[R] installation step for RSperl
Hi, I try to use R within perl. however, I have a bit difficulty to install RSperl. I followd steps from http://www.omegahat.org/RSPerl/. but still can' t make it work. could someone list a fe w clean steps that I can follow to install it? cheers -- Yuandan Zhang å¼ å æ¦ . [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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] add colors to persp plot to reflect levels of z values
Hi, I try to use persp to draw perspective plots of surfaces in a region. the data matrix is 606x354 here is my simple code: r-read.table (file='prod.asc.txt', header=F) r[r==-]-NA # no values in surrounding region r-as.matrix(r) y-seq(1:ncol(r)) #354 cols x-seq(1:nrow(r)) #606 rows png (file=prod.png) persp(x,y, r, theta = 100, phi = 30, expand=0.5, col =10, ltheta=120, shade = 0.75, ticktype='detailed', d=.4, lty=0, border=NULL) dev.off() as the data points are very dense, i set the lty to 0. r ranges from 200 to 600. I want to add a series of colors (say 10) to reflect the levels (eg 10) of r values. how to do this? regards, -- Yuandan __ R-help@stat.math.ethz.ch 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] write out data in format
Hi, how to write out data frame in format? for examples, I wrote out a data using 'write.table(siredata, file='siredata.txt', row.names=F, quote=F)'. it produced data alike this: 2882 1 0 0 0 0 L1600481991910012 L160001190196 2883 0.79 0.21 0 0 21 L1622881993930001 L1600481991910012 2884 0.84 0.16 0 0 23 L1622881993930005 L1600481991910012 2885 0.9 0.1 0 0 23 L1622881993930027 L1600481991910012 2886 0.87 0.13 0 0 23 L1622881993930038 L1600481991910012 2887 0.9 0.1 0 0 27 L1622881993930111 L1600481991910012 2888 0.81 0.19 0 0 22 L1622881993930113 L1600481991910012 In fact i want it formated as 2882 1.00 0.00 0.00 0.00 0 L1600481991910012 L160001190196 2883 0.79 0.21 0.00 0.00 21 L1622881993930001 L1600481991910012 2884 0.84 0.16 0.00 0.00 23 L1622881993930005 L1600481991910012 2885 0.90 0.10 0.00 0.00 23 L1622881993930027 L1600481991910012 2886 0.87 0.13 0.00 0.00 23 L1622881993930038 L1600481991910012 2887 0.90 0.10 0.00 0.00 27 L1622881993930111 L1600481991910012 2888 0.81 0.19 0.00 0.00 22 L1622881993930113 L1600481991910012 Thanks for your help Yuandan __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] simplified Chinese and traditional Chinese translation for R manuals
Guohui, Great effort for translating this document into Chinese. I will certainly read through and send some feedback to you. Best Yuandan Guohui Ding wrote: Hi, every one, I have translated An Introduction to R into simplified Chinese and traditional Chinese. You can browse them from these two URL: simplified Chinese: http://www.biosino.org/pages/newhtm/r/schtml/index.html#Top traditional Chinese: http://www.biosino.org/pages/newhtm/r/tchtml/ I have distributed these document in HTML format. That is because there is something wrong with the format change between the PDF format and texinfo format in Chinese. However, I will overcome this problem soon. If some website on R have some interest to these Chinese translation, you can get all the HTML document of them from me. The other four manuals is being translated now, and I will distribute them in the future. The Chinese translation for An Introduction to R is a beta version, and will need some modification and your suggestion. More information was in the document. R is a great sofeware. I like it and I will do something for it. Wish You Will Enjoy It! You can send a email to me. Any suggestion and comment are welcome! __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Who can tell me some packages for population genetic structure's simulation?
