, adj=0.1, col=1)
mtext(1st treatm, line=0.6, adj=0.5, col=1)
mtext(1st treatm, line=0.6, adj=0.9, col=1)
}
for(aux in 1:4){
plot(2,2)
mtext(1st treatm, cex=1, line=1.7, adj=0.1, col=1)
mtext(2nd treatm, cex=1, line=1.7, adj=0.5, col=2)
mtext(3rd treatm, cex=1, line=1.7, adj=0.9, col=3)
mtext(2nd treatm, line=0.6, adj=0.1, col=2)
mtext(2nd treatm, line=0.6, adj=0.5, col=2)
mtext(2nd treatm, line=0.6, adj=0.9, col=2)
}
The code above does more or less what I want and
I wrote it to simplify my explanation to you all.
But what I really need is to put on top of each plot
an entire string with color embedded into, so to say.
A sort of 1st treatm 2nd treatm 3rd treatm string with
informations able to colour the word 1st treatm in black,
the word 2nd treatm in red and so on.
I need this because I have my descriptions in a vector like
c(1st treatm 2nd treatm 3rd treatm,
2nd treatm 3rd treatm 1st treatm,
...)
What I have in mind is something similar to the latex code
\color{black}{1st treatm} \color{red}{2nd treatm} \color{green}{3rd treatm}
Which pages of the R manual should I have to read to solve my problem ?
Thanks in advance
--
Ottorino-Luca Pantani, Università di Firenze
Dip.to di Scienze delle Produzioni Vegetali,
del Suolo e dell'Ambiente Forestale (DiPSA)
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Re: [R] macro variable in R?
Why don't use a list?
m - list()
for(i in 1:10) {
m[[i]] - matrix(NA, i, i)
}
then access them as m[[7]][1,6]
Ciao!
mario
On 22-Apr-10 18:08, karena wrote:
I need to create 10 matrices. say matrix 1-10.
matrix_1 is 1 by 1
matrix_2 is 2 by 2
matrix_3 is 3 by 3
.
.
.
matrix_10 is 10 by 10
I am just wondering if there are some functions in R that are similar to the
macro variables in SAS. so I can create these 10 matrices by doing:
for (i in 1: 10) {
matrix_$i- matrix(nrow=i, ncol=i)
}
rather thank creating these matrices one by one manually.
Anyone have any suggestions?
thanks,
karena
--
Ing. Mario Valle
Data Analysis and Visualization Group|
http://www.cscs.ch/~mvalle
Swiss National Supercomputing Centre (CSCS) | Tel: +41 (91) 610.82.60
v. Cantonale Galleria 2, 6928 Manno, Switzerland | Fax: +41 (91) 610.82.82
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Re: [R] macro variable in R?
maybe
for (i in 1:10) assign(paste(matrix, i, sep=_), matrix(nrow=i, ncol=i))
suffices?
On Thu, Apr 22, 2010 at 5:08 PM, karena dr.jz...@gmail.com wrote:
I need to create 10 matrices. say matrix 1-10.
matrix_1 is 1 by 1
matrix_2 is 2 by 2
matrix_3 is 3 by 3
.
.
.
matrix_10 is 10 by 10
I am just wondering if there are some functions in R that are similar to the
macro variables in SAS. so I can create these 10 matrices by doing:
for (i in 1: 10) {
matrix_$i - matrix(nrow=i, ncol=i)
}
rather thank creating these matrices one by one manually.
Anyone have any suggestions?
thanks,
karena
--
View this message in context:
http://r.789695.n4.nabble.com/macro-variable-in-R-tp2020772p2020772.html
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and provide commented, minimal, self-contained, reproducible code.
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Re: [R] macro variable in R?
Hi,
On Thu, Apr 22, 2010 at 12:08 PM, karena dr.jz...@gmail.com wrote:
I need to create 10 matrices. say matrix 1-10.
matrix_1 is 1 by 1
matrix_2 is 2 by 2
matrix_3 is 3 by 3
.
.
.
matrix_10 is 10 by 10
I am just wondering if there are some functions in R that are similar to the
macro variables in SAS. so I can create these 10 matrices by doing:
for (i in 1: 10) {
matrix_$i - matrix(nrow=i, ncol=i)
}
rather thank creating these matrices one by one manually.
Anyone have any suggestions?
I believe the most idiomatic R way is to make a list of length 10:
R mats - lapply(1:10, function(x) matrix(0, nrow=x, ncol=x))
Then reference them like so:
R mats[[1]]
If you *really* want them to be in your global namespace, you have two options:
1. You can slightly modify the `mat` list I made above with more
variable-friendly names and then `attach` it (or use `with`):
R names(mats) - paste(m, 1:10, sep=)
R attach(mats)
R m2
[,1] [,2]
[1,]00
[2,]00
2. Or you could forget the `lapply` from above use `assign` in a for loop:
R for (i in 1:10) {
assign(sprintf('mat%d', i), matrix(0, nrow=i, ncol=i))
}
R mat2
[,1] [,2]
[1,]00
[2,]00
Other notes: using attach isn't really best practice -- look into using `with`
Documentation you should read:
?lapply
?attach
?with
?assign
-steve
--
Steve Lianoglou
Graduate Student: Computational Systems Biology
| Memorial Sloan-Kettering Cancer Center
| Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact
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Re: [R] R loop.
You did not give a good description of your problem, or what you wanted as a
solution (what is a 'button'), or a reasonable idea of what you data is.
Here is one solution
x - read.table(textConnection(Deafness, EYA4, DIAPH1, MYO7A, TECTA,
COL11A2, POU4F3, MYH9, ACTG1, MYO6),
as.is=TRUE, sep=',')
output - file('output.txt', 'w')
for (i in seq(nrow(x))){
for (j in 2:ncol(x)){
cat(x[i,1], ',', x[i,j], '\n', file=output)
}
}
close(output)
output.txt file*
Deafness , EYA4
Deafness , DIAPH1
Deafness , MYO7A
Deafness , TECTA
Deafness , COL11A2
Deafness , POU4F3
Deafness , MYH9
Deafness , ACTG1
Deafness , MYO6
On Thu, Apr 22, 2010 at 7:07 AM, mhalsham mhals...@bradford.ac.uk wrote:
Thanks a lot for the help, but its not what I needed.
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and provide commented, minimal, self-contained, reproducible code.
--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem that you are trying to solve?
[[alternative HTML version deleted]]
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[R] Arima online forecasting
I'd like to have an online horizon=k forecast with Arima, something like:
library(forecast)
air.model = Arima(AirPassengers[0:100], c(1,0,1),
seasonal=list(order=c(0,1,1), period=12))
for(i in 0:(length(AirPassengers)-100)) {
air.model2 = Arima(AirPassengers[0:(100+i)], model=air.model)
cat(forecast(air.model2, h=2)$mean, '\n')
}
But this approach, even if not fitting the model from scratch, is still very
slow for big timeseries.
Some hints to speed it up?
Thanks,
Matteo
[[alternative HTML version deleted]]
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[R] Error in plotting non-linear regression
Hello everyone,
I'm trying to draw the non-linear regression curve to look at the
distance decay relationship between distance and correlation values. But
I'm not able to plot the curve as I'm struggling with the following
error (parameters without starting value in 'data': x) and found no
answers online.*
*Can anyone help...
--
Muhammad*
*s1 cm
10 0.57223196
2 10 0.33110049
3 20 0.11163181
4 30 0.10242237
5 40 0.09254315
6 50 0.02739370
7 60 0.02567137
8 70 0.02492397
9 80 0.03206637
10 90 0.02487381
11 100 0.01747584
12 110 0.15977533
13 120 0.13317708
new - data.frame(s1,cm)
plot(s1,cm)
f - function(x,a,b){a*exp(-b*x)}
fm - nls(cm~f(x,a,b),data=new,start=c(a=1,b=1))
co - coef(fm)
curve(f(x,a=co[1],b=co[2]),add=TRUE,col=blue)
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Re: [R] macro variable in R?
On Apr 22, 2010, at 12:24 PM, Steve Lianoglou wrote:
Hi,
On Thu, Apr 22, 2010 at 12:08 PM, karena dr.jz...@gmail.com wrote:
I need to create 10 matrices. say matrix 1-10.
matrix_1 is 1 by 1
matrix_2 is 2 by 2
matrix_3 is 3 by 3
.
.
.
matrix_10 is 10 by 10
I am just wondering if there are some functions in R that are
similar to the
macro variables in SAS. so I can create these 10 matrices by doing:
for (i in 1: 10) {
matrix_$i - matrix(nrow=i, ncol=i)
}
rather thank creating these matrices one by one manually.
Anyone have any suggestions?
