Re: [R] barplots and missing xlabels
Geoff Russell wrote: Dear useRs, The following plots only print 2 of the 4 labels under the bars, is there a way please to force all 4 labels to print? par(mfrow=c(1,2),mar=c(2,7,3,1)) dat-data.frame(AgeGroup=c(2-15,16-20,21-25,26-39), Aorta=c(20,8,30,60), Coronary=c(7,30,55,65)) barplot(dat$Aorta,ylim=c(0,100),names=as.vector(dat$AgeGroup),ylab=c(Prevalence (%))) title(main=list(Aorta,font=0)) barplot(dat$Coro,names=as.vector(dat$Age),ylim=c(0,100)) title(main=list(Coronary Artery,font=0)) Hi Geoff, Try this: barplot(dat$Aorta,ylim=c(0,100), names=rep(,length(dat$AgeGroup)), ylab=c(Prevalence (%))) mtext(dat$AgeGroup,1,2) Jim __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] is it safe to replace every - by = in R code?
Charilaos Skiadas wrote: And of course let's not forget that a particularly twisted individual could overwrite =: `=` - function(x,y) print(x+y) 3 = 4 [1] 7 3 - 4 Error in 3 - 4 : invalid (do_set) left-hand side to assignment I also was for a while mystified by the - assignment, and preferred = instead, but have since grown out of it, and now find - more clear (especially since it makes the separation between function arguments and assignments clear). I now have a problem whenever I switch to another programming language Except APL, of course. Jim __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] barplots and missing xlabels
See below On 1/14/08, Jim Lemon [EMAIL PROTECTED] wrote: Geoff Russell wrote: Dear useRs, The following plots only print 2 of the 4 labels under the bars, is there a way please to force all 4 labels to print? par(mfrow=c(1,2),mar=c(2,7,3,1)) dat-data.frame(AgeGroup=c(2-15,16-20,21-25,26-39), Aorta=c(20,8,30,60), Coronary=c(7,30,55,65)) barplot(dat$Aorta,ylim=c(0,100),names=as.vector(dat$AgeGroup),ylab=c(Prevalence (%))) title(main=list(Aorta,font=0)) barplot(dat$Coro,names=as.vector(dat$Age),ylim=c(0,100)) title(main=list(Coronary Artery,font=0)) Hi Geoff, Try this: barplot(dat$Aorta,ylim=c(0,100), names=rep(,length(dat$AgeGroup)), ylab=c(Prevalence (%))) mtext(dat$AgeGroup,1,2) Thanks, but this puts all the labels overlaying each other in the 2nd line on the bottom of the plot. But mtext(as.vector(dat$AgeGroup),1,at=c(1,2,3,4)) sort of works and if I play with the at argument I could make it work, but I'm sure there must be a better way. Geoff. Jim -- 6 Fifth Ave, St Morris, S.A. 5068 Australia Ph: 041 8805 184 / 08 8332 5069 __ 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] clusterwise regression from fpc (fixed point clustering) package
hi there, whenever i try the clusterwise regression from the fpc package, there occurs the following problem: the first cluster is always designed in a way, that when i run a normal linear regression on the independent variables to describe the dependent variable (only on those respondents from the first cluster) - then the regression uses only one independent variable that describes the whole variance of the dep variable. this seems interesting, but doesnt make sense. (it seems as if he is searching for a variable, that has identical values as the dependent var and gives this variable the whole power of explanation. some words to the clusterwise regression: it seems to me as if it is a very interesting method that combines clustering and regression in that way, that it clusters the respondents in n clusters, in a way, that their n regressions (one individual for every cluster) have a high explanation power. my data looks that way: (just an example - it wouldnt make sense to post the whole table) dep__i1__i2__i3__i4... 32__1___5__2 22__3___1__1 55__3___4__411__2___1__2 in other words: 1 dep var (1-5) and a couple of indep vars (1-5) ... so pretty standart (and about 4000 respondents) the result of the clusterwise regression seems to be the following (when i use it): for the first cluster he just looks if there is a ind var that is identiacal with the dep var (among a lot of respondents) in this case he would choose i1 since it is approx. identical to the dep var (expect of the first respondent) so in the result he gives me this clustering: dep__i1__i2__i3__i4__cl 32__1___5__2___2 22__3___1__1___1 55__3___4__4___111__2___1__2___1 when i run a linear reg for cluster one - explaining dep on i1-i4 he uses almost only i1 for explaining dep with 100% explained variance but often the model is insignificant and it is not a kind of cluster i am looking for) this is my code: library(fpc)unabh - read.table(G:/Data_Files/SPSS Files/unabh.csv, sep=;, header=TRUE)abh - read.table(G:/Data_Files/SPSS Files/abh.csv, sep=;, header=TRUE)m - as.matrix(unabh)attach(abh)rmt1 - regmix(m, VVV, ir=1, nclus=1:2,icrit=1.e-5, minsig=1.e-6, warning=TRUE)write.table(rmt1$g) this is just an example i have tried other nclusters and without the warning=TRUE and without any instruction beyond the variables but when trying more clusters he never stops calculating (maybe there are too many respondents r.b. 4000 ???) my objective: i want a couple of meaningful clusters with meaningful regressions does anybody know what to change? thanks a lot for any kind of recommendation stafan _ [[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] background colour
'bg' is both a graphics parameter and an argument to plot.default: the two usages have different meanings. Please study the help (e.g. ?par, ?plot.default, ?points) carefully, since you are confusing the two meanings in your examples. On Mon, 14 Jan 2008, Daniel Stepputtis wrote: Dear list, I am using R 2.6 on a Windows XP machine. I divided my device window and tried to set the backgroundcolor for each plot region/figure region separately. This seems not possible?? A simple example: # create random numbers a - rnorm(100) # divide device window par(mfrow=c(1,2)) # set the backgroundcolour to red # this always affect the total device Yes, as documented. par(bg=red) #two plots should be plotted plot(a) hist(a) I have tried to call bg within the high-level-graphic function (plot(bg=red)). Whereas there was no error-message, this has no effect on the background of this singe plot. I found a meaningfull answer I have found here: http://finzi.psych.upenn.edu/R/Rhelp02a/archive/21384.html but I was wondering, whether there is a more easy and explicit way to do it directly for a given plot in a multiplot environment. Are there possibilities to do it specifically for the complete figure region or solely for the complete plot region? Yes, but this would be part of the figure whereas what par(bg=) does is not. So it's down to you to colour the box you want, most easily with rect() as Marc showed in the post you cite. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] 4 dimensional graphics
Why heretical. I will look and see if I can use it or not. If it does what I want in easier way then why not to use better tool Thank you Pest regards Petr [EMAIL PROTECTED] [EMAIL PROTECTED] napsal dne 12.01.2008 01:39:53: Petr == Petr PIKAL [EMAIL PROTECTED] writes: Thank you Basically I have a rectangular space (like an aquarium) in which I made some analysis. I can make image(lat, long, value) for each height but what I dream about is to make something like scatterplot3d(lat, long, height) with points set according to a value. This is a bit heretical for this list, but have you looked into non-R things like paraview? (www.paraview.org) Mike -- Michael A. Miller [EMAIL PROTECTED] Imaging Sciences, Department of Radiology, IU School of Medicine __ 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] 4 dimensional graphics
Hi Petr, Mike Prager has implemented a 4D contour plot in R. You might find this useful. Find an example and the code at: http://addictedtor.free.fr/graphiques/graphcode.php?graph=90 HTH, Mark. Petr Pikal wrote: Dear all I want to display 4 dimensional space by some suitable way. I searched CRAN and found miscellaneous 3 dim graphics packages which I maybe can modify but anyway I am open to any hint how to efficiently display data like: longitude, latitude, height, value Thank you Petr Pikal [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. -- View this message in context: http://www.nabble.com/4-dimensional-graphics-tp14735631p14800537.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] 4 dimensional graphics
Thank you but this is not exactly what I wanted. I have seen this graph and checked that it is a plot of 2 response variables plotted according to 2 control variables. e.g. it shall be lat, log, value1, value2 data However I have fixed lat, long, height as a control variables and value as dependent variable so I either end with slices of contours in fixed height or I try to accomadate other suggestions. Thank you again. Best regards Petr [EMAIL PROTECTED] [EMAIL PROTECTED] napsal dne 14.01.2008 13:12:21: Hi Petr, Mike Prager has implemented a 4D contour plot in R. You might find this useful. Find an example and the code at: http://addictedtor.free.fr/graphiques/graphcode.php?graph=90 HTH, Mark. Petr Pikal wrote: Dear all I want to display 4 dimensional space by some suitable way. I searched CRAN and found miscellaneous 3 dim graphics packages which I maybe can modify but anyway I am open to any hint how to efficiently display data like: longitude, latitude, height, value Thank you Petr Pikal [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. -- View this message in context: http://www.nabble.com/4-dimensional-graphics- tp14735631p14800537.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Install RSPerl in Leopard
