[R] climatological standard deviation
Hello R users, I have a montly time series over a several year period. It's easy to compute a monthly climatology (12 values), Now, I would like to calculate the corresponding standard deviation, ie the 12 values calculated from the january values, february values, etc. What's the best way for such a calculation ? Regards, Yogesh -- Yogesh K. Tiwari (Dr.rer.nat), Scientist, Indian Institute of Tropical Meteorology, Homi Bhabha Road, Pashan, Pune-411008 INDIA Phone: 0091-99 2273 9513 (Cell) : 0091-20-258 93 600 (O) (Ext.250) Fax : 0091-20-258 93 825 [[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] How to draw the graph of f(x,y) = x * y ?
Paul you might find the view() function in the 'elliptic' package useful. This function implements various methods to visualize functions over the complex plane. HTH rksh Paul Smith wrote: Dear All, The function curve() draws the graph of functions from R to R. Is there some homologous function to curve() to draw functions from R^2 to R? Thanks in advance, 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. -- Robin K. S. Hankin Senior Research Associate Cambridge Centre for Climate Change Mitigation Research (4CMR) Department of Land Economy University of Cambridge [EMAIL PROTECTED] 01223-764877 __ 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] Options for viewing / using results from lm
Hello,
Thanks for the response.
However, I have this problem with view.
View(fit1)
Error: could not find function View
I have R 2.4.1 and even tried loading 'utils'.
As for saving residuals in a spreadsheet I used something like this:
res.fit1-fit1$residuals
res.fit2-fit2$residuals
write.csv(res.fit1, file=res.fit1.csv)
write.csv(res.fit2, file=res.fit2.csv)
Thanks,
M Just
On Tue, Sep 23, 2008 at 9:07 PM, Greg Snow [EMAIL PROTECTED] wrote:
The View function (note the uppercase V) is in the utils package, one of
the standard ones that loads automatically.
--
*From:* Michael Just [EMAIL PROTECTED]
*Sent:* Tuesday, September 23, 2008 2:49 PM
*To:* Greg Snow
*Cc:* r-help@r-project.org; [EMAIL PROTECTED]
*Subject:* Re: [R] Options for viewing / using results from lm
Greg,
Thanks for the pseudocode and cbind suggestions I think these should be
quite helpful. What package is the function 'view' in? As for exporting
elsewhere, basically I would to have the values of residuals saved in a
spreadsheet in addition to any visualizations created within R.
Thanks,
M Just
On Tue, Sep 23, 2008 at 3:26 PM, Greg Snow [EMAIL PROTECTED] wrote:
You can do things like this pseudocode:
fit1 - lm( y ~ x1, data=mydata )
fit2 - lm( y ~ x2, data=mydata )
fit3 - lm( y ~ x1*x2, data=mydata )
...
mydata$r1 - resid(fit1)
mydata$r2 - resid(fit2)
mydata$r3 - resid(fit3)
Or
mydata - cbind(mydata, r1=resid(fit1), r2=resid(fit2), ...
To view the data in a spreadsheet like table:
View(mydata)
And scroll over to the r columns, using indexing or the subset function
can reorder the columns to make this easier.
A simple plot:
pairs( mydata[ , paste('r',1:10, sep='')], col=c('red','green','blue')[
mydata$g1 ],
+ panel=panel.smooth )
Or there are various other ways to explore the data within R. If you
really feel the need to use another tool, do like the above, then use
write.table to export it to a csv file or paste it to a spreadsheet. There
is also the rggobi package which will automate the exporting to the ggobi
program which allows a lot more visualization options.
Hope this helps,
--
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
[EMAIL PROTECTED]
801.408.8111
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
project.org] On Behalf Of Michael Just
Sent: Tuesday, September 23, 2008 2:06 PM
To: r-help@r-project.org
Cc: [EMAIL PROTECTED]
Subject: Re: [R] Options for viewing / using results from lm
Hello,
Why do you think it is better done in another program? Keeping it in R
saves you from the exporting, which you say you are having trouble
with.
I think it might be better for viewing capabilities. If I had columns
of
residuals right next to each other I could spot differences amongst
locations. Right? If I can take the residual values and put them back
into
my main data file I can then have the options to use grouping values
that
exist there. (Like I asked here:
http://tolstoy.newcastle.edu.au/R/e5/help/08/09/2186.html)
Q2: How can I take the residuals and create an object(s) for further
http://tolstoy.newcastle.edu.au/R/e5/help/08/09/2259.html#2265qlink2
*
analysis.
*
**
See ?residuals.
Try the following:
x - sample(1:20, 100, replace=TRUE)
y - rnorm(100)
fit.lm - lm(y ~ x)
plot(residuals(fit.lm))
plot(x,residuals(fit.lm))
When I was thinking further analysis, for example, could I take the
residuals for all metrics in one extent and compare them to all
residuals
for all metrics in another extent? Even though the were created with 16
different models?
In 'plot(residuals(fit.lm))' what is the index 'counting'?
Thank you kindly for you $0.25,
Cheers,
M Just
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[R] Antwort: Re: WG: Problem during porting R-2.7.2 on HP-UP 11.11 PA-Risc
Dear Peter, thank you so much for the information and quick help, this was my problem to get the configure run. please see the results: R is now configured for hppa2.0w-hp-hpux11.11 Source directory: . Installation directory:/opt/R C compiler:gcc -std=gnu99 -g -O2 Fortran 77 compiler: f90 -g C++ compiler: g++ -g -O2 Fortran 90/95 compiler:f90 -g Obj-C compiler: Interfaces supported: External libraries: Additional capabilities: PNG, JPEG, iconv, MBCS, NLS Options enabled: shared BLAS, R profiling Recommended packages: yes configure: WARNING: you cannot build DVI versions of the R manuals configure: WARNING: you cannot build PDF versions of the R manuals But now i have a new problem during the make, we get a error from the compiler. Please Peter can you look / help again? 141 Lines Compiled f90 -g -c eigen.f -o eigen.o eigen.f external subroutine BALANC external subroutine BALBAK external subroutine CBABK2 external subroutine CBAL external subroutine CDIV external subroutine COMQR external subroutine COMQR2 external subroutine CORTH external subroutine CSROOT external subroutine ELMHES external subroutine ELTRAN external function EPSLON external subroutine HQR external subroutine HQR2 external subroutine HTRIBK external subroutine HTRIDI external function PYTHAG external subroutine TQL1 external subroutine TQL2 external subroutine TQLRAT external subroutine TRED1 external subroutine TRED2 external subroutine RG external subroutine RS external subroutine CG external subroutine CH 3502 Lines Compiled Make: Don't know how to make #. Stop. *** Error exit code 1 Stop. *** Error exit code 1 Stop. *** Error exit code 1 Stop. - Ok, this makes no sense in this moment ;-) ZLI/sw2/R-2.7.2 make install mkdir /opt/R/bin/lib mkdir /opt/R/bin/lib/R installing doc ... mkdir /opt/R/bin/lib/R/doc mkdir /opt/R/share mkdir /opt/R/share/man mkdir /opt/R/share/man/man1 ../tools/install-sh -c -m 644 ../NEWS /opt/R/bin/lib/R/doc help2man: can't get `--version' info from ../bin/R *** Error exit code 127 Stop. *** Error exit code 1 Stop. Viele Grüße Claus-Juergen Neumann Global RD Information Technology and Information Management Phone: +49 621 60-27453, Mobile: +49 172 7437400, Fax: +49 621 60-27092, E-Mail: [EMAIL PROTECTED] Postal Address: BASF SE, AP/CLS - LI444, D-67117 Limburgerhof, Germany BASF - The Chemical Company BASF SE, Registered Office: 67056 Ludwigshafen, Germany Companies' Register: Amtsgericht Ludwigshafen, Registration No.: HRB 6000 Chairman of the Supervisory Board: Juergen Strube Board of Executive Directors: Juergen Hambrecht, Chairman; Eggert Voscherau, Vice Chairman; Kurt Bock, Martin Brudermueller, John Feldmann, Andreas Kreimeyer, Stefan Marcinowski, Harald Schwager Peter Dalgaard [EMAIL PROTECTED] at.ku.dk An [EMAIL PROTECTED] 23.09.2008 15:35Kopie r-help@r-project.org Thema Re: [R] WG: Problem during porting R-2.7.2 on HP-UP 11.11 PA-Risc [EMAIL PROTECTED] wrote: Claus-Juergen Neumann/BASF-AG/B ASF An r-help@r-project.org 23.09.2008 12:49 Kopie Thema Problem during porting R-2.7.2 on HP-UP 11.11 PA-Risc Dear R-Team, we had some problem to install R-2.7.2 on HP-UX 11.11 on PA-Risc platform. 1.) i load down the Software and made a extract of the tar-file in a specific Directory. 2.) i follow the instructions on the
Re: [R] cannot allocate memory
DumpsterBear wrote: I am getting Error: cannot allocate vector of size 197 MB. I know that similar problems were discussed a lot already, but I didn't find any satisfactory answers so far! Details: *** I have XP (32bit) with 4GB ram. At the time when the problem appeared I had 1.5GB of available physical memory. *** I increased R memory limit to 3GB via memory.limit(3000) Have you told Windows to allow processes of more than 2GB? *** I did gs() and got gc(), I think. Uwe Ligges used (Mb) gc trigger (Mb) max used (Mb) Ncells147534 4.0 407500 10.9407500 10.9 Vcells 104939449 800.7 186388073 1422.1 185874684 1418.2 The garbage collection didn't help. Any ideas? Many thanks in advance! -- Adam __ 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] Antwort: Re: WG: Problem during porting R-2.7.2 on HP-UP 11.11 PA-Risc
[EMAIL PROTECTED] wrote: Make: Don't know how to make #. Stop. *** Error exit code 1 Sounds like you are using a make which doesn' t understand comments (??!). You might need to install GNU make and possibly set MAKE=gmake or some such to make sure that you are using the right one. At least that is the sort of thing you needed to do on Solaris five years ago... Isn't this in the admin manual? -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ 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] Logistic regression
Dear all, I am currently learning to run logistic regression models with R. Would someone tell me what this exactly means: Estimated scale (compare to 1 ) 1.746724 If the value is higher or lower than 1, what should I do? The complete results of the model were as follows: Generalized linear mixed model fit using Laplace Formula: success ~ diffca + (1 | partner1) + (1 | partner2) + (1 | target) Data: cascoresept08.df Family: binomial(logit link) AIC BIC logLik deviance 105.8 121.8 -47.89 95.79 Random effects: Groups Name Variance Std.Dev. partner1 (Intercept) 5.e-10 2.2361e-05 partner2 (Intercept) 5.e-10 2.2361e-05 target (Intercept) 1.0461e+00 1.0228e+00 number of obs: 182, groups: partner1, 19; partner2, 19; target, 13 Estimated scale (compare to 1 ) 1.746724 Fixed effects: Estimate Std. Error z value Pr(|z|) (Intercept) -4.5053 0.9174 -4.911 9.06e-07 *** diffca 0.7631 0.1130 6.756 1.42e-11 *** I thank you in advance! Annie __ 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] Bug in is ?
7 is an integer, but it's also a real. In R '?is' and '?is.integer' are clear that you're testing the class(es) of objects, not their values. I can't comment on the relationship with S Programming hth Keith J [EMAIL PROTECTED] wrote in message news:[EMAIL PROTECTED] This is really bothering me! In the Dr. Venables and Dr. Ripley's book S Programming Page 105 shows that c(is(10,integer),is(10.5,integer)) [1] T F But I try this in R 2.7.2 it shows c(is(10,integer),is(10.5,integer)) [1] FALSE FALSE Does anyone know what is going on here? Appreciate, Chunhao Quoting Yihui Xie [EMAIL PROTECTED]: Yes, everyone will agree 7 is an integer, but I don't think computers will agree too :-) R thinks it's a double-precision number, except when you explicitly specify it as an integer (say, as.integer()). class(7) [1] numeric is.double(7) [1] TRUE Regards, Yihui -- Yihui Xie [EMAIL PROTECTED] Phone: +86-(0)10-82509086 Fax: +86-(0)10-82509086 Mobile: +86-15810805877 Homepage: http://www.yihui.name School of Statistics, Room 1037, Mingde Main Building, Renmin University of China, Beijing, 100872, China On Wed, Sep 24, 2008 at 12:40 PM, [EMAIL PROTECTED] wrote: Hi R users Is there anything wrong in is function? (R 2.7.2) I believe that everyone will agree that 7 is an integer, right? but why R shows 7 is not an integer is.integer(7) [1] FALSE is(7,integer) [1] FALSE is(as.integer(7), integer) [1] TRUE Thank you very much in advance Chunhao __ 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] match.call in a function
Dear UseRs,
please find below a simple example which exemplifies my question.
In words, I'd like to write a function which prints formula and outcomes only
when results are not assigned or recalling the already assigned object, as e.g.
glm.
I'm sure a solution is rather simple and straightforward and it has something
to do with match.call (maybe), but I'm not able to see it.
Thanks in advance for any help
Carlo G. Camarda
# my simple function
myFUN - function(a, b, method){
res - ifelse(method==1, a+b, a-b)
object - list(res=res, call=match.call())
return(object)
}
# assigning to A
A - myFUN(2,4,1)
# recalling A or don't assign ...
A
myFUN(2,4,1)
# ... what I'd like (somehow) to have when
# I don't assign myFUN to another obj
# or when I recall the obj itself
My simple analysis
Call: myFUN(a = 2, b = 4, method = 1)
a: 2
b: 4
Outcome: 6
-
Carlo Giovanni Camarda
Research Scientist
Konrad-Zuse-Straße 1
18057 Rostock - Germany
Phone: +49 381 2081 172
Fax: +49 381 2081 472
[EMAIL PROTECTED]
http://www.demogr.mpg.de/en/staff/camarda/default.htm
-
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This mail has been sent through the MPI for Demographic ...{{dropped:10}}
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Re: [R] cannot allocate memory
Em Ter, 2008-09-23 às 21:42 -0400, DumpsterBear escreveu: I am getting Error: cannot allocate vector of size 197 MB. I know that similar problems were discussed a lot already, but I didn't find any satisfactory answers so far! Details: *** I have XP (32bit) with 4GB ram. At the time when the problem appeared I had 1.5GB of available physical memory. *** I increased R memory limit to 3GB via memory.limit(3000) *** I did gs() and got used (Mb) gc trigger (Mb) max used (Mb) Ncells147534 4.0 407500 10.9407500 10.9 Vcells 104939449 800.7 186388073 1422.1 185874684 1418.2 The garbage collection didn't help. Any ideas? Many thanks in advance! Adam, First, is possible 32bit XP use all your 4Gb? Second, I think you say gc whem say gs, so in my computer (Ubuntu 64bit with 4Gb): gc() used (Mb) gc trigger (Mb) max used (Mb) Ncells 188975 10.1 407500 21.8 35 18.7 Vcells 169133 1.3 786432 6.0 786378 6.0 gc(reset=T) used (Mb) gc trigger (Mb) max used (Mb) Ncells 188951 10.1 407500 21.8 188951 10.1 Vcells 168893 1.3 786432 6.0 168893 1.3 If you read gc help: reset: logical; if 'TRUE' the values for maximum space used are reset to the current values. Other issue is options for rgui command. Have a option --max-mem-size that you modify to expand you RAM avaiable -- Bernardo Rangel Tura, M.D,MPH,Ph.D National Institute of Cardiology Brazil __ 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] Modifying output to Google Docs
Ajay ohri wrote: Hi List, Graphical output to PDF's ,RTF ,CSV is known through R. Can it be modified for outputting to Google Docs (which is basically uploaded files ,published to become html pages) Is there any package on this ? Hi Ajay, Do you mean transforming R output into HTML? The R2HTML package does this, and the htmlize and R2html functions in the prettyR package do so as well. Jim __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Modifying output to Google Docs
Do I mean R output to Google docs, like in Google spreadsheets which are different from a spreadsheet published as an html or Presentations in Google Docs, which are much different tahn ordinary html presentations. See examples here of Google Docs- https://spreadsheets.google.com/ccc?key=pS9vSxWuwOlmcp-m7LUaAKAhl=en Thats an example of country wise medals in Olympics , and see if you can switch to Sheet3 which has graphs. Ajay www.decisionstats.com On Wed, Sep 24, 2008 at 3:05 PM, Jim Lemon [EMAIL PROTECTED] wrote: Ajay ohri wrote: Hi List, Graphical output to PDF's ,RTF ,CSV is known through R. Can it be modified for outputting to Google Docs (which is basically uploaded files ,published to become html pages) Is there any package on this ? Hi Ajay, Do you mean transforming R output into HTML? The R2HTML package does this, and the htmlize and R2html functions in the prettyR package do so as well. Jim -- Regards, Ajay Ohri http://tinyurl.com/liajayohri [[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] R2HTML: output from for-loops
Werner Wernersen wrote: Hi, I am trying to prepare a report with R2HTML using HTMLStart(outdir=./html, filename=report, echo=T, HTMLframe=F) then, for instance, I want to get the output of a loop: for (i in 1:20) print(summary(rnorm(1000))) but only the first of summaries really ends up in the html file. What am I doing wrongly? Hi Werner, I don't think you are doing anything wrong. I tried running a loop with the htmlize function in the prettyR package and it seems to work okay. Jim __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] extract species in a phylog tree
Hi, I am working with a phylog tree and I would like to extract a subset of the tree based on the species names (conserving the evolutionary distance and relationships between the pairs of species I am interested in). I see there is an option to select a subset of the tree using node names (phylog.extract), but this is not what I need since one node could take me to several species, some of which I am not interested in. This happens, for example, when I have a phylogenetic tree for, say, all bird species of North America, but I am only interested on those 20 that occur in my community, and I would like to extract the phylog tree for these species. Would anyone have any advice on how to proceed? Thanks a lot, Christine [[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] read.table readLines behaviour?