I believe the most idiomatic R way is to make a list of length 10:
R mats - lapply(1:10, function(x) matrix(0, nrow=x, ncol=x))
A somewhat similar method using Map:
mtxlist - Map(matrix, rep(0,10), 1:10, 1:10)
names(mtxlist) - paste(matrix, 1:10, sep=_)
mtxlist$matrix_1
mtxlist$matrix_10
Or with nested Map/mapply calls:
mtxlist - Map(assign, paste(matx, 1:10, sep=_), Map(matrix,
rep(0,10), 1:10, 1:10) )
And if you wanted to have all of those individual mtx_n's floating
around:
mapply(assign,
paste(matx, 1:4, sep=_),
Map(matrix, 1:4, 1:4, 1:4),
MoreArgs=list( envir=.GlobalEnv) )
Then reference them like so:
R mats[[1]]
If you *really* want them to be in your global namespace, you have
two options:
1. You can slightly modify the `mat` list I made above with more
variable-friendly names and then `attach` it (or use `with`):
R names(mats) - paste(m, 1:10, sep=)
R attach(mats)
R m2
[,1] [,2]
[1,]00
[2,]00
2. Or you could forget the `lapply` from above use `assign` in a for
loop:
R for (i in 1:10) {
assign(sprintf('mat%d', i), matrix(0, nrow=i, ncol=i))
}
R mat2
[,1] [,2]
[1,]00
[2,]00
Other notes: using attach isn't really best practice -- look into
using `with`
Documentation you should read:
?lapply
?attach
?with
?assign
-steve
--
Steve Lianoglou
Graduate Student: Computational Systems Biology
| Memorial Sloan-Kettering Cancer Center
| Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact
__
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and provide commented, minimal, self-contained, reproducible code.
David Winsemius, MD
West Hartford, CT
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Re: [R] R crashing oddly
Hi Uwe,
I downloaded R 2.11.0 and the latest version of nlme. I am still getting the
problem. I should also note that I got a message from Viechtbauer Wolfgang
saying that he had experienced a similar problem using nlme.
I have pasted the code below. (The data is generated in the first ~15
lines). I have bunch of debug() statements, which may or may not be useful.
The code is not as elegant as it could be since I have been constantly
editing it to try to track down the bug (I replaced the corMatrix C routine
with R code). FYI, the objective of the code is to simultaneously fit
temporal and spatial correlation (adding one corExp matrix plus another)
where the nuggets are constrained to add to 1.
I really hope you have a chance to look at this. Thanks so much!!
## BEGIN
N - 100
x - round(sin(rep(1:23/2,length.out=N)),digits=2)+1:N*2/N
y - round(cos(rep(1:23/2,length.out=N)),digits=2)+1:N*2/N
g - rep(1:5,each=N/5)
a - round(runif(N,0,10))
t - 1:N
r - runif(N,0,5)
e - 5*sin(4*x) +
5*cos(4*y) +
5*sin(t) +
2*g +
a +
r
e - round(e)
df - data.frame(x,y,g,a,t,r,e)
df - df[-c(22,23,67),]
library(nlme)
corSPT - function(a,b) {
object - list(time=a,space=b)
class(object) - c(corSPT,corSpatial,corStruct)
attr(object, formula) - formula(object)
attr(object, nugget) - attr(object[[time]], nugget)
attr(object, metric) - attr(object[[time]], metric)
attr(object, fixed) - attr(object[[time]], fixed)
return(object)
}
coef.corSPT - function(object,...) {
c(time=coef(object[[time]],...),space=coef(object[[space]],...)[1])
}
coef-.corSPT - function (object, ..., value) {
value - as.numeric(value)
if (length(value) != 3) {
stop(Cannot change the length of the parameter of a corSPT object)
}
object[[time]][] - value[1:2]
object[[space]][] - c(value[3],-value[2]) # nugget for space is
determined by the nugget for time
attr(object, factor) - NULL
attr(object, factor) - corFactor(object)
attr(object, logDet) - NULL
attr(object, logDet) - logDet(object)
object
}
Initialize.corSPT - function (object, data, ...) {
if (!is.null(attr(object[[time]], minD))) {
return(object)
}
object[[time]] -
getS3method(Initialize,corStruct)(object[[time]], data)
object[[space]] -
getS3method(Initialize,corStruct)(object[[space]], data)
object[[time]][1] - log(object[[time]][1])
object[[space]][1] - log(object[[space]][1])
object[[time]][2] - log(object[[time]][2]/(1 -
object[[time]][2]))
object[[space]][2] - -object[[time]][2]
attr(object,groups) - attr(object[[time]],groups)
attr(object,Dim) - attr(object[[time]],Dim)
attr(object,covariate) - NULL
attr(object, nugget) - attr(object[[time]], nugget)
attr(object[[time]],minD) - min(unlist(attr(object[[time]],
covariate)))
attr(object[[space]],minD) - min(unlist(attr(object[[space]],
covariate)))
attr(object, minD) - NULL
###
corD - Dim(object[[time]])
attr(object[[time]],covariate) - lapply(seq(corD$M),function(M) {
x - attr(object[[time]],covariate)[[M]]
l - corD$len[M]
g - rep(seq(l),(l-1):0)
mat - do.call(rbind,lapply(seq(l),function(G) {c(rep(0,G),x[g==G])}))
mat - mat + t(mat)
})
attr(object[[space]],covariate) - lapply(seq(corD$M),function(M) {
x - attr(object[[space]],covariate)[[M]]
l - corD$len[M]
g - rep(seq(l),(l-1):0)
mat - do.call(rbind,lapply(seq(l),function(G) {c(rep(0,G),x[g==G])}))
mat - mat + t(mat)
})
###
attr(object, factor) - corFactor(object)
attr(object, logDet) - -attr(attr(object, factor), logDet)
object
}
corMatrix.corSPT - function(object,covariate = NULL,corr=TRUE, ...) {
if (corr) {
temp - coef(object[[time]],unconstrained=FALSE)
cat(temp)
time.rng - temp[1]
time.nug - temp[2]
temp - coef(object[[space]],unconstrained=FALSE)
space.rng - temp[1]
space.nug - temp[2]
cor.time - lapply(attr(object[[time]],covariate),function(mat)
(1-time.nug)*exp(-mat/time.rng))
cor.space - lapply(attr(object[[space]],covariate),function(mat)
(1-space.nug)*exp(-mat/space.rng))
x - lapply(seq(length(cor.time)),function(mat)
round(cor.time[[mat]]+cor.space[[mat]],4))
attr(x, logDet) - NULL
} else {
d - Dim(object)
gg - rep(seq(d$M),each=d$len^2)
cf - corFactor(object)
lD - attr(cf, logDet)
x - lapply(seq(d$M),function(mm) {mat - cf[gg==mm];
matrix(mat,nrow=d$len[mm])})
attr(x,logDet) - lD
}
return(x)
}
corFactor.corSPT - getS3method(corFactor,corStruct)
logDet.corSPT - getS3method(logDet,corStruct)
recalc.corSPT - getS3method(recalc,corStruct)
formula.corSPT - function(object,...) {
a - as.character(formula(object[[time]]))
b - as.character(formula(object[[space]]))
a - strsplit(a[2],split=|,fixed=TRUE)[[1]]
b - strsplit(b[2],split=|,fixed=TRUE)[[1]]
as.formula(paste(~,a[1],+,b[1],|,a[2]))
}
Dim.corSPT - function(object,...) {
[R] simple question
Hi how can I find, in a vector of characters, which is the most frequent one? Thanks Gabriele Zoppoli, MD Ph.D. Fellow, Experimental and Clinical Oncology and Hematology, University of Genova, Genova, Italy Guest Researcher, LMP, NCI, NIH, Bethesda MD Work: 301-451-8575 Mobile: 301-204-5642 Email: zoppo...@mail.nih.gov __ 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] Error in plotting non-linear regression
On 2010-04-22 11:09, Muhammad Rahiz wrote:
Hello everyone,
I'm trying to draw the non-linear regression curve to look at the
distance decay relationship between distance and correlation values. But
I'm not able to plot the curve as I'm struggling with the following
error (parameters without starting value in 'data': x) and found no
answers online.*
*Can anyone help...
--
Muhammad*
* s1 cm
1 0 0.57223196
2 10 0.33110049
3 20 0.11163181
4 30 0.10242237
5 40 0.09254315
6 50 0.02739370
7 60 0.02567137
8 70 0.02492397
9 80 0.03206637
10 90 0.02487381
11 100 0.01747584
12 110 0.15977533
13 120 0.13317708
new - data.frame(s1,cm)
plot(s1,cm)
f - function(x,a,b){a*exp(-b*x)} fm -
nls(cm~f(x,a,b),data=new,start=c(a=1,b=1)) co - coef(fm)
Presumably you want f(s1,a,b) in your nls call.
-Peter Ehlers
curve(f(x,a=co[1],b=co[2]),add=TRUE,col=blue)
__
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http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Peter Ehlers
University of Calgary
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Re: [R] Amusing coincidence
On Apr 22, 2010, at 10:34 AM, Ted Harding wrote: On 22-Apr-10 15:19:45, Barry Rowlingson wrote: On Thu, Apr 22, 2010 at 3:27 PM, peter dalgaard pda...@gmail.com wrote: ...that this Danish movie would have an official release today: http://www.imdb.com/title/tt1434443/ Does it have music by this composer: http://www.imdb.com/name/nm1731203/ and stills photography by: http://www.imdb.com/name/nm2083657/ ? Nah, it was all outsourced to http://www.imdb.com/name/nm0264036/ Ted. And of course, a member of the screen writing team is http://www.imdb.com/title/tt0134119/ :-) Regards, Marc Schwartz __ 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] simple question
Hello, What about test - c(rep(c(A,C,G,T), 20),C) table(test) I am not sure that is an apt representation of the data and problem you are trying to solve. It also occurred to me that each character may not be its own element in the vector. If that is so, you would need to do something a little differently. Let us know. Josh On Thu, Apr 22, 2010 at 10:36 AM, Zoppoli, Gabriele (NIH/NCI) [G] zoppo...@mail.nih.gov wrote: Hi how can I find, in a vector of characters, which is the most frequent one? Thanks Gabriele Zoppoli, MD Ph.D. Fellow, Experimental and Clinical Oncology and Hematology, University of Genova, Genova, Italy Guest Researcher, LMP, NCI, NIH, Bethesda MD Work: 301-451-8575 Mobile: 301-204-5642 Email: zoppo...@mail.nih.gov __ 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. -- Joshua Wiley Senior in Psychology University of California, Riverside http://www.joshuawiley.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] simple question
Hi Gabriele,
This is one way but I'm sure that there is an optimal way of doing so...
x - c(A,B,C,C,C,C,C,B,B)
name - unique(x) # get unique characters
freq - c()
for (a in 1:length(name)){
freq[a] - sum(x==name[a])}# get frequency
out - cbind(name,freq)
Muhammad
Zoppoli, Gabriele (NIH/NCI) [G] wrote:
Hi
how can I find, in a vector of characters, which is the most frequent one?