There are others too, such as genetics qtl qtlsim bqtl Eduwin Pakpahan wrote: download this package gap - genetic analysis package. E On 6/2/05, luan_sheng [EMAIL PROTECTED] wrote: hi,everyone,I am beginner for R. I want to use R for simulating population genetic structrue of different generations. This thesis include alleles of 1-10 loci. Does a package like this exist? thanks for you. __ G __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] dependency help for FC2 rpm
On 29 Mar 2005 22:04:51 +0200 Peter Dalgaard [EMAIL PROTECTED] wrote: Steve Sherman [EMAIL PROTECTED] writes: I am having difficulty with dependencies for the R rpm for Fedora Core 2. In attempting to load R-2.0.0.0.fdr.1.fc2.i386.rpm it fails the libtk8.4.so dependency even though I have this library loaded. The library is located in: /usr/local/lib. How might I tell R where to find this library? I am new to Linux and loading rpms so I am hoping there is a simple answer and that the problem is related to my inexperience. Thanks in advance for any assistance. It is most likely the rpm looks for this lib at /usr/lib, you may create a symbolic link eg cd /usr/lib ln -s /usr/local/libtk8.4.so . of cource, you must have a root access to do this. You need to install the RPM dependencies that it depends on. A libtk8.4.so in /usr/local/lib doesn't come from a standard RPM. You need to install the tk (and tcl) RPM from CD's or a Fedora repository. -- O__ Peter Dalgaard Blegdamsvej 3 c/ /'_ --- Dept. of Biostatistics 2200 Cph. N (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Tool for update
Hi, Is there any tool to check if there is update version of a package available? I look for things alike YUM for linux? YD __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] switching to Linux, suggestions?
I have both desktop and laptop with Fedora core 3. R 2.0.1 are working well on all PCs. There is a problem with Fedora core 3 on HP nx500 laptop. The display resolution is 1024x768 according to HP's description. However, during the installation, there were only two options on display resolution 800x600 640x480. I tried various ways, but can't set it to 1024x768. any one have fix for this. Yuandan On Sun, 12 Dec 2004 15:23:40 -0500 Thomas W Volscho [EMAIL PROTECTED] wrote: Dear List, I have acquired a new desktop and wanted to put a free OS on it. I am trying Fedora Core 1, but not sure what the best Linux OS is for using R 2.0.1? Thank you in advance for your input, Tom Volscho Thomas W. Volscho Graduate Student Dept. of Sociology U-2068 University of Connecticut Storrs, CT 06269 Phone: (860) 486-3882 http://vm.uconn.edu/~twv1 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Re : LOOPS
On Mon, 6 Dec 2004 13:36:37 +1300
[EMAIL PROTECTED] wrote:
Dear lists,
I want to construct a loop in R, but don't know how to do it. I can do it
in SAS, but I prefer in R (which I am hoping I will off SAS for good
soon). Could anyone help me to convert the SAS codes to equivalent R codes.
Basically, the following codes were written to establish the sire gametes
or phases for daughter design for one markers two alleles.
Here are the SAS code:
You may try this code. There may be better code from others.
m-array(0, 795) #phase
for ( i in 1:744) { # sire
for (j in 745:1540) { # progeny
if (sire[j] == anim[i] ) { #check if the progeny j is sired by animal i
if (m1[j]==m1[i]m2[j]==m2[i] ) { m[j]=0; next}
if ( m1[j]==m1[i]) { m[j] = 1; next}
if (m1[j]==m2[i]) { m[j==2; next}
.