Quoting Peter Dalgaard [EMAIL PROTECTED]: [EMAIL PROTECTED] wrote: Hi, I have been using 'read.table' regularly to read tab-delimited text files with data. No problem, until now. Now I have a file that appeared to have read fine, and the data inside looks correct (structure etc), except I only had 15000+ rows out of the expected 24000. Using 'readLines' instead, and breaking up the data by tabs, gives me the expected result. I do not understand why this is happening and I can't find anything obvious in the data to explain the bahaviour... Does anybody have an explanation? something to watch out for? Hmm: - completely blank lines - filling - quotes My bet would be on the last one. Does read.delim work better? I just tried 'read.delim', and it reads the file just fine xxx-read.delim(All_norm_calls.txt, header=T, sep=\t) dim(xxx) [1] 2400011 I'll check for quotes etc. Thanks! Also, just in case: Check length(probesets) after the readLines call. I did the first time. It gives me the expected 20001 lines (the first one is the header) Jose -- Dr. Jose I. de las Heras Email: [EMAIL PROTECTED] The Wellcome Trust Centre for Cell BiologyPhone: +44 (0)131 6513374 Institute for Cell Molecular BiologyFax: +44 (0)131 6507360 Swann Building, Mayfield Road University of Edinburgh Edinburgh EH9 3JR UK -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. __ 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 readLines behaviour?
The result was 11, 24001 times, as I expected originally. hmmm... JOse Quoting Gabor Grothendieck [EMAIL PROTECTED]: Try looking at the result of count.fields to diagnose it. On Tue, Sep 23, 2008 at 5:19 AM, [EMAIL PROTECTED] wrote: Hi, I have been using 'read.table' regularly to read tab-delimited text files with data. No problem, until now. Now I have a file that appeared to have read fine, and the data inside looks correct (structure etc), except I only had 15000+ rows out of the expected 24000. Using 'readLines' instead, and breaking up the data by tabs, gives me the expected result. I do not understand why this is happening and I can't find anything obvious in the data to explain the bahaviour... Does anybody have an explanation? something to watch out for? If I run this I get the incomplete set: oldprobesets-read.table(All_norm_calls.txt,sep=\t,header=T,stringsAsFactors=F) dim(oldprobesets) [1] 1573311 but I get the right data if I use: probesets-readLines(All_norm_calls.txt) tmp-matrix(ncol=11,nrow=24000) for (i in 1:24000) tmp[i,]-unlist(strsplit(probesets[i+1],split=\t)) colnames(tmp)-unlist(strsplit(probesets[1],split=\t)) probesets-data.frame(tmp,stringsAsFactors=F) dim(probesets) [1] 2400011 Here's my sessionInfo output: sessionInfo() R version 2.7.0 (2008-04-22) i386-pc-mingw32 locale: LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United Kingdom.1252;LC_MONETARY=English_United Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252 attached base packages: [1] stats graphics grDevices datasets tcltk utils methods [8] base other attached packages: [1] limma_2.14.0 svSocket_0.9-5 svIO_0.9-5 R2HTML_1.59svMisc_0.9-5 [6] svIDE_0.9-5 loaded via a namespace (and not attached): [1] tools_2.7.0 Thanks! Jose -- Dr. Jose I. de las Heras Email: [EMAIL PROTECTED] The Wellcome Trust Centre for Cell BiologyPhone: +44 (0)131 6513374 Institute for Cell Molecular BiologyFax: +44 (0)131 6507360 Swann Building, Mayfield Road University of Edinburgh Edinburgh EH9 3JR UK -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. __ 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. Jose I. de las Heras Email: [EMAIL PROTECTED] The Wellcome Trust Centre for Cell BiologyPhone: +44 (0)131 6513374 Institute for Cell Molecular BiologyFax: +44 (0)131 6507360 Swann Building, Mayfield Road University of Edinburgh Edinburgh EH9 3JR UK -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. __ 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] lattice: Color in Barchart legend
Dear list,
with the code below I produce the right graph, but the colours of the
legend are different from the colours of the graph. The colours of the
graph are the desired colours.
Thanks for any help.
Patrick
library(lattice)
pal1 - rgb(196, 255, 255, max = 255)
pal2 - rgb( 0, 35, 196, max = 255)
df - data.frame( Gruppe = c(A, B, A, B),
Kat = c(x1, x1, w1, w1),
value= c(1,2, 4, 5))
barchart(value ~ Kat, group= Gruppe,
panel = function(y,x,...){
panel.barchart(x,y, ..., col=c(pal1, pal2))
}, data = df,
auto.key = list(points = FALSE, rectangles = TRUE,
columns = 2, space = bottom)
)
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Re: [R] How to convert backslash to slash?
Shengqiao Li wrote: On Tue, 23 Sep 2008, Duncan Murdoch wrote: On 23/09/2008 4:00 PM, Shengqiao Li wrote: How to use sub, gsub, etc. to replace \ in a string to /? For example,convert C:\foo\bar to C:/foo/bar. If those are R strings, there are no backslashes in the first one. It has a formfeed and a backspace in it. I did notice that this string was special. It's a legimate R string. If f and b are replaced by d, it will not. I didn't say it was not legitimate, I said that it contains no backslashes. If you replace f or b with d, you do not have a legitimate string. My purpose is to convert a Windows file path (eg. copied from Explorer location bar) to a R file path through some R function inside R terminal. The File-Change dir... takes a file path like C:\Acer, but setwd function will fail. That's not true. If you enter a backslash in the string, setwd() works fine. Your problem is that you are confusing R source code with the strings that it represents. The R source code for the file path C:\Acer is C:\\Acer. The R source code C:\foo\bar contains no backslashes, it contains the characters C, :, formfeed, o, o, backspace, a, r. If you have the string C:\Acer in the Windows clipboard, then you can read it from there using readClipboard(). (There are many other ways to read the clipboard as well; using 'clipboard' as a filename generally works.) You can then pass it to setwd(), and it will be fine. Duncan Murdoch I guess there must be some ways in R to replace a backslash by slash, eg. C:\Acer - C:/Acer. The first problem may be how to pass and save this kind of strings. encodeString does not work for this, it will just ignore \. Shengqiao Li 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-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] lattice: Color in Barchart legend
Hi,
you can use par.settings to get a consistent color scheme,
pal1 - rgb(196, 255, 255, max = 255)
pal2 - rgb( 0, 35, 196, max = 255)
df - data.frame( Gruppe = c(A, B, A, B),
Kat = c(x1, x1, w1, w1),
value= c(1,2, 4, 5))
barchart(value ~ Kat, group= Gruppe,
par.settings = list(superpose.polygon = list(col=c(pal1, pal2)) ),
panel = function(y,x,...){
panel.barchart(x,y, ...)
}, data = df,
auto.key = list(points = FALSE, rectangles = TRUE,
columns = 2, space = bottom)
)
HTH,
baptiste
On 24 Sep 2008, at 11:37, Patrick Hausmann wrote:
Dear list,
with the code below I produce the right graph, but the colours of
the legend are different from the colours of the graph. The colours
of the graph are the desired colours.
Thanks for any help.
Patrick
library(lattice)
pal1 - rgb(196, 255, 255, max = 255)
pal2 - rgb( 0, 35, 196, max = 255)
df - data.frame( Gruppe = c(A, B, A, B),
Kat = c(x1, x1, w1, w1),
value= c(1,2, 4, 5))
barchart(value ~ Kat, group= Gruppe,
panel = function(y,x,...){
panel.barchart(x,y, ..., col=c(pal1, pal2))
}, data = df,
auto.key = list(points = FALSE, rectangles = TRUE,
columns = 2, space = bottom)
)
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_
Baptiste Auguié
School of Physics
University of Exeter
Stocker Road,
Exeter, Devon,
EX4 4QL, UK
Phone: +44 1392 264187
http://newton.ex.ac.uk/research/emag
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[R] hexbin object to vector (shapefile)
Is it possible to convert an hexbin object like hexbin(rep(1:100,each=100),rep(1:100,100),xbins=10) and convert it to a vectorial (shp) format? Paulo - This electronic mail transmission including any attachment hereof, contains information that is private and confidential, and it is only for the use of the person and at the e-mail address above indicated. If you have received this electronic mail transmission in error, please destroy it and notify me immediately through e-mail address: [EMAIL PROTECTED] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Changing a plot
Hello list, I've been working on this problem for a while and I haven't been able to come up with a solution. I have a couple of functions that plot a bunch of data, then a single point on top of it. What I want is to be able to change the plot of the point without replotting all the data. Consider the following example: x = rnorm(100,1,0.5) y = rnorm(100,1,0.5) plot(x,y,pch=16) points(x[35],y[35],pch=19,col=6,cex=3) What I want to be able to do is to change the purple point to a different value without replotting everything. I know this seems like an odd suggestion, but it comes up a lot with the work I'm doing. I've prepared a package on CRAN called ResearchMethods for a course I'm working on, and there are several functions in there who's GUIs could work better if I could figure this out. If anyone has any ideas, or needs some further explanation, feel free to contact me. Thanks a lot, Sam Stewart __ 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] Generating series of distributions with the same skewness and different kurtosis or with same kurtosis and different skewness?
Check out JohnsonFit in SuppDists. On Tue, Sep 23, 2008 at 10:59 AM, zhijie zhang [EMAIL PROTECTED] wrote: Dear R users, I hope to explain the concepts of skewness and kurtosis by generating series of distributions with same skewness and different kurtosis or with same kurtosis and different skewness, but it seems that i cannot find the right functions. I have searched the mailing list, but no answers were found. Is it possible to do that in R? Which function could be used? Thanks a lot. -- With Kind Regards, oooO: (..): :\.(:::Oooo:: ::\_)::(..):: :::)./::: ::(_/ : [***] Zhi Jie,Zhang ,PHD Tel:+86-21-54237149 Dept. of Epidemiology,School of Public Health,Fudan University Address:No. 138 Yi Xue Yuan Road,Shanghai,China Postcode:200032 Email:[EMAIL PROTECTED] [EMAIL PROTECTED] Website: www.statABC.com [***] oooO: (..): :\.(:::Oooo:: ::\_)::(..):: :::)./::: ::(_/ : [[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] Bug in is ?
KJ == Keith Jewell [EMAIL PROTECTED]
on Wed, 24 Sep 2008 09:46:08 +0100 writes:
KJ 7 is an integer, but it's also a real.
KJ In R '?is' and '?is.integer' are clear that you're testing the
class(es) of
KJ objects, not their values.
KJ I can't comment on the relationship with S Programming
I can:
In S, and S-plus upto version 3.4,
numeric constants such as '7' where double as they are in R.
Then in S-plus 5.1, they became integer,
and there were tools so users could change all(!!) their S
scripts to use '7.' instead of '7' in all places where numeric
constants were seen, in order to keep behavior back compatible.
R never made such a step (backwards ;-), and never will,
notably since in R we had introduced the explicit long (= long
integer) constants, using the 'L' suffix,
i.e., 7L is integer
7 is double
Note however that for both, is.numeric(.) is fulfilled and
class(.) and mode(.) return numeric.
Only typeof(.), storage.mode(.) or str(.)
(or functions building on these) tell you the difference.
Martin Maechler, ETH Zurich and R core team
[And, yes, if you think further and are wondering:
If we'd design things from scratch, we would only have S4
classes and double would be a proper class and
numeric would be the class union of {integer, double}
]
KJ [EMAIL PROTECTED] wrote in message
KJ news:[EMAIL PROTECTED]
This is really bothering me! In the Dr. Venables and Dr. Ripley's book
S
Programming Page 105
shows that
c(is(10,integer),is(10.5,integer))
[1] T F
But I try this in R 2.7.2 it shows
c(is(10,integer),is(10.5,integer))
[1] FALSE FALSE
Does anyone know what is going on here?
Appreciate,
Chunhao
Quoting Yihui Xie [EMAIL PROTECTED]:
Yes, everyone will agree 7 is an integer, but I don't think
computers will agree too :-) R thinks it's a double-precision number,
except when you explicitly specify it as an integer (say,
as.integer()).
class(7)
[1] numeric
is.double(7)
[1] TRUE
Regards,
Yihui
--
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Phone: +86-(0)10-82509086 Fax: +86-(0)10-82509086
Mobile: +86-15810805877
Homepage: http://www.yihui.name
School of Statistics, Room 1037, Mingde Main Building,
Renmin University of China, Beijing, 100872, China
On Wed, Sep 24, 2008 at 12:40 PM, [EMAIL PROTECTED] wrote:
Hi R users
Is there anything wrong in is function? (R 2.7.2)
I believe that everyone will agree that 7 is an integer, right? but
why R
shows 7 is not an integer
is.integer(7)
[1] FALSE
is(7,integer)
[1] FALSE
is(as.integer(7), integer)
[1] TRUE
Thank you very much in advance
Chunhao
KJ __
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http://www.R-project.org/posting-guide.html
KJ and provide commented, minimal, self-contained, reproducible code.
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Re: [R] How to convert backslash to slash?
On Wed, 24 Sep 2008, Duncan Murdoch wrote: Shengqiao Li wrote: On Tue, 23 Sep 2008, Duncan Murdoch wrote: On 23/09/2008 4:00 PM, Shengqiao Li wrote: How to use sub, gsub, etc. to replace \ in a string to /? For example,convert C:\foo\bar to C:/foo/bar. If those are R strings, there are no backslashes in the first one. It has a formfeed and a backspace in it. I did notice that this string was special. It's a legimate R string. If f and b are replaced by d, it will not. I didn't say it was not legitimate, I said that it contains no backslashes. If you replace f or b with d, you do not have a legitimate string. My purpose is to convert a Windows file path (eg. copied from Explorer location bar) to a R file path through some R function inside R terminal. The File-Change dir... takes a file path like C:\Acer, but setwd function will fail. That's not true. If you enter a backslash in the string, setwd() works fine. Your problem is that you are confusing R source code with the strings that it represents. The R source code for the file path C:\Acer is C:\\Acer. The R source code C:\foo\bar contains no backslashes, it contains the characters C, :, formfeed, o, o, backspace, a, r. If you have the string C:\Acer in the Windows clipboard, then you can read it from there using readClipboard(). (There are many other ways to read the clipboard as well; using 'clipboard' as a filename generally works.) You can then pass it to setwd(), and it will be fine. Thank you for your reply. readClipboard is a partial solution to this case. More generally, if I want to wrtie a R program in which users are asked to input a file path. I want this program to be robust and tolerant, that is users can type in C:\Acer or C:/Acer. What's the way to do this? Shengqiao Li Duncan Murdoch I guess there must be some ways in R to replace a backslash by slash, eg. C:\Acer - C:/Acer. The first problem may be how to pass and save this kind of strings. encodeString does not work for this, it will just ignore \. Shengqiao Li 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-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 draw the graph of f(x,y) = x * y ?
On Wed, Sep 24, 2008 at 4:05 AM, Ben Bolker [EMAIL PROTECTED] wrote: The function curve() draws the graph of functions from R to R. Is there some homologous function to curve() to draw functions from R^2 to R? There is a curve3d function in the emdbook package on CRAN. Thanks, Ben and Robin. I think curve3d should be included in the base of R. It would help many users, I believe. I do not know whether curve3d could be extended to draw constant functions and functions like f(x,y) = x. With the current version, I get the following: curve3d(1) Error in curve3d(1) : 'expr' must be a function or an expression containing 'x' and 'y' curve3d(x) Error in eval(expr, envir, enclos) : could not find function x 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.
Re: [R] How to convert backslash to slash?
It probably depends on how you are prompting the user for input. Here is what happens with 'readline' and you will see that the string after input does have the backslashes escaped. x - readline(Input File: ) Input File: c:\dir1\dir2\file.name x [1] c:\\dir1\\dir2\\file.name gsub(, /, x) # notice the double escape [1] c:/dir1/dir2/file.name On Wed, Sep 24, 2008 at 8:53 AM, Shengqiao Li [EMAIL PROTECTED] wrote: On Wed, 24 Sep 2008, Duncan Murdoch wrote: Shengqiao Li wrote: On Tue, 23 Sep 2008, Duncan Murdoch wrote: On 23/09/2008 4:00 PM, Shengqiao Li wrote: How to use sub, gsub, etc. to replace \ in a string to /? For example,convert C:\foo\bar to C:/foo/bar. If those are R strings, there are no backslashes in the first one. It has a formfeed and a backspace in it. I did notice that this string was special. It's a legimate R string. If f and b are replaced by d, it will not. I didn't say it was not legitimate, I said that it contains no backslashes. If you replace f or b with d, you do not have a legitimate string. My purpose is to convert a Windows file path (eg. copied from Explorer location bar) to a R file path through some R function inside R terminal. The File-Change dir... takes a file path like C:\Acer, but setwd function will fail. That's not true. If you enter a backslash in the string, setwd() works fine. Your problem is that you are confusing R source code with the strings that it represents. The R source code for the file path C:\Acer is C:\\Acer. The R source code C:\foo\bar contains no backslashes, it contains the characters C, :, formfeed, o, o, backspace, a, r. If you have the string C:\Acer in the Windows clipboard, then you can read it from there using readClipboard(). (There are many other ways to read the clipboard as well; using 'clipboard' as a filename generally works.) You can then pass it to setwd(), and it will be fine. Thank you for your reply. readClipboard is a partial solution to this case. More generally, if I want to wrtie a R program in which users are asked to input a file path. I want this program to be robust and tolerant, that is users can type in C:\Acer or C:/Acer. What's the way to do this? Shengqiao Li Duncan Murdoch I guess there must be some ways in R to replace a backslash by slash, eg. C:\Acer - C:/Acer. The first problem may be how to pass and save this kind of strings. encodeString does not work for this, it will just ignore \. Shengqiao Li 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-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem that you are trying to solve? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] rgl: ellipse3d with axes
Last week I asked about data ellipses with rgl:::ellipse3d() with lines
showing the principal axes.
(The goal is a visual demonstration of PCA as a rotation of variable
space to component space.)
I was trying, unsuccessfully, to use princomp() to generate the PCA axes
and plot them using
segments3d:
PC - princomp(trees)
sdev - PC$sdev # component standard deviations
sd - sqrt(diag(cov)) # variable standard deviations
# vectors in variable space of principal components
vec - matrix(mu,3,3, byrow=TRUE) + diag(sd) %*% PC$loadings
for (j in 1:3) {
mat - rbind(mu, vec[j,])
segments3d(mat, col=red)
}
However, it occurred to me that these axes are just the orthogonal axes
of the unit sphere
that is transformed (using chol()) in ellipse3d, so plotting the axes
transformed in the
same way would give me what I want.
Looking at the result returned by ellipse3d, I see a normals component,
but I'm not sure if this
represents what I want, or, if it is, how to use it to draw the ellipse
major axes in the plot.
e1 -ellipse3d(cov, centre=mu, level=0.68)
str(e1)
List of 6
$ vb : num [1:4, 1:386] 4.95 2.64 2.03 1.00 6.74 ...
$ ib : num [1:4, 1:384] 1 195 99 196 51 197 99 195 27 198 ...