Thanks
Gabriele Zoppoli, MD
Ph.D. Fellow, Experimental and Clinical Oncology and Hematology, University of
Genova, Genova, Italy
Guest Researcher, LMP, NCI, NIH, Bethesda MD
Work: 301-451-8575
Mobile: 301-204-5642
Email: zoppo...@mail.nih.gov
__
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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.
__
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Re: [R] simple question
On Apr 22, 2010, at 1:36 PM, Zoppoli, Gabriele (NIH/NCI) [G] wrote: Hi how can I find, in a vector of characters, which is the most frequent one? a - sample(letters[1:10], 100, replace=TRUE) table(a) a a b c d e f g h i j 10 7 7 13 7 12 1 14 15 14 max(table(a)) [1] 15 which.max(table(a)) i 9 # so the ninth element in the table is the max table(a)[which.max(table(a))] i 15 # but the table entry needs to be extracted if you want the count. Thanks Gabriele Zoppoli, MD Ph.D. Fellow, Experimental and Clinical Oncology and Hematology, University of Genova, Genova, Italy Guest Researcher, LMP, NCI, NIH, Bethesda MD Work: 301-451-8575 Mobile: 301-204-5642 Email: zoppo...@mail.nih.gov __ 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. David Winsemius, MD West Hartford, CT __ 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] Error in plotting non-linear regression
It now works. Thanks both.
Muhammad
Peter Ehlers wrote:
On 2010-04-22 11:09, Muhammad Rahiz wrote:
Hello everyone,
I'm trying to draw the non-linear regression curve to look at the
distance decay relationship between distance and correlation values. But
I'm not able to plot the curve as I'm struggling with the following
error (parameters without starting value in 'data': x) and found no
answers online.*
*Can anyone help...
--
Muhammad*
* s1 cm
1 0 0.57223196
2 10 0.33110049
3 20 0.11163181
4 30 0.10242237
5 40 0.09254315
6 50 0.02739370
7 60 0.02567137
8 70 0.02492397
9 80 0.03206637
10 90 0.02487381
11 100 0.01747584
12 110 0.15977533
13 120 0.13317708
new - data.frame(s1,cm)
plot(s1,cm)
f - function(x,a,b){a*exp(-b*x)} fm -
nls(cm~f(x,a,b),data=new,start=c(a=1,b=1)) co - coef(fm)
Presumably you want f(s1,a,b) in your nls call.
-Peter Ehlers
curve(f(x,a=co[1],b=co[2]),add=TRUE,col=blue)
__
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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.
__
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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] simple question
Gabriele -
How about this:
data-c(A,A,A,B,B,C,D)
data
[1] A A A B B C D
table(data)
data
A B C D
3 2 1 1
Thanks,
Lee
. . . people who focus only on 'what is' will create more of 'what is.'
People who focus mostly on 'what could be' will begin to create 'what
could be.' ~ Laura Beth Jones
Lee P. Adams | Fuel Emissions Strategy | Luminant Energy |
lee.ad...@luminant.com | 214.875.8737 Office | 214.701.0687 Mobile
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org]
On Behalf Of Zoppoli, Gabriele (NIH/NCI) [G]
Sent: Thursday, April 22, 2010 12:37 PM
To: r-help@r-project.org
Subject: [R] simple question
Hi
how can I find, in a vector of characters, which is the most frequent
one?
Thanks
Gabriele Zoppoli, MD
Ph.D. Fellow, Experimental and Clinical Oncology and Hematology,
University of Genova, Genova, Italy
Guest Researcher, LMP, NCI, NIH, Bethesda MD
Work: 301-451-8575
Mobile: 301-204-5642
Email: zoppo...@mail.nih.gov
__
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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.
Confidentiality Notice: This email message, including an...{{dropped:10}}
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Re: [R] overlaying a levelplot on a map plot
Mixing base/lattice graphics can be tricky, but is possible.
http://www.bioconductor.org/CRAN/web/packages/gridBase/vignettes/gridBase.pdf
Also, did you look at Chapter 13 of the lattice book?
http://lmdvr.r-forge.r-project.org/figures/figures.html
Kevin
On Wed, Apr 21, 2010 at 2:08 PM, David Winsemius dwinsem...@comcast.netwrote:
On Apr 21, 2010, at 2:27 PM, Simon Goodman wrote:
I've generated a levelplot showing the density distribution of a species
derived from survey transects, with lon, lat co-ordinates.
I'd like to overlay this on a map of the study region specified by:
map('worldHires', xlim = range(mlon), ylim = range(mlat)), where mlon,
mlat
specifies the study region.
?map
No documentation for 'map' in specified packages and libraries:
you could try '??map'
??map
require(maps)
Loading required package: maps
map
So map uses base graphics.
I've tried plotting the map first, then using the options: 'add=TRUE,
axes=FALSE' in the levelplot,
levelplot is a lattice function. You will have failure with most efforts to
mix base and grid graphics.
but this doesn't work - a new plot is
generated for the level plot despite the 'add' option. If I try to add the
map on top of the level plot, they are not to the same scale.
Any suggestions on how to get round this.
Thanks
--
View this message in context:
http://n4.nabble.com/overlaying-a-levelplot-on-a-map-plot-tp2019419p2019419.html
Sent from the R help mailing list archive at Nabble.com.
__
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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.
David Winsemius, MD
West Hartford, CT
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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.
--
Kevin Wright
[[alternative HTML version deleted]]
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Re: [R] compare variables and take largest value?
Try this: apply(replace(v - rbind(v1, v2, v3), is.nan(v), 0), 2, max) On Thu, Apr 22, 2010 at 12:24 PM, Vlatka Matkovic Puljic v.matkovic.pul...@gmail.com wrote: Only thing that when I put na.rm=FALSE, R is puting in v4 NA (as is largest) and I want to see NA as zero (0, smallest value) 2010/4/22 Vlatka Matkovic Puljic v.matkovic.pul...@gmail.com Thanx a lot! That's it! 2010/4/22 Duncan Murdoch murdoch.dun...@gmail.com On 22/04/2010 11:07 AM, Vlatka Matkovic Puljic wrote: Hi! I have v1, v2 and v3 (data in v. ranges 1 to 4) v1 [1] 1 1 1 1 NaN 1 1 4 1 1 3 v2 [1] 1 1 1 1 1 1 1 1 1 1 1 v3 [1] 1 1 1 1 1 1 1 1 1 1 1 I want R to compare entries in v1,v2,v3 and in v4 to put largest value (NA=0). For example. first line v4 would be 1, but last line v4 would be 3. What function should I use? pmax. Duncan Murdoch __ 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. -- ** Vlatka Matkovic Puljic 095/8618 171 -- ** Vlatka Matkovic Puljic 095/8618 171 [[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. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O [[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] Multicolor main title in a plot or mtext
Perhaps this helps?
http://blog.revolution-computing.com/2009/01/multicolor-text-in-r.html
Kevin
On Thu, Apr 22, 2010 at 11:18 AM, Ottorino-Luca Pantani
ottorino-luca.pant...@unifi.it wrote:
Dear R-users, the problem I'm facing today is to write a
multicolor main title in a plot.
I would like to have 3/4 colors to help people in the
audience to visually realize what is what in a 4x2 plot array
On top of each plot I would like to have two lines.
The 1st line will indicate what is plotted
The 2nd line will indicate a a reference
Graphically speaking I would like a result similar to this (simplified)
one:
par(mfrow=c(2,4))
for(aux in 1:4){
plot(1,1)
mtext(1st treatm, cex=1, line=1.7, adj=0.1, col=1)
mtext(2nd treatm, cex=1, line=1.7, adj=0.5, col=2)
mtext(3rd treatm, cex=1, line=1.7, adj=0.9, col=3)
mtext(1st treatm, line=0.6, adj=0.1, col=1)
mtext(1st treatm, line=0.6, adj=0.5, col=1)
mtext(1st treatm, line=0.6, adj=0.9, col=1)
}
for(aux in 1:4){
plot(2,2)
mtext(1st treatm, cex=1, line=1.7, adj=0.1, col=1)
mtext(2nd treatm, cex=1, line=1.7, adj=0.5, col=2)
mtext(3rd treatm, cex=1, line=1.7, adj=0.9, col=3)
mtext(2nd treatm, line=0.6, adj=0.1, col=2)
mtext(2nd treatm, line=0.6, adj=0.5, col=2)
mtext(2nd treatm, line=0.6, adj=0.9, col=2)
}
The code above does more or less what I want and
I wrote it to simplify my explanation to you all.