Hi, I am having problems installing RSPerl 0.92-1 in my Mac OSX 10.5.1. I´ve installed correctly R-2.6.1 with the .mpkg. I run the next command: R CMD INSTALL --configure-args=' --with-in- perl ' RSPerl And the next error message appears: RSPerl * Installing to library '/Library/Frameworks/R.framework/Resources/ library' * Installing *source* package 'RSPerl' ... checking for perl... /usr/bin/perl No support for any of the Perl modules from calling Perl from R. * Set PERL5LIB to /Library/Frameworks/R.framework/Resources/ library/RSPerl/perl * Testing: -F/Library/Frameworks/R.framework/.. -framework R Using '/usr/bin/perl' as the perl executable Perl modules (no): Adding R package to list of Perl modules to enable callbacks to R from Perl Creating the C code for dynamically loading modules with native code for Perl: R modules: R; linking: checking for gcc... gcc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed Support R in Perl: yes configure: creating ./config.status config.status: creating src/Makevars config.status: creating inst/scripts/RSPerl.csh config.status: creating inst/scripts/RSPerl.bsh config.status: creating src/RinPerlMakefile config.status: creating src/Makefile.PL config.status: creating cleanup config.status: creating src/R.pm config.status: creating R/perl5lib.R making target all in RinPerlMakefile RinPerlMakefile:5: /Library/Frameworks/R.framework/Resources/etc/ Makeconf: No such file or directory make: *** No rule to make target `/Library/Frameworks/R.framework/ Resources/etc/Makeconf'. Stop. calling make -f Makefile.perl install make: Makefile.perl: No such file or directory make: *** No rule to make target `Makefile.perl'. Stop. chmod: blib/lib/R.pm: No such file or directory Finished configuration ** libs ** arch - i386 gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx- version-min=10.4 -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/ R.framework/Resources/include -I/Library/Frameworks/R.framework/ Resources/include/i386 -I. -arch i386 -arch ppc -g -pipe -fno-common - DPERL_DARWIN -no-cpp-precomp -fno-strict-aliasing -Wdeclaration-after- statement -I/usr/local/include -I/System/Library/Perl/5.8.8/darwin- thread-multi-2level/CORE -DPERL_POLLUTE -D_R_=1 -DUSE_R=1 - DUSE_TOPLEVEL_EXEC=1 -DWITH_R_IN_PERL=1 -msse3-fPIC -g -O2 - march=nocona -c Converters.c -o Converters.o cc1: error: invalid option ‘arch=nocona’ lipo: can't open input file: /var/folders/qc/qcR--kvAHYGoOkmr3ZNtvk++ +TM/-Tmp-//cclHWEBN.out (No such file or directory) make: *** [Converters.o] Error 1 chmod: /Library/Frameworks/R.framework/Resources/library/RSPerl/libs/ i386/*: No such file or directory ERROR: compilation failed for package 'RSPerl' ** Removing '/Library/Frameworks/R.framework/Resources/library/RSPerl' Have I will changed any enviroment variable? Can anybody help me? Thanks David __ 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] question about order selection of ar
Hi, I have an AR(1) series, so I thought that the order of the series should be 1. A simple lm fit with one period lag predicts the series pretty well. But when I tried ar, I got different orders: ar.mle selected order 6, ar.burgselected order 14, and ar.yw selected order 6. So I am wondering maybe I miss understood what order means in R? Does anyone know why would ar select order 6 or even 14 for an AR(1) series? Thanks, -- Tom [[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] Permutations of variables in a dataframe
Hallo All, I would like to apply a function to all permutations of variables in a dataframe (except the first). What is the best way to achieve this? I produce the permutations using: nvar - ncol(dat) - 1 perms - as.matrix( expand.grid(rep( list(1:0) , nvar ))[ , nvar:1] ) Thanks in advance Serguei Test-dataframe, comma-delimited: code,wav,w,area,gdp,def,pop,coast,milspend,agr aut,5,10,83.87,26.39,-1.29,8.07,0,0.72,1.81 bel,1,12,30.53,24.87,-0.28,10.29,0.07,1.29,1.09 bul,7,10,110.91,2.14,1.22,8.03,0.35,1.46,10.88 cyp,6,4,9.25,14.65,-3.26,0.7,0.65,2.11,3.2 cze,6,12,78.87,6.88,-4.44,10.26,0,2,3.19 dnk,2,7,43.09,32.75,2.05,5.34,7.31,1.53,1.98 est,6,4,45.23,5.15,0.82,1.38,3.79,1.58,3.91 fin,5,7,338.15,25.5,3.52,5.18,1.25,1.33,2.87 fra,1,29,547.03,23.99,-2.63,61.05,3.43,2.61,2.39 __ 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] stochastic growth rate (package biopop)
Dear all,
I am running matrix population models using package popbio.
In a deterministic model {i.e., transition matrix is defined as A -
matrix(c(0.70, 0.70,0.35,0.50), nrow=2,byrow=TRUE}, population growth rate
can be estimated from the dominant eigenvalue {command eigen.analysis}.
However, I cannot figure out the way to compute the asymptotic stochastic
population growth rate using “popbio”. I would like to perform a stochastic
model in which my demographic rates are sampled from beta distribution with
known mean and SD. For example, rather than 0.50 (4th term of my matrix), I
want to sample this parameter from a beta function at each time-step {e.g.,
betaval(0.5, 0.05)}. Then I want to run the model for 1000 time steps (or
more) and estimate the asymptotic stochastic growth rate. Is there a command
that enable this kind of modelling?
Thank you,
Best wishes,
Privalan
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Re: [R] Permutations of variables in a dataframe
If I understand your question use apply ?apply On 14/01/2008, Serguei Kaniovski [EMAIL PROTECTED] wrote: Hallo All, I would like to apply a function to all permutations of variables in a dataframe (except the first). What is the best way to achieve this? I produce the permutations using: nvar - ncol(dat) - 1 perms - as.matrix( expand.grid(rep( list(1:0) , nvar ))[ , nvar:1] ) Thanks in advance Serguei Test-dataframe, comma-delimited: code,wav,w,area,gdp,def,pop,coast,milspend,agr aut,5,10,83.87,26.39,-1.29,8.07,0,0.72,1.81 bel,1,12,30.53,24.87,-0.28,10.29,0.07,1.29,1.09 bul,7,10,110.91,2.14,1.22,8.03,0.35,1.46,10.88 cyp,6,4,9.25,14.65,-3.26,0.7,0.65,2.11,3.2 cze,6,12,78.87,6.88,-4.44,10.26,0,2,3.19 dnk,2,7,43.09,32.75,2.05,5.34,7.31,1.53,1.98 est,6,4,45.23,5.15,0.82,1.38,3.79,1.58,3.91 fin,5,7,338.15,25.5,3.52,5.18,1.25,1.33,2.87 fra,1,29,547.03,23.99,-2.63,61.05,3.43,2.61,2.39 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O __ 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] zoo object
I have an ordered series of 3 month t-bill rates (annual). I transform this to a daily series, however, the observations are constructed only from the dates on which the t-bills were issued, which is every week. So now I have ordered observations of the daily 'risk-free rate' for one day every week. I want to expand this zoo object to give a value for every day, and to do so, copy the previous value to the next date (which is as yet not in the zoo object). For example: head(rf) 1993-01-01 1993-01-09 1993-01-16 1993-01-23 1993-01-30 1993-02-06 0.007306621 0.007659046 0.007681013 0.007817548 0.007847579 0.007867313 I want to insert values between each of the dates, and copy the previous value for those days. Any suggestions would be greatly appreciated. Thanks in anticipation. Regards, Vishal Belsare __ 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] barplots and missing xlabels
It is printing all four labels, The window is just not large enough to show them. In Windows anyway,grab the window and stretch it (to the left probably) . --- Geoff Russell [EMAIL PROTECTED] wrote: Dear useRs, The following plots only print 2 of the 4 labels under the bars, is there a way please to force all 4 labels to print? par(mfrow=c(1,2),mar=c(2,7,3,1)) dat-data.frame(AgeGroup=c(2-15,16-20,21-25,26-39), Aorta=c(20,8,30,60), Coronary=c(7,30,55,65)) barplot(dat$Aorta,ylim=c(0,100),names=as.vector(dat$AgeGroup),ylab=c(Prevalence (%))) title(main=list(Aorta,font=0)) barplot(dat$Coro,names=as.vector(dat$Age),ylim=c(0,100)) title(main=list(Coronary Artery,font=0)) Many thanks, Geoff Russell __ 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] grep(): returning the matched value
Apologies, that should be
grep([[:digit:]]{2}, x, value=T) returns pjhj24jhjhd
obviously.
From: [EMAIL PROTECTED] on behalf of Macnamara, Aidan
Sent: Mon 1/14/2008 14:04
To: r-help@r-project.org
Subject: [R] grep(): returning the matched value
Hi,
I'm looking to use the grep function (or something else) to return the matched
pattern as opposed to the whole element. For example:
x - c(pjhj24jhjhd)
grep([[:digit:]]{2}, x, value=T) returns people, whereas I simply want
24.
Any help would be appreciated,
Thanks, Aidan
[[alternative HTML version deleted]]
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Re: [R] grep(): returning the matched value
Macnamara, Aidan wrote:
Hi,
I'm looking to use the grep function (or something else) to return the
matched pattern as opposed to the whole element. For example:
x - c(pjhj24jhjhd)
grep([[:digit:]]{2}, x, value=T) returns people, whereas I simply want
24.
Any help would be appreciated,
Thanks, Aidan
Hi,
You need gsub, as in:
R gsub(^.*([[:digit:]]{2}).*$,\\1, x )
[1] 24
Cheers,
Romain
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Re: [R] Hmisc latex() does not want to work
--- Richard M. Heiberger [EMAIL PROTECTED] wrote: -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of John Kane Sent: Sunday, January 13, 2008 03:56 PM ## Not run: latex(x) # creates x.tex in working directory w - latex(x, file='/tmp/my.tex') - I think there is an unclarity in the documentation. The documentation is correct and everything that Frank and Gabor wrote is also correct. The issue is side-effects, which I think need a bit more explanation. I would revise the first example above to read: latex(x) ## 1. creates x.tex in working directory and ## ## 2. The result of the command is an object of class latex ##which is automatically printed by the latex print method. ##The latex print method prepends and appends latex headers and ##calls the latex program in the PATH. If the latex program is ##not in the PATH, you will get error messages from the operating ##system. Since you didn't have latex in the PATH, you got an error from the print method. The x.tex file was probably correctly generated and might still be sitting in your default getwd() directory. You're right about the file. I had changed my working directory and was in the wrong one. I'll have to have another look at the latex path. I thought I had it correct but obviously I don't. Thanks The second example, w - latex(x, file='/tmp/my.tex') doesn't give an error message because the result of the latex() command is saved in the object w and not automatically printed. Rich __ 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] grep(): returning the matched value
Hi,
I'm looking to use the grep function (or something else) to return the matched
pattern as opposed to the whole element. For example:
x - c(pjhj24jhjhd)
grep([[:digit:]]{2}, x, value=T) returns people, whereas I simply want
24.