$ primitivetype: chr quad
$ homogeneous : logi TRUE
$ material : list()
$ normals : num [1:4, 1:386] 0.290 -0.902 -0.320 1.000 0.635 ...
- attr(*, class)= chr qmesh3d
-Michael
--
Michael Friendly Email: friendly AT yorku DOT ca
Professor, Psychology Dept.
York University Voice: 416 736-5115 x66249 Fax: 416 736-5814
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Re: [R] How to convert backslash to slash?
Shengqiao Li wrote: On Wed, 24 Sep 2008, Duncan Murdoch wrote: Shengqiao Li wrote: On Tue, 23 Sep 2008, Duncan Murdoch wrote: On 23/09/2008 4:00 PM, Shengqiao Li wrote: How to use sub, gsub, etc. to replace \ in a string to /? For example,convert C:\foo\bar to C:/foo/bar. If those are R strings, there are no backslashes in the first one. It has a formfeed and a backspace in it. I did notice that this string was special. It's a legimate R string. If f and b are replaced by d, it will not. I didn't say it was not legitimate, I said that it contains no backslashes. If you replace f or b with d, you do not have a legitimate string. My purpose is to convert a Windows file path (eg. copied from Explorer location bar) to a R file path through some R function inside R terminal. The File-Change dir... takes a file path like C:\Acer, but setwd function will fail. That's not true. If you enter a backslash in the string, setwd() works fine. Your problem is that you are confusing R source code with the strings that it represents. The R source code for the file path C:\Acer is C:\\Acer. The R source code C:\foo\bar contains no backslashes, it contains the characters C, :, formfeed, o, o, backspace, a, r. If you have the string C:\Acer in the Windows clipboard, then you can read it from there using readClipboard(). (There are many other ways to read the clipboard as well; using 'clipboard' as a filename generally works.) You can then pass it to setwd(), and it will be fine. Thank you for your reply. readClipboard is a partial solution to this case. More generally, if I want to wrtie a R program in which users are asked to input a file path. I want this program to be robust and tolerant, that is users can type in C:\Acer or C:/Acer. What's the way to do this? Just treat their input as data, not as source code. Backslashes are not special in data. 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] Bug in persp?
Dear All, I am not sure whether the following can be considered a bug: x - seq(-1,1,length=20) y - x z - matrix(1,20,20) persp(x,y,z) Error in persp.default(x, y, z) : invalid 'z' limits It works with: persp(x,y,z,zlim=c(0,1.5)) Should not persp set the z limits by default when the matrix to draw is constant? 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.
Re: [R] bandwidth selection for locpoly
Don't think it's in kernSmooth, but locfit has such facility. See
Loader's book for details.
Best,
Andy
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Chinthaka Kuruwita
Sent: Tuesday, September 23, 2008 12:18 PM
To: r-help@r-project.org
Subject: [R] bandwidth selection for locpoly
Hello All,
Is there a local bandwidth selection routine for local polynomial
regression (locpoly) ?
Thanks
Chinthaka Kuruwita
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[R] qplot, stacked area, own colourscheme
Dear list, I would like to apply my own colours to a stacked area plot, done with qplot, but I have not succeeded... What do I have so far (I am dealing with the development of cover of specific groups of plants): library(ggplot2) library(RODBC) channel - odbcConnect(myusername, case=tolower) sql - select trial, cover_of, dateofsurvey, cover from mytable mydata - (sqlQuery(channel, sql)) What I get is the following dataframe (simplified, there are more categories, not real data): trial cover_ofdateofsurveycover 1ZU-316 Cover dead material 2004-09-160 2ZU-316 Cover grasses 2004-09-16 16 3ZU-316 Cover herbs 2004-09-16 14 4ZU-316 Cover legumes 2004-09-16 10 5ZU-316 Cover open soil 2004-09-16 30 6ZU-316 Cover dead material 2005-09-185 7ZU-316 Cover grasses 2005-09-18 26 8ZU-316 Cover herbs 2005-09-18 14 9ZU-316 Cover legumes 2005-09-18 15 10 ZU-316 Cover open soil 2005-09-18 20 11 ZU-316 Cover dead material 2006-09-067 12 ZU-316 Cover grasses 2006-09-06 36 13 ZU-316 Cover herbs 2006-09-06 20 14 ZU-316 Cover legumes 2006-09-06 15 15 ZU-316 Cover open soil 2006-09-06 20 . . . With the following command I get a nice graph (development of cover over the years): qplot(dateofsurvey, cover, data=mydata, geom=area, fill=cover_of, main = Development of cover, ZU-316, ylab=projective Cover[%], xlab = Year) As I have those categories (cover grasses, cover herbs...) I would like to assign special colours to each (for example cover grasses = dark green, cover open soil = brown ...), but I did not get it so far. I tried several variations with area_geom, scale_manual but without success... For example (which does not work, it just shows the standard colourscheme): mycolorscheme - c(khaki, darkgreen, lightgreen, yellow, saddlebrown) mycolors - rep(mycolorscheme,3) myplot - qplot(dateofsurvey, wert, data=mydata, geom=area, fill=cover_of, main = Development of cover, ZU-316, ylab=projective Cover[%], xlab = Year) myplot + geom_area(colour = mycolours) What am I doing wrong? Thank you in advance, Albin -- | Albin Blaschka, Mag.rer.nat. | Etrichstrasse 26, A-5020 Salzburg | * www.albinblaschka.info * www.thinkanimal.info * | - It's hard to live in the mountains, hard but not hopeless! __ 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 convert backslash to slash?
On Wed, 24 Sep 2008, jim holtman wrote: It probably depends on how you are prompting the user for input. Here is what happens with 'readline' and you will see that the string after input does have the backslashes escaped. x - readline(Input File: ) Input File: c:\dir1\dir2\file.name x [1] c:\\dir1\\dir2\\file.name gsub(, /, x) # notice the double escape [1] c:/dir1/dir2/file.name Great! Thanks. By the way, it would be nice if R have a third way to quote a string and automatically escape the backslashes in memory. For instance: #not run now s- `C:\Acer' print(s) [1] C:\\Acer On Wed, Sep 24, 2008 at 8:53 AM, Shengqiao Li [EMAIL PROTECTED] wrote: On Wed, 24 Sep 2008, Duncan Murdoch wrote: Shengqiao Li wrote: On Tue, 23 Sep 2008, Duncan Murdoch wrote: On 23/09/2008 4:00 PM, Shengqiao Li wrote: How to use sub, gsub, etc. to replace \ in a string to /? For example,convert C:\foo\bar to C:/foo/bar. If those are R strings, there are no backslashes in the first one. It has a formfeed and a backspace in it. I did notice that this string was special. It's a legimate R string. If f and b are replaced by d, it will not. I didn't say it was not legitimate, I said that it contains no backslashes. If you replace f or b with d, you do not have a legitimate string. My purpose is to convert a Windows file path (eg. copied from Explorer location bar) to a R file path through some R function inside R terminal. The File-Change dir... takes a file path like C:\Acer, but setwd function will fail. That's not true. If you enter a backslash in the string, setwd() works fine. Your problem is that you are confusing R source code with the strings that it represents. The R source code for the file path C:\Acer is C:\\Acer. The R source code C:\foo\bar contains no backslashes, it contains the characters C, :, formfeed, o, o, backspace, a, r. If you have the string C:\Acer in the Windows clipboard, then you can read it from there using readClipboard(). (There are many other ways to read the clipboard as well; using 'clipboard' as a filename generally works.) You can then pass it to setwd(), and it will be fine. Thank you for your reply. readClipboard is a partial solution to this case. More generally, if I want to wrtie a R program in which users are asked to input a file path. I want this program to be robust and tolerant, that is users can type in C:\Acer or C:/Acer. What's the way to do this? Shengqiao Li Duncan Murdoch I guess there must be some ways in R to replace a backslash by slash, eg. C:\Acer - C:/Acer. The first problem may be how to pass and save this kind of strings. encodeString does not work for this, it will just ignore \. Shengqiao Li 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-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem that you are trying to solve? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] time calculation for simulation
Hello list, I want to compare time needed for a simulation between R and Ra (time optimized loops). Does anybody know, how I can count time needed for a simulation in R? Bests, Ralph __ 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] qplot, stacked area, own colourscheme
On Wed, Sep 24, 2008 at 8:39 AM, Albin Blaschka [EMAIL PROTECTED] wrote: Dear list, I would like to apply my own colours to a stacked area plot, done with qplot, but I have not succeeded... What do I have so far (I am dealing with the development of cover of specific groups of plants): library(ggplot2) library(RODBC) channel - odbcConnect(myusername, case=tolower) sql - select trial, cover_of, dateofsurvey, cover from mytable mydata - (sqlQuery(channel, sql)) What I get is the following dataframe (simplified, there are more categories, not real data): trial cover_ofdateofsurveycover 1ZU-316 Cover dead material 2004-09-160 2ZU-316 Cover grasses 2004-09-16 16 3ZU-316 Cover herbs 2004-09-16 14 4ZU-316 Cover legumes 2004-09-16 10 5ZU-316 Cover open soil 2004-09-16 30 6ZU-316 Cover dead material 2005-09-185 7ZU-316 Cover grasses 2005-09-18 26 8ZU-316 Cover herbs 2005-09-18 14 9ZU-316 Cover legumes 2005-09-18 15 10 ZU-316 Cover open soil 2005-09-18 20 11 ZU-316 Cover dead material 2006-09-067 12 ZU-316 Cover grasses 2006-09-06 36 13 ZU-316 Cover herbs 2006-09-06 20 14 ZU-316 Cover legumes 2006-09-06 15 15 ZU-316 Cover open soil 2006-09-06 20 . . . With the following command I get a nice graph (development of cover over the years): qplot(dateofsurvey, cover, data=mydata, geom=area, fill=cover_of, main = Development of cover, ZU-316, ylab=projective Cover[%], xlab = Year) As I have those categories (cover grasses, cover herbs...) I would like to assign special colours to each (for example cover grasses = dark green, cover open soil = brown ...), but I did not get it so far. I tried several variations with area_geom, scale_manual but without success... For example (which does not work, it just shows the standard colourscheme): mycolorscheme - c(khaki, darkgreen, lightgreen, yellow, saddlebrown) mycolors - rep(mycolorscheme,3) myplot - qplot(dateofsurvey, wert, data=mydata, geom=area, fill=cover_of, main = Development of cover, ZU-316, ylab=projective Cover[%], xlab = Year) myplot + geom_area(colour = mycolours) You want to modify the scale (the thing that converts data values to colours), not the geom: + scale_fill_manual(values = mycolorscheme) (And it's fill you want to change, not colour) This will also update the legend. Hadley -- http://had.co.nz/ __ 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 calculation for simulation
?system.time On Wed, Sep 24, 2008 at 9:46 AM, Ralph Scherer [EMAIL PROTECTED] wrote: Hello list, I want to compare time needed for a simulation between R and Ra (time optimized loops). Does anybody know, how I can count time needed for a simulation in R? Bests, Ralph __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem that you are trying to solve? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] climatological standard deviation
Dear Yogesh, Send us a minimal reproducive code, with a sample of your data structure. It will help us to help you :-) Best wishes, miltinho astronauta brazil On Wed, Sep 24, 2008 at 2:00 AM, Yogesh Tiwari [EMAIL PROTECTED]wrote: Hello R users, I have a montly time series over a several year period. It's easy to compute a monthly climatology (12 values), Now, I would like to calculate the corresponding standard deviation, ie the 12 values calculated from the january values, february values, etc. What's the best way for such a calculation ? Regards, Yogesh -- Yogesh K. Tiwari (Dr.rer.nat), Scientist, Indian Institute of Tropical Meteorology, Homi Bhabha Road, Pashan, Pune-411008 INDIA Phone: 0091-99 2273 9513 (Cell) : 0091-20-258 93 600 (O) (Ext.250) Fax : 0091-20-258 93 825 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.htmlhttp://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] rgl: ellipse3d with axes
Michael Friendly wrote:
Last week I asked about data ellipses with rgl:::ellipse3d() with lines
showing the principal axes.
(The goal is a visual demonstration of PCA as a rotation of variable
space to component space.)
I was trying, unsuccessfully, to use princomp() to generate the PCA axes
and plot them using
segments3d:
PC - princomp(trees)
sdev - PC$sdev # component standard deviations
sd - sqrt(diag(cov)) # variable standard deviations
# vectors in variable space of principal components
vec - matrix(mu,3,3, byrow=TRUE) + diag(sd) %*% PC$loadings
for (j in 1:3) {
mat - rbind(mu, vec[j,])
segments3d(mat, col=red)
}
However, it occurred to me that these axes are just the orthogonal axes
of the unit sphere
that is transformed (using chol()) in ellipse3d, so plotting the axes
transformed in the
same way would give me what I want.
Looking at the result returned by ellipse3d, I see a normals component,
but I'm not sure if this
represents what I want, or, if it is, how to use it to draw the ellipse
major axes in the plot.
e1 -ellipse3d(cov, centre=mu, level=0.68)
str(e1)
List of 6
$ vb : num [1:4, 1:386] 4.95 2.64 2.03 1.00 6.74 ...
$ ib : num [1:4, 1:384] 1 195 99 196 51 197 99 195 27 198 ...
$ primitivetype: chr quad
$ homogeneous : logi TRUE
$ material : list()
$ normals : num [1:4, 1:386] 0.290 -0.902 -0.320 1.000 0.635 ...
- attr(*, class)= chr qmesh3d
The normals component contains the surface normals. It is used to help
in rendering the surface, but isn't much use for your purposes.
Unfortunately, I'm not familiar enough with the internals of princomp to
tell you how to get the axes you want.
Duncan Murdoch
-Michael
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[R] rowSums()
Say I have the following data:
testDat - data.frame(A = c(1,NA,3), B = c(NA, NA, 3))
testDat
A B
1 1 NA
2 NA NA
3 3 3
rowsums() with na.rm=TRUE generates the following, which is not desired:
rowSums(testDat[, c('A', 'B')], na.rm=T)
[1] 1 0 6
rowsums() with na.rm=F generates the following, which is also not
desired:
rowSums(testDat[, c('A', 'B')], na.rm=F)
[1] NA NA 6
I see why this occurs, but what I hope to have returned would be:
[1] 1 NA 6
To get what I want I could do the following, but normally my ideas are
bad ideas and there are codified and proper ways to do things.
rr - numeric(nrow(testDat))
for(i in 1:nrow(testDat)) rr[i] - if(all(is.na(testDat[i,]))) NA else
sum(testDat[i,], na.rm=T)
rr
[1] 1 NA 6
Is there a proper way to do this? In my real data, nrow is over
100,000
Thanks,
Harold
sessionInfo()
R version 2.7.2 (2008-08-25)
i386-pc-mingw32
locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_MONETARY=English_United
States.1252;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_1.2 lattice_0.17-13 statmod_1.3.6
loaded via a namespace (and not attached):
[1] grid_2.7.2
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Re: [R] How to convert backslash to slash?
Your users will have to learn that if they are inputting quoted
strings into R, then, by convention, a backslash is used to 'escape'
certain character sequences and if you want a backslash, you have to
escape it ('\\'). You can also have your users upgrade to a system
that does not use backslashes in its file names, or learn that you can
alway use a virgule (/) in the file names.
On Wed, Sep 24, 2008 at 9:59 AM, Shengqiao Li [EMAIL PROTECTED] wrote:
On Wed, 24 Sep 2008, jim holtman wrote:
It probably depends on how you are prompting the user for input. Here
is what happens with 'readline' and you will see that the string after
input does have the backslashes escaped.
x - readline(Input File: )
Input File: c:\dir1\dir2\file.name
x
[1] c:\\dir1\\dir2\\file.name
gsub(, /, x) # notice the double escape
[1] c:/dir1/dir2/file.name
Great! Thanks. By the way, it would be nice if R have a third way to quote a
string and automatically escape the backslashes in memory. For instance:
#not run now
s- `C:\Acer'
print(s)
[1] C:\\Acer
On Wed, Sep 24, 2008 at 8:53 AM, Shengqiao Li [EMAIL PROTECTED] wrote:
On Wed, 24 Sep 2008, Duncan Murdoch wrote:
Shengqiao Li wrote:
On Tue, 23 Sep 2008, Duncan Murdoch wrote:
On 23/09/2008 4:00 PM, Shengqiao Li wrote:
How to use sub, gsub, etc. to replace \ in a string to /?
For example,convert C:\foo\bar to C:/foo/bar.
If those are R strings, there are no backslashes in the first one. It
has a formfeed and a backspace in it.
I did notice that this string was special. It's a legimate R string.
If
f and b are replaced by d, it will not.
I didn't say it was not legitimate, I said that it contains no
backslashes. If you replace f or b with d, you do not have a legitimate
string.
My purpose is to convert a Windows file path (eg. copied from Explorer
location bar) to a R file path through some R function inside R
terminal.
The File-Change dir... takes a file path like C:\Acer, but setwd
function will fail.
That's not true. If you enter a backslash in the string, setwd() works
fine.
Your problem is that you are confusing R source code with the strings
that
it represents. The R source code for the file path C:\Acer is
C:\\Acer.
The
R source code C:\foo\bar contains no backslashes, it contains the
characters C, :, formfeed, o, o, backspace, a, r.
If you have the string C:\Acer in the Windows clipboard, then you can
read
it from there using readClipboard(). (There are many other ways to read
the
clipboard as well;
using 'clipboard' as a filename generally works.) You can then pass it
to
setwd(), and it will be fine.
Thank you for your reply. readClipboard is a partial solution to this
case.
More generally, if I want to wrtie a R program in which users are asked
to
input a file path. I want this program to be robust and tolerant, that is
users can type in C:\Acer or C:/Acer. What's the way to do this?
Shengqiao Li
Duncan Murdoch
I guess there must be some ways in R to replace a backslash by slash,
eg.
C:\Acer - C:/Acer. The first problem may be how to pass and save this
kind
of strings. encodeString does not work for this, it will just ignore
\.
Shengqiao Li
Duncan Murdoch
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http://www.R-project.org/posting-guide.html
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--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem that you are trying to solve?
--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem that you are trying to solve?