But what I really need is to put on top of each plot
an entire string with color embedded into, so to say.
A sort of 1st treatm 2nd treatm 3rd treatm string with
informations able to colour the word 1st treatm in black,
the word 2nd treatm in red and so on.
I need this because I have my descriptions in a vector like
c(1st treatm 2nd treatm 3rd treatm,
2nd treatm 3rd treatm 1st treatm,
...)
What I have in mind is something similar to the latex code
\color{black}{1st treatm} \color{red}{2nd treatm} \color{green}{3rd treatm}
Which pages of the R manual should I have to read to solve my problem ?
Thanks in advance
--
Ottorino-Luca Pantani, Università di Firenze
Dip.to di Scienze delle Produzioni Vegetali,
del Suolo e dell'Ambiente Forestale (DiPSA)
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PLEASE do read the posting guide
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and provide commented, minimal, self-contained, reproducible code.
--
Kevin Wright
[[alternative HTML version deleted]]
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[R] Accessing outside data sources for stock data?
Hi All, I apologize if this is not the right forum for this question. I know there used to be a package for R that connected to opentick's (open source) stock market data. However, opentick closed up about a year ago. Does anyone know of a similar package that connects to IQfeed's stock market data (or another source of historical stock market data)? Thanks, Brigid [[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] overlaying a levelplot on a map plot
On Apr 22, 2010, at 2:24 PM, Kevin Wright wrote:
Mixing base/lattice graphics can be tricky, but is possible.
http://www.bioconductor.org/CRAN/web/packages/gridBase/vignettes/gridBase.pdf
That could be quite useful in the future. Thanks for that.
Also, did you look at Chapter 13 of the lattice book?
http://lmdvr.r-forge.r-project.org/figures/figures.html
I did look at the actual book, and upon doing so yet again, I would
say that my comments were an accurate, if pithy, summary of the
message I take away from what very little regarding base graphics
appears in that chapter.
--
David.
Kevin
On Wed, Apr 21, 2010 at 2:08 PM, David Winsemius dwinsem...@comcast.net
wrote:
On Apr 21, 2010, at 2:27 PM, Simon Goodman wrote:
I've generated a levelplot showing the density distribution of a
species
derived from survey transects, with lon, lat co-ordinates.
I'd like to overlay this on a map of the study region specified by:
map('worldHires', xlim = range(mlon), ylim = range(mlat)), where
mlon, mlat
specifies the study region.
?map
No documentation for 'map' in specified packages and libraries:
you could try '??map'
??map
require(maps)
Loading required package: maps
map
So map uses base graphics.
I've tried plotting the map first, then using the options:
'add=TRUE,
axes=FALSE' in the levelplot,
levelplot is a lattice function. You will have failure with most
efforts to mix base and grid graphics.
but this doesn't work - a new plot is
generated for the level plot despite the 'add' option. If I try to
add the
map on top of the level plot, they are not to the same scale.
Any suggestions on how to get round this.
Thanks
--
David Winsemius, MD
West Hartford, CT
__
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and provide commented, minimal, self-contained, reproducible code.
[R] R and S-Plus: Two programs separated by a common language?
Hello Everyone, My company purchased S-Plus before it was bought out by Tibco. My understanding is that we own version 7.0 outright. So far, I've been learning in R but thought I might also try working in S-Plus. My understanding is that S-Plus has some useful extra features. Another potential benefit would be the ability to purchase technical support, which I thought might help me to learn the S language. I was just wondering if anyone could give me some advice about the wisdom or folly of trying to use both products. For example, how well do the two play together? If I learn to do something using a package in R, is their some way to bring that into S-Plus? I've noticed that some R packages, such as MASS and Hmisc are in S-Plus but are unsupported. Others, such as reshape, appear not to be in the program but I thought maybe they could be imported. I know that R and S-Plus code are supposed to be very similar. I was just wondering how similar. Yesterday, I ran some code from the MASS package in S-Plus but the program didn't produce the graph I exepected to see. I've been able to use windows() in R to correct this, but S-Plus doesn't recognize that. So I was wondering how often code written in one program would fail to work in the other. Any insights you can offer will be most appreciated. Thanks, 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] read.table understands comment field and ignores text
Hi I'm trying to import a large csv file without quotes around each field. This creates some problems when there are # characters in certain strings as R understands its comment field and ignores the rest of the line. Here's an example: var1, var2, var3, var4 one, two, three, four Use this in R to get off clipboard: read.table(clipboard, header=F, sep=,,na.strings=c(NULL, ), dec=., strip.white=TRUE, fill=T) Now try it with this table: var1, var2, var3, var4 one#, two, three, four Notice R ignores everything after the # character. Is this something that can be fixed? -- View this message in context: http://r.789695.n4.nabble.com/read-table-understands-comment-field-and-ignores-text-tp2021036p2021036.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] read.table understands comment field and ignores text
On Apr 22, 2010, at 2:05 PM, Jack T. wrote: Hi I'm trying to import a large csv file without quotes around each field. This creates some problems when there are # characters in certain strings as R understands its comment field and ignores the rest of the line. Here's an example: var1, var2, var3, var4 one, two, three, four Use this in R to get off clipboard: read.table(clipboard, header=F, sep=,,na.strings=c(NULL, ), dec=., strip.white=TRUE, fill=T) Now try it with this table: var1, var2, var3, var4 one#, two, three, four Notice R ignores everything after the # character. Is this something that can be fixed? Change the 'comment.char' argument to : read.table(, comment.char = ) See ?read.table for more information. HTH, Marc Schwartz __ 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] read.table understands comment field and ignores text
On Apr 22, 2010, at 3:05 PM, Jack T. wrote: Hi I'm trying to import a large csv file without quotes around each field. This creates some problems when there are # characters in certain strings as R understands its comment field and ignores the rest of the line. Here's an example: var1, var2, var3, var4 one, two, three, four Use this in R to get off clipboard: read.table(clipboard, header=F, sep=,,na.strings=c(NULL, ), dec=., strip.white=TRUE, fill=T) Now try it with this table: var1, var2, var3, var4 one#, two, three, four Notice R ignores everything after the # character. Is this something that can be fixed? ?read.table Read the documentation with particular attention to comment.char -- David Winsemius, MD West Hartford, CT __ 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] read.table understands comment field and ignores text
Oh man, totally missed that one! Thanks so much for the reminder. -- View this message in context: http://r.789695.n4.nabble.com/read-table-understands-comment-field-and-ignores-text-tp2021036p2021055.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] mixed model with subject-specific variance structure
Hi All, I built a mixed model with subject-specific variance structure in SAS and it works quite well. Now I intended to implement the same model in R using lme with weights option. Following is the SAS code and the corresponding R code: SAS: proc mixed data=source; class id trial group valence scan; model y=group|valence|scan; repeated /sub=id(trial) group=id type=AR(1); run; R vf1Ident-varIdent(~1|id) vf1Ident.ini-Initialize(vf1Ident,grouped.data) model-lme(fixed=y~group*valence*scan,data=grouped.data,correlation=corAR1(),weights=vf1Ident.ini); The result shows :convergence error code = 1 message = iteration limit reached without convergence (9) I searched the help archive and likely the weights option does not work well. Any suggestion to implement the subject-specific variance structure in R? Thanks, Yonghua [[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] What is the test statistics in perm.test
Hi, The permutation test for two samples in R is function perm.test(). I could not figure out what is the statistics it estimate and how many permutation it did in default? Thanks, [[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] index ordering
Hi All! I have a problem that I do not know it how it is necessary to query an index belonging to a given value. Somebody would help? [[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] index ordering
On Apr 22, 2010, at 3:45 PM, tamas barjak wrote: Hi All! I have a problem that I do not know it how it is necessary to query an index belonging to a given value. I bit hard to tell without an example but suspect you want: ?which -- David Winsemius, MD West Hartford, CT __ 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] Compare two data frames
Hi
Sounds like the 'compare' package might do some of what you want.
Paul
On 23/04/2010 1:41 a.m., Doran, Harold wrote:
I wonder if there is a more efficient way to do this task. Suppose I
have two data frames, such as
d1- data.frame(x = c(1,2,3), y = c(4,5,6), z = c(7,8,9))
d2- d1[, c('y', 'x')]
The first dataframe d1 has more variables than d2 and the variable
columns are in a different order.
So, what I want to do is compare the two frames on the variables that
are common between the two. First I find the common variables between
the two dataframes
common_order- intersect(colnames(d1), colnames(d2))
Then, I have to put the variables in d2 in the same order as d1 as
d2- d2[, common_order]
Then, I keep only the variables in common between d1 and d2 as
d1- d1[, common_order]
Then, finally I can do the compare on the common variables now in the
same order.
all.equal(d1, d2)
None of this is horribly difficult, but it requires a couple of steps
that I am wondering might be eliminated.