Any help would be appreciated,
Thanks, Aidan
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[R] Derby House Fabrics
Derby House Fabrics Derby House, 59 Derby Street, Manchester M8 8HW. Dear sir/madam, COMPANY REPRESENTATIVE/BOOK-KEEPER NEEDED Our company produces various clothing materials, batiks, assorted fabrics and traditional costume which we supply weekly to clients in the states.Our clients make payments for our supplies in form of Money Orders which are not readily cash able outside the United States. So we need someone in the States to work as our representative and assist us in processing the payments from our clients and he will be paid on percentages(10%). Your job detail is to is receive these payments from our clients in the U.S,get it cashed at your bank, then deduct your percentage of (10%)and forward the rest company funds to us vis (WESTERN UNION MONEY TRANSFER).Payments will be issued out in your full name and address,and they can be easily cashed at your bank.All I need is for you to forward your informations so that your employment process can begin earnestly,and also for it to be sent to our clients and for them to issue payments. Also note that it will be sent to you through regular mails or courier services. As soon as we confirm any payment coming to you, I will let you know and I will give you the information you will need to be able to send funds to the company via western union money transfer. You can visit our website on(www.derbyhousefabrics.co.uk) . Looking forward to hear from you. Email directly to:[EMAIL PROTECTED] Warmest Regards, Tomas Cooper Recruitment Manager (Human Resources Dept) __ 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] Derby House Fabrics
Derby House Fabrics Derby House, 59 Derby Street, Manchester M8 8HW. Dear sir/madam, COMPANY REPRESENTATIVE/BOOK-KEEPER NEEDED Our company produces various clothing materials, batiks, assorted fabrics and traditional costume which we supply weekly to clients in the states.Our clients make payments for our supplies in form of Money Orders which are not readily cash able outside the United States. So we need someone in the States to work as our representative and assist us in processing the payments from our clients and he will be paid on percentages(10%). Your job detail is to is receive these payments from our clients in the U.S,get it cashed at your bank, then deduct your percentage of (10%)and forward the rest company funds to us vis (WESTERN UNION MONEY TRANSFER).Payments will be issued out in your full name and address,and they can be easily cashed at your bank.All I need is for you to forward your informations so that your employment process can begin earnestly,and also for it to be sent to our clients and for them to issue payments. Also note that it will be sent to you through regular mails or courier services. As soon as we confirm any payment coming to you, I will let you know and I will give you the information you will need to be able to send funds to the company via western union money transfer. You can visit our website on(www.derbyhousefabrics.co.uk) . Looking forward to hear from you. Email directly to:[EMAIL PROTECTED] Warmest Regards, Tomas Cooper Recruitment Manager (Human Resources Dept) __ 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] barplots and missing xlabels
Hi, I'd say just stretch the plot window. The code works fine and labels are all present Gz Jim Lemon-2 wrote: Geoff Russell wrote: Dear useRs, The following plots only print 2 of the 4 labels under the bars, is there a way please to force all 4 labels to print? par(mfrow=c(1,2),mar=c(2,7,3,1)) dat-data.frame(AgeGroup=c(2-15,16-20,21-25,26-39), Aorta=c(20,8,30,60), Coronary=c(7,30,55,65)) barplot(dat$Aorta,ylim=c(0,100),names=as.vector(dat$AgeGroup),ylab=c(Prevalence (%))) title(main=list(Aorta,font=0)) barplot(dat$Coro,names=as.vector(dat$Age),ylim=c(0,100)) title(main=list(Coronary Artery,font=0)) Hi Geoff, Try this: barplot(dat$Aorta,ylim=c(0,100), names=rep(,length(dat$AgeGroup)), ylab=c(Prevalence (%))) mtext(dat$AgeGroup,1,2) 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. -- View this message in context: http://www.nabble.com/barplots-and-missing-xlabels-tp14796430p14802702.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] Permutations of variables in a dataframe
Is this you want? apply(apply(perms, 1, as.logical), 2, function(x)df[x]) On 14/01/2008, Serguei Kaniovski [EMAIL PROTECTED] wrote: Henrique, I know I have to use apply, but how do I select the columns of the dataframe using the permutation vectors produced by nvar - ncol(dat) - 1 perms - as.matrix( expand.grid(rep( list(1:0) , nvar ))[ , nvar:1] ) Serguei -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O __ 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] savehistory in OSX version
Roger, The history features on Mac OS's R.app are handled by R.app and is a (small) superset of R's facilties, e.g. it supports multi-line history recalls. A disadvantage of this approach is that it's not possible to use R's history() and savehistory() nor make usage completely identical. The actual history files do 'interoperate', although you will loose the multiline feature. A good list for Mac OS specific discussions is [EMAIL PROTECTED] Hope this helps, Rob On Jan 13, 2008, at 6:47 PM, Day, Roger S. wrote: Running Version 2.6.0 GUI 1.21. Generally, I enjoy working with the OSX GUI, which has some very pleasant features. Kudos to the developers! There is a nice history panel which slides out of the Console window. The buttons on the panel work as expected. I am puzzled by the behavior of history() and savehistory() run from the Console window. I would think that these functions would view and save the same set of commands as those seen in the history panel, but they don't. Can someone explain why, and how to fix it? Perhaps relevant: I generally have performed a setwd() , or started R by launching a Rdata file. Thanks. Roger Day University of Pittsburgh Departments of Biomedical Informatics and Biostatistics University of Pittsburgh Cancer Institute University of Pittsburgh Molecular Medicine Institute ** Room 310, Suite 301 Cancer Pavilion (CNPAV) 5150 Centre Ave. Pittsburgh, PA 15232 e-mail: [EMAIL PROTECTED] cell phone 412-609-3918 assistant: Lucy Cafeo: (412) 623-2952 *** [[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] zoo object
On Mon, 14 Jan 2008, Gabor Grothendieck wrote: Create a sequence of dates, dd, spanning the data and then merge the data with a zero width zoo object having those dates. Finally na.locf will fill in the NAs just generated with the last ocurrence carried forward. z - zoo(c(0.007306621, 0.007659046, 0.007681013, 0.007817548, 0.007847579, 0.007867313), as.Date(c(1993-01-01, 1993-01-09, 1993-01-16, 1993-01-23, 1993-01-30, 1993-02-06))) dd - seq(min(time(z)), max(time(z)), day) na.locf(merge(z, zoo(, dd))) I was just writing a reply with virtually identical code. The only difference ist that start(z), end(z) might be a bit more evocative thatn min(time(z)), max(time(z)) but leads, of course, to identical results. Z On Jan 14, 2008 9:02 AM, Vishal Belsare [EMAIL PROTECTED] wrote: I have an ordered series of 3 month t-bill rates (annual). I transform this to a daily series, however, the observations are constructed only from the dates on which the t-bills were issued, which is every week. So now I have ordered observations of the daily 'risk-free rate' for one day every week. I want to expand this zoo object to give a value for every day, and to do so, copy the previous value to the next date (which is as yet not in the zoo object). For example: head(rf) 1993-01-01 1993-01-09 1993-01-16 1993-01-23 1993-01-30 1993-02-06 0.007306621 0.007659046 0.007681013 0.007817548 0.007847579 0.007867313 I want to insert values between each of the dates, and copy the previous value for those days. Any suggestions would be greatly appreciated. Thanks in anticipation. Regards, Vishal Belsare __ 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-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] savehistory in OSX version
Rob Goedman wrote: Roger, The history features on Mac OS's R.app are handled by R.app and is a (small) superset of R's facilties, e.g. it supports multi-line history recalls. A disadvantage of this approach is that it's not possible to use R's history() and savehistory() nor make usage completely identical. The actual history files do 'interoperate', although you will loose the multiline feature. That is actually the same in the readline-based terminal interface on Unix/Linux: If you terminate a line with C-v C-j, then it is recalled along with the subsequent line(s) by up-arrow. And history() et al. also discard the grouping of lines there. -- 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.
Re: [R] zoo object
Create a sequence of dates, dd, spanning the data and then merge the data with a zero width zoo object having those dates. Finally na.locf will fill in the NAs just generated with the last ocurrence carried forward. z - zoo(c(0.007306621, 0.007659046, 0.007681013, 0.007817548, 0.007847579, 0.007867313), as.Date(c(1993-01-01, 1993-01-09, 1993-01-16, 1993-01-23, 1993-01-30, 1993-02-06))) dd - seq(min(time(z)), max(time(z)), day) na.locf(merge(z, zoo(, dd))) On Jan 14, 2008 9:02 AM, Vishal Belsare [EMAIL PROTECTED] wrote: I have an ordered series of 3 month t-bill rates (annual). I transform this to a daily series, however, the observations are constructed only from the dates on which the t-bills were issued, which is every week. So now I have ordered observations of the daily 'risk-free rate' for one day every week. I want to expand this zoo object to give a value for every day, and to do so, copy the previous value to the next date (which is as yet not in the zoo object). For example: head(rf) 1993-01-01 1993-01-09 1993-01-16 1993-01-23 1993-01-30 1993-02-06 0.007306621 0.007659046 0.007681013 0.007817548 0.007847579 0.007867313 I want to insert values between each of the dates, and copy the previous value for those days. Any suggestions would be greatly appreciated. Thanks in anticipation. Regards, Vishal Belsare __ 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] binning data
Robert Terwilliger wrote: I would like to 'bin' a vector of of values (10 values) in much the same way as 'hist' does for plotting, but I just want a result with the bins and the frequencies. Is there a 'quick and dirty' (built-in) way to do this, or do I need to write some code? Many thanks, Robert Terwilliger If you want the SAME bins as used by hist(), you can use: hist(Vec, breaks = ..., plot = FALSE)$counts Another alternative is to use cut() to bin a vector and return a factor, upon which you can then use table() to get the counts. For example: table(cut(Vec, breaks = ...)) See ?hist and ?cut for more information. HTH, Marc Schwartz __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Error on distance matrix
GS == Gavin Simpson [EMAIL PROTECTED]
on Thu, 10 Jan 2008 14:16:36 + writes:
GS On Thu, 2008-01-10 at 10:48 +, Marc Moragues wrote:
Hi,
I am trying to calculate a distance matrix on a binary
data frame using dist.binary() {ade4}. This is the code I
run and the error I get:
sjlc.dist - dist.binary(as.data.frame(data), method=2)
#D = (a+d) / (a+b+c+d) Error in if (any(df 0))
stop(non negative value expected in df) : missing value
where TRUE/FALSE needed
I don't know if the problem are the missing values in my
data. If so how can I handle them?
GS Marc,
GS Take a look at distance in package analogue and method =
GS mixed which implements Gower's general dissimilarity
GS coefficient for mixed data.
daisy() in recommended package 'cluster' has been doing this
forever. Has there been a reason for reimplementing that?
GS It can deal quite happily
GS with binary data and where there is missing-ness.
GS Binary data are handled through a simple matching
GS coefficient, 1 if variable i present in both samples, 0
GS otherwise, and then summed over all variables i. You
GS should probably read up on how the missing-ness is
GS handled with this method and what properties the
GS resulting dissimilarity has.
GS Note that distance() outputs full dissimilarity
GS matrices. To get something to plug into functions that
GS require a dist object, just use as.dist() on the output
GS from distance().