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[R] Error results from MS Access via RODBC
I have an MS Access database with one table and one column holding rep(1:10) I use: library(RODBC) channel - odbcConnect(test) sqlQuery(channel, paste(SELECT col FROM tblTest), believeNRows=FALSE) and get: 49 50 51 52 53 54 55 56 57 12337 What? The above should, of course, read: 1 2 3 4 5 6 7 8 9 10 I tried the 'odbcQuery' / 'sqlGetResults' dance. But no love... From a console, 'mdb-sql' and 'isql' gives correct output, so the odbc seems to be working OK. Text columns show up fine when I select them with the above RODBC procedure. I've fiddled with pretty much all the options that go with 'sqlQuery' with the same output every time. I've compacted and repaired the database. I've created other mdb's, with the same result. When I connect to other DB's via RODBC, like MySQL, data is correct... What am I missing? Some output: -- ~# dpkg -l libmdb* mdbtools ii libmdbodbc 0.5.99.0.6pre1.0.20 MDB tools ODBC module ii libmdbtools 0.5.99.0.6pre1.0.20 mdbtools libraries ii mdbtools 0.5.99.0.6pre1.0.20 JET / MS Access database (MDB) tools -- ~# mdb-ver db.mdb JET4 -- R odbcGetInfo(channel) DBMS_Name DBMS_Ver Driver_ODBC_Ver Data_Source_Name test Driver_Name test Driver_Ver test ODBC_Ver 03.52 Server_Name 03.52 -- R version platform: i486-pc-linux-gnu arch: i486 os: linux-gnu system: i486, linux-gnu status major: 2 minor: 7.2 year: 2008 month: 08 day: 25 svn rev: 46428 language: R version.string R version 2.7.2 (2008-08-25) -- R sessionInfo() R version 2.7.2 (2008-08-25) i486-pc-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] RODBC_1.2-3 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] lower / upper case letters in a plot
Hi, How can I generate lower case letters for my axis-titles? Thanks, Jörg __ 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] cannot allocate memory
I am getting Error: cannot allocate vector of size 197 MB. I know that similar problems were discussed a lot already, but I didn't find any satisfactory answers so far! Details: *** I have XP (32bit) with 4GB ram. At the time when the problem appeared I had 1.5GB of available physical memory. *** I increased R memory limit to 3GB via memory.limit(3000) Have you told Windows to allow processes of more than 2GB? Yes, I did. But this only matters if R requests a memory block of size bigger than 2GB at one time. As I wrote, I had 1.5GB available of physical memory out of my 4GB. gc(), I think. Yes, indeed. Many thanks, Adam __ 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] Changing a plot
R Help rhelp.stats at gmail.com writes: Hello list, I've been working on this problem for a while and I haven't been able to come up with a solution. I have a couple of functions that plot a bunch of data, then a single point on top of it. What I want is to be able to change the plot of the point without replotting all the data. Consider the following example: x = rnorm(100,1,0.5) y = rnorm(100,1,0.5) plot(x,y,pch=16) points(x[35],y[35],pch=19,col=6,cex=3) What I want to be able to do is to change the purple point to a different value without replotting everything. R's default (base) graphics model is a 'canvas' -- things get drawn, but nothing ever gets erased. (The cheap solution is to overplot in the background color, but that won't work if there's stuff underneath the point that you want to preserve.) You probably need to move to the grid graphics package (hint: buy or borrow Paul Murrell's book) to do something like this. Ben Bolker __ 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] rgl: ellipse3d with axes
Duncan Murdoch wrote: The normals component contains the surface normals. It is used to help in rendering the surface, but isn't much use for your purposes. Unfortunately, I'm not familiar enough with the internals of princomp to tell you how to get the axes you want. Duncan Murdoch OK, then let me repharase it. The axes of the unit sphere are like axes - matrix( c(0, 0, -1, 0, 0, 1, 0, -1, 0, 0, 1, 0, -1, 0, 0, 1, 0, 0), 6, 3, byrow=TRUE) taken in pairs. I'd like to transform these coordinates the same was as in ellipse3d() and add them to the plot. -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. York University Voice: 416 736-5115 x66249 Fax: 416 736-5814 4700 Keele Streethttp://www.math.yorku.ca/SCS/friendly.html Toronto, ONT M3J 1P3 CANADA __ 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] qplot, stacked area, own colourscheme
hadley wickham schrieb: On Wed, Sep 24, 2008 at 8:39 AM, Albin Blaschka [EMAIL PROTECTED] wrote: [snip] As I have those categories (cover grasses, cover herbs...) I would like to assign special colours to each (for example cover grasses = dark green, cover open soil = brown ...), but I did not get it so far. I tried several variations with area_geom, scale_manual but without success... You want to modify the scale (the thing that converts data values to colours), not the geom: + scale_fill_manual(values = mycolorscheme) (And it's fill you want to change, not colour) This will also update the legend. Hadley Thank you very much, it works now - the right keywords were the problem: it seems I went wrong because for me scale had only a meaning in a spatial context (mother tongue is german), for example scale on a map or scale (range) of an axis...and I was fixed to changeing colours, but fill is now logical... best wishes, Albin -- | Albin Blaschka, Mag.rer.nat. | Etrichstrasse 26, A-5020 Salzburg | * www.albinblaschka.info * www.thinkanimal.info * | - It's hard to live in the mountains, hard but not hopeless! __ 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] lower / upper case letters in a plot
check: ?tolower() Best, Dimitris Jörg Groß wrote: Hi, How can I generate lower case letters for my axis-titles? Thanks, Jörg __ 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. -- Dimitris Rizopoulos Assistant Professor Department of Biostatistics Erasmus Medical Center Address: PO Box 2040, 3000 CA Rotterdam, the Netherlands Tel: +31/(0)10/7043478 Fax: +31/(0)10/7043014 __ 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] rowSums()
I guess this would be the fastest way would be:
rs - rowSums( testDat, na.rm=T)
rs[ which( rowMeans(is.na(testDat)) == 1 ) ] - NA
since both rowSums and rowMeans are internally coded in C.
Regards, Adai
Doran, Harold wrote:
Say I have the following data:
testDat - data.frame(A = c(1,NA,3), B = c(NA, NA, 3))
testDat
A B
1 1 NA
2 NA NA
3 3 3
rowsums() with na.rm=TRUE generates the following, which is not desired:
rowSums(testDat[, c('A', 'B')], na.rm=T)
[1] 1 0 6
rowsums() with na.rm=F generates the following, which is also not
desired:
rowSums(testDat[, c('A', 'B')], na.rm=F)
[1] NA NA 6
I see why this occurs, but what I hope to have returned would be:
[1] 1 NA 6
To get what I want I could do the following, but normally my ideas are
bad ideas and there are codified and proper ways to do things.
rr - numeric(nrow(testDat))
for(i in 1:nrow(testDat)) rr[i] - if(all(is.na(testDat[i,]))) NA else
sum(testDat[i,], na.rm=T)
rr
[1] 1 NA 6
Is there a proper way to do this? In my real data, nrow is over
100,000
Thanks,
Harold
sessionInfo()
R version 2.7.2 (2008-08-25)
i386-pc-mingw32
locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_MONETARY=English_United
States.1252;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_1.2 lattice_0.17-13 statmod_1.3.6
loaded via a namespace (and not attached):
[1] grid_2.7.2
__
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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] Changing a plot
One way is to keep a copy of the original and then return to it when you
need it.
x - rnorm(100,1,0.5)
y - rnorm(100,1,0.5)
plot(x,y,pch=16)
original - recordPlot()
for( i in 1:10 ){
points( x[i], y[i], pch=19, col=yellow, cex=3)
points( x[i], y[i], pch=16)
Sys.sleep(1) # slow the graphs a bit
replayPlot(original)
}
Regards, Adai
R Help wrote:
Hello list,
I've been working on this problem for a while and I haven't been able
to come up with a solution.
I have a couple of functions that plot a bunch of data, then a single
point on top of it. What I want is to be able to change the plot of
the point without replotting all the data. Consider the following
example:
x = rnorm(100,1,0.5)
y = rnorm(100,1,0.5)
plot(x,y,pch=16)
points(x[35],y[35],pch=19,col=6,cex=3)
What I want to be able to do is to change the purple point to a
different value without replotting everything.
I know this seems like an odd suggestion, but it comes up a lot with
the work I'm doing. I've prepared a package on CRAN called
ResearchMethods for a course I'm working on, and there are several
functions in there who's GUIs could work better if I could figure this
out.
If anyone has any ideas, or needs some further explanation, feel free
to contact me.
Thanks a lot,
Sam Stewart
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Re: [R] rowSums()
On 9/24/2008 10:06 AM, Doran, Harold wrote:
Say I have the following data:
testDat - data.frame(A = c(1,NA,3), B = c(NA, NA, 3))
testDat
A B
1 1 NA
2 NA NA
3 3 3
rowsums() with na.rm=TRUE generates the following, which is not desired:
rowSums(testDat[, c('A', 'B')], na.rm=T)
[1] 1 0 6
rowsums() with na.rm=F generates the following, which is also not
desired:
rowSums(testDat[, c('A', 'B')], na.rm=F)
[1] NA NA 6
I see why this occurs, but what I hope to have returned would be:
[1] 1 NA 6
To get what I want I could do the following, but normally my ideas are
bad ideas and there are codified and proper ways to do things.
rr - numeric(nrow(testDat))
for(i in 1:nrow(testDat)) rr[i] - if(all(is.na(testDat[i,]))) NA else
sum(testDat[i,], na.rm=T)
rr
[1] 1 NA 6
Is there a proper way to do this? In my real data, nrow is over
100,000
I don't know if it is proper, but here is a slightly different way
that I find easier to read:
apply(testDat, 1, function(x){
ifelse(all(is.na(x)), NA, sum(x, na.rm=TRUE))
})
[1] 1 NA 6
hope this helps,
Chuck
Thanks,
Harold
sessionInfo()
R version 2.7.2 (2008-08-25)
i386-pc-mingw32
locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_MONETARY=English_United
States.1252;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_1.2 lattice_0.17-13 statmod_1.3.6
loaded via a namespace (and not attached):
[1] grid_2.7.2
__
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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.
--
Chuck Cleland, Ph.D.
NDRI, Inc. (www.ndri.org)
71 West 23rd Street, 8th floor
New York, NY 10010
tel: (212) 845-4495 (Tu, Th)
tel: (732) 512-0171 (M, W, F)
fax: (917) 438-0894
__
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] lower / upper case letters in a plot
Oh, ok ... perhaps it was the wrong description; I want lowered cases... In LaTeX I get them with x_1 for example. Or x^2 for upper cases. But how can I make this in R? Am 24.09.2008 um 16:17 schrieb Dimitris Rizopoulos: check: ?tolower() Best, Dimitris Jörg Groß wrote: Hi, How can I generate lower case letters for my axis-titles? Thanks, Jörg __ 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. -- Dimitris Rizopoulos Assistant Professor Department of Biostatistics Erasmus Medical Center Address: PO Box 2040, 3000 CA Rotterdam, the Netherlands Tel: +31/(0)10/7043478 Fax: +31/(0)10/7043014 __ 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 convert backslash to slash?
On Wed, Sep 24, 2008 at 9:59 AM, Shengqiao Li [EMAIL PROTECTED] wrote: On Wed, 24 Sep 2008, jim holtman wrote: It probably depends on how you are prompting the user for input. Here is what happens with 'readline' and you will see that the string after input does have the backslashes escaped. x - readline(Input File: ) Input File: c:\dir1\dir2\file.name x [1] c:\\dir1\\dir2\\file.name gsub(, /, x) # notice the double escape [1] c:/dir1/dir2/file.name Great! Thanks. By the way, it would be nice if R have a third way to quote a string and automatically escape the backslashes in memory. For instance: #not run now s- `C:\Acer' print(s) [1] C:\\Acer I agree that that some sort of facility would be convenient. Creating latex output is another situation where not having to escape backslashes would be convenient. Other languages do have special purpose constructs for this. __ 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] lower / upper case letters in a plot
so you mean subscripts and superscripts, then check: ?plotmath Best, Dimitris Jörg Groß wrote: Oh, ok ... perhaps it was the wrong description; I want lowered cases... In LaTeX I get them with x_1 for example. Or x^2 for upper cases. But how can I make this in R? Am 24.09.2008 um 16:17 schrieb Dimitris Rizopoulos: check: ?tolower() Best, Dimitris Jörg Groß wrote: Hi, How can I generate lower case letters for my axis-titles? Thanks, Jörg __ 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. -- Dimitris Rizopoulos Assistant Professor Department of Biostatistics Erasmus Medical Center Address: PO Box 2040, 3000 CA Rotterdam, the Netherlands Tel: +31/(0)10/7043478 Fax: +31/(0)10/7043014 __ 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. -- Dimitris Rizopoulos Assistant Professor Department of Biostatistics Erasmus Medical Center Address: PO Box 2040, 3000 CA Rotterdam, the Netherlands Tel: +31/(0)10/7043478 Fax: +31/(0)10/7043014 __ 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] rowSums()
try the following:
testDat - data.frame(A = c(1,NA,3), B = c(NA, NA, 3))
ind - rowSums(is.na(testDat)) == length(testDat)
out - rowSums(testDat, na.rm = TRUE)
out[ind] - NA
out
I hope it helps.
Best,
Dimitris
Doran, Harold wrote:
Say I have the following data:
testDat - data.frame(A = c(1,NA,3), B = c(NA, NA, 3))
testDat
A B
1 1 NA
2 NA NA
3 3 3
rowsums() with na.rm=TRUE generates the following, which is not desired:
rowSums(testDat[, c('A', 'B')], na.rm=T)
[1] 1 0 6
rowsums() with na.rm=F generates the following, which is also not
desired:
rowSums(testDat[, c('A', 'B')], na.rm=F)
[1] NA NA 6
I see why this occurs, but what I hope to have returned would be:
[1] 1 NA 6
To get what I want I could do the following, but normally my ideas are
bad ideas and there are codified and proper ways to do things.
rr - numeric(nrow(testDat))
for(i in 1:nrow(testDat)) rr[i] - if(all(is.na(testDat[i,]))) NA else
sum(testDat[i,], na.rm=T)
rr
[1] 1 NA 6
Is there a proper way to do this? In my real data, nrow is over
100,000
Thanks,
Harold
sessionInfo()
R version 2.7.2 (2008-08-25)
i386-pc-mingw32
locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_MONETARY=English_United
States.1252;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_1.2 lattice_0.17-13 statmod_1.3.6
loaded via a namespace (and not attached):
[1] grid_2.7.2
__
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.
--
Dimitris Rizopoulos
Assistant Professor
Department of Biostatistics
Erasmus Medical Center
Address: PO Box 2040, 3000 CA Rotterdam, the Netherlands
Tel: +31/(0)10/7043478
Fax: +31/(0)10/7043014
__
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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] lower / upper case letters in a plot
An example would help. You generally control the titles using arguments like main, xlab, ylab, sub in the plotting functions or afterwards using title() function. You can get the upper/lower case using toupper()/tolower() functions. See help(par), help(title), help(tolower). Here is an example: string - My x-axis corresponding to something plot( rnorm(10), xlab=toupper(string) ) Regards, Adai Jörg Groß wrote: Hi, How can I generate lower case letters for my axis-titles? Thanks, Jörg __ 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] rowSums()
on 09/24/2008 09:06 AM Doran, Harold wrote:
Say I have the following data:
testDat - data.frame(A = c(1,NA,3), B = c(NA, NA, 3))
testDat
A B
1 1 NA
2 NA NA
3 3 3
rowsums() with na.rm=TRUE generates the following, which is not desired:
rowSums(testDat[, c('A', 'B')], na.rm=T)
[1] 1 0 6
rowsums() with na.rm=F generates the following, which is also not
desired:
rowSums(testDat[, c('A', 'B')], na.rm=F)
[1] NA NA 6
I see why this occurs, but what I hope to have returned would be:
[1] 1 NA 6
To get what I want I could do the following, but normally my ideas are
bad ideas and there are codified and proper ways to do things.
rr - numeric(nrow(testDat))
for(i in 1:nrow(testDat)) rr[i] - if(all(is.na(testDat[i,]))) NA else
sum(testDat[i,], na.rm=T)
rr
[1] 1 NA 6
Is there a proper way to do this? In my real data, nrow is over
100,000
Thanks,
Harold
The behavior you observe is documented in ?rowSums in the Value section:
If there are no values in a range to be summed over (after removing
missing values with na.rm = TRUE), that component of the output is set
to 0 (*Sums) or NA (*Means), consistent with sum and mean.
So:
sum(c(NA, NA), na.rm = TRUE)
[1] 0
As per the definition of the sum of an empty set being 0, which I got
burned on myself a while back.
You could feasibly use:
Res - rowSums(testDat, na.rm = TRUE)
is.na(Res) - rowSums(is.na(testDat)) == ncol(testDat)
HTH,
Marc Schwartz
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] rowSums()
On 9/24/2008 10:38 AM, Marc Schwartz wrote:
on 09/24/2008 09:06 AM Doran, Harold wrote:
Say I have the following data:
testDat - data.frame(A = c(1,NA,3), B = c(NA, NA, 3))
testDat
A B
1 1 NA
2 NA NA
3 3 3
rowsums() with na.rm=TRUE generates the following, which is not desired:
rowSums(testDat[, c('A', 'B')], na.rm=T)
[1] 1 0 6
rowsums() with na.rm=F generates the following, which is also not
desired:
rowSums(testDat[, c('A', 'B')], na.rm=F)
[1] NA NA 6
I see why this occurs, but what I hope to have returned would be:
[1] 1 NA 6
To get what I want I could do the following, but normally my ideas are
bad ideas and there are codified and proper ways to do things.
rr - numeric(nrow(testDat))
for(i in 1:nrow(testDat)) rr[i] - if(all(is.na(testDat[i,]))) NA else
sum(testDat[i,], na.rm=T)
rr
[1] 1 NA 6
Is there a proper way to do this? In my real data, nrow is over
100,000
Thanks,
Harold
The behavior you observe is documented in ?rowSums in the Value section:
If there are no values in a range to be summed over (after removing
missing values with na.rm = TRUE), that component of the output is set
to 0 (*Sums) or NA (*Means), consistent with sum and mean.
Based on the difference in behavior for Sums and Means, this might be
another possibility:
rowMeans(testDat, na.rm=TRUE) * rowSums(!is.na(testDat))
[1] 1 NA 6
So:
sum(c(NA, NA), na.rm = TRUE)
[1] 0
As per the definition of the sum of an empty set being 0, which I got
burned on myself a while back.
You could feasibly use:
Res - rowSums(testDat, na.rm = TRUE)
is.na(Res) - rowSums(is.na(testDat)) == ncol(testDat)
HTH,
Marc Schwartz
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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.
--
Chuck Cleland, Ph.D.