}
}
}
do i=1 to 744;
do j=745 to 1540;
m[j]=0;
if sire[j]=anml[i] then do;
if m1[j]=m1[i] and m2[j]=m2[i] then m[j]=0;
else if m1[j]=m1[i] then m[j] =1;
else if m1[j]=m2[i] then m[j==2;
else if m2[j]=m1[i] then m[j]=1;
else if m2[j]=m2[i] then m[j]=2;
else m[j]=0;
end do;
end;
end;
Thanks Stella
___
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--
--
Yuandan Zhang, PhD
Animal Genetics and Breeding Unit
The University of New England
Armidale, NSW, Australia, 2351
E-mail: [EMAIL PROTECTED]
Phone:(61) 02 6773 3786
Fax: (61) 02 6773 3266
http://agbu.une.edu.au
AGBU is a joint venture of NSW Primary Industries
and The University of New England to undertake
genetic RD for Australia's Livestock Industries
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Re: [R] A possible way to reduce basic questions
I would like to add a few points on the increasing size of r-help. 1. this is a possitive sign that more and more people migrate to R. For starting users of R or a R package, the r-help is unique way to seek answers. Gradually, once starting, I trust, users are finding ways to search answers. 2. DO NOT disencourage users to ask bassic questions, this may scare starters away from R. I believe, most of us experienced such transsion, from basic questions to good familarity with R or some R packages. We should encourage experienced users contribute to Q-A. 3. We may start forming interesting groups to deal with some specifical questions. It is true that not everyone using all packages, or not many people mastering on all packages, but a few users may know almost every aspect of some packages. If a task force can analyse the previous questions, cluster them and identify a number of key areas, this may be a useful start to group people. Directing questions to target groups may produce quick and fruitful answers. Yuandan On Thu, 2 Dec 2004 17:17:21 + Tim Cutts [EMAIL PROTECTED] wrote: On 2 Dec 2004, at 1:23 am, Gabor Grothendieck wrote: Jim Lemon bitwrit at ozemail.com.au writes: I have been thinking about how to reduce the number of basic questions that elicit the ...ahem... robust debate that has occurred about how to answer The traffic on r-help could be reduced by creating a second list where more elementary questions are asked. But how many people here would read it, and help the novices (like me) out? There is always the danger that novice lists just become write-only lists. Tim -- Dr Tim Cutts Informatics Systems Group, Wellcome Trust Sanger Institute GPG: 1024D/E3134233 FE3D 6C73 BBD6 726A A3F5 860B 3CDD 3F56 E313 4233 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Animal Genetics and Breeding Unit The University of New England Armidale, NSW, Australia, 2351 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] combine two strings
x-paste(string1, string2, sep=) On Thu, 2 Dec 2004 18:23:28 -0500 Ben-Yang Liao [EMAIL PROTECTED] wrote: Hello, I would like to combine two strings while using R. For instance, string1 - abcde string2 - WXYZ I'd like to combine string1 and string2 into Sting3; and string3 should be abcdeWXZY. Would you please tell me how to do it? Thank you very much Ben-Yang [[alternative HTML version deleted]] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Getting R to emit an image file as a pipe or Base64 stream: Mac OSX 10.3 - R 2.0.1
If you want to call R from perl, why don't you do a simple system call like: $callR=/usr/loca/bin/R CMD BATCH plotscript.R; system ($callR); It is not necessary to start X display if anything can be done in background On Fri, 3 Dec 2004 12:07:24 +1100 (EST) Thuan-Jin Kee [EMAIL PROTECTED] wrote: Hi All, Anybody know how to make R emit base64 encoded text in some way that perl can grab it, instead of planting a file on your harddrive when calling JPEG or PNG? I've managed to get these scripts to work and put a file on the harddisk #!/usr/bin/perl -Wall # by jin kee. a simple script to demonstrate # the needed steps to get R to emit a jpeg. use strict; my($callR, $callRold); # need to start X if is isn't already started. `open /Applications/Utilities/X11.app`; #need to get let the R program know where to look #for the display immediately before calling #the R executible. $callR =MARKER; DISPLAY=:0.0; export DISPLAY; /usr/bin/R --vanilla plotscript.R; MARKER system($callR); # end script #!