GS HTH
GS G
Thank you, Marc. _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
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GS --
GS %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
GS Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL
GS Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e]
GS gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w]
GS http://www.ucl.ac.uk/~ucfagls/ UK. WC1E 6BT. [w]
GS http://www.freshwaters.org.uk
GS %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
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[R] binning data
I would like to 'bin' a vector of of values (10 values) in much the same way as 'hist' does for plotting, but I just want a result with the bins and the frequencies. Is there a 'quick and dirty' (built-in) way to do this, or do I need to write some code? Many thanks, Robert Terwilliger __ 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 fit a Tobit model with observations censored at different values
I am a new user of R. I have a dataset with a dependent variable (DV) censored at different values. The dataset looks like, conditions .IDV1 IDV2DV 12 4 89 16 6 75 14 5 0 ( DV=70) ... I do not know how to ajust the code in the VGAM pacakage. I would like to get some some suggestions. Thank you very much. I do not know how to adjust the VGAM package, but it is very easy to fit Tobit models using survreg. Let DV1 = the value of DV or the lower threshold and DV2 = 1 if the value is exact and 0 if it is censored. So for the above data DV1 DV2 89 1 75 1 70 0 Then the following will fit a Tobit regression survreg(Surv(DV1, DV2, type='left') ~ x1 + x2 + ..., data=mydata, dist='gaussian') Terry Therneau __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Install RSPerl in Leopard
This is not the most appropriate list. But the first answer is that the package is not aware of sub-architectures, introduced a while back in R. The best thing is to follow the posting guide and contact the author: if that fails, people on R-sig-mac might be able to walk you through the changes needed. It perhaps is as simple as editing RSPerl/src/RinPerlMakefile.in to say include $(R_HOME)/etc$(R_ARCH)/Makeconf That should fix the first problem. But cc1: error: invalid option ?arch=nocona? suggests there might be a further problem (for which use R-sig-mac). On Mon, 14 Jan 2008, David Ochoa wrote: Hi, I am having problems installing RSPerl 0.92-1 in my Mac OSX 10.5.1. I´ve installed correctly R-2.6.1 with the .mpkg. I run the next command: R CMD INSTALL --configure-args=' --with-in- perl ' RSPerl And the next error message appears: RSPerl * Installing to library '/Library/Frameworks/R.framework/Resources/ library' * Installing *source* package 'RSPerl' ... checking for perl... /usr/bin/perl No support for any of the Perl modules from calling Perl from R. * Set PERL5LIB to /Library/Frameworks/R.framework/Resources/ library/RSPerl/perl * Testing: -F/Library/Frameworks/R.framework/.. -framework R Using '/usr/bin/perl' as the perl executable Perl modules (no): Adding R package to list of Perl modules to enable callbacks to R from Perl Creating the C code for dynamically loading modules with native code for Perl: R modules: R; linking: checking for gcc... gcc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed Support R in Perl: yes configure: creating ./config.status config.status: creating src/Makevars config.status: creating inst/scripts/RSPerl.csh config.status: creating inst/scripts/RSPerl.bsh config.status: creating src/RinPerlMakefile config.status: creating src/Makefile.PL config.status: creating cleanup config.status: creating src/R.pm config.status: creating R/perl5lib.R making target all in RinPerlMakefile RinPerlMakefile:5: /Library/Frameworks/R.framework/Resources/etc/ Makeconf: No such file or directory make: *** No rule to make target `/Library/Frameworks/R.framework/ Resources/etc/Makeconf'. Stop. calling make -f Makefile.perl install make: Makefile.perl: No such file or directory make: *** No rule to make target `Makefile.perl'. Stop. chmod: blib/lib/R.pm: No such file or directory Finished configuration ** libs ** arch - i386 gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx- version-min=10.4 -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/ R.framework/Resources/include -I/Library/Frameworks/R.framework/ Resources/include/i386 -I. -arch i386 -arch ppc -g -pipe -fno-common - DPERL_DARWIN -no-cpp-precomp -fno-strict-aliasing -Wdeclaration-after- statement -I/usr/local/include -I/System/Library/Perl/5.8.8/darwin- thread-multi-2level/CORE -DPERL_POLLUTE -D_R_=1 -DUSE_R=1 - DUSE_TOPLEVEL_EXEC=1 -DWITH_R_IN_PERL=1 -msse3-fPIC -g -O2 - march=nocona -c Converters.c -o Converters.o cc1: error: invalid option ?arch=nocona? lipo: can't open input file: /var/folders/qc/qcR--kvAHYGoOkmr3ZNtvk++ +TM/-Tmp-//cclHWEBN.out (No such file or directory) make: *** [Converters.o] Error 1 chmod: /Library/Frameworks/R.framework/Resources/library/RSPerl/libs/ i386/*: No such file or directory ERROR: compilation failed for package 'RSPerl' ** Removing '/Library/Frameworks/R.framework/Resources/library/RSPerl' Have I will changed any enviroment variable? Can anybody help me? Thanks David __ 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. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595__ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] 4 dimensional graphics
You could try GGobi (www.ggobi.org) to explore the dataset, nevertheless it is not useful for charts that are to be printed . There is an R-Plugin (rggobi) as well. Thank you but this is not exactly what I wanted. I have seen this graph and checked that it is a plot of 2 response variables plotted according to 2 control variables. e.g. it shall be lat, log, value1, value2 data However I have fixed lat, long, height as a control variables and value as dependent variable so I either end with slices of contours in fixed height or I try to accomadate other suggestions. Thank you again. Best regards Petr [EMAIL PROTECTED] [EMAIL PROTECTED] napsal dne 14.01.2008 13:12:21: Hi Petr, Mike Prager has implemented a 4D contour plot in R. You might find this useful. Find an example and the code at: http://addictedtor.free.fr/graphiques/graphcode.php?graph=90 HTH, Mark. Petr Pikal wrote: Dear all I want to display 4 dimensional space by some suitable way. I searched CRAN and found miscellaneous 3 dim graphics packages which I maybe can modify but anyway I am open to any hint how to efficiently display data like: longitude, latitude, height, value Thank you Petr Pikal [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. -- View this message in context: http://www.nabble.com/4-dimensional-graphics- tp14735631p14800537.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ 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] stochastic growth rate (package popbio)
privalan wrote:
However, I cannot figure out the way to compute the asymptotic stochastic
population growth rate using “popbio”. I would like to perform a
stochastic model in which my demographic rates are sampled from beta
distribution with known mean and SD. For example, rather than 0.50 (4th
term of my matrix), I want to sample this parameter from a beta function
at each time-step {e.g., betaval(0.5, 0.05)}.
I guess you can't do this right now, but it shouldn't be too difficult to
add an option to accept an expression as input to stoch.growth.rate or
stoch.projection in the next version of popbio.
Maybe this will get you started.
A-expression(c(0.70, 0.70,0.35, betaval(0.5, 0.05)))
## stoch.growth.rate(A) ## this doesn't work yet, so try...
matrix(eval(A), nrow=2,byrow=TRUE)
## code from simulation section in stoch.growth.rate
## just replace A with matrix(eval(A), nrow=2,byrow=TRUE)
maxt-1
r-numeric(maxt)
n0-c(1,1)
for (t in 1:maxt)
{
n0- matrix(eval(A), nrow=2,byrow=TRUE) %*% n0
N-sum(n0)
r[t]-log(N)
n0-n0/N
}
loglsim-mean(r)
dse-1.96*sqrt(var(r)/maxt)
CI-c(loglsim-dse, loglsim+dse)
loglsim
#[1] 0.09982282
CI
#[1] 0.0994700 0.1001757
# check
eigen.analysis( matrix(c(0.70, 0.70,0.35,0.50), nrow=2,byrow=TRUE))$lambda1
exp(loglsim)
Thanks,
Chris
--
View this message in context:
http://www.nabble.com/stochastic-growth-rate-%28package-biopop%29-tp14800951p14806622.html
Sent from the R help mailing list archive at Nabble.com.
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[R] Ceiling to the nearest ten?
R-users, Is there a function for ceiling to the nearest ten? a - 1:10*4 a [1] 4 8 12 16 20 24 28 32 36 40 The resulting vector should look like this (ceiling to the nearest ten) [1] 10 10 20 20 20 30 30 40 40 40 Thanks in advance Lauri __ 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] Ceiling to the nearest ten?
Lauri Nikkinen wrote: R-users, Is there a function for ceiling to the nearest ten? a - 1:10*4 a [1] 4 8 12 16 20 24 28 32 36 40 The resulting vector should look like this (ceiling to the nearest ten) [1] 10 10 20 20 20 30 30 40 40 40 Divide and conquer: a [1] 4 8 12 16 20 24 28 32 36 40 ceiling(a/10)*10 [1] 10 10 20 20 20 30 30 40 40 40 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.
Re: [R] Ceiling to the nearest ten?
A suggestion for a family of such functions: ceilGenerator - function(num) function(x) num * ceiling(x / num) ceil10 - ceilGenerator(10) ceil20 - ceilGenerator(20) ceil10(1:10 * 4) ceil20(1:10 * 4) Lauri Nikkinen wrote: R-users, Is there a function for ceiling to the nearest ten? a - 1:10*4 a [1] 4 8 12 16 20 24 28 32 36 40 The resulting vector should look like this (ceiling to the nearest ten) [1] 10 10 20 20 20 30 30 40 40 40 Thanks in advance Lauri __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- View this message in context: http://www.nabble.com/Ceiling-to-the-nearest-ten--tp14806582p14806624.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] Ceiling to the nearest ten?
a - 1:10*4 ceiling(a/10)*10 [1] 10 10 20 20 20 30 30 40 40 40 -Original Message- Lauri Nikkinen Is there a function for ceiling to the nearest ten? a - 1:10*4 a [1] 4 8 12 16 20 24 28 32 36 40 The resulting vector should look like this (ceiling to the nearest ten) [1] 10 10 20 20 20 30 30 40 40 40 Thanks in advance Lauri __ 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] Ceiling to the nearest ten?
Oh, yeah, too simple... Thank you all! 2008/1/14, Richard M. Heiberger [EMAIL PROTECTED]: a - 1:10*4 ceiling(a/10)*10 [1] 10 10 20 20 20 30 30 40 40 40 -Original Message- Lauri Nikkinen Is there a function for ceiling to the nearest ten? a - 1:10*4 a [1] 4 8 12 16 20 24 28 32 36 40 The resulting vector should look like this (ceiling to the nearest ten) [1] 10 10 20 20 20 30 30 40 40 40 Thanks in advance Lauri __ 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] Ceiling to the nearest ten?