NDRI, Inc. (www.ndri.org)
71 West 23rd Street, 8th floor
New York, NY 10010
tel: (212) 845-4495 (Tu, Th)
tel: (732) 512-0171 (M, W, F)
fax: (917) 438-0894
__
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] *solved* lower / upper case letters in a plot
Great thanks and sorry for my bad english! Am 24.09.2008 um 16:32 schrieb Dimitris Rizopoulos: so you mean subscripts and superscripts, then check: ?plotmath Best, Dimitris Jörg Groß wrote: Oh, ok ... perhaps it was the wrong description; I want lowered cases... In LaTeX I get them with x_1 for example. Or x^2 for upper cases. But how can I make this in R? Am 24.09.2008 um 16:17 schrieb Dimitris Rizopoulos: check: ?tolower() Best, Dimitris Jörg Groß wrote: Hi, How can I generate lower case letters for my axis-titles? Thanks, Jörg __ 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. -- Dimitris Rizopoulos Assistant Professor Department of Biostatistics Erasmus Medical Center Address: PO Box 2040, 3000 CA Rotterdam, the Netherlands Tel: +31/(0)10/7043478 Fax: +31/(0)10/7043014 __ 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. -- Dimitris Rizopoulos Assistant Professor Department of Biostatistics Erasmus Medical Center Address: PO Box 2040, 3000 CA Rotterdam, the Netherlands Tel: +31/(0)10/7043478 Fax: +31/(0)10/7043014 __ 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 convert backslash to slash?
I agree that that some sort of facility would be convenient. Creating latex output is another situation where not having to escape backslashes would be convenient. And regular expressions, of course. Hadley -- http://had.co.nz/ __ 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] Counting character occurrences in data frame
Thanks Charles, ftable() works perfectly.
-Original Message-
From: Charles C. Berry [mailto:[EMAIL PROTECTED]
Sent: Tuesday, September 23, 2008 5:06 PM
To: Hutchinson,David [PYR]
Cc: r-help@r-project.org
Subject: Re: [R] Counting character occurrences in data frame
See
?ftable
?as.data.frame
?xtabs
e.g.
ftable( xtabs( ~code+year+month, your.df ), col.vars=1 )
as.data.frame( xtabs(~code+year+month, your.df ) )
HTH,
Chuck
On Tue, 23 Sep 2008, Hutchinson,David [PYR] wrote:
Hi R-Users,
I have a data frame containing year, month, day, and code columns. The
code column is a unique character of set ('E','A','B') - I am trying
to
determine an efficient way of summarizing the count of each of these
codes by month and year without having to use for...loops and subsets.
Does anyone have any suggestions?
Thanks in advance,
Dave
Here is a snapshot of my data frame:
year month day code
8006 193512 1E
8007 193512 2
8008 193512 3E
8009 193512 4
8010 193512 5E
8011 193512 6E
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Charles C. Berry(858) 534-2098
Dept of Family/Preventive
Medicine
E mailto:[EMAIL PROTECTED] UC San Diego
http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego
92093-0901
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[R] How do I Convert 1 to the number 1?
Is there an elegant way in R to change a number reported as a less-than number in text format, 1 for example, to the numeric equivalent 1? I have been trying to use as.numeric, but have not come up with anything clever yet. Tom -- View this message in context: http://www.nabble.com/How-do-I-Convert-%22%3C1%22-to-the-number-1--tp19651018p19651018.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] rgl: ellipse3d with axes
On 24/09/2008 10:12 AM, Michael Friendly wrote: Duncan Murdoch wrote: The normals component contains the surface normals. It is used to help in rendering the surface, but isn't much use for your purposes. Unfortunately, I'm not familiar enough with the internals of princomp to tell you how to get the axes you want. Duncan Murdoch OK, then let me repharase it. The axes of the unit sphere are like axes - matrix( c(0, 0, -1, 0, 0, 1, 0, -1, 0, 0, 1, 0, -1, 0, 0, 1, 0, 0), 6, 3, byrow=TRUE) taken in pairs. I'd like to transform these coordinates the same was as in ellipse3d() and add them to the plot. That's easy, but it doesn't give you the principal axes of the ellipse. Just use axes %*% chol(cov) If you start with a unit sphere, this will give you points on its surface, but not the ones you want. For those you need the SVD or eigenvectors. This looks like it does what you want: axes - matrix( c(0, 0, 0, # added origin 0, 0, -1, 0, 0, 1, 0, -1, 0, 0, 1, 0, -1, 0, 0, 1, 0, 0), 7, 3, byrow=TRUE) axes - axes[c(1,2,1,3,1,4,1,5,1,6,1,7),] # add the origin before each cov - cov(trees) eigen - eigen(cov) shade3d(ellipse3d(cov, t=1, alpha=0.2, col='red')) segments3d(axes %*% sqrt(diag(eigen$values)) %*% t(eigen$vectors)) 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] How to draw the graph of f(x,y) = x * y ?
You could always try F(x,y) = f(x) + 0*y That is zero out the degenerate dimensions. Of course you'll be plotting what is essentially a two dimensional object as if it were three dimensional. The degeneracy in y means a 2-D curve will be extruded along the Y dimension. Robert Farley Metro www.Metro.net -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Paul Smith Sent: Wednesday, September 24, 2008 06:20 To: [EMAIL PROTECTED] Subject: Re: [R] How to draw the graph of f(x,y) = x * y ? On Wed, Sep 24, 2008 at 4:05 AM, Ben Bolker [EMAIL PROTECTED] wrote: The function curve() draws the graph of functions from R to R. Is there some homologous function to curve() to draw functions from R^2 to R? There is a curve3d function in the emdbook package on CRAN. Thanks, Ben and Robin. I think curve3d should be included in the base of R. It would help many users, I believe. I do not know whether curve3d could be extended to draw constant functions and functions like f(x,y) = x. With the current version, I get the following: curve3d(1) Error in curve3d(1) : 'expr' must be a function or an expression containing 'x' and 'y' curve3d(x) Error in eval(expr, envir, enclos) : could not find function x 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] looping through variables
Hello everyone,
I have the following problem:
My analysis includes many predictor variables (50) in the form of
raster maps (asc), but I am trying to avoid having to type all their
names over and over again in the analysis (e.g. for vectorisation, for
deletion of NA's, etc.)
So ideally I would like to store them in some way that their names
only have to be typed once and can always be referred back to.
First step would be to automate the vectorisation of the raster maps:
# these are the raster maps which need to combined somehow ??
variables - (temperature, precipitation, elevation, vegcover)
VariablesNew=c()
For (i in 1:length(variables)) {
Varnew - as.vector(variables[i])
VariablesNew - cbind(VariablesNew, Varnew)
}
This should return a data frame called VariablesNew with each column
representing one of the variables.
So the BIG QUESTION is how to input the variable names that they can
be referred to easily and, the variable itself can be pulled out and
not just its name!!
I believe this cant be too difficult??
Thanx in advance,
Katrin
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Re: [R] How to convert backslash to slash?
On 24/09/2008 10:53 AM, hadley wickham wrote: I agree that that some sort of facility would be convenient. Creating latex output is another situation where not having to escape backslashes would be convenient. And regular expressions, of course. There were proposals to do this last year (I think you participated in the discussion), but there was no agreement on how to do it. One was triple quotes as in Python, e.g. '''c:\foo\bar''' and another was some variation on heredocs from several languages, or \verb from TeX. 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] keep the row indexes/names when do aggregate
Hi, R-users, If I have a data frame like this: x-data.frame(g=c(g1,g2,g1,g1,g2),v=c(1,7,3,2,8)) g v 1 g1 1 2 g2 7 3 g1 3 4 g1 2 5 g2 8 It contains two groups, g1 and g2. Now for each group I want the max v: aggregate(x$v,list(g=x$g),max) g x 1 g1 3 2 g2 8 Beautiful. But what if I want to keep the row index of (g1 3) and (g2 8) in the original x? So I want is: do something g x 3 g1 3 5 g2 8 Of course it'd may make much more sense if the row indexes are some row names that I want to keep. Is there a simple way to do that? Thanks a lot! Z _ [[elided Hotmail spam]] [[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] rgl: ellipse3d with axes
On 24/09/2008 11:11 AM, Duncan Murdoch wrote: On 24/09/2008 10:12 AM, Michael Friendly wrote: Duncan Murdoch wrote: The normals component contains the surface normals. It is used to help in rendering the surface, but isn't much use for your purposes. Unfortunately, I'm not familiar enough with the internals of princomp to tell you how to get the axes you want. Duncan Murdoch OK, then let me repharase it. The axes of the unit sphere are like axes - matrix( c(0, 0, -1, 0, 0, 1, 0, -1, 0, 0, 1, 0, -1, 0, 0, 1, 0, 0), 6, 3, byrow=TRUE) taken in pairs. I'd like to transform these coordinates the same was as in ellipse3d() and add them to the plot. That's easy, but it doesn't give you the principal axes of the ellipse. Just use axes %*% chol(cov) If you start with a unit sphere, this will give you points on its surface, but not the ones you want. For those you need the SVD or eigenvectors. This looks like it does what you want: axes - matrix( c(0, 0, 0, # added origin 0, 0, -1, 0, 0, 1, 0, -1, 0, 0, 1, 0, -1, 0, 0, 1, 0, 0), 7, 3, byrow=TRUE) axes - axes[c(1,2,1,3,1,4,1,5,1,6,1,7),] # add the origin before each Why did I add the origin? It's not needed, your axes were fine. Sorry. 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] Weights for polr
Thanks for directing my attention to the survey package and svyolr(). Best, Greg . Gregory Wawro [EMAIL PROTECTED] Associate Professor phone: 212-854-8540 Dept. of Political Science fax:212-222-0598 741 International Affairs http://www.columbia.edu/~gjw10/ Columbia University New York, NY 10027 . On Mon, 22 Sep 2008, Thomas Lumley wrote: On Mon, 22 Sep 2008, Gregory Wawro wrote: Hello, I'm estimating an ordered logit model on a probability weighted survey sample. You could use svyolr() in the survey package. polr permits case weights with the weights option, but I cannot figure out from existing documentation what it actually does with these weights. They are frequency weights. I'm concerned about this because I get somewhat different results using Stata's ologit command with the pweights option You should get the same point estimates, but different standard errors. and very different results using proc logistic in SAS with its weight option. Again, it should be the same point estimates but different standard errors. So my basic question is whether or not it is appropriate to use the weight option for polr with my data. No. -thomas Thomas Lumley Assoc. Professor, Biostatistics [EMAIL PROTECTED] University of Washington, Seattle __ 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] keep the row indexes/names when do aggregate
Rather than aggregate, use order and duplicated as in this post: https://stat.ethz.ch/pipermail/r-help/2008-September/173139.html On Wed, Sep 24, 2008 at 11:21 AM, zhihuali [EMAIL PROTECTED] wrote: Hi, R-users, If I have a data frame like this: x-data.frame(g=c(g1,g2,g1,g1,g2),v=c(1,7,3,2,8)) g v 1 g1 1 2 g2 7 3 g1 3 4 g1 2 5 g2 8 It contains two groups, g1 and g2. Now for each group I want the max v: aggregate(x$v,list(g=x$g),max) g x 1 g1 3 2 g2 8 Beautiful. But what if I want to keep the row index of (g1 3) and (g2 8) in the original x? So I want is: do something g x 3 g1 3 5 g2 8 Of course it'd may make much more sense if the row indexes are some row names that I want to keep. Is there a simple way to do that? Thanks a lot! Z _ [[elided Hotmail spam]] [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] (nlme) Repeated measures with continuous covariate in lme
Dear readers, I have a basic question about how to use lme for my design. I haven't been able to find an example in r-help that made it clear to me how to tackle this problem and unfortunately I also cannot get hold of Pinheiro Bates 2000. I hope someone can help. Data for the response variable foan were collected in: · 60 plots · plots were re-sampled yearly for 15 years (certain years are missing for certain plots) · plots are divided over 4 reserves (but not equally, so the design is unbalanced) · rain is a continuous covariate, which has the same value for all plots within one year. Since plots are random within reserves, but reserves can be seen as fixed factors, it seems I should use a mixed-model and so I have come up with the following models: model.1 - lme(foan ~ year * reserve, data=data, random= ~1 | plot) model.2 - lme(foan ~ year * reserve, data=data, random= ~year | plot) Model.2 does not provide a better fit than model.1, so apparently the slope of the relationship between foan and year does not vary for plots. I want to know if (and how) the response variable changes over the years, while correcting for variance explained by rain. My question is how to incorporate rain in this model. Can I simply use: model.3 - lme(foan ~ year * reserve * rain, data=data, random= ~ 1 | plot) This somehow seems wrong (forgive my ignorance) since rain has the same value within each year. On the other hand it has different values within each plot. I hope someone can point me in the right direction. Thanks in advance, Robert Buitenwerf South African Environmental Observation Network Phalaborwa South Africa _ [[elided Hotmail spam]] [[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] Graph question
If I have a set of data comprising a list of numbers of eggs on mosquito guts that range from 1 to 157. How can I get R to draw a barchart of the distribution of the data (i.e. x axis= number of eggs on a gut, y axis=number of mosquitoes found with that number of eggs)? Data is listed below. Thanks, Georgina Number of eggs on each mosquito gut: [1] 1 1 1 1 4 2 1 12 12 1 2 1 12 6 11 33 33 94 17 [20] 3 14 12 54 1 16 10 7 12 4 7 22 1 34 2 11 34 22 27 [39] 4 1 27 1 1 157 1 7 31 3 6 24 6 7 23 10 54 3 12 [58] 12 5 2 27 2 7 6 84 3 68 1 4 6 41 1 50 27 30 14 [77] 3 1 1 1 30 1 68 1 7 1 10 5 11 4 19 1 7 9 33 [96] 2 33 57 12 6 2 57 3 115 19 22 10 19 6 11 30 57 4 PhD Student Division of Infection and Immunity B5-29, GBRC 120 University Place Glasgow G12 8TA Tel: 0141 330 5650 __ 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] climatological standard deviation- (question re-posted)
Sorry for re-posting the question, I did not get any reply. Kindly reply please if any one can. ### Hello R users, I have a montly time series over a several year period. It's easy to compute a monthly climatology (12 values), Now, I would like to calculate the corresponding standard deviation, ie the 12 values calculated from the january values, february values, etc. What's the best way for such a calculation ? Regards, Yogesh -- Yogesh K. Tiwari (Dr.rer.nat), Scientist, Indian Institute of Tropical Meteorology, Homi Bhabha Road, Pashan, Pune-411008 INDIA Phone: 0091-99 2273 9513 (Cell) : 0091-20-258 93 600 (O) (Ext.250) Fax : 0091-20-258 93 825 -- Yogesh K. Tiwari (Dr.rer.nat), Scientist, Indian Institute of Tropical Meteorology, Homi Bhabha Road, Pashan, Pune-411008 INDIA Phone: 0091-99 2273 9513 (Cell) : 0091-20-258 93 600 (O) (Ext.250) Fax : 0091-20-258 93 825 [[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] Simulations / repetitions help!
Dear all, My question concerns using repetitions and simulations (loops?) in R. I am very new R user, so any help that can be offered would be greatly appreciated! I am using fitdistr() to determine the distribution of empirical univariate datasets, and ks.test to assess the goodness of fit. Because the null distribution of the KS statistic is not known when the distribution parameters are estimated from the data I would like to use simulations to generate a more accurate p-value (following the methods explained in the second to last paragraph on page 11 of Clauset et al. [2007] available at http://arxiv.org/abs/0706.1062 - also attached) Specifically: I would like to generate a random dataset (‘x’) from a distribution (e.g. exponential): x-rweibull(1500,shape,scale) calculate the parameters of the best-fit distribution: fitdistr(x,weibull) shape scale 14.8727621811.098046257 ( 0.250069835) ( 0.002030626) and assess the goodness-of-fit of ‘x’ to this best-fit distribution. ks.test(x,pweibull,14.9,1.1) data: x D = 0.215, p-value 2.2e-16 alternative hypothesis: two-sided I would like to repeat this c.500 times using a new random dataset each time, calculating D for each dataset relative to its own best fit model (i.e. using the parameters generated by fitdistr each time). As a final output I would like a matrix listing all 500 D values. I am very new to R, so any advice anyone could give me (no matter how simple it may seem) would be greatly appreciated! Many thanks Lauren http://www.nabble.com/file/p19648673/clauset_et_al_2007.pdf clauset_et_al_2007.pdf -- View this message in context: http://www.nabble.com/Simulations---repetitions-help%21-tp19648673p19648673.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] t tests/ANOVA
I have a set of data that comprises genome numbers in single eggs from three different parasite clones - 3D7, HB3, and MIX. I can draw a boxplot of the genome numbers for each clonefed but how do I carry out a t test or ANOVA to compare if the means are signifcantly different? (Data is listed below) Many thanks, Georgina Humphreys clonefedgenomes HB3 21.3 HB3 23.5 HB3 25.9 3D7 27.2 HB3 28.1 MIX 35.1 MIX 37.9 MIX 42.1 MIX 42.4 HB3 46.3 HB3 46.3 MIX 48.4 MIX 52.1 HB3 54.6 MIX 55.4 3D7 57.6 HB3 58.4 3D7 62.1 MIX 63.6 MIX 66.5 3D7 69.1 3D7 76.2 MIX 77.5 MIX 80.4 MIX 85.5 MIX 85.9 HB3 96 HB3 106.3 3D7 108.1 MIX 113.8 MIX 117.4 MIX 118 3D7 122.8 3D7 131.4 MIX 138.7 MIX 142.6 MIX 143 3D7 144 MIX 151.6 MIX 155.2 MIX 162.4 MIX 168.4 MIX 169.3 3D7 172.3 HB3 173 HB3 191.9 MIX 192.7 HB3 200 MIX 206.3 3D7 210.2 HB3 223.7 HB3 223.9 3D7 232.1 HB3 238.6 MIX 240.8 3D7 254.3 3D7 257.6 3D7 261.8 3D7 269.9 HB3 277 MIX 289.1 MIX 293.2 MIX 295.2 MIX 295.7 MIX 310.4 3D7 311.9 3D7 311.9 MIX 313.1 MIX 317.8 MIX 332.2 3D7 334.9 3D7 338.2 MIX 340 MIX 360.5 3D7 372.8 3D7 376.6 HB3 390.3 MIX 419.1 3D7 420 MIX 427.4 MIX 443 MIX 449.7 MIX 452.8 MIX 501.4 3D7 502.9 3D7 505.5 3D7 506.3 3D7 529 MIX 534.4 MIX 540.6 MIX 542 3D7 545.2 MIX 547.2 MIX 554.2 MIX 556.5 3D7 564.9 3D7 575.1 3D7 580.6 MIX 591.5 3D7 655.5 3D7 666.1 3D7 667.2 3D7 699 3D7 741.2 3D7 744.8 3D7 752.2 MIX 795.9 3D7 810.9 HB3 816.4 MIX 849.2 3D7 852.9 3D7 875.4 3D7 891.3 MIX 906.5 MIX 922.3 MIX 949.6 MIX 986.1 MIX 994.3 MIX 1005.3 MIX 1061.3 MIX 1159.5 3D7 1163.2 MIX 1177.5 3D7 1211.3 3D7 1249.7 3D7 1318.3 MIX 1579.3 MIX 1585.2 MIX 1590.3 MIX 1788.7 MIX 2012.9 3D7 2067.4 PhD Student Division of Infection and Immunity B5-29, GBRC 120 University Place Glasgow G12 8TA Tel: 0141 330 5650 __ 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 do I Convert 1 to the number 1?