/usr/bin/R peg(~/Desktop/test.jpg); plot(rnorm(100)); dev.off(); q(save = no); My sysadmin says that the apache user can't write to the disk due to security policy, so he wants to know if I can emit the jpeg as a base64 stream and embedd it into the dynamically generated tag using a DATA tag to inline the image. http://www.elf.org/essay/inline-image.html http://www.faqs.org/rfcs/rfc2397.html i've tried searching the R-project.org site and help.search() and no luck. Yours Jin __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- -- Yuandan Zhang, PhD Animal Genetics and Breeding Unit The University of New England Armidale, NSW, Australia, 2351 E-mail: [EMAIL PROTECTED] Phone:(61) 02 6773 3786 Fax: (61) 02 6773 3266 http://agbu.une.edu.au AGBU is a joint venture of NSW Primary Industries and The University of New England to undertake genetic RD for Australia's Livestock Industries __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Installing gregmisc under windows 2000
That seems not the case under linux in term of installation. You can install this bundle in the same way as installing an individul package. eg R CMD INSTALL CRAN/contrib/main/gregmisc_2.0.0.tar.gz to get all constituent packages installed. On Wed, 24 Nov 2004 22:14:14 + (GMT) Prof Brian Ripley [EMAIL PROTECTED] wrote: gregmisc is a bundle, not a package. Its description on CRAN is gregmisc Bundle of gtools, gdata, gmodels, gplots so try one of those packages. -- -- Yuandan Zhang, PhD Animal Genetics and Breeding Unit The University of New England Armidale, NSW, Australia, 2351 E-mail: [EMAIL PROTECTED] Phone:(61) 02 6773 3786 Fax: (61) 02 6773 3266 http://agbu.une.edu.au AGBU is a joint venture of NSW Primary Industries and The University of New England to undertake genetic RD for Australia's Livestock Industries __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Search engine for LINUX MOZILLA
Thanks for instructions, it works. here are a few simple steps which may be useful for others too. 1 GET SOURCE: Following the link http://www.MedAnalytics.com/INSTALL, go and download http://www.MedAnalytics.com/j2re-1_4_2_01-linux-i586-rpm.bin 2 INSTALL: chown 007 j2re-1_4_2_01-linux-i586-rpm.bin ./j2re-1_4_2_01-linux-i586-rpm.bin you will get j2re-1_4_2_01-linux-i586.rpm have root access rpm -Uh j2re-1_4_2_01-linux-i586.rpm 3 create a symbolic link eg cd /usr/local/mozilla/plugins ln -s /usr/java/j2re1.4.2_01/plugin/i386/ns610-gcc32/libjavaplugin_oji.so . 4 configure broswer to java enabled Edit = Preferences = Advanced, tick 'Enable Java' __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] gdata package for genetics
Hi, I try to install genetics_1.1.1.tar.gz and get following errors. it looks for a package call 'gdata'. I looked and search r-project web, did not find any thing R CMD INSTALL src/contrib/genetics_1.1.1.tar.gz * Installing *source* package 'genetics' ... ** R ** data ** inst ** preparing package for lazy loading Error in loadNamespace(i[[1]], c(lib.loc, .libPaths()), keep.source) : There is no package called 'gdata' Execution halted ERROR: lazy loading failed for package 'genetics' ** Removing '/usr/local/lib/R/library/genetics' ** Restoring previous '/usr/local/lib/R/library/genetics' Can you help me out this? Yuandan __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Search engine for LINUX MOZILLA
Hi, I am looking for help on searc engine at R htmlhelp page. Here is the system settings: R 2.0.0 (2004-10-04). Installed at Linux RH 9.0 (kernal 2.4.20-8) and FC2 (kernal 2.5.8). The web broswer is Mozilla 1.7 Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.7) Gecko/20040616 From help.start(), web broswer started ok. However, the search engine does not respond. The status bar only shows done. In Windows settings, it shows Applet started or something similar. I tried a few plugins, did not work. Any suggest? Yuandan __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] anova, multiple comparison
hi, I try to used R to do one-way anova. here is the simple code f1- lm (y ~ block, data=yd) there are 8 levels of factor block, I also want produce multiple pairwise comparisons for the 8 levels of block, inlcuding mean and std err for each of the 8 lelevls. It is tidious to do pair test. I looked the manuals, find no clues. any suggest? Regards, Yuandan __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] RW1081.exe installation
Hi, I download R 1.081 for windows (RW1081.exe). I tried to install it on windows 98 or windows xp, it stoped and stated that 'This program must be run under Win32'. Any one have suggestion how to fix it ? Thanks Yuandan __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