Harold
sessionInfo()
R version 2.10.1 (2009-12-14) i386-pc-mingw32
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 States.1252
attached base packages: [1] stats graphics grDevices utils
datasets methods base
other attached packages: [1] MiscPsycho_1.6 statmod_1.4.6
loaded via a namespace (and not attached): [1] tools_2.10.1
__ 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.
--
Dr Paul Murrell
Department of Statistics
The University of Auckland
Private Bag 92019
Auckland
New Zealand
64 9 3737599 x85392
p...@stat.auckland.ac.nz
http://www.stat.auckland.ac.nz/~paul/
__
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] R2.11.0 - rasterImage() and barplot fill-patterns
Hi On 23/04/2010 12:10 a.m., Tal Galili wrote: Hello Peter, Thank you, and the R core team, for the new release. I see that in R 2.11.0 there is now support for rendering of raster (bitmap) images through rasterImage(). I am wondering - can this be used to create a texture/fill-pattern for hist()/barplot() ? That is one possible application (see http://developer.r-project.org/Raster/raster-RFC.html) Paul (A request made several times throughout the years on the mailing list. For example: http://osdir.com/ml/lang.r.general/2005-07/msg00799.html ) (I am also sending this e-mail to the maintainers of lattice, ggplot2 and gplots in the hope for more perspectives) With much respect, Tal Contact Details:--- Contact me: tal.gal...@gmail.com | 972-52-7275845 Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) | www.r-statistics.com (English) -- On Thu, Apr 22, 2010 at 12:01 PM, Peter Dalgaardpd@cbs.dk wrote: I've rolled up R-2.11.0.tar.gz a short while ago. This is a development release which contains a number of new features. Also, a number of mostly minor bugs have been fixed. See the full list of changes below. NOTE: The build platform has been changed for this release. Please watch out extra carefully for anomalies. You can get it from http://cran.r-project.org/src/base/R-2/R-2.11.0.tar.gz or wait for it to be mirrored at a CRAN site nearer to you. Binaries for various platforms will appear in due course. For the R Core Team Peter Dalgaard These are the md5sums for the freshly created files, in case you wish to check that they are uncorrupted: MD5 (AUTHORS) = ac9746b4845ae81f51cfc99262f5 MD5 (COPYING) = eb723b61539feef013de476e68b5c50a MD5 (COPYING.LIB) = a6f89e2100d9b6cdffcea4f398e37343 MD5 (FAQ) = 5b653442bedab476a4eff7468192fb5f MD5 (INSTALL) = 70447ae7f2c35233d3065b004aa4f331 MD5 (NEWS) = 59017734fb8474f98f994c7a5a27f9fb MD5 (ONEWS) = a8c985af5ad5e9c7e0a9f502d07baeb4 MD5 (OONEWS) = 4f004de59e24a52d0f500063b4603bcb MD5 (R-latest.tar.gz) = c6c1e866299f533617750889c729bfb3 MD5 (README) = 433182754c05c2cf7a04ad0da474a1d0 MD5 (RESOURCES) = 020479f381d5f9038dcb18708997f5da MD5 (THANKS) = f2ccf22f3e20ebaa86f8ee5cc6b0f655 MD5 (R-2/R-2.11.0.tar.gz) = c6c1e866299f533617750889c729bfb3 This is the relevant part of the NEWS file: CHANGES IN R VERSION 2.11.0 SIGNIFICANT USER-VISIBLE CHANGES o Packages must have been installed under R= 2.10.0, as the current help system is the only one now supported. o A port to 64-bit Windows is now available as well as binary package repositiories: see the 'R Administration and Installation Manual'. o Argument matching for primitive functions is now done in the same way as for interpreted functions except for the deliberate exceptions call switch .C .Fortran .Call .External all of which use positional matching for their first argument, and also some internal-use-only primitives. o The default device for command-line R at the console on Mac OS X is now quartz() and not X11(). NEW FEATURES o The 'open' modes for connections are now interpreted more consistently. open = r is now equivalent to open = rt for all connections. The default open = now means rt for all connections except the compressed file connections gzfile(), bzfile() and xzfile() for which it means rb. o R CMD INSTALL now uses the internal untar() in package utils: this ensures that all platforms can install bzip2- and xz-compressed tarballs. In case this causes problems (as it has on some Windows file systems when run from Cygwin tools) it can be overridden by the environment variable R_INSTALL_TAR: setting this to a modern external tar program will speed up unpacking of large (tens of Mb or more) tarballs. o help(try.all.packages = TRUE) is much faster (although the time taken by the OS to find all the packages the first time it is used can dominate the time). o R CMD check has a new option '--timings' to record per-example timings in filepkg.Rcheck/pkg-Ex.timings. o The TRE library has been updated to version 0.8.0 (minor bugfixes). o grep[l], [g]sub and [g]regexpr now work in bytes in an 8-bit locales if there is no marked UTF-8 input string: this will be somewhat faster, and for [g]sub() give the result in the native encoding rather than in UTF-8 (which returns to the behaviour prior to R 2.10.0). o A new argument 'skipCalls' has been added to browser() so that it can report the original context when called by other debugging functions. o
Re: [R] index ordering
Ah. Close to what David suggested... Try: ?which.max Contact Details:--- Contact me: tal.gal...@gmail.com | 972-52-7275845 Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) | www.r-statistics.com (English) -- On Thu, Apr 22, 2010 at 10:57 PM, tamas barjak tamas.bar...@gmail.comwrote: Of course! max(dbinom(0:20, 20, 0.4)) [1] 0.1797058 I would like the place of the maximum for this. The value is found, I do not know it only which index belongs to. [[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] Subject: R and S-Plus: Two programs separated by a common language?
Paul
Just as in your implied analogy there are significant differences
beneath the surface between these programs despite superficial
similarities.
You will soon get frustrated trying to use both simultaneously as you
will not be sure that the critical step you've discovered in one will
work in the other. Most basic functions will work but I suspect that you
will soon discover some development or feature in the R pantheon that
will not translate readily to S-PLUS (and certainly not versions before
8.1).
The reasons for these differences are the result of fundamental
differences in architectures.
I used S-PLUS for 12 years, and I still need to use it occasionally the
most useful feature is the oft-despised Windows GUI. This is because it
provides a ready means to start to use a function that perhaps I only
use infrequently. However the GUI soon looses its appeal as I start to
solve a problem and almost immediately return to the scripting or
command line interface.
In R there are many useful starting points (help, apropos, views and a
simple search mechanism) that replace this comfortable feature, but
there is a learning curve to 'how do I find out how to find out in R'.
There are a range of helpful 'Starting R' books and they are worth the
effort of buying and reading.
Many companies, including the one I work for, offer support of all kinds
in R (as well as S-PLUS).
However the best help is the mechanism you have just used: an active and
mostly friendly R community. In addition there is a plethora of R
community groups, London, Chicago, New York come to mind - drop along to
some of them. And start to use R.
Regards
John James
Mango
- Original Message -
From: r-help-boun...@r-project.org r-help-boun...@r-project.org
To: r-help@r-project.org r-help@r-project.org
Sent: Thu Apr 22 20:00:13 2010
Subject: [R] R and S-Plus: Two programs separated by a common language?
Hello Everyone,
My company purchased S-Plus before it was bought out by Tibco. My
understanding is that we own version 7.0 outright.
So far, I've been learning in R but thought I might also try working in
S-Plus. My understanding is that S-Plus has some useful extra features.
Another potential benefit would be the ability to purchase technical
support, which I thought might help me to learn the S language.
I was just wondering if anyone could give me some advice about the
wisdom or folly of trying to use both products. For example, how well do
the two play together? If I learn to do something using a package in R,
is their some way to bring that into S-Plus? I've noticed that some R
packages, such as MASS and Hmisc are in S-Plus but are unsupported.
Others, such as reshape, appear not to be in the program but I thought
maybe they could be imported.
I know that R and S-Plus code are supposed to be very similar. I was
just wondering how similar. Yesterday, I ran some code from the MASS
package in S-Plus but the program didn't produce the graph I exepected
to see. I've been able to use windows() in R to correct this, but S-Plus
doesn't recognize that. So I was wondering how often code written in one
program would fail to work in the other.
Any insights you can offer will be most appreciated.
Thanks,
Paul
LEGAL NOTICE
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Re: [R] overlaying a levelplot on a map plot
Thanks for those pointers making some progress now
The following will put the levelplot on to the map, but the not with the
co-ordinates aligned...
The level plot appears on a slightly larger scale compared to the underlying
map.
In both the map and levelplot, the coordinates are in lon, lat decimal
degrees.
Hopefully I'm nearly there, with 1 or 2 tweaks.
library(gridBase)
mlat-c(n1,n2)
mlon-c(n3,n4)
map('worldHires', xlim = range(mlon), ylim = range(mlat))
axis(1);axis(2);axis(3);axis(4)
lvl.plot-levelplot(z~x+y,xyz,pretty=TRUE,at=at,col.regions=cl)
vps - baseViewports()
pushViewport(vps$inner, vps$figure, vps$plot)
pushViewport(viewport(print(lvl.plot, newpage=FALSE)))
popViewport()
popViewport(3)
However after the line 'pushViewport(viewport(print(lvl.plot,
newpage=FALSE)))' an error is returned:
Error in unit(x, default.units) :
(list) object cannot be coerced to type 'double'
--
View this message in context:
http://r.789695.n4.nabble.com/overlaying-a-levelplot-on-a-map-plot-tp2019419p2021128.html
Sent from the R help mailing list archive at Nabble.com.
__
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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] Compare two data frames
Why does:
nm - intersect(names(d1),names(d2))
identical(d1[,nm], d2[,nm])
not do it?