Dear Tom, I don't know whether it qualifies as elegant or clever, but you should be able to use sub(), as in as.numeric(sub(, , c(1, -2, 1))) [1] 1 -2 1 I hope this helps, John On Wed, 24 Sep 2008 08:08:21 -0700 (PDT) Tom La Bone [EMAIL PROTECTED] wrote: Is there an elegant way in R to change a number reported as a less-than number in text format, 1 for example, to the numeric equivalent 1? I have been trying to use as.numeric, but have not come up with anything clever yet. Tom -- View this message in context: http://www.nabble.com/How-do-I-Convert-%22%3C1%22-to-the-number-1--tp19651018p19651018.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. John Fox, Professor Department of Sociology McMaster University Hamilton, Ontario, Canada http://socserv.mcmaster.ca/jfox/ __ 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] Bug in is ?
Thank you for all of you. Intuitively, 7 is an integer for people who
live in this planet. It is just very difficult for me to believe that
R does not think 7 is an integer but 7L is.
is.integer(7) # R 2.7.2
[1] FALSE
Thus, based on Martin's comments, I try it again on the S-PLUS 8.0 and
it shows
is.integer(7) # S-PLUS 8.0
[1] T
Hopefully, someday and someone will fix it therefore, R users don't
need to use as.integer(7) to tell R that 7 is an integer.
Thanks again
Chunhao
Quoting Martin Maechler [EMAIL PROTECTED]:
KJ == Keith Jewell [EMAIL PROTECTED]
on Wed, 24 Sep 2008 09:46:08 +0100 writes:
KJ 7 is an integer, but it's also a real.
KJ In R '?is' and '?is.integer' are clear that you're testing
the class(es) of
KJ objects, not their values.
KJ I can't comment on the relationship with S Programming
I can:
In S, and S-plus upto version 3.4,
numeric constants such as '7' where double as they are in R.
Then in S-plus 5.1, they became integer,
and there were tools so users could change all(!!) their S
scripts to use '7.' instead of '7' in all places where numeric
constants were seen, in order to keep behavior back compatible.
R never made such a step (backwards ;-), and never will,
notably since in R we had introduced the explicit long (= long
integer) constants, using the 'L' suffix,
i.e., 7L is integer
7 is double
Note however that for both, is.numeric(.) is fulfilled and
class(.) and mode(.) return numeric.
Only typeof(.), storage.mode(.) or str(.)
(or functions building on these) tell you the difference.
Martin Maechler, ETH Zurich and R core team
[And, yes, if you think further and are wondering:
If we'd design things from scratch, we would only have S4
classes and double would be a proper class and
numeric would be the class union of {integer, double}
]
KJ [EMAIL PROTECTED] wrote in message
KJ news:[EMAIL PROTECTED]
This is really bothering me! In the Dr. Venables and Dr.
Ripley's book S
Programming Page 105
shows that
c(is(10,integer),is(10.5,integer))
[1] T F
But I try this in R 2.7.2 it shows
c(is(10,integer),is(10.5,integer))
[1] FALSE FALSE
Does anyone know what is going on here?
Appreciate,
Chunhao
Quoting Yihui Xie [EMAIL PROTECTED]:
Yes, everyone will agree 7 is an integer, but I don't think
computers will agree too :-) R thinks it's a double-precision number,
except when you explicitly specify it as an integer (say,
as.integer()).
class(7)
[1] numeric
is.double(7)
[1] TRUE
Regards,
Yihui
--
Yihui Xie [EMAIL PROTECTED]
Phone: +86-(0)10-82509086 Fax: +86-(0)10-82509086
Mobile: +86-15810805877
Homepage: http://www.yihui.name
School of Statistics, Room 1037, Mingde Main Building,
Renmin University of China, Beijing, 100872, China
On Wed, Sep 24, 2008 at 12:40 PM, [EMAIL PROTECTED] wrote:
Hi R users
Is there anything wrong in is function? (R 2.7.2)
I believe that everyone will agree that 7 is an integer,
right? but
why R
shows 7 is not an integer
is.integer(7)
[1] FALSE
is(7,integer)
[1] FALSE
is(as.integer(7), integer)
[1] TRUE
Thank you very much in advance
Chunhao
KJ __
KJ R-help@r-project.org mailing list
KJ https://stat.ethz.ch/mailman/listinfo/r-help
KJ PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
KJ and provide commented, minimal, self-contained, reproducible code.
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Re: [R] climatological standard deviation- (question re-posted)
-Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Yogesh Tiwari Sent: Wednesday, September 24, 2008 5:43 AM To: [EMAIL PROTECTED] Subject: [R] climatological standard deviation- (question re-posted) Sorry for re-posting the question, I did not get any reply. Kindly reply please if any one can. ### Hello R users, I have a montly time series over a several year period. It's easy to compute a monthly climatology (12 values), Now, I would like to calculate the corresponding standard deviation, ie the 12 values calculated from the january values, february values, etc. What's the best way for such a calculation ? Regards, Yogesh -- Yogesh K. Tiwari (Dr.rer.nat), Scientist, Indian Institute of Tropical Meteorology, Homi Bhabha Road, Pashan, Pune-411008 INDIA Actually, you did get a response from someone asking for more information about what you were doing, and for some sample data so that the advice given would actually be useful. I presume everyone is waiting for the additional information. Dan Daniel J. Nordlund Washington State Department of Social and Health Services Planning, Performance, and Accountability Research and Data Analysis Division Olympia, WA 98504-5204 __ 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] climatological standard deviation- (question re-posted)
On Wed, Sep 24, 2008 at 8:43 AM, Yogesh Tiwari [EMAIL PROTECTED] wrote: Sorry for re-posting the question, I did not get any reply. Kindly reply please if any one can. Most likely that's because you didn't clearly explain the problem. Please read the posting guide (see link at bottom of each and every message on this list), and provide an example of your data, a clear description of what you're trying to do, and what you have tried that hasn't worked. Sarah ### Hello R users, I have a montly time series over a several year period. It's easy to compute a monthly climatology (12 values), Now, I would like to calculate the corresponding standard deviation, ie the 12 values calculated from the january values, february values, etc. What's the best way for such a calculation ? Regards, Yogesh -- -- Sarah Goslee http://www.functionaldiversity.org __ 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] Why horizontal bars instead of a line
Since x$GrSe isn't a number, what do you expect R to do? On Wed, Sep 24, 2008 at 11:28 AM, Schreiber, Stefan [EMAIL PROTECTED] wrote: Hey list! It looks simple, though it's not possible for me to plot the following properly: (some made-up data) GrSeClone1 Clone2 Clone3 Clone4 Clone... G1999 2 3 6 5 G2000 2 5 7 4 G2001 5 3 7 3 G2002 4 5 8 3 G... GrSe=Growing Season. I've read the file as x and then tried:plot(x$GrSe,x$Clone1) The output is 4 horizontal bars. Even if I write plot(x$GrSe,x$Clone1,type=n) R is still plotting! I figured already that if I delete the G in front of the years it'll work, however, I'd like to keep the G. Is that possible? Hope it is an appropriate question for the list. Thanks, Stefan -- Sarah Goslee http://www.functionaldiversity.org __ 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] climatological standard deviation- (question re-posted)
package zoo rollapply if I had to guess at what you want to do, but heed the advice given above. On Wed, Sep 24, 2008 at 12:11 PM, Sarah Goslee [EMAIL PROTECTED] wrote: On Wed, Sep 24, 2008 at 8:43 AM, Yogesh Tiwari [EMAIL PROTECTED] wrote: Sorry for re-posting the question, I did not get any reply. Kindly reply please if any one can. Most likely that's because you didn't clearly explain the problem. Please read the posting guide (see link at bottom of each and every message on this list), and provide an example of your data, a clear description of what you're trying to do, and what you have tried that hasn't worked. Sarah ### Hello R users, I have a montly time series over a several year period. It's easy to compute a monthly climatology (12 values), Now, I would like to calculate the corresponding standard deviation, ie the 12 values calculated from the january values, february values, etc. What's the best way for such a calculation ? Regards, Yogesh -- -- Sarah Goslee http://www.functionaldiversity.org __ 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. -- Stephen Sefick Research Scientist Southeastern Natural Sciences Academy Let's not spend our time and resources thinking about things that are so little or so large that all they really do for us is puff us up and make us feel like gods. We are mammals, and have not exhausted the annoying little problems of being mammals. -K. Mullis __ 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] Graph question
look at histogram and densityplot in the lattice package On Wed, Sep 24, 2008 at 9:26 AM, Georgina Sarah Humphreys [EMAIL PROTECTED] wrote: If I have a set of data comprising a list of numbers of eggs on mosquito guts that range from 1 to 157. How can I get R to draw a barchart of the distribution of the data (i.e. x axis= number of eggs on a gut, y axis=number of mosquitoes found with that number of eggs)? Data is listed below. Thanks, Georgina Number of eggs on each mosquito gut: [1] 1 1 1 1 4 2 1 12 12 1 2 1 12 6 11 33 33 94 17 [20] 3 14 12 54 1 16 10 7 12 4 7 22 1 34 2 11 34 22 27 [39] 4 1 27 1 1 157 1 7 31 3 6 24 6 7 23 10 54 3 12 [58] 12 5 2 27 2 7 6 84 3 68 1 4 6 41 1 50 27 30 14 [77] 3 1 1 1 30 1 68 1 7 1 10 5 11 4 19 1 7 9 33 [96] 2 33 57 12 6 2 57 3 115 19 22 10 19 6 11 30 57 4 PhD Student Division of Infection and Immunity B5-29, GBRC 120 University Place Glasgow G12 8TA Tel: 0141 330 5650 __ 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. -- Stephen Sefick Research Scientist Southeastern Natural Sciences Academy Let's not spend our time and resources thinking about things that are so little or so large that all they really do for us is puff us up and make us feel like gods. We are mammals, and have not exhausted the annoying little problems of being mammals. -K. Mullis __ 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] weights option in lmer
Hi all, I am trying to run a linear mixed effect models in lmer() from the lme4 package using the weights option. I am using the R version 2.7.2 (2008-08-25) and lmer version in lme4_0.999375-26, which I think it is the latest version! I am getting and error message when I add the option weights in the lmer function. This is the error message I get Error en mer_finalize(ans) : Calculated PWRSS for a LMM is negative. I have been reading in the last few weeks all the forum questions and answers about this issue. Certainly this has been discussed MANY times before especially with older versions of lmer (much less in the newer versions). I have been trying different things following peoples advice with not happy end, even I tried older version of lmer where the weight option was not giving an error message but it was not affecting the model at all, hoping maybe It did work some time in the past. This is an simple example of one of my models with varying intercept and slope. I am looking how the mean size of fish has been changing over time in different stocks. This is a simple model but it will get more complicated in the future. I just need to make the option of weights to work before the model becomes more complex. MODEL WITH NO WEIGHTS M1- lmer(meansize_scaled~year + (year |stock ), data=cas) # two levels M1 Linear mixed model fit by REML Formula: meansize_scaled ~ year + (year | stock) Data: cas AIC BIC logLik deviance REMLdev -2777 -2742 1395-2807 -2789 Random effects: Groups NameVariance Std.Dev. Corr stock (Intercept) 1.0964e-02 0.1047097 year3.2435e-06 0.0018010 -0.273 Residual 2.0193e-02 0.1421010 Number of obs: 2692, groups: stock, 9 Fixed effects: Estimate Std. Error t value (Intercept) 0.4869771 0.0360736 13.500 year0.0001034 0.0006642 0.156 Correlation of Fixed Effects: (Intr) year -0.341 MODEL WITH WEIGHTS. M2- lmer(meansize_scaled~year + (year |stock ), data=cas, weights=N_fish) # two level model Error en mer_finalize(ans) : Calculated PWRSS for a LMM is negative As you see above I get the message error. I read read read in the [R] and [R-sig-ME] and I did not get any clear solutions to the weight problem in lmer. My feeling is that the weight option in lmer just not work! At least at the present time, maybe in the future it will change. Can anybody share with me how they have deal with this issue? Should I give up with lmer and try to do this analysis using other tools? maybe try to learn the function lme from nlme package? I just would like to know if I need to give up with weight option in lmer or if I am missing something obvious but I did not find it yet. I want to emphasize that I really appreciate all the hard work of everybody (specially Douglas Bates) for always working hard answering everybody´s questions and improving the lmer function!! SincerelyMaria ))):) ))):) ))):) ))):) ))):) ))):) ))):) ))):) Maria Jose Juan Jorda Phd Student AZTI - Tecnalia / Unidad de Investigación Marina Herrera Kaia Portualde z/g 20110 Pasaia, Gipuzkoa, Spain Recursos Marinos y Pesquerias Depart. Biologia Animal, Vegetal y Ecologia Universidade A Coruña Campus A Zapateira s/n 15071, A Coruña, Spain Tel. +34981167000 ext. 2204 Fax. +34981167065 [EMAIL PROTECTED] _ [[elided Hotmail spam]] [[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] rgl: ellipse3d with axes
Thanks Duncan ( others)
Here is a function that does what I want in this case, and tries to do
it to work generally
with ellipse3d. (Note that I reverse the order of centre and scale
'cause I was bitten
by trying ellipse3d.axes(cov, mu))
# draw axes in the data ellipse computed by ellipse3d
ellipse3d.axes -
function (x, centre = c(0, 0, 0), scale = c(1, 1, 1), level = 0.95,
t = sqrt(qchisq(level, 3)), which = 1:3, ...)
{
stopifnot(is.matrix(x)) # should test for square, symmetric
cov - x[which, which]
eigen - eigen(cov)
# coordinate axes, (-1, 1), in pairs
axes - matrix(
c(0, 0, -1, 0, 0, 1,
0, -1, 0, 0, 1, 0,
-1, 0, 0,1, 0, 0), 6, 3, byrow=TRUE)
# transform to PC axes
axes - axes %*% sqrt(diag(eigen$values)) %*% t(eigen$vectors)
result - scale3d(axes, t, t, t)
if (!missing(scale))
if (length(scale) != 3) scale - rep(scale, length.out=3)
result - scale3d(result, scale[1], scale[2], scale[3])
if (!missing(centre))
if (length(centre) != 3) scale - rep(centre, length.out=3)
result - translate3d(result, centre[1], centre[2], centre[3])
segments3d(result, ...)
invisible(result)
}
Test case:
library(rgl)
data(iris)
iris3 - iris[,1:3]
cov - cov(iris3)
mu - mean(iris3)
col -c(blue, green, red)[iris$Species]
plot3d(iris3, type=s, size=0.5, col=col, cex=2, box=FALSE)
plot3d( ellipse3d(cov, centre=mu, level=0.68), col=gray, alpha=0.2,
add = TRUE)
axes - ellipse3d.axes(cov, centre=mu)
One thing I can't explain, compared to your example is why the my axes
extend outside the ellipse,
whereas yours didn't.
One final remark- I knew that axes %*% chol(cov) did not give the
orthogonal PC axes I wanted,
but at least it gave me something on the right scale and location. But
these axes also turn out to be
useful for visualizing multivariate scatter and statistical concepts.
chol() gives the factorization of
cov that corresponds to the Gram-Schmidt orthogonalization of a data
matrix -- orthogonal axes
in the order x1, x2|x1, x3|x1, x2, ..., and vector length and
orientation in this coordinate system
correspond to Type I SS in linear models.
Thus, I could see generalizing my ellipse3d.axes function further to
allow a type=c(pca, chol)
argument.
-Michael
Duncan Murdoch wrote:
That's easy, but it doesn't give you the principal axes of the
ellipse. Just use
axes %*% chol(cov)
If you start with a unit sphere, this will give you points on its
surface, but not the ones you want. For those you need the SVD or
eigenvectors. This looks like it does what you want:
axes - matrix(
c(0, 0, 0, # added origin
0, 0, -1, 0, 0, 1,
0, -1, 0, 0, 1, 0,
-1, 0, 0, 1, 0, 0), 7, 3, byrow=TRUE)
axes - axes[c(1,2,1,3,1,4,1,5,1,6,1,7),] # add the origin before each
cov - cov(trees)
eigen - eigen(cov)
shade3d(ellipse3d(cov, t=1, alpha=0.2, col='red'))
segments3d(axes %*% sqrt(diag(eigen$values)) %*% t(eigen$vectors))
Duncan Murdoch
--
Michael Friendly Email: friendly AT yorku DOT ca
Professor, Psychology Dept.
York University Voice: 416 736-5115 x66249 Fax: 416 736-5814
4700 Keele Streethttp://www.math.yorku.ca/SCS/friendly.html
Toronto, ONT M3J 1P3 CANADA
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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] Bug in is ?
Have you tried is.integer(7.0) in S-Plus? (I have)
Do you think 7.0 is integer?
IMHO in R there is nothing to be fixed (in this regard) except your
understanding.
This is a computer language, not English; intuition isn't reliable, so we
have help pages.
is.integer(x) is not intended to indicate whether the value of x is a whole
number, it indicates whether x has class integer.
All objects of class integer have whole number values, but not all objects
with whole number values have class integer.
If you want to know whether a value is a whole number you could try (but
there may be a better way, and beware of computer precision)
x == as.integer(x)
If you want a value to be stored in an object of class integer you'd
better say so (using as.integer or L or ...), else how is R to know what you
want? As Martin has pointed out, the system could guess based on the
presence or absence of a decimal point; I share his opinion that this would
be a bad thing.
Nuff said.