Rob Robinson wrote:
Perhaps not the most elegant but 10*ceiling(x/10) usually works for me...
I thought maybe adding five and rounding to the nearest -1 decimal
places might be quicker:
round(a+5,-1)
[1] 10 10 20 20 20 30 30 40 40 40
gives same as:
ceiling(a/10)*10
[1] 10 10 20 20 20 30 30 40 40 40
but it's not quicker:
system.time(for(i in 1:100){round(a+5,-1)})
[1] 17.505 0.116 19.538 0.000 0.000
system.time(for(i in 1:100){ceiling(a/10)*10})
[1] 5.212 0.048 5.726 0.000 0.000
which surprised me, given that the ceiling example has a multiply and a
divide to do before working out the ceiling, whereas the round just has
an add to do before working out the rounding, and I can't immediately
see why ceilinging should be faster than roundinging:
system.time(for(i in 1:100){ceiling(a)})
[1] 2.724 0.044 3.053 0.000 0.000
system.time(for(i in 1:100){round(a)})
[1] 12.397 0.092 14.339 0.000 0.000
but maybe if I think about it a bit more I'll see...
Barry
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Re: [R] Error in solve.default message using lme
What it probably means is that you can't make a silk purse out of a sow's
ear: all those missings in your your data do not allow you to estimate the
model(s) that you've specified.
If you don't know what this means, I suggest you seek the help of a local
statistician.
--
Bert Gunter
Genentech
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On
Behalf Of Leonardo
Sent: Monday, January 14, 2008 8:51 AM
To: r-help@r-project.org
Subject: [R] Error in solve.default message using lme
Dear All,
Im using lme to analyze a time series gene expression data. I dont have
all animals in all times, the number of animals in each time is different
and I have lots of NA values.
An example file can be downloaded at lbmp.fcav.unesp.br/leonardo and the
code used is the following:
teste-read.table(file='example.csv',sep=',',header=T)
B-1366
library(nlme)
pValueTime-matrix(nrow=B,ncol=2)
colnames(pValueTime)-c('geneID','pValue.Time')
for (i in 1:B) {
print(i)
gene = teste$gene [i]
keep-teste$gene==gene
MTemp =as.numeric( teste$M [keep])
timeTemp = as.factor(teste$time [keep])
animalTemp = as.factor(teste$animal [keep])
tempMM.HA-lme(MTemp~timeTemp,random=~1|animalTemp,method='ML',
na.action=na.omit)
tempMM.H0-lme(MTemp~1,random=~1|animalTemp,method='ML',
na.action=na.omit)
pValueTime[i,1]-gene
pValueTime[i,2]-anova(tempMM.HA,tempMM.H0)[2,9]
}
Im getting the following error message:
Error in solve.default(estimates[dimE[1] - (p:1), dimE[2] - (p:1), drop =
FALSE]) :
system is computationally singular: reciprocal condition number =
1.64483e-17
I dont know what this message means, so any help/suggestion will be very
appreciated.
sessionInfo()
R version 2.6.0 (2007-10-03)
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] nlme_3.1-86
loaded via a namespace (and not attached):
[1] grid_2.6.0 lattice_0.17-2 tools_2.6.0
Best regards,
Leonardo
MSc. Leonardo Bernardes da Rocha
Doctorate Student - Animal Science
Department of Tecnology
College of Agricultural and Veterinary Sciences
São Paulo State University
Jaboticabal, SP - Brazil
Phone: +55 16 32092675 (Ext. 206)
Email: [EMAIL PROTECTED]
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[R] problems with .svg
Dear everybody! I am making a graph in R and employ pstoedit to expot the .pdf-output to .svg. When I open the .svg with firefox I get the .svg-code shown wit the following header: Mit dieser XML-Datei sind anscheinend keine Style-Informationen verknüpft. Nachfolgend wird die Baum-Ansicht des Dokuments angezeigt. Which information should how be included? Thank you in advance. Yours, Mag. Ferri Leberl __ 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] problems with .svg
Are you sure this is an R problem? I guess it is not, but rather a pstoedit problem. You can use the RSVGDevice package, or the Cairo package to export your graphics directly into SVG from R. Gabor On Mon, Jan 14, 2008 at 07:10:13PM +0100, Mag. Ferri Leberl wrote: Dear everybody! I am making a graph in R and employ pstoedit to expot the .pdf-output to .svg. When I open the .svg with firefox I get the .svg-code shown wit the following header: Mit dieser XML-Datei sind anscheinend keine Style-Informationen verknüpft. Nachfolgend wird die Baum-Ansicht des Dokuments angezeigt. Which information should how be included? Thank you in advance. Yours, Mag. Ferri Leberl __ 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. -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ 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] Ceiling to the nearest ten?
On 1/14/08, Jim Price [EMAIL PROTECTED] wrote:
A suggestion for a family of such functions:
ceilGenerator - function(num)
function(x) num * ceiling(x / num)
ceil10 - ceilGenerator(10)
ceil20 - ceilGenerator(20)
ceil10(1:10 * 4)
ceil20(1:10 * 4)
libraray(reshape)
round_any(100, 40, floor)
round_any(100, 40, ceiling)
round_any(101, 40)
# in reshape package
round_any - function (x, accuracy, f = round) {
f(x/accuracy) * accuracy
}
which is a pretty similar idea.
Hadley
--
http://had.co.nz/
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[R] lm predict warning: prediction from a rank-deficient fit may be misleading
Hi all, I´m getting this warning with predict form lm.fit model, but the prediction still works. I have read some old messages, and Prof. Ripley said that the matrix is collinear. Interestingly, when i make a regression like lag2 ~ lag1 + lag0 i do not get this message. Only with higher dimensions, like lag3 ~ lag2 + lag1 + lag0. It´s difficult to me to debug, because the regression is done with 45 or more points. Any suggestion? I used SVD matrix to reduce the space dimensionality and it works fine, but i want to make lm and rlm work too. Thanks for your attention. José Augusto M. de Andrade Jr. Undergraduate Student Business Administration University of São Paulo __ 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] Is R on Windows multi-threaded
I hope to get a new version of snow released in a couple of weeks that will work on Windows using a Windows Rmpi version or, at least on a local machine, a socket interface. luke On Sat, 12 Jan 2008, Prof Brian Ripley wrote: On Fri, 11 Jan 2008, Greg Snow wrote: Someone else suggested the snow package, but I don't think it is available for windows. It is. From http://cran.r-project.org/bin/windows/contrib/2.6/ReadMe Although the packages ROracle, and snow pass make check, it seems to be dangerous to distribute them: I do not have the software available these packages depend on. It compiles from the sources, and using snow alone you can run socket clusters on Windows (by default it expects ssh to be running, and Windows machines rarely run an ssh daemon so as to accept incoming ssh). The caution is that the packages runs no tests so needs manual intervention to test it, and in particular most people will want to run snow over Rmpi which does not compile on Windows without more software (and some effort). It might be worth modifying snow to more easily run multiple processes on a single machine. I have been able to get the nws package to work on a duel core machine using windows and it did speed up my tests (and was fairly straight forward to use). Dueling cores can be apt From: [EMAIL PROTECTED] on behalf of Rees, David Sent: Fri 1/11/2008 7:28 AM To: r-help@r-project.org Subject: [R] Is R on Windows multi-threaded Hi, A previous thread suggests that R on Windows is multi-threaded http://tolstoy.newcastle.edu.au/R/help/03b/6946.html When I'm running R 2.5.1 on a dual core pc I get Rgui.exe uses up to 50% of the available cpu and the rest is not used. i.e. it only uses one cpu. I'm soon going to get a nice shiny new 8 cpu machine which it would be very nice to fully utilize. Is there any way to get R to use all the cpus - should this happen automatically? Many thanks, Regards, David [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Luke Tierney Chair, Statistics and Actuarial Science Ralph E. Wareham Professor of Mathematical Sciences University of Iowa Phone: 319-335-3386 Department of Statistics andFax: 319-335-3017 Actuarial Science 241 Schaeffer Hall email: [EMAIL PROTECTED] Iowa City, IA 52242 WWW: http://www.stat.uiowa.edu __ 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] Ceiling to the nearest ten?
Well the help page for ceiling and round states that ceiling only works
on numeric vectors, but round can work on complex vectors as well.
Perhaps the extra overhead of checking for complex numbers is part of
the extra time taken by round.
Also, ceiling rounds up to an integer, round needs to deal with the
digits specification and that will add some overhead as well.
--
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
[EMAIL PROTECTED]
(801) 408-8111
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Barry Rowlingson
Sent: Monday, January 14, 2008 10:48 AM
To: [EMAIL PROTECTED]
Cc: [EMAIL PROTECTED]; 'Lauri Nikkinen'
Subject: Re: [R] Ceiling to the nearest ten?
Rob Robinson wrote:
Perhaps not the most elegant but 10*ceiling(x/10) usually
works for me...
I thought maybe adding five and rounding to the nearest -1
decimal places might be quicker:
round(a+5,-1)
[1] 10 10 20 20 20 30 30 40 40 40
gives same as:
ceiling(a/10)*10
[1] 10 10 20 20 20 30 30 40 40 40
but it's not quicker:
system.time(for(i in 1:100){round(a+5,-1)})
[1] 17.505 0.116 19.538 0.000 0.000
system.time(for(i in 1:100){ceiling(a/10)*10})
[1] 5.212 0.048 5.726 0.000 0.000
which surprised me, given that the ceiling example has a
multiply and a divide to do before working out the ceiling,
whereas the round just has an add to do before working out
the rounding, and I can't immediately see why ceilinging
should be faster than roundinging:
system.time(for(i in 1:100){ceiling(a)})
[1] 2.724 0.044 3.053 0.000 0.000
system.time(for(i in 1:100){round(a)})
[1] 12.397 0.092 14.339 0.000 0.000
but maybe if I think about it a bit more I'll see...
Barry
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[R] multinomial confidence interval
Hi R users! Is there a function that extracts the simultaneous confidence intervals for multinomial proportions as described by Sison and Glaz 1995? or anyone else for that matter? I have seen that SAS has macro for this ( http://www.jstatsoft.org/v05/i06) and i was wondering if R had something similar? Thank you and have a great day ahead! - [[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] binning data
On 15/01/2008, at 5:13 AM, Robert Terwilliger wrote:
I would like to 'bin' a vector of of values (10 values) in much
the same way as 'hist' does for plotting, but I just want a result
with the bins and the frequencies.