-- Bert
Bert Gunter
Nonclinical Biostatistics
467-7374
http://devo.gene.com/groups/devo/depts/ncb/home.shtml
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of Paul Murrell
Sent: Thursday, April 22, 2010 12:54 PM
To: Doran, Harold
Cc: r help
Subject: Re: [R] Compare two data frames
Hi
Sounds like the 'compare' package might do some of what you want.
Paul
On 23/04/2010 1:41 a.m., Doran, Harold wrote:
I wonder if there is a more efficient way to do this task. Suppose I
have two data frames, such as
d1- data.frame(x = c(1,2,3), y = c(4,5,6), z = c(7,8,9))
d2- d1[, c('y', 'x')]
The first dataframe d1 has more variables than d2 and the variable
columns are in a different order.
So, what I want to do is compare the two frames on the variables that
are common between the two. First I find the common variables between
the two dataframes
common_order- intersect(colnames(d1), colnames(d2))
Then, I have to put the variables in d2 in the same order as d1 as
d2- d2[, common_order]
Then, I keep only the variables in common between d1 and d2 as
d1- d1[, common_order]
Then, finally I can do the compare on the common variables now in the
same order.
all.equal(d1, d2)
None of this is horribly difficult, but it requires a couple of steps
that I am wondering might be eliminated.
Harold
sessionInfo()
R version 2.10.1 (2009-12-14) i386-pc-mingw32
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 States.1252
attached base packages: [1] stats graphics grDevices utils
datasets methods base
other attached packages: [1] MiscPsycho_1.6 statmod_1.4.6
loaded via a namespace (and not attached): [1] tools_2.10.1
__ 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.
--
Dr Paul Murrell
Department of Statistics
The University of Auckland
Private Bag 92019
Auckland
New Zealand
64 9 3737599 x85392
p...@stat.auckland.ac.nz
http://www.stat.auckland.ac.nz/~paul/
__
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] How to insert gridlines in lattice density plot
Greetings. How can I insert gridlines in the following density plot call? Must one compose a panel function? 'data.frame': 46 obs. of 2 variables: $ fallrates: num 5.2 7.1 7.1 9.8 3.7 7.5 5 6.2 1.5 2.9 ... $ prepost : Factor w/ 2 levels post,pre: 2 2 2 2 2 2 2 2 2 2 ... library(lattice) densityplot(~fallrates, groups = prepost, kernal=triangular, lwd=2, plot.points = TRUE, ref = TRUE, auto.key = list(columns = 2), main=Estimated fall rate density, pre and post intevention) Thank you for your consideration and comments. Giles Crane __ 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] legend problem
Dear R users, I have been plotting several graphics in only one page. I intend to plot only one legend in each page. Since the graphics are inside a loop I have to do it automatically. The main problem is that inside the loop I work with differente types of variables, I mean , the range is different for each one. I have already tried : par(xpd=TRUE) pos-par(usr) legend(pos[1],pos[3]-(pos[3]*.05),c(Modelo,Observado),col = c(blue,orange),cex=1.0, pch=15) I would like to be able to plot the legend outer the graphics region. Something like I've done with title. You can see one figure an attached file. I really appreciate any help. Nilza Barros -- Abraço, Nilza Barros __ 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] How to insert gridlines in lattice density plot
Must one compose a panel function? Depending on what you want exactly, no. Add the argument type=g to your call. (e.g. densityplot(~fallrates, groups = prepost,type=g,... ) See ?panel.xyplot and recall that lattice passes down arguments that it does not know what to do with to the panel function. Bert Gunter Genentech Nonclinical Biostatistics -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Giles Sent: Thursday, April 22, 2010 1:31 PM To: r-help@r-project.org Subject: [R] How to insert gridlines in lattice density plot Greetings. How can I insert gridlines in the following density plot call? Must one compose a panel function? 'data.frame': 46 obs. of 2 variables: $ fallrates: num 5.2 7.1 7.1 9.8 3.7 7.5 5 6.2 1.5 2.9 ... $ prepost : Factor w/ 2 levels post,pre: 2 2 2 2 2 2 2 2 2 2 ... library(lattice) densityplot(~fallrates, groups = prepost, kernal=triangular, lwd=2, plot.points = TRUE, ref = TRUE, auto.key = list(columns = 2), main=Estimated fall rate density, pre and post intevention) Thank you for your consideration and comments. Giles Crane __ 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] using which to select range of values
Another solution (whether this is better/worse, prettier/uglier, etc./etc. is in the eye of the beholder): library(TeachingDemos) x0 - rnorm(100) x0[ 0 %% x0 %% 1.5 ] Hope this helps, -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r- project.org] On Behalf Of Muhammad Rahiz Sent: Thursday, April 22, 2010 9:21 AM To: r-help@r-project.org Subject: [R] using which to select range of values Hi all, I would like to get the array index for a range of values, say 0 x 1.5. I'm wondering if there is an alternative for the following which I've done x0 - rnorm(100) x1 - ifelse(x0 0 x0 1.5,t,f) x2 - which(x1==t,arr.ind=TRUE) x0[x2] Thanks. -- Muhammad __ 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] How to insert gridlines in lattice density plot
On Apr 22, 2010, at 4:52 PM, Bert Gunter wrote: Must one compose a panel function? Depending on what you want exactly, no. Add the argument type=g to your call. (e.g. densityplot(~fallrates, groups = prepost,type=g,... ) See ?panel.xyplot and recall that lattice passes down arguments that it does not know what to do with to the panel function. I found that type=g interfered with execution of the ,,, plot.points=TRUE, ... directive and got better success with ... , type=c(p, g) -- David. Bert Gunter Genentech Nonclinical Biostatistics -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org ] On Behalf Of Giles Sent: Thursday, April 22, 2010 1:31 PM To: r-help@r-project.org Subject: [R] How to insert gridlines in lattice density plot Greetings. How can I insert gridlines in the following density plot call? Must one compose a panel function? 'data.frame': 46 obs. of 2 variables: $ fallrates: num 5.2 7.1 7.1 9.8 3.7 7.5 5 6.2 1.5 2.9 ... $ prepost : Factor w/ 2 levels post,pre: 2 2 2 2 2 2 2 2 2 2 ... library(lattice) densityplot(~fallrates, groups = prepost, kernal=triangular, lwd=2, plot.points = TRUE, ref = TRUE, auto.key = list(columns = 2), main=Estimated fall rate density, pre and post intevention) Thank you for your consideration and comments. Giles Crane __ 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. David Winsemius, MD West Hartford, CT __ 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] How to insert gridlines in lattice density plot
Thank you Burt Gunter and David Winsemius, I confirmed David's comment. One must use type=c(p,g) in order to get both the grid and points. So, to use densityplot well, we must be quite aware of the options for panel.xyplot! Cordially, Giles Crane __ 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] overlaying a levelplot on a map plot
You don't have to use map() to draw the map.
m - map(..., plot = FALSE)
xyplot(y ~ x, m, type = l, aspect = iso,
par.settings = list(axis.line = list(col = transparent)))
or inside a panel function, assuming appropriate scales:
panel.xyplot(m$x, m$y, ...)
On 23 April 2010 04:38, David Winsemius dwinsem...@comcast.net wrote:
On Apr 22, 2010, at 2:24 PM, Kevin Wright wrote:
Mixing base/lattice graphics can be tricky, but is possible.
http://www.bioconductor.org/CRAN/web/packages/gridBase/vignettes/gridBase.pdf
That could be quite useful in the future. Thanks for that.
Also, did you look at Chapter 13 of the lattice book?
http://lmdvr.r-forge.r-project.org/figures/figures.html
I did look at the actual book, and upon doing so yet again, I would say that
my comments were an accurate, if pithy, summary of the message I take away
from what very little regarding base graphics appears in that chapter.
--
David.
Kevin
On Wed, Apr 21, 2010 at 2:08 PM, David Winsemius dwinsem...@comcast.net
wrote:
On Apr 21, 2010, at 2:27 PM, Simon Goodman wrote:
I've generated a levelplot showing the density distribution of a species
derived from survey transects, with lon, lat co-ordinates.
I'd like to overlay this on a map of the study region specified by:
map('worldHires', xlim = range(mlon), ylim = range(mlat)), where mlon,
mlat
specifies the study region.
?map
No documentation for 'map' in specified packages and libraries:
you could try '??map'
??map
require(maps)
Loading required package: maps
map
So map uses base graphics.
I've tried plotting the map first, then using the options: 'add=TRUE,
axes=FALSE' in the levelplot,
levelplot is a lattice function. You will have failure with most efforts
to mix base and grid graphics.
but this doesn't work - a new plot is
generated for the level plot despite the 'add' option. If I try to add
the
map on top of the level plot, they are not to the same scale.
Any suggestions on how to get round this.