Keith J
[EMAIL PROTECTED] wrote in message
news:[EMAIL PROTECTED]
Thank you for all of you. Intuitively, 7 is an integer for people who
live in this planet. It is just very difficult for me to believe that R
does not think 7 is an integer but 7L is.
is.integer(7) # R 2.7.2
[1] FALSE
Thus, based on Martin's comments, I try it again on the S-PLUS 8.0 and it
shows
is.integer(7) # S-PLUS 8.0
[1] T
Hopefully, someday and someone will fix it therefore, R users don't need
to use as.integer(7) to tell R that 7 is an integer.
Thanks again
Chunhao
Quoting Martin Maechler [EMAIL PROTECTED]:
KJ == Keith Jewell [EMAIL PROTECTED]
on Wed, 24 Sep 2008 09:46:08 +0100 writes:
KJ 7 is an integer, but it's also a real.
KJ In R '?is' and '?is.integer' are clear that you're testing the
class(es) of
KJ objects, not their values.
KJ I can't comment on the relationship with S Programming
I can:
In S, and S-plus upto version 3.4,
numeric constants such as '7' where double as they are in R.
Then in S-plus 5.1, they became integer,
and there were tools so users could change all(!!) their S
scripts to use '7.' instead of '7' in all places where numeric
constants were seen, in order to keep behavior back compatible.
R never made such a step (backwards ;-), and never will,
notably since in R we had introduced the explicit long (= long
integer) constants, using the 'L' suffix,
i.e., 7L is integer
7 is double
Note however that for both, is.numeric(.) is fulfilled and
class(.) and mode(.) return numeric.
Only typeof(.), storage.mode(.) or str(.)
(or functions building on these) tell you the difference.
Martin Maechler, ETH Zurich and R core team
[And, yes, if you think further and are wondering:
If we'd design things from scratch, we would only have S4
classes and double would be a proper class and
numeric would be the class union of {integer, double}
]
KJ [EMAIL PROTECTED] wrote in message
KJ news:[EMAIL PROTECTED]
This is really bothering me! In the Dr. Venables and Dr.
Ripley's book S
Programming Page 105
shows that
c(is(10,integer),is(10.5,integer))
[1] T F
But I try this in R 2.7.2 it shows
c(is(10,integer),is(10.5,integer))
[1] FALSE FALSE
Does anyone know what is going on here?
Appreciate,
Chunhao
Quoting Yihui Xie [EMAIL PROTECTED]:
Yes, everyone will agree 7 is an integer, but I don't think
computers will agree too :-) R thinks it's a double-precision
number,
except when you explicitly specify it as an integer (say,
as.integer()).
class(7)
[1] numeric
is.double(7)
[1] TRUE
Regards,
Yihui
--
Yihui Xie [EMAIL PROTECTED]
Phone: +86-(0)10-82509086 Fax: +86-(0)10-82509086
Mobile: +86-15810805877
Homepage: http://www.yihui.name
School of Statistics, Room 1037, Mingde Main Building,
Renmin University of China, Beijing, 100872, China
On Wed, Sep 24, 2008 at 12:40 PM, [EMAIL PROTECTED] wrote:
Hi R users
Is there anything wrong in is function? (R 2.7.2)
I believe that everyone will agree that 7 is an integer,
right? but
why R
shows 7 is not an integer
is.integer(7)
[1] FALSE
is(7,integer)
[1] FALSE
is(as.integer(7), integer)
[1] TRUE
Thank you very much in advance
Chunhao
KJ __
KJ R-help@r-project.org mailing list
KJ https://stat.ethz.ch/mailman/listinfo/r-help
KJ PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
KJ and provide commented, minimal, self-contained, reproducible
code.
__
R-help@r-project.org mailing list
[R] logistic regression model validation through bootstrapping
I'm new to R and to validation of logistic regression models via bootstrapping. I see that there are various approaches to bootstrapping, and I am wondering (1) which approach would be best for internal validation of predictive discrimination, (2) are there any good resources that could be recommended to explain the optimal approach, and (3) what packages in R should I use to achieve this approach. Many thanks for the input. Alison Van Dyke MD/PhD Candidate, Class of 2011 Cancer Biology Wayne State University [EMAIL PROTECTED] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] logistic regression model validation through bootstrapping
Van Dyke, Alison wrote: I'm new to R and to validation of logistic regression models via bootstrapping. I see that there are various approaches to bootstrapping, and I am wondering (1) which approach would be best for internal validation of predictive discrimination, (2) are there any good resources that could be recommended to explain the optimal approach, and (3) what packages in R should I use to achieve this approach. Many thanks for the input. Alison Van Dyke MD/PhD Candidate, Class of 2011 Cancer Biology Wayne State University [EMAIL PROTECTED] One possibility: library(Design) ?validate.lrm -- Frank E Harrell Jr Professor and Chair School 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.
Re: [R] rgl: ellipse3d with axes
On 24/09/2008 12:32 PM, Michael Friendly wrote:
Thanks Duncan ( others)
Here is a function that does what I want in this case, and tries to do
it to work generally
with ellipse3d. (Note that I reverse the order of centre and scale
'cause I was bitten
by trying ellipse3d.axes(cov, mu))
# draw axes in the data ellipse computed by ellipse3d
ellipse3d.axes -
function (x, centre = c(0, 0, 0), scale = c(1, 1, 1), level = 0.95,
t = sqrt(qchisq(level, 3)), which = 1:3, ...)
{
stopifnot(is.matrix(x)) # should test for square, symmetric
cov - x[which, which]
eigen - eigen(cov)
# coordinate axes, (-1, 1), in pairs
axes - matrix(
c(0, 0, -1, 0, 0, 1,
0, -1, 0, 0, 1, 0,
-1, 0, 0,1, 0, 0), 6, 3, byrow=TRUE)
# transform to PC axes
axes - axes %*% sqrt(diag(eigen$values)) %*% t(eigen$vectors)
result - scale3d(axes, t, t, t)
if (!missing(scale))
if (length(scale) != 3) scale - rep(scale, length.out=3)
result - scale3d(result, scale[1], scale[2], scale[3])
if (!missing(centre))
if (length(centre) != 3) scale - rep(centre, length.out=3)
result - translate3d(result, centre[1], centre[2], centre[3])
segments3d(result, ...)
invisible(result)
}
Test case:
library(rgl)
data(iris)
iris3 - iris[,1:3]
cov - cov(iris3)
mu - mean(iris3)
col -c(blue, green, red)[iris$Species]
plot3d(iris3, type=s, size=0.5, col=col, cex=2, box=FALSE)
plot3d( ellipse3d(cov, centre=mu, level=0.68), col=gray, alpha=0.2,
add = TRUE)
axes - ellipse3d.axes(cov, centre=mu)
One thing I can't explain, compared to your example is why the my axes
extend outside the ellipse,
whereas yours didn't.
That's just because you specified level in the ellipse3d call, but not
in the ellipes3d.axes call.
One thing that looks a little strange is that the PC axes don't appear
to be orthogonal: this is because the scaling is not the same on all
coordinates. It might look better doing the first plot as
plot3d(iris3, type=s, size=0.5, col=col, cex=2, box=FALSE, aspect=iso)
Duncan Murdoch
One final remark- I knew that axes %*% chol(cov) did not give the
orthogonal PC axes I wanted,
but at least it gave me something on the right scale and location. But
these axes also turn out to be
useful for visualizing multivariate scatter and statistical concepts.
chol() gives the factorization of
cov that corresponds to the Gram-Schmidt orthogonalization of a data
matrix -- orthogonal axes
in the order x1, x2|x1, x3|x1, x2, ..., and vector length and
orientation in this coordinate system
correspond to Type I SS in linear models.
Thus, I could see generalizing my ellipse3d.axes function further to
allow a type=c(pca, chol)
argument.
-Michael
Duncan Murdoch wrote:
That's easy, but it doesn't give you the principal axes of the
ellipse. Just use
axes %*% chol(cov)
If you start with a unit sphere, this will give you points on its
surface, but not the ones you want. For those you need the SVD or
eigenvectors. This looks like it does what you want:
axes - matrix(
c(0, 0, 0, # added origin
0, 0, -1, 0, 0, 1,
0, -1, 0, 0, 1, 0,
-1, 0, 0, 1, 0, 0), 7, 3, byrow=TRUE)
axes - axes[c(1,2,1,3,1,4,1,5,1,6,1,7),] # add the origin before each
cov - cov(trees)
eigen - eigen(cov)
shade3d(ellipse3d(cov, t=1, alpha=0.2, col='red'))
segments3d(axes %*% sqrt(diag(eigen$values)) %*% t(eigen$vectors))
Duncan Murdoch
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to draw the graph of f(x,y) = x * y ?
On Wed, Sep 24, 2008 at 4:14 PM, Farley, Robert [EMAIL PROTECTED] wrote: You could always try F(x,y) = f(x) + 0*y That is zero out the degenerate dimensions. Of course you'll be plotting what is essentially a two dimensional object as if it were three dimensional. The degeneracy in y means a 2-D curve will be extruded along the Y dimension. -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Paul Smith Sent: Wednesday, September 24, 2008 06:20 To: [EMAIL PROTECTED] Subject: Re: [R] How to draw the graph of f(x,y) = x * y ? On Wed, Sep 24, 2008 at 4:05 AM, Ben Bolker [EMAIL PROTECTED] wrote: The function curve() draws the graph of functions from R to R. Is there some homologous function to curve() to draw functions from R^2 to R? There is a curve3d function in the emdbook package on CRAN. Thanks, Ben and Robin. I think curve3d should be included in the base of R. It would help many users, I believe. I do not know whether curve3d could be extended to draw constant functions and functions like f(x,y) = x. With the current version, I get the following: curve3d(1) Error in curve3d(1) : 'expr' must be a function or an expression containing 'x' and 'y' curve3d(x) Error in eval(expr, envir, enclos) : could not find function x Thanks, Robert. your suggestion works to plot f(x,y) = x + 0*y, but it does not work in the case of f(x,y) = 1 + 0*x +0*y. 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] Fortunes Candidates from Keith Jewell?
IMHO Keith Jewell has a couple of jewels here (sorry Keith -- couldn't resist): nice possible fortunes package candidates: IMHO in R there is nothing to be fixed (in this regard) except your understanding. This is a computer language, not English; intuition isn't reliable, so we have help pages. Cheers to all, Bert Gunter __ 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] Bug in is ?
Hi Keith,
No doubt, 7.0 is integer in math. But if people can write 7 why people
need to write 7.0 (I do not see any reason to do this). My point is
that R maybe can do something like S-plus. No point to argue. don't
you think so?
Thanks
Chunhao
Quoting Keith Jewell [EMAIL PROTECTED]:
Have you tried is.integer(7.0) in S-Plus? (I have)
Do you think 7.0 is integer?
IMHO in R there is nothing to be fixed (in this regard) except your
understanding.
This is a computer language, not English; intuition isn't reliable, so we
have help pages.
is.integer(x) is not intended to indicate whether the value of x is a whole
number, it indicates whether x has class integer.
All objects of class integer have whole number values, but not all objects
with whole number values have class integer.
If you want to know whether a value is a whole number you could try (but
there may be a better way, and beware of computer precision)
x == as.integer(x)
If you want a value to be stored in an object of class integer you'd
better say so (using as.integer or L or ...), else how is R to know what you
want? As Martin has pointed out, the system could guess based on the
presence or absence of a decimal point; I share his opinion that this would
be a bad thing.
Nuff said.
Keith J
[EMAIL PROTECTED] wrote in message
news:[EMAIL PROTECTED]
Thank you for all of you. Intuitively, 7 is an integer for people who
live in this planet. It is just very difficult for me to believe that R
does not think 7 is an integer but 7L is.
is.integer(7) # R 2.7.2
[1] FALSE
Thus, based on Martin's comments, I try it again on the S-PLUS 8.0 and it
shows
is.integer(7) # S-PLUS 8.0
[1] T
Hopefully, someday and someone will fix it therefore, R users don't need
to use as.integer(7) to tell R that 7 is an integer.
Thanks again
Chunhao
Quoting Martin Maechler [EMAIL PROTECTED]:
KJ == Keith Jewell [EMAIL PROTECTED]
on Wed, 24 Sep 2008 09:46:08 +0100 writes:
KJ 7 is an integer, but it's also a real.
KJ In R '?is' and '?is.integer' are clear that you're testing the
class(es) of
KJ objects, not their values.
KJ I can't comment on the relationship with S Programming
I can:
In S, and S-plus upto version 3.4,
numeric constants such as '7' where double as they are in R.
Then in S-plus 5.1, they became integer,
and there were tools so users could change all(!!) their S
scripts to use '7.' instead of '7' in all places where numeric
constants were seen, in order to keep behavior back compatible.
R never made such a step (backwards ;-), and never will,
notably since in R we had introduced the explicit long (= long
integer) constants, using the 'L' suffix,
i.e., 7L is integer
7 is double
Note however that for both, is.numeric(.) is fulfilled and
class(.) and mode(.) return numeric.
Only typeof(.), storage.mode(.) or str(.)
(or functions building on these) tell you the difference.
Martin Maechler, ETH Zurich and R core team
[And, yes, if you think further and are wondering:
If we'd design things from scratch, we would only have S4
classes and double would be a proper class and
numeric would be the class union of {integer, double}
]
KJ [EMAIL PROTECTED] wrote in message
KJ news:[EMAIL PROTECTED]
This is really bothering me! In the Dr. Venables and Dr.
Ripley's book S
Programming Page 105
shows that
c(is(10,integer),is(10.5,integer))
[1] T F
But I try this in R 2.7.2 it shows
c(is(10,integer),is(10.5,integer))
[1] FALSE FALSE
Does anyone know what is going on here?
Appreciate,
Chunhao
Quoting Yihui Xie [EMAIL PROTECTED]:
Yes, everyone will agree 7 is an integer, but I don't think
computers will agree too :-) R thinks it's a double-precision
number,
except when you explicitly specify it as an integer (say,
as.integer()).
class(7)
[1] numeric
is.double(7)
[1] TRUE
Regards,
Yihui
--
Yihui Xie [EMAIL PROTECTED]
Phone: +86-(0)10-82509086 Fax: +86-(0)10-82509086
Mobile: +86-15810805877
Homepage: http://www.yihui.name
School of Statistics, Room 1037, Mingde Main Building,
Renmin University of China, Beijing, 100872, China
On Wed, Sep 24, 2008 at 12:40 PM, [EMAIL PROTECTED] wrote:
Hi R users
Is there anything wrong in is function? (R 2.7.2)
I believe that everyone will agree that 7 is an integer,
right? but
why R
shows 7 is not an integer
is.integer(7)
[1] FALSE
is(7,integer)
[1] FALSE
is(as.integer(7), integer)
[1] TRUE
Thank you very much in advance
Chunhao
KJ __
KJ R-help@r-project.org mailing list
KJ https://stat.ethz.ch/mailman/listinfo/r-help
KJ PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
KJ and provide
Re: [R] Options for viewing / using results from lm
I don't remember which version View was added in, but it was more recent than
2.4.1. I would suggest upgrading (2.4.1 is ancient in R terms).
You can get something similar with:
invisible(edit(mydata))
But you will have to close the window to continue with R (View lets you look at
the data (but not edit it), while still working at the command prompt).
--
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
[EMAIL PROTECTED]
801.408.8111
From: Michael Just [mailto:[EMAIL PROTECTED]
Sent: Wednesday, September 24, 2008 1:03 AM
To: Greg Snow
Cc: r-help@r-project.org; [EMAIL PROTECTED]
Subject: Re: [R] Options for viewing / using results from lm
Hello,
Thanks for the response.
However, I have this problem with view.
View(fit1)
Error: could not find function View
I have R 2.4.1 and even tried loading 'utils'.
As for saving residuals in a spreadsheet I used something like this:
res.fit1-fit1$residuals
res.fit2-fit2$residuals
write.csv(res.fit1, file=res.fit1.csv)
write.csv(res.fit2, file=res.fit2.csv)
Thanks,
M Just
On Tue, Sep 23, 2008 at 9:07 PM, Greg Snow [EMAIL PROTECTED]mailto:[EMAIL
PROTECTED] wrote:
The View function (note the uppercase V) is in the utils package, one of the
standard ones that loads automatically.
From: Michael Just [EMAIL PROTECTED]mailto:[EMAIL PROTECTED]]
Sent: Tuesday, September 23, 2008 2:49 PM
To: Greg Snow
Cc: r-help@r-project.orgmailto:r-help@r-project.org; [EMAIL
PROTECTED]mailto:[EMAIL PROTECTED]
Subject: Re: [R] Options for viewing / using results from lm
Greg,
Thanks for the pseudocode and cbind suggestions I think these should be quite
helpful. What package is the function 'view' in? As for exporting elsewhere,
basically I would to have the values of residuals saved in a spreadsheet in
addition to any visualizations created within R.
Thanks,
M Just
On Tue, Sep 23, 2008 at 3:26 PM, Greg Snow [EMAIL PROTECTED]mailto:[EMAIL
PROTECTED] wrote:
You can do things like this pseudocode:
fit1 - lm( y ~ x1, data=mydata )
fit2 - lm( y ~ x2, data=mydata )
fit3 - lm( y ~ x1*x2, data=mydata )
...
mydata$r1 - resid(fit1)
mydata$r2 - resid(fit2)
mydata$r3 - resid(fit3)
Or
mydata - cbind(mydata, r1=resid(fit1), r2=resid(fit2), ...
To view the data in a spreadsheet like table:
View(mydata)
And scroll over to the r columns, using indexing or the subset function can
reorder the columns to make this easier.
A simple plot:
pairs( mydata[ , paste('r',1:10, sep='')], col=c('red','green','blue')[
mydata$g1 ],
+ panel=panel.smooth )
Or there are various other ways to explore the data within R. If you really
feel the need to use another tool, do like the above, then use write.table to
export it to a csv file or paste it to a spreadsheet. There is also the
rggobi package which will automate the exporting to the ggobi program which
allows a lot more visualization options.
Hope this helps,
--
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
[EMAIL PROTECTED]mailto:[EMAIL PROTECTED]
801.408.8111
-Original Message-
From: [EMAIL PROTECTED]mailto:[EMAIL PROTECTED] [mailto:[EMAIL
PROTECTED]mailto:[EMAIL PROTECTED]
project.orghttp://project.org] On Behalf Of Michael Just
Sent: Tuesday, September 23, 2008 2:06 PM
To: r-help@r-project.orgmailto:r-help@r-project.org
Cc: [EMAIL PROTECTED]mailto:[EMAIL PROTECTED]
Subject: Re: [R] Options for viewing / using results from lm
Hello,
Why do you think it is better done in another program? Keeping it in R
saves you from the exporting, which you say you are having trouble
with.