Is there a 'quick and dirty' (built-in) way to do this, or do I need
to write some code?
?hist
(Hint: Look at ``Value''. Also look at the ``plot'' argument.)
cheers,
Rolf Turner
##
Attention:\ This e-mail message is privileged and confid...{{dropped:9}}
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] is it safe to replace every - by = in R code?
Thank you (all) for the helpful explanations! My own R code tends to simpler constructs, but now perhaps we can start having obfuscated code competitions: something common in Perl, but I have not seen in R (yet). Anyone up for the challenge? Best wishes, Mark -- Dr. Mark Wardle Specialist registrar, Neurology Cardiff, UK __ 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] Need help with xspline error message in R 2.6.1 on Windows XP
I am attempting to generate a series of plots with cubic B-Splines and
the code I am using is generating the following error message that I
have been unable to resolve.
Error in grid.Call.graphics(L_xspline, x$x, x$y, x$shape, x$open,
x$arrow, : add_point - reached MAXNUMPTS (25200)
This is the code that generates this error.
plot.results - function(dfn) {
dt - read.table(dfn)
shp - rep(1, as.numeric(length(dt$year)))
shp[1] - shp[as.numeric(length(dt$year))] - 0
grid.rect()
pushViewport(plotViewport(c(5.1, 4.1, 4.1, 2.1)))
pushViewport(dataViewport(dt$year, dt$mean))
grid.rect()
grid.xaxis()
grid.yaxis()
grid.points(dt$year, dt$mean, pch=16)
grid.xspline(dt$year, dt$mean, shape=shp, open=TRUE,
gp=gpar(col=red))
popViewport(2)
}
plot.results(section01_model_results.dat)
And here is the data that is being used:
year mean
1 2010 6738
2 2015 8793
3 2020 11699
4 2025 15951
5 2030 22492
6 2035 33289
7 2040 52917
I have tried changing the values in the shape vector and have noticed
that a value of 0 does not generate the error; however, it also does not
plot a line or curve. I have also tried values for the shape vector of
-1, 0.1, 0.2, and 0.5.
I think my problem may be unit related, but am unclear how to specify
that my control points are user units (or to convert user units to what
ever xspline might prefer).
Walter Anderson
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Re: [R] is it safe to replace every - by = in R code?
Jonathan Baron [EMAIL PROTECTED] writes: I think it is worth pointing out that, if you use ESS with (X)emacs, - (with spaces) is produced when you type _. It requires only two keystrokes (shift and -), and the spaces are done for you. The = sign requires three because you need to type the spaces on each side. Is there a way to turn this off? I sometimes have to use variable names with underscores in them (not by my choice) and having to defeat ESS's attempts to replace the underscores with '-' can really be annoying. -- Jeff __ 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] is it safe to replace every - by = in R code?
The answer in emacs is always Yes. Type _ twice, and it will become an underscore. See C-h k _ For the full help page. -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Jeffrey J. Hallman Is there a way to turn this off? I sometimes have to use variable names with underscores in them (not by my choice) and having to defeat ESS's attempts to replace the underscores with '-' can really be annoying. -- Jeff __ 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] Listing the data contents of a package
Hi R users, Simply question: On the command line, how do I list the datasets contained within a package, e.g. MASS? I scanned the mailing list history but was unable to find the answer. Thanks in advance. Gregory - [[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] Listing the data contents of a package
data(package=MASS) On 14/01/2008, Gregory Gentlemen [EMAIL PROTECTED] wrote: Hi R users, Simply question: On the command line, how do I list the datasets contained within a package, e.g. MASS? I scanned the mailing list history but was unable to find the answer. Thanks in advance. Gregory - [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O __ 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] Listing the data contents of a package
?data -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare [EMAIL PROTECTED] (801) 408-8111 -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Gregory Gentlemen Sent: Monday, January 14, 2008 1:18 PM To: r-help@r-project.org Subject: [R] Listing the data contents of a package Hi R users, Simply question: On the command line, how do I list the datasets contained within a package, e.g. MASS? I scanned the mailing list history but was unable to find the answer. Thanks in advance. Gregory - [[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] Need help with xspline error message in R 2.6.1 on Windows XP
Walter,
Try adding the argument default.units = native to your grid.xspline call.
Erik Iverson
Anderson, Walter wrote:
I am attempting to generate a series of plots with cubic B-Splines and
the code I am using is generating the following error message that I
have been unable to resolve.
Error in grid.Call.graphics(L_xspline, x$x, x$y, x$shape, x$open,
x$arrow, : add_point - reached MAXNUMPTS (25200)
This is the code that generates this error.
plot.results - function(dfn) {
dt - read.table(dfn)
shp - rep(1, as.numeric(length(dt$year)))
shp[1] - shp[as.numeric(length(dt$year))] - 0
grid.rect()
pushViewport(plotViewport(c(5.1, 4.1, 4.1, 2.1)))
pushViewport(dataViewport(dt$year, dt$mean))
grid.rect()
grid.xaxis()
grid.yaxis()
grid.points(dt$year, dt$mean, pch=16)
grid.xspline(dt$year, dt$mean, shape=shp, open=TRUE,
gp=gpar(col=red))
popViewport(2)
}
plot.results(section01_model_results.dat)
And here is the data that is being used:
year mean
1 2010 6738
2 2015 8793
3 2020 11699
4 2025 15951
5 2030 22492
6 2035 33289
7 2040 52917
I have tried changing the values in the shape vector and have noticed
that a value of 0 does not generate the error; however, it also does not
plot a line or curve. I have also tried values for the shape vector of
-1, 0.1, 0.2, and 0.5.
I think my problem may be unit related, but am unclear how to specify
that my control points are user units (or to convert user units to what
ever xspline might prefer).
Walter Anderson
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Re: [R] Need help with xspline error message in R 2.6.1 on Windows XP
Erik, That worked perfectly! Thank you very much! Walter Anderson -Original Message- From: Erik Iverson Sent: Monday, January 14, 2008 2:37 PM To: Anderson, Walter Cc: r-help@r-project.org Subject: Re: [R] Need help with xspline error message in R 2.6.1 on Windows XP Walter, Try adding the argument default.units = native to your grid.xspline call. Erik Iverson __ 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] Some simple questions about neural networks
Have you ever gotten any response from this post? I have similar questions regarding the AMORE package. Efferz wrote: Hi, I have some simple questions and annotations about neural networks: 1) Which R-package (or which software) would you use to train and validate a multilayer (2 hidden layers) feed forward neural network. I think AMORE is the only one that can do this task in R. 2) When using neural networks for time series prediction (macroeconomic financial time series), how would you precede to avoid overfitting? Split the sample in two subsamples, train the NN in the first subsample and then test it on the validation set? What is a good split ratio 1/2, 2/3, 3/4? Are there procedureces which endogenize this step. 3) How to select the parameters like the global.learnging.rate, the momentum.global, the activation functions of the hidden layer neurons, the training method, the n.shows and show.step numbers, the probability vector,... when setting up a neural net with AMORE or the initial weights, decay,... when setting up a neural net with NNET? Are these all econometrican choice variables and must be exogenously specified. My own experience shows that the results are far from robust and highly sensitive to an alternative parameter choice. Even when using the same parameter setup re-training and re-validation delivers different results (unless you use the set.seed command). How to get results that are replicable? I think there is a great danger of getting spurious results when snooping the parameter space. Or are there any reasons why to use a decay of 0.1 instead 0.11 or a momentum of 0.4 instead of 0.5, or ... Is it a good choice to use if possible the default values? Therefore I am very skeptical if those new and highly sophisticated non-linear methods (neural networks, svm, etc.) perform really better in time series prediction than the classical linear methods. Besides the problem which variables to use as predictors, how to choose the calibration window (rolling expanding, rolling fixed), one faces the additional choice of model parameters. How do you think about it? Any ideas? Any experiences? Best Martin [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- View this message in context: http://www.nabble.com/Some-simple-questions-about-neural-networks-tp12898957p14814193.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] barplots and missing xlabels
On 1/15/08, -Halcyon- [EMAIL PROTECTED] wrote: Hi, I'd say just stretch the plot window. The code works fine and labels are all present The labels didn't appear on my pdf output but the following code worked fine xpos-barplot(dat$Aorta,ylim=c(0,100), names=rep(,length(dat$AgeGroup)), ylab=c(Prevalence (%))) mtext(as.vector(dat$AgeGroup),1,2,at=xpos) Many thanks, Geoff. Gz Jim Lemon-2 wrote: Geoff Russell wrote: Dear useRs, The following plots only print 2 of the 4 labels under the bars, is there a way please to force all 4 labels to print? par(mfrow=c(1,2),mar=c(2,7,3,1)) dat-data.frame(AgeGroup=c(2-15,16-20,21-25,26-39), Aorta=c(20,8,30,60), Coronary=c(7,30,55,65)) barplot(dat$Aorta,ylim=c(0,100),names=as.vector(dat$AgeGroup),ylab=c(Prevalence (%))) title(main=list(Aorta,font=0)) barplot(dat$Coro,names=as.vector(dat$Age),ylim=c(0,100)) title(main=list(Coronary Artery,font=0)) Hi Geoff, Try this: barplot(dat$Aorta,ylim=c(0,100), names=rep(,length(dat$AgeGroup)), ylab=c(Prevalence (%))) mtext(dat$AgeGroup,1,2) 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. -- View this message in context: http://www.nabble.com/barplots-and-missing-xlabels-tp14796430p14802702.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. -- 6 Fifth Ave, St Morris, S.A. 5068 Australia Ph: 041 8805 184 / 08 8332 5069 __ 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] savehistory in OSX version
Thanks, Rob, I'm still unsure on the key question. Is there any way in R.app to save the commands run in the Console into a *.history or .Rhistory file, by running a command on the Console, whether savehistory() or some other function call? (I'm trying to semi-automate a regular backup procedure while in a very long interactive session at risk of hanging.) Can you say more what you mean by interoperate here? Roger -Original Message- From: Rob Goedman [mailto:[EMAIL PROTECTED] Sent: Monday, January 14, 2008 10:21 AM To: Day, Roger S. Cc: r-help@r-project.org Subject: Re: [R] savehistory in OSX version Roger, The history features on Mac OS's R.app are handled by R.app and is a (small) superset of R's facilties, e.g. it supports multi-line history recalls. A disadvantage of this approach is that it's not possible to use R's history() and savehistory() nor make usage completely identical. The actual history files do 'interoperate', although you will loose the multiline feature. A good list for Mac OS specific discussions is [EMAIL PROTECTED] Hope this helps, Rob On Jan 13, 2008, at 6:47 PM, Day, Roger S. wrote: Running Version 2.6.0 GUI 1.21. Generally, I enjoy working with the OSX GUI, which has some very pleasant features. Kudos to the developers! There is a nice history panel which slides out of the Console window. The buttons on the panel work as expected. I am puzzled by the behavior of history() and savehistory() run from the Console window. I would think that these functions would view and save the same set of commands as those seen in the history panel, but they don't. Can someone explain why, and how to fix it? Perhaps relevant: I generally have performed a setwd() , or started R by launching a Rdata file. Thanks. Roger Day University of Pittsburgh Departments of Biomedical Informatics and Biostatistics University of Pittsburgh Cancer Institute University of Pittsburgh Molecular Medicine Institute ** Room 310, Suite 301 Cancer Pavilion (CNPAV) 5150 Centre Ave. Pittsburgh, PA 15232 e-mail: [EMAIL PROTECTED] cell phone 412-609-3918 assistant: Lucy Cafeo: (412) 623-2952 *** [[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] R from within a web page