Thanks
--
David Winsemius, MD
West Hartford, CT
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Felix Andrews / 安福立
Postdoctoral Fellow
Integrated Catchment Assessment and Management (iCAM) Centre
Fenner School of Environment and Society [Bldg 48a]
The Australian National University
Canberra ACT 0200 Australia
M: +61 410 400 963
T: + 61 2 6125 4670
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[R] ROC curve in randomSurvivalForest
I'm using randomSurvivalForest to predict survival from a rather small sample. As it's not enough data to have training and validation set, I rely on the Estimate of error rate computed by the randomForest. If I understand the method correctly, it repeatedly partitions the data into varying training/validation sets during the learning steps, which also produces the estimate of error. My questions is, would it be possible to compute a ROC curve during RF training? A possible approach I considered would be to train the RF on a subset of the data and create a ROC curve from the prediction on the remaining data. By repeating this process, I would get the variation of the ROC curve for the different possible data subsets. But this seems to be not such an elegant solution, as this could be done during one instance of RF learning. It would be very helpful, if someone could point to an approach on how to do this. Nick Fankhauser __ 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] Why does 'apply(.., 1, .., ..)' transpose result
I am sorry if this is documented in apply's dcumentation or completely obvious, I could not find or work it out. Given an matricies Q: 2x3, R:1x3 and S:1x2 apply(Q, 1, '-', R) is 3x2 and apply(Q, 2, '-', S) is 2x3 Why? cheers Worik Q [,1] [,2] [,3] [1,]123 [2,] 10 11 12 R [1] 1 4 7 S [1] 1 4 apply(Q, 1, '-', R) [,1] [,2] [1,]09 [2,] -27 [3,] -45 apply(Q, 2, '-', S) [,1] [,2] [,3] [1,]012 [2,]678 [[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] simple question
Or use this handy-dandy function:
smode-function(x){
xtab-table(x)
modes-xtab[max(xtab)==xtab]
mag-as.numeric(modes[1]) #in case mult. modes, this is safer
themodes-names(modes)
mout-list(themodes=themodes,modeval=mag)
return(mout)
}
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Re: [R] how to reorder of groups and specify ylim for each row in lattice barchart
On 2010-04-21 21:13, zhenjiang xu wrote: R experts, Is there anyway to reorder inside each group? In the following example, the bar of year 1932 is always plotted before the bar of year 1931, may I change the order inside each groups of bars? Do you mean a different order in different panels? That seems to me to defeat the purpose of panels. I can't think of an easy way to do that. library(lattice) barchart(yield ~ variety | site,data=barley, groups = year, layout = c(1,6),auto.key = list(points = FALSE, rectangles = TRUE, space = right),ylab = Barley Yield (bushels/acre),scales = list(x = list(rot = 45))) Another questions is: may I specify the various ranges of y axis for each row of the panels? In the example of above, how can I change the y range of Waseca panel to (40,70) from the default (0,80)? Please notice I don't want to set arguement scales = list(y=list(relation='free')), for the automatic various setting of ranges for different panels isn't good enough for me. Basically I'd like to manually control y ranges. You can use scales() with y=list(relation='free', ylim=mylist) where mylist is a list of ylims: mylim - list(c(0,30), c(40,80), ) -Peter Ehlers Thank you! -- Peter Ehlers University of Calgary __ 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] cell-based high-throughput chemical compound screens package?
Hi I'm looking for a package to perform quality control, normalization and analysis of high throughput cell-based chemical screens. I know that the cellHTS2 package provides this for siRNA screens. Does anybody know if something like what I'm looking for exists? Thank you! Gabriele Zoppoli, MD Ph.D. Fellow, Experimental and Clinical Oncology and Hematology, University of Genova, Genova, Italy Guest Researcher, LMP, NCI, NIH, Bethesda MD Work: 301-451-8575 Mobile: 301-204-5642 Email: zoppo...@mail.nih.gov __ 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] overlaying a levelplot on a map plot
You are plotting the entire lattice plot (including axes, margins etc)
in the grid viewport. What you want to do is to call the panel
function, panel.levelplot(), instead.
However, why not just
mm - map('worldHires', plot = FALSE)
levelplot(z~x+y,xyz, mm = mm, panel = function(..., mm) {
panel.levelplot(...)
panel.lines(mm$x, mm$y)
})
On 23 April 2010 06:16, Simon Goodman s.j.good...@leeds.ac.uk wrote:
Thanks for those pointers making some progress now
The following will put the levelplot on to the map, but the not with the
co-ordinates aligned...
The level plot appears on a slightly larger scale compared to the underlying
map.
In both the map and levelplot, the coordinates are in lon, lat decimal
degrees.
Hopefully I'm nearly there, with 1 or 2 tweaks.
library(gridBase)
mlat-c(n1,n2)
mlon-c(n3,n4)
map('worldHires', xlim = range(mlon), ylim = range(mlat))
axis(1);axis(2);axis(3);axis(4)
lvl.plot-levelplot(z~x+y,xyz,pretty=TRUE,at=at,col.regions=cl)
vps - baseViewports()
pushViewport(vps$inner, vps$figure, vps$plot)
pushViewport(viewport(print(lvl.plot, newpage=FALSE)))
popViewport()
popViewport(3)
However after the line 'pushViewport(viewport(print(lvl.plot,
newpage=FALSE)))' an error is returned:
Error in unit(x, default.units) :
(list) object cannot be coerced to type 'double'
--
View this message in context:
http://r.789695.n4.nabble.com/overlaying-a-levelplot-on-a-map-plot-tp2019419p2021128.html
Sent from the R help mailing list archive at Nabble.com.
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and provide commented, minimal, self-contained, reproducible code.
--
Felix Andrews / 安福立
Postdoctoral Fellow
Integrated Catchment Assessment and Management (iCAM) Centre
Fenner School of Environment and Society [Bldg 48a]
The Australian National University
Canberra ACT 0200 Australia
M: +61 410 400 963
T: + 61 2 6125 4670
E: felix.andr...@anu.edu.au
CRICOS Provider No. 00120C
--
http://www.neurofractal.org/felix/
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[R] Practical work with logistic regression
Dear all, I have a couple of short noob questions for whoever can take them. I'm from a very non-stats background so sorry for offending anybody with stupid questions ! :-) I have been using logistic regression care of glm to analyse a binary dependent variable against a couple of independent variables. All has gone well so far. In my work I have to compare the accuracy of analysis to a C4.5 machine learning approach. With the machine learning, a straight-forward measure of the quality of the classifier is simply the percentage of correctly classified instances. I can calculate this for the resultant model by comparing predictions to original values 'manually'. My question: is this not automatically - or easily - calculated in the produced model or the summary of that model? I want to use my model in real time to produce results for new inputs. Basically this model is to be used as a classifier for a robot in real time. Can anyone suggest the best way that a produced model can be used directly in external code once the model has been developed in R? If my external code is in Java, then using jri is one option. A more efficient method would be to take the intercept and coefficients and actually code up the function in the appropriate programming language. Has anyone ever tried doing this? Apologies again for the stupid questions, but the sooner I get some of these things straight, the better. Claus __ 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 of R CMD check
Hi ,
This maybe a bug. I checked my another package, the same problem occurred.
See below for detailed information.
##check log##
* using log directory 'D:/StatSoft/R/MyPackage/sbar.Rcheck'
* using R version 2.10.1 (2009-12-14)
* using session charset: ISO8859-1
* checking for file 'sbar/DESCRIPTION' ... OK
* this is package 'sbar' version '0.0-1'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking for executable files ... OK
* checking whether package 'sbar' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the name space can be loaded with stated dependencies ...
OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking examples ... ERROR
Running examples in 'sbar-Ex.R' failed.
###sbar-Ex.R###
### * HEADER
###
attach(NULL, name = CheckExEnv)
assign(nameEx,
local({
s - __{must remake R-ex/*.R}__
function(new) {
if(!missing(new)) s - new else s
}
}),
pos = CheckExEnv)
## Add some hooks to label plot pages for base and grid graphics
assign(base_plot_hook,
function() {
pp - par(c(mfg,mfcol,oma,mar))
if(all(pp$mfg[1:2] == c(1, pp$mfcol[2]))) {
outer - (oma4 - pp$oma[4]) 0; mar4 - pp$mar[4]
mtext(sprintf(help(\%s\), nameEx()), side = 4,
line = if(outer)max(1, oma4 - 1) else min(1, mar4 - 1),
outer = outer, adj = 1, cex = .8, col = orchid, las=3)
}
},
pos = CheckExEnv)
assign(grid_plot_hook,
function() {
grid::pushViewport(grid::viewport(width=grid::unit(1, npc) -
grid::unit(1, lines), x=0, just=left))
grid::grid.text(sprintf(help(\%s\), nameEx()),
x=grid::unit(1, npc) + grid::unit(0.5,
lines),
y=grid::unit(0.8, npc), rot=90,
gp=grid::gpar(col=orchid))
},
pos = CheckExEnv)
setHook(plot.new, get(base_plot_hook, pos = CheckExEnv))
setHook(persp,get(base_plot_hook, pos = CheckExEnv))
setHook(grid.newpage, get(grid_plot_hook, pos = CheckExEnv))
assign(cleanEx,
function(env = .GlobalEnv) {
rm(list = ls(envir = env, all.names = TRUE), envir = env)
RNGkind(default, default)
set.seed(1)
options(warn = 1)
.CheckExEnv - as.environment(CheckExEnv)
delayedAssign(T, stop(T used instead of TRUE),
assign.env = .CheckExEnv)
delayedAssign(F, stop(F used instead of FALSE),
assign.env = .CheckExEnv)
sch - search()
newitems - sch[! sch %in% .oldSearch]
for(item in rev(newitems)) detach(item, character.only=TRUE)
missitems - .oldSearch[! .oldSearch %in% sch]
if(length(missitems))
warning(items , paste(missitems, collapse=, ),
have been removed from the search path)
},
pos = CheckExEnv)
assign(ptime, proc.time(), pos = CheckExEnv)