I think it might be better for viewing capabilities. If I had columns
of
residuals right next to each other I could spot differences amongst
locations. Right? If I can take the residual values and put them back
into
my main data file I can then have the options to use grouping values
that
exist there. (Like I asked here:
http://tolstoy.newcastle.edu.au/R/e5/help/08/09/2186.html)
Q2: How can I take the residuals and create an object(s) for further
http://tolstoy.newcastle.edu.au/R/e5/help/08/09/2259.html#2265qlink2*
analysis.
*
**
See ?residuals.
Try the following:
x - sample(1:20, 100, replace=TRUE)
y - rnorm(100)
fit.lm - lm(y ~ x)
plot(residuals(fit.lm))
plot(x,residuals(fit.lm))
When I was thinking further analysis, for example, could I take the
residuals for all metrics in one extent and compare them to all
residuals
for all metrics in another extent? Even though the were created with 16
different models?
In 'plot(residuals(fit.lm))' what is the index 'counting'?
Thank you kindly for you $0.25,
Cheers,
M Just
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PLEASE do read the posting guide http://www.R-project.org/posting-
[R] lattice xyplot symbols instead of colors and legend matching plot symbols or colors
I would like to use the data below where the plots are close to what I want. Instead of color I would like to use different symbols, and have the symbols in the legend match the graphs. I am also going to add a regression line to these I know about the type=r (which is fine for these particular graphs) argument, but it fits the subsets instead of the entire data set-- should I use a list of regression fits in the order of the arguments in an abline panel to do this? Ok, I think that is all for right now. If I need to clarify please tell me. thanks f - structure(list(GPP = c(1.213695235, 3.817313822, 1.267930498, 10.45692825, 3.268295623, 3.505286001, 4.468225245, 0.915653726, 1.635617261, 3.726133898, 1.363453706, 13.99650967, 0.417618143, 0.741080504, 0.412440872, 3.515743675, 8.248491445, 1.537773727, 3.249103284, 0.768531626, 2.633107621, 3.113199095, 0.773824094, 0.680150068, 0.026385752, 0.369310858, 8.049276658, 7.487378383, 0.763580377, 0.333244629, 5.475999014, 9.235631398), TSS = c(2.8, 8.4, 11, 1.3, 4.2, 2, 3.4, 14, 8.2, 3.1, 1.4, 0.9, 6.1, 9.2, 11, 1.2, 1.3, 11, 8.5, 13, 4.4, 1.4, 2.1, 25, 9.3, 6.1, 1.6, 1.5, 24, 9.6, 1.8, 1.4), Iron = c(0.74, 0.54, 0.23, 0.13, 0.4, 0.13, 0.15, 0.58, 0.38, 0.22, 0.13, 0.07, 0.32, 0.26, 0.86, 0.13, 0.09, 0.58, 0.35, 0.59, 0.33, 0.19, 0.21, 0.81, 0.34, 0.31, 0.07, 0.16, 0.54, 0.36, 0.13, 0.07), TIN.TP = c(3.117647059, 2.736842105, 2.25, 22, 3, 2.428571429, 6.428571429, NA, NA, 2.384615385, 3, NA, 3.25, NA, 3.16667, 9, 23, 3.5, 11, 3.91667, 3.4, 3.4, 8.75, 2.7, 3.58333, 2.75, 17, NA, 2.9, 2.5, 2.5, 11), RiverMile = c(148L, 179L, 185L, 202L, 179L, 185L, 190L, 119L, 148L, 179L, 185L, 202L, 119L, 202L, 148L, 190L, 202L, 148L, 202L, 119L, 179L, 185L, 190L, 61L, 119L, 148L, 202L, 202L, 119L, 148L, 185L, 202L)), .Names = c(GPP, TSS, Iron, TIN.TP, RiverMile), class = data.frame, row.names = c(1L, 2L, 3L, 5L, 6L, 7L, 8L, 9L, 10L, 11L, 12L, 13L, 15L, 16L, 19L, 22L, 23L, 30L, 34L, 36L, 37L, 38L, 39L, 43L, 44L, 45L, 46L, 47L, 49L, 50L, 51L, 52L)) xyplot(GPP~(1/Iron)+(1/TSS)+TIN.TP, groups=RiverMile,data=f, scales=list(relation=free), pch=20, auto.key=TRUE) -- Stephen Sefick Research Scientist Southeastern Natural Sciences Academy Let's not spend our time and resources thinking about things that are so little or so large that all they really do for us is puff us up and make us feel like gods. We are mammals, and have not exhausted the annoying little problems of being mammals. -K. Mullis __ 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] possible interesting R projects for undergrads
Dear R People: I finally (Yay!) got R installed in a classroom! Anyhow, I have a respectful request, please: could anyone recommend some nice undergrad projects in R, please? This is in a statistical computation class; first time being run. Thanks, Erin -- Erin Hodgess Associate Professor Department of Computer and Mathematical Sciences University of Houston - Downtown mailto: [EMAIL PROTECTED] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Add title in sink output and possibility of plot-like output for text
Hello, I have been using sink to create text file outputs. sink(summ_model1and2.txt) summary(model1) summary(model2) sink() Q1: Is there a way I could add a line of the text above the summary to act like a title? Also, I have been using the following to save plots from the lm function: pdf(small.bin.ENN_MN_withQ.pdf) par(mfrow = c(2, 2), oma = c(0, 0, 2, 0)) plot(small.bin.ENN_MN) plot(small.bin.ENN_MN.q) dev.off() Q2: Is there a way I could save the output from 'summary' into a c(2,2) window like I do with the plots? Thank you kindly, Cheers, M Just [[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] Generating series of distributions with the same skewness and different kurtosis or with same kurtosis and different skewness?
And here is one way of using JohnsonFit to display how a distribution changes
with changes in the moments:
library(TeachingDemos)
library(SuppDists)
tmpfun - function(m1=0,m2=1,m3=-0.2,m4=3.7, xmin=-3, xmax=3){
parms - JohnsonFit( c(m1,m2,m3,m4), 'use')
plot(function(x) dJohnson(x,parms), xmin, xmax)
}
tmplst - list( Parameters=list(
m1=list('slider', init=0, from=-1, to=1, resolution=0.1),
m2=list('slider', init=1, from=0 , to=3, resolution=0.1),
m3=list('slider', init=-0.2, from=-1, to=1, resolution=0.1),
m4=list('slider', init=3.7, from=0 , to=10, resolution=0.5)),
xmin=list('numentry', init=-3, width=5),
xmax=list('numentry', init=3 , width=5) )
tkexamp( tmpfun, tmplst, plotloc='left' )
of course assuming that you have SuppDists and TeachingDemos packages
installed, play around with this (and possibly change parameters and/or limits
in tmplst) before demoing it as there are many combinations of the parameters
that cause errors.
--
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
[EMAIL PROTECTED]
801.408.8111
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
project.org] On Behalf Of Gabor Grothendieck
Sent: Wednesday, September 24, 2008 6:29 AM
To: zhijie zhang
Cc: [EMAIL PROTECTED]
Subject: Re: [R] Generating series of distributions with the same
skewness and different kurtosis or with same kurtosis and different
skewness?
Check out JohnsonFit in SuppDists.
On Tue, Sep 23, 2008 at 10:59 AM, zhijie zhang [EMAIL PROTECTED]
wrote:
Dear R users,
I hope to explain the concepts of skewness and kurtosis by
generating
series of distributions with same skewness and different kurtosis or
with
same kurtosis and different skewness, but it seems that i cannot find
the
right functions.
I have searched the mailing list, but no answers were found.
Is it possible to do that in R? Which function could be used?
Thanks a lot.
--
With Kind Regards,
oooO:
(..):
:\.(:::Oooo::
::\_)::(..)::
:::)./:::
::(_/
:
[**
*]
Zhi Jie,Zhang ,PHD
Tel:+86-21-54237149
Dept. of Epidemiology,School of Public Health,Fudan University
Address:No. 138 Yi Xue Yuan Road,Shanghai,China
Postcode:200032
Email:[EMAIL PROTECTED] [EMAIL PROTECTED]
Website: www.statABC.com
[**
*]
oooO:
(..):
:\.(:::Oooo::
::\_)::(..)::
:::)./:::
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:
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Re: [R] Proper power computation for one-sided binomial tests.
Thank you Peter. That is incredibly helpfyul, and much much smaller! Best, Collin. __ 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] Modifying output to Google Docs
The command line app is fine, although there are some potential security issues or annoyances with a smooth work flow. But it would be more flexible and powerful to do it directly in R. And we don't need to know or program in C. The RCurl (https, getForm() and postForm()) and XML packages provide all we need. It took a couple of hours of reading the Google documentation, designing and writing the R code and _testing_, but in relatively few lines of code, the RGoogleDocs package enables an R user to query, delete, download and upload documents to her Google account. This was one of the motivations for developing the XML and RCurl packages, i.e. to be able to quickly develop utilities in R to communicate with Web apps. So Ajay's suggestion was a nice exercise to see if the packages do make it easy. The package currently has no Rd files, but there is a brief user's guide. The package is available from http://www.omegahat.org/RGoogleDocs For binary files, you will want to grab a beta-version of RCurl at http://www.omegahat.org/Prerelease/RCurl_0.91-0.tar.gz D. Barry Rowlingson wrote: 2008/9/23 Ajay ohri [EMAIL PROTECTED]: By outputting PDF directly to a Google Doc, it becomes light and portable for people to view and collaborate on projects in different parts of the world. If you extend this to Google spreadsheets this functionality is especially useful for financial reporting or marketing metrics reports or collaborative presentations to be made. There's command-line tools (written in python, but probably in other languages elsewhere) to do this: http://code.google.com/p/gdatacopier/ their example is: ./gdoc-cp.py --username [EMAIL PROTECTED] --import --local files/doc.txt --title New Document So all you need to do is call that from R with system() and wrap it up in some R functions. Barry __ 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] Modifying output to Google Docs
Wow. Dont you get to name it on me or something (like the RPackageGoogleAjayDoc ?) Just kidding This is fabulous and the reason this community is so innovative Now if only someone can create a package for me to use R from Amazon EC2 and be free of the damn RAM problem forever to create it as a SaaS. Regards, Ajay On Wed, Sep 24, 2008 at 11:29 PM, Duncan Temple Lang [EMAIL PROTECTED] wrote: The command line app is fine, although there are some potential security issues or annoyances with a smooth work flow. But it would be more flexible and powerful to do it directly in R. And we don't need to know or program in C. The RCurl (https, getForm() and postForm()) and XML packages provide all we need. It took a couple of hours of reading the Google documentation, designing and writing the R code and _testing_, but in relatively few lines of code, the RGoogleDocs package enables an R user to query, delete, download and upload documents to her Google account. This was one of the motivations for developing the XML and RCurl packages, i.e. to be able to quickly develop utilities in R to communicate with Web apps. So Ajay's suggestion was a nice exercise to see if the packages do make it easy. The package currently has no Rd files, but there is a brief user's guide. The package is available from http://www.omegahat.org/RGoogleDocs For binary files, you will want to grab a beta-version of RCurl at http://www.omegahat.org/Prerelease/RCurl_0.91-0.tar.gz D. Barry Rowlingson wrote: 2008/9/23 Ajay ohri [EMAIL PROTECTED]: By outputting PDF directly to a Google Doc, it becomes light and portable for people to view and collaborate on projects in different parts of the world. If you extend this to Google spreadsheets this functionality is especially useful for financial reporting or marketing metrics reports or collaborative presentations to be made. There's command-line tools (written in python, but probably in other languages elsewhere) to do this: http://code.google.com/p/gdatacopier/ their example is: ./gdoc-cp.py --username [EMAIL PROTECTED] --import --local files/doc.txt --title New Document So all you need to do is call that from R with system() and wrap it up in some R functions. Barry __ 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. -- Regards, Ajay Ohri http://tinyurl.com/liajayohri [[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] Proper power computation for one-sided binomial tests.
Am 23.09.2008 um 23:57 schrieb Peter Dalgaard: For this kind of problem I'd go directly for the binomial distribution. If the actual probability is 0, this is essentially deterministic and you can look at binom.test(0,99,p=.03, alt=less) This means that you don't sample from the p=.03 population? Note that there is a 5 per cent chance to have 0 failures in 99 trials with p=.03. __ 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] Why horizontal bars instead of a line
Remember that computers are not as smart as you. Some smart people have written instructions for the computer on what to do in certain cases, but they can't anticipate everything, so when you tell the computer to do something that was different from what is anticipated, it either gives an error or the results of a wrong guess. In your case, since GrSe has a G in the front and your data is probably in a data frame, the plot function sees a factor (generally what gets created automatically when characters are seen) and passes the data to plot.factor which plots boxplots (and with 1 point per year, the 5 number summary for the boxplot gives all the same value, hence the horizontal line). What you probably want to do is to plot your clone data against a numerical representation of the year (without the G), but suppress the axis labels and add the labels yourself (with the G), see ?axis for detail on doing this. Hope this helps, -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare [EMAIL PROTECTED] 801.408.8111 -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] project.org] On Behalf Of Schreiber, Stefan Sent: Wednesday, September 24, 2008 9:28 AM To: r-help@r-project.org Subject: [R] Why horizontal bars instead of a line Hey list! It looks simple, though it's not possible for me to plot the following properly: (some made-up data) GrSeClone1 Clone2 Clone3 Clone4 Clone... G1999 2 3 6 5 G2000 2 5 7 4 G2001 5 3 7 3 G2002 4 5 8 3 G... GrSe=Growing Season. I've read the file as x and then tried:plot(x$GrSe,x$Clone1) The output is 4 horizontal bars. Even if I write plot(x$GrSe,x$Clone1,type=n) R is still plotting! I figured already that if I delete the G in front of the years it'll work, however, I'd like to keep the G. Is that possible? Hope it is an appropriate question for the list. Thanks, Stefan [[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] lattice xyplot symbols instead of colors and legend matching plot symbols or colors
xyplot(GPP~(1/Iron)+(1/TSS)+TIN.TP, groups=RiverMile,data=f,
scales=list(relation=free), par.settings = list(
superpose.symbol = list(
pch = c(1:7),
fill = c(red, blue),
col = black)), auto.key=TRUE,
panel=function(...){
panel.xyplot(...)
panel.abline(lm(GPP~I(1/Iron), data=f))
panel.abline(lm(GPP~I(1/TSS), data=f))
panel.abline(lm(GPP~I(TIN.TP), data=f))
})
now how do I get the panel abline to only plot in the appropriate
panel GPP~1/Iron and the regression line for this panel only in that
panel
thanks
On Wed, Sep 24, 2008 at 1:15 PM, stephen sefick [EMAIL PROTECTED] wrote:
I would like to use the data below where the plots are close to what I
want. Instead of color I would like to use different symbols, and
have the symbols in the legend match the graphs. I am also going to
add a regression line to these I know about the type=r (which is
fine for these particular graphs) argument, but it fits the subsets
instead of the entire data set-- should I use a list of regression
fits in the order of the arguments in an abline panel to do this? Ok,
I think that is all for right now. If I need to clarify please tell
me.
thanks
f - structure(list(GPP = c(1.213695235, 3.817313822, 1.267930498,
10.45692825, 3.268295623, 3.505286001, 4.468225245, 0.915653726,
1.635617261, 3.726133898, 1.363453706, 13.99650967, 0.417618143,
0.741080504, 0.412440872, 3.515743675, 8.248491445, 1.537773727,
3.249103284, 0.768531626, 2.633107621, 3.113199095, 0.773824094,
0.680150068, 0.026385752, 0.369310858, 8.049276658, 7.487378383,
0.763580377, 0.333244629, 5.475999014, 9.235631398), TSS = c(2.8,
8.4, 11, 1.3, 4.2, 2, 3.4, 14, 8.2, 3.1, 1.4, 0.9, 6.1, 9.2,
11, 1.2, 1.3, 11, 8.5, 13, 4.4, 1.4, 2.1, 25, 9.3, 6.1, 1.6,
1.5, 24, 9.6, 1.8, 1.4), Iron = c(0.74, 0.54, 0.23, 0.13, 0.4,
0.13, 0.15, 0.58, 0.38, 0.22, 0.13, 0.07, 0.32, 0.26, 0.86, 0.13,
0.09, 0.58, 0.35, 0.59, 0.33, 0.19, 0.21, 0.81, 0.34, 0.31, 0.07,
0.16, 0.54, 0.36, 0.13, 0.07), TIN.TP = c(3.117647059, 2.736842105,
2.25, 22, 3, 2.428571429, 6.428571429, NA, NA, 2.384615385, 3,
NA, 3.25, NA, 3.16667, 9, 23, 3.5, 11, 3.91667, 3.4,
3.4, 8.75, 2.7, 3.58333, 2.75, 17, NA, 2.9,
2.5, 2.5, 11), RiverMile = c(148L, 179L, 185L, 202L,
179L, 185L, 190L, 119L, 148L, 179L, 185L, 202L, 119L, 202L, 148L,
190L, 202L, 148L, 202L, 119L, 179L, 185L, 190L, 61L, 119L, 148L,
202L, 202L, 119L, 148L, 185L, 202L)), .Names = c(GPP, TSS,
Iron, TIN.TP, RiverMile), class = data.frame, row.names = c(1L,
2L, 3L, 5L, 6L, 7L, 8L, 9L, 10L, 11L, 12L, 13L, 15L, 16L, 19L,
22L, 23L, 30L, 34L, 36L, 37L, 38L, 39L, 43L, 44L, 45L, 46L, 47L,
49L, 50L, 51L, 52L))
xyplot(GPP~(1/Iron)+(1/TSS)+TIN.TP, groups=RiverMile,data=f,
scales=list(relation=free), pch=20, auto.key=TRUE)
--
Stephen Sefick
Research Scientist
Southeastern Natural Sciences Academy
Let's not spend our time and resources thinking about things that are
so little or so large that all they really do for us is puff us up and
make us feel like gods. We are mammals, and have not exhausted the
annoying little problems of being mammals.
-K. Mullis
--
Stephen Sefick
Research Scientist
Southeastern Natural Sciences Academy
Let's not spend our time and resources thinking about things that are
so little or so large that all they really do for us is puff us up and
make us feel like gods. We are mammals, and have not exhausted the
annoying little problems of being mammals.
-K. Mullis
__
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.