Hi all , I need to create some graphics from/for an Apache server . With php I extract data from a PostgreSQL db , and i'd like to create some graphic from the data . I have 2 questions : 1) I've tried with an exec(/usr/local/bin/R --vanilla myfile.R) and exec(/usr/local/bin/R --no-save myfile.R myfile.out.R ) . Both command work from a shell but not called from within a php page . Myfile.R is generated by the php code and is actually something like this : y - c(16.0938,16.1562,16.0938,16.1875,[...]); x-c(0.29,0.34,0.39,0.44,0.49,0.54,0.59,[...]); png(file=/var/www/htdocs/temp.png,bg=transparent); plot(x,y,type=h,col=2,xlab=Time,ylab=Temperature,lwd=3); dev.off() The resulting image is 0 byte . 2)One axis represent time , so actually I have some empties spaces ( when I execute myfile.R from shell ) because the graphic is built in 100 basis and not 60 . Could someone please help ? Thx in advance David __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Problem using ROracle
Hi, I am trying to use ROracle installed on a Solaris (i386 platform) with Oracle client 10.2. The installation took quite some troubleshooting, but eventually I could load ROracle library from R, but here is the trace and error: library(ROracle) Loading required package: DBI drv-dbDriver(Oracle) con-dbConnect(drv,username/[EMAIL PROTECTED]) Error in oraNewConnection(drv, ...) : RS-DBI driver: (ORA-12154: TNS:could not resolve the connect identifier specified) However, when I try to connect to oracle thru sqlplus, I have no problem: sqlplus username/[EMAIL PROTECTED] would work, I could retrieve data from the database. By google this error, I was trying everything in TNSNAMES.ORA file, I tried a numeric ip, tried directly copy the connection string from TNSNAMES.ORA, none seems to work. Also, error messages will be recorded in sqlnet.log if I use sqlplus and intentionally use a wrong connection string. But with the ROracle error message above, it is not recoded in sqlnet.log. Can some guru help? Thanks I advance. Shuping Zhang [[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] Listing the data contents of a package
Dear Gregory, data(package=MASS) will do what you want. Regards, John On Mon, 14 Jan 2008 15:17:54 -0500 (EST) Gregory Gentlemen [EMAIL PROTECTED] wrote: Hi R users, Simply question: On the command line, how do I list the datasets contained within a package, e.g. MASS? I scanned the mailing list history but was unable to find the answer. Thanks in advance. Gregory __ 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] Heatmap problem
Hi all, I am making a heatmap using gplots. I have two problems; a solution to any one will be greatly appreciated: 1. I have a file with genes and samples from two groups of patients. I don't want to cluster samples; just the genes. The samples should stay in the same order as in the datafile. Any way to do this? 2. Or, I can split the datafile into the two patient groups and make heatmaps and present two pictures, but the ranges of values are different. Therefore, I want to adjust the range on the color key to be the same in both heatmaps. That is, instead of being 0 to 800 and 0 to 1500, both should have 0 to 1500. Please help!! Many thanks, -Davendra Sohal, MD, MPH Research Fellow Albert Einstein College of Medicine, Bronx, NY, USA. [[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] re adline detection problems
I ran into identical readline problems. For me appealing to the sysadmin to install readline correctly with rpms or the like was not an option. I needed a personal copy of R which I could update and add packages to at my own discretion. So I 1. got readline 5.2 from gnu.org. 2. From readline extracted distribution root folder, called ./configure --prefix=/myreadlinehome; make; make install 3. From R extracted distribution root folder, executed the following configure command ./configure LDFLAGS=-L/myreadlinehome/lib --prefix=/myrhome CPPFLAGS=-I/myreadlinehome/include/ Performing those steps allowed me to build a version of R with all the familiar up/down arrow tab completion etc. -- View this message in context: http://www.nabble.com/readline-detection-problems-tp2719581p14816968.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] Loading only particular columns from csv file...
Dear all,
I'm trying to process HUGE datasets with R. It's very fast, but I would like
to optimize it a bit more, by focusing one one column at time. say file
is 1GB big and has 100 columns. In order to prevent out of memory
problems I need to load one column at the time the only problem is
that read.table doesn't support this feature
Is there some thick which will do the magic?
Thank you in advance.
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Re: [R] Loading only particular columns from csv file...
See the colClasses= argument of read.table where you can use NULL.
On Jan 14, 2008 6:02 PM, Marko Milicic [EMAIL PROTECTED] wrote:
Dear all,
I'm trying to process HUGE datasets with R. It's very fast, but I would like
to optimize it a bit more, by focusing one one column at time. say file
is 1GB big and has 100 columns. In order to prevent out of memory
problems I need to load one column at the time the only problem is
that read.table doesn't support this feature
Is there some thick which will do the magic?
Thank you in advance.
--
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Re: [R] R from within a web page
Hello Professor Ripley Have you read ?png ? You almost certainly don't have an X11 server accessible, and alternatives are described there. There ? 2)One axis represent time , so actually I have some empties spaces ( when I execute myfile.R from shell ) because the graphic is built in 100 basis and not 60 . I don't even understand the words here. I'm sorry but I'm not a native english speaker ... so maybe I was not very clear ... I'll try again . The axis represents values from 1 to 100 , while I use just values from 1 to 60 ( 1 hour ) . So I get white spaces for those 40 values left . David __ 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] plot POSIXct format data
Hi, everyone I've been trying to make a scatter plot of POSIXct format data to see the difference between two start time. Like X: [1] 1995-05-26 19:00:00 1995-05-27 01:00:00 1995-05-27 07:00:00 [4] 1995-06-29 01:00:00 1995-06-29 07:00:00 1995-06-30 13:00:00 [7] 1995-06-30 19:00:00 1995-07-01 01:00:00 1995-07-01 07:00:00 .. Y: [1] 1995-05-26 19:00:00 1995-05-27 01:00:00 1995-05-27 07:00:00 [4] 1995-06-29 01:00:00 1995-06-29 07:00:00 1995-06-30 13:00:00 [7] 1995-06-30 19:00:00 1995-07-01 01:00:00 1995-07-01 07:00:00 ... But it seems plot(x,y) doesn't work, y have to be numeric format. Is there any special command for that or I should change the format of the data? Thanks Jingru Dai School of Mathematical Sciences Rm 454, Building 28 Monash University, 3800 Victoria, Australia __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R from within a web page
On Tue, 15 Jan 2008, David Galligani wrote: Hello Professor Ripley Have you read ?png ? You almost certainly don't have an X11 server accessible, and alternatives are described there. There ? On the web page. 2)One axis represent time , so actually I have some empties spaces ( when I execute myfile.R from shell ) because the graphic is built in 100 basis and not 60 . I don't even understand the words here. I'm sorry but I'm not a native english speaker ... so maybe I was not very clear ... I'll try again . The axis represents values from 1 to 100 , while I use just values from 1 to 60 ( 1 hour ) . So I get white spaces for those 40 values left . Without knowing how you got 100 David -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] plot POSIXct format data
When I try this: x - as.POSIXct(Sys.Date() + 0:9) plot(x, x) plot(x ~ x) The first one does give me dates on both axes but the second one gives numbers on the Y axis. Note that you can always not print the axis with plot and then do it yourself with axis or Axis. This works for me: plot(x ~ x, yaxt = n) Axis(x, side = 2) R.version.string # Windows Vista [1] R version 2.6.1 Patched (2007-12-06 r43610) On Jan 14, 2008 6:37 PM, Jingru Dai [EMAIL PROTECTED] wrote: Hi, everyone I've been trying to make a scatter plot of POSIXct format data to see the difference between two start time. Like X: [1] 1995-05-26 19:00:00 1995-05-27 01:00:00 1995-05-27 07:00:00 [4] 1995-06-29 01:00:00 1995-06-29 07:00:00 1995-06-30 13:00:00 [7] 1995-06-30 19:00:00 1995-07-01 01:00:00 1995-07-01 07:00:00 .. Y: [1] 1995-05-26 19:00:00 1995-05-27 01:00:00 1995-05-27 07:00:00 [4] 1995-06-29 01:00:00 1995-06-29 07:00:00 1995-06-30 13:00:00 [7] 1995-06-30 19:00:00 1995-07-01 01:00:00 1995-07-01 07:00:00 ... But it seems plot(x,y) doesn't work, y have to be numeric format. Is there any special command for that or I should change the format of the data? Thanks Jingru Dai School of Mathematical Sciences Rm 454, Building 28 Monash University, 3800 Victoria, Australia __ 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] savehistory in OSX version
Roger, On Jan 14, 2008, at 1:14 PM, Day, Roger S. wrote: Thanks, Rob, I'm still unsure on the key question. Is there any way in R.app to save the commands run in the Console into a *.history or .Rhistory file, by running a command on the Console, whether savehistory() or some other function call? Right now, there isn't in R.app. (I'm trying to semi-automate a regular backup procedure while in a very long interactive session at risk of hanging.) Can you say more what you mean by interoperate here? The history file is updated on exiting R, which is clearly of no use to you. The updated history file can be read by both R and R.app, this is the interoperable part. If I recall correctly (it has been a few years!), to do what you need, would require a call back from R. I seem to remember this would not be hard to do but at that time was not available. Don't think it is today either. A possible approach is to run long interactive sessions from within the editor. Add a couple of statements and submit selection to R. If you're using the internal editor, save the file before submitting. From within an external editor, saving is less critical. Rob Roger -Original Message- From: Rob Goedman [mailto:[EMAIL PROTECTED] Sent: Monday, January 14, 2008 10:21 AM To: Day, Roger S. Cc: r-help@r-project.org Subject: Re: [R] savehistory in OSX version Roger, The history features on Mac OS's R.app are handled by R.app and is a (small) superset of R's facilties, e.g. it supports multi-line history recalls. A disadvantage of this approach is that it's not possible to use R's history() and savehistory() nor make usage completely identical. The actual history files do 'interoperate', although you will loose the multiline feature. A good list for Mac OS specific discussions is [EMAIL PROTECTED] project.org. Hope this helps, Rob On Jan 13, 2008, at 6:47 PM, Day, Roger S. wrote: Running Version 2.6.0 GUI 1.21. Generally, I enjoy working with the OSX GUI, which has some very pleasant features. Kudos to the developers! There is a nice history panel which slides out of the Console window. The buttons on the panel work as expected. I am puzzled by the behavior of history() and savehistory() run from the Console window. I would think that these functions would view and save the same set of commands as those seen in the history panel, but they don't. Can someone explain why, and how to fix it? Perhaps relevant: I generally have performed a setwd() , or started R by launching a Rdata file. Thanks. Roger Day University of Pittsburgh Departments of Biomedical Informatics and Biostatistics University of Pittsburgh Cancer Institute University of Pittsburgh Molecular Medicine Institute ** Room 310, Suite 301 Cancer Pavilion (CNPAV) 5150 Centre Ave. Pittsburgh, PA 15232 e-mail: [EMAIL PROTECTED] cell phone 412-609-3918 assistant: Lucy Cafeo: (412) 623-2952 *** [[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] Loading only particular columns from csv file...