## at least one package changes these via ps.options(), so do this
## before loading the package.
## Use postscript as incomplete files may be viewable, unlike PDF.
## Choose a size that is close to on-screen devices, fix paper
grDevices::ps.options(width = 7, height = 7, paper = a4, reset = TRUE)
grDevices::postscript(paste(pkgname, -Ex.ps, sep=))
assign(par.postscript, graphics::par(no.readonly = TRUE), pos =
CheckExEnv)
options(contrasts = c(unordered = contr.treatment, ordered =
contr.poly))
options(pager = console)
library('sbar')
assign(.oldSearch, search(), pos = 'CheckExEnv')
assign(.oldNS, loadedNamespaces(), pos = 'CheckExEnv')
cleanEx(); nameEx(stKDE.simcomp)
### * stKDE.simcomp
flush(stderr()); flush(stdout())
### Name: stKDE.simcomp
### Here, just copied my example codes, so i ignored here to save space.
### * FOOTER
###
cat(Time elapsed: , proc.time() - get(ptime, pos = 'CheckExEnv'),\n)
grDevices::dev.off()
###
### Local variables: ***
### mode: outline-minor ***
### outline-regexp: \\( \\)?### [*]+ ***
### End: ***
quit('no')
2010/4/22 Dennis Murphy djmu...@gmail.com
Hi Jane,
I was just hoping to
[R] Remove duplicated rows
Hi all, I have a dataset similar to the following NameDateValue A 1/01/2000 4 A 2/01/2000 4 A 3/01/2000 5 A 4/01/2000 4 A 5/01/2000 1 B 6/01/2000 2 B 7/01/2000 1 B 8/01/2000 1 I would like R to remove duplicates based on column 1 and 3 only. In addition, I would like R to remove duplicates based on the underlying and overlying row only. For example, for A, I would like to remove row 2 only and keep row 1, 3 and 4. I have tried: unique() and replicated(), but I do not have much success. I have also tried: dataset-c(1,diff(dataset)!=0), but I don't know how to apply it to this multi-column situation. Any help would be greatly appreciated. Thanks in advance, Chris -- View this message in context: http://r.789695.n4.nabble.com/Remove-duplicated-rows-tp2023065p2023065.html Sent from the R help mailing list archive at Nabble.com. [[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] User inputs
Thank you very much Dieter and Don. This solves my problem. :) -- View this message in context: http://r.789695.n4.nabble.com/User-inputs-tp2018251p2023067.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] Practical work with logistic regression
confusionMatrix in the caret package can be used to replace your manual procedure. You could try using RWeka, the R interface to the java Weka software. Once you have it working you could then directly interface your java program to Weka without involving R. On Thu, Apr 22, 2010 at 9:29 PM, Claus O'Rourke claus.orou...@gmail.com wrote: Dear all, I have a couple of short noob questions for whoever can take them. I'm from a very non-stats background so sorry for offending anybody with stupid questions ! :-) I have been using logistic regression care of glm to analyse a binary dependent variable against a couple of independent variables. All has gone well so far. In my work I have to compare the accuracy of analysis to a C4.5 machine learning approach. With the machine learning, a straight-forward measure of the quality of the classifier is simply the percentage of correctly classified instances. I can calculate this for the resultant model by comparing predictions to original values 'manually'. My question: is this not automatically - or easily - calculated in the produced model or the summary of that model? I want to use my model in real time to produce results for new inputs. Basically this model is to be used as a classifier for a robot in real time. Can anyone suggest the best way that a produced model can be used directly in external code once the model has been developed in R? If my external code is in Java, then using jri is one option. A more efficient method would be to take the intercept and coefficients and actually code up the function in the appropriate programming language. Has anyone ever tried doing this? Apologies again for the stupid questions, but the sooner I get some of these things straight, the better. Claus __ 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] time difference
thank you! this really helps!
On Thu, Apr 22, 2010 at 7:00 PM, jim holtman jholt...@gmail.com wrote:
?strptime
Read the documentation and you will find reference to %OSn
x - strptime('13:45:34.123', format=%H:%M:%OS)
x
[1] 2010-04-22 13:45:34
format(x, format=%H:%M:%OS3)
[1] 13:45:34.123
On Thu, Apr 22, 2010 at 2:58 AM, Carol Gao carol.g...@gmail.com wrote:
Hi,
Does anyone know how to take a time difference when the format of the time
is as 13:22:23.586? I am trying to take the difference of time between
stock
transactions and need to keep the three decimal places for seconds. I have
tried *diff(strptime(x, %H:%M:%S.000))*, but apperantly that doesn't
work.
Carol Gao
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--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem that you are trying to solve?
[[alternative HTML version deleted]]
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[R] packages gdata / gtools - installation in R 2.11.0
Dear R-list members, I have just downloaded R version 2.11.0. Then I installed package gdata. At the end of the installation, a warning message said that package gtools could not be found. Package gdata was, after the installation, included in the Package Index in the help files. Messages during installation (which was made through the menu Packages / Instal package(s), choosing the Austria site, R running on Windows XP): utils:::menuInstallPkgs() Warning: dependency ‘gtools’ is not available trying URL 'http://cran.at.r-project.org/bin/windows/contrib /2.11/gdata_2.7.1.zip' Content type 'application/zip' length 830646 bytes (811 Kb) opened URL downloaded 811 Kb package 'gdata' successfully unpacked and MD5 sums checked When I tried to use (in R 2.11.0) package gdata and its function write.fwf, I got the messages below: library(gdata) Error in loadNamespace(i[[1L]], c(lib.loc, .libPaths())) : there is no package called 'gtools' Error: package/namespace load failed for 'gdata' write.fwf(x,'test-01.txt') Error: could not find function write.fwf (** Note: x is a data frame **) Package gdata is correctly installed in my R 2.10.1, and both packages gdata and gtools appear in the list of available packages when I try to install some package in R 2.10.1 through the menu Packages / Instal package(s), choosing the Austria site. But when I try to install some package in R 2.11.0 through the menu, only package gdata appears in the list of available packages - package gtools does not appear in that list. Both packages are listed on the CRAN (Austria) package Web page. It seems that R 2.11.0 is somehow not seeing the package gtools. Is there any way around this situation? How to correctly install package gdata (which depends on gtools) in R 2.11.0? Both R 2.10.1 and R 2.11.0 are running on Windows XP, in the same computer. Thank you very much. Paulo Barata Paulo Barata Fundacao Oswaldo Cruz - Oswaldo Cruz Foundation Rua Leopoldo Bulhoes 1480 - 8A 21041-210 Rio de Janeiro - RJ Brazil E-mail: pbar...@infolink.com.br E-mail: paulo.bar...@ensp.fiocruz.br __ 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] Practical work with logistic regression
Claus O'Rourke wrote: Dear all, I have a couple of short noob questions for whoever can take them. I'm from a very non-stats background so sorry for offending anybody with stupid questions ! :-) I have been using logistic regression care of glm to analyse a binary dependent variable against a couple of independent variables. All has gone well so far. In my work I have to compare the accuracy of analysis to a C4.5 machine learning approach. With the machine learning, a straight-forward measure of the quality of the classifier is simply the percentage of correctly classified instances. I can calculate this for the resultant model by comparing predictions to original values 'manually'. My question: is this not automatically - or easily - calculated in the produced model or the summary of that model? The percent classified correctly is an improper scoring rule that will lead to a selection of a bogus model. You can easily find examples where adding a very important variable to a binary logistic model results in a decrease in the percent correct. Frank I want to use my model in real time to produce results for new inputs. Basically this model is to be used as a classifier for a robot in real time. Can anyone suggest the best way that a produced model can be used directly in external code once the model has been developed in R? If my external code is in Java, then using jri is one option. A more efficient method would be to take the intercept and coefficients and actually code up the function in the appropriate programming language. Has anyone ever tried doing this? Apologies again for the stupid questions, but the sooner I get some of these things straight, the better. Claus __ 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. -- Frank E Harrell Jr Professor and ChairmanSchool of Medicine Department of Biostatistics Vanderbilt University __ 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 with plotting lines linking two sets of points?
Hello everyone, I'm trying to plot the initial and final size of some tadpoles and look at their growth rates (slope of line). They are divided into 6 densities, and so far I have plotted the initial and final sizes (these are means for a pool), and color coded for the 6 densities, but I want a line to connect the initial and final value for each pool (also color coded by density). Any ideas? I'm hoping to see what the effect of density is on growth, and there are 4 replicates for each density. The initial and final sizes are staggered, 1/2 were measured at age 7.3 and 11, and the other 1/2 were measured at age 8.5 and 12. here's a sample pool age age2 density body_length body_length2 11 7.4 11.3 25 0.887 1.322550 22 7.4 11.3 100 0.921 1.152000 33 7.4 11.3 250 0.896 1.136300 44 7.4 11.3 75 0.723 0.955950 55 7.4 11.3 500 0.755 1.113300 66 7.4 11.3 50 0.869 1.169833 and as far as i've gotten plot(age,body_length,pch=as.numeric(school), col=as.numeric(density), xlim=c(6,13), ylim=c(0.7,1.6)) points(age2, body_length2, pch=as.numeric(school), col=as.numeric(density)) http://n4.nabble.com/forum/FileDownload.jtp?type=nid=2023096name=Screen_shot_2010-04-22_at_11.03.08_PM.png thanks! kristiina -- View this message in context: http://r.789695.n4.nabble.com/help-with-plotting-lines-linking-two-sets-of-points-tp2023096p2023096.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.