On Mon, 14 Jan 2008, Marko Milicic wrote:
Dear all,
I'm trying to process HUGE datasets with R. It's very fast, but I would like
to optimize it a bit more, by focusing one one column at time. say file
is 1GB big and has 100 columns. In order to prevent out of memory
problems I need to load one column at the time the only problem is
that read.table doesn't support this feature
Is there some thick which will do the magic?
There is a unix utility called 'cut' that enables stuff like
columns.1.3.5.to.7 - read.table( pipe( cut -f1,3,5-7 myfile ) )
and if you have numeric data only, using scan() directly will save some space.
HTH,
Chuck
Thank you in advance.
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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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Re: [R] plot POSIXct format data
On Tue, 15 Jan 2008, Jingru Dai wrote: Hi, everyone I've been trying to make a scatter plot of POSIXct format data to see the difference between two start time. Like X: [1] 1995-05-26 19:00:00 1995-05-27 01:00:00 1995-05-27 07:00:00 [4] 1995-06-29 01:00:00 1995-06-29 07:00:00 1995-06-30 13:00:00 [7] 1995-06-30 19:00:00 1995-07-01 01:00:00 1995-07-01 07:00:00 .. Y: [1] 1995-05-26 19:00:00 1995-05-27 01:00:00 1995-05-27 07:00:00 [4] 1995-06-29 01:00:00 1995-06-29 07:00:00 1995-06-30 13:00:00 [7] 1995-06-30 19:00:00 1995-07-01 01:00:00 1995-07-01 07:00:00 ... But it seems plot(x,y) doesn't work, y have to be numeric format. Is there any special command for that or I should change the format of the data? It's possible, but there is not a canned solution. You could look at the code of graphics:::plot.POSIXct and modify to treat x the same way as y. Or simply use plot(x,y, xaxt=n, yaxt=n) axis.POSIXct(1, x) axis.POSIXct(2, y) Thanks Jingru Dai School of Mathematical Sciences Rm 454, Building 28 Monash University, 3800 Victoria, Australia -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Overlay plots from different data sets using the Lattice package
#After spending the entire day working on this question, I have
decided to reach out for support:
#I am trying to overlay a densityplot from one data set over a
histogram of another, if I were to plot the two individually, they
would look like:
# data frame construction
data.frame.A - data.frame(rnorm(12*8), c(rep(one, 4), rep(two,
4), rep(three, 4)), c(red, orange, yellow, green))
names(data.frame.A) - c(vals, factor.1, factor.2)
data.frame.B - data.frame(rnorm(12*15), c(rep(one, 4), rep(two,
4), rep(three, 4)), c(red, orange, yellow, green))
names(data.frame.B) - names(data.frame.A)
# stand alone plots
histogram(~ vals|factor.1*factor.2, data.frame.A, type = density)
densityplot(~ vals | factor.1*factor.2, data.frame.B, plot.points = F)
# I found http://www.ats.ucla.edu/STAT/R/faq/overlay_trellis.htm
xyplot(write~read | ses.f, hsb2,
panel=function(x, y, subscripts){
panel.xyplot(x, y, pch=16)
panel.lmline(x, y, lty=4)
panel.xyplot(hsb2$science[subscripts], hsb2$math[subscripts], pch=3)
panel.lmline(hsb2$science[subscripts], hsb2$math[subscripts])
}, as.table=T, subscripts=T)
# but it seems that the overlay only works in cases where the data
comes from the same data.frame and has the same subscripting.
# I have attempted a variety of incarnations of:
histogram(~ vals|factor.1*factor.2, data.frame.A, type = density,
panel=function(x, ...){
panel.histogram(x,...)
panel.densityplot(~ vals | factor.1*factor.2, data.frame.B,
plot.points = F) })
# which obviously doesn't work.
# I'm not sure if the problem lies in my poor understanding of writing
functions or my poor understanding of Lattice. Is it indeed possible?
# Thank you for your time.
# Erin
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Re: [R] Overlay plots from different data sets using the Lattice package
On Jan 14, 2008 7:30 PM, Erin Steiner [EMAIL PROTECTED] wrote: #After spending the entire day working on this question, I have decided to reach out for support: #I am trying to overlay a densityplot from one data set over a histogram of another, if I were to plot the two individually, they would look like: # data frame construction data.frame.A - data.frame(rnorm(12*8), c(rep(one, 4), rep(two, 4), rep(three, 4)), c(red, orange, yellow, green)) names(data.frame.A) - c(vals, factor.1, factor.2) data.frame.B - data.frame(rnorm(12*15), c(rep(one, 4), rep(two, 4), rep(three, 4)), c(red, orange, yellow, green)) names(data.frame.B) - names(data.frame.A) # stand alone plots histogram(~ vals|factor.1*factor.2, data.frame.A, type = density) densityplot(~ vals | factor.1*factor.2, data.frame.B, plot.points = F) It isn't lattice, but this is pretty easy to do with ggplot2: install.packages(ggplot2) library(ggplot2) qplot(vals, ..density.., data = data.frame.A, geom=histogram, facets = factor.1 ~ factor.2, binwidth = 1) + geom_density(data=data.frame.B) In ggplot2, every layer on the plot can have a different dataset. You can find out more about ggplot2 at http://had.co.nz/ggplot2/, but I'm still working on the documentation for these more advanced features. 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] Overlay plots from different data sets using the Lattice package
On 1/14/08, Erin Steiner [EMAIL PROTECTED] wrote:
#After spending the entire day working on this question, I have
decided to reach out for support:
#I am trying to overlay a densityplot from one data set over a
histogram of another, if I were to plot the two individually, they
would look like:
# data frame construction
data.frame.A - data.frame(rnorm(12*8), c(rep(one, 4), rep(two,
4), rep(three, 4)), c(red, orange, yellow, green))
names(data.frame.A) - c(vals, factor.1, factor.2)
data.frame.B - data.frame(rnorm(12*15), c(rep(one, 4), rep(two,
4), rep(three, 4)), c(red, orange, yellow, green))
names(data.frame.B) - names(data.frame.A)
The first step would be to combine the two data sources:
df.comb - make.groups(data.frame.A, data.frame.B)
I would then just overlay two density plots:
densityplot(~vals | factor.1 * factor.2, df.comb,
groups = which, plot.points=FALSE,
auto.key = TRUE)
but you could do a histogram and a densityplot too:
histogram(~vals | factor.1 * factor.2, df.comb,
type = density,
groups = which,
panel = panel.superpose,
panel.groups = function(x, group.number, col, ...) {
if (group.number == 1)
panel.histogram(x, ...)
else
panel.densityplot(x, ..., plot.points = FALSE)
})
-Deepayan
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Re: [R] plot POSIXct format data
Hi, Gabor It works now, thanks. The tricky part is I imported my data from Excel and converted the data into POSIXct format using command strptime(). So I thought they were already converted into dates and times class. I added as.POSIct, now it works alright. Thanks for that Gabor Grothendieck wrote: When I try this: x - as.POSIXct(Sys.Date() + 0:9) plot(x, x) plot(x ~ x) The first one does give me dates on both axes but the second one gives numbers on the Y axis. Note that you can always not print the axis with plot and then do it yourself with axis or Axis. This works for me: plot(x ~ x, yaxt = n) Axis(x, side = 2) R.version.string # Windows Vista [1] R version 2.6.1 Patched (2007-12-06 r43610) On Jan 14, 2008 6:37 PM, Jingru Dai [EMAIL PROTECTED] wrote: Hi, everyone I've been trying to make a scatter plot of POSIXct format data to see the difference between two start time. Like X: [1] 1995-05-26 19:00:00 1995-05-27 01:00:00 1995-05-27 07:00:00 [4] 1995-06-29 01:00:00 1995-06-29 07:00:00 1995-06-30 13:00:00 [7] 1995-06-30 19:00:00 1995-07-01 01:00:00 1995-07-01 07:00:00 .. Y: [1] 1995-05-26 19:00:00 1995-05-27 01:00:00 1995-05-27 07:00:00 [4] 1995-06-29 01:00:00 1995-06-29 07:00:00 1995-06-30 13:00:00 [7] 1995-06-30 19:00:00 1995-07-01 01:00:00 1995-07-01 07:00:00 ... But it seems plot(x,y) doesn't work, y have to be numeric format. Is there any special command for that or I should change the format of the data? Thanks Jingru Dai School of Mathematical Sciences Rm 454, Building 28 Monash University, 3800 Victoria, Australia __ 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] navigating ggplot viewports
list(...) I can not get at the grid viewports in a ggplot2 plot. I know there is supposed to be a viewport called panel_1_1 but downViewport() can't find it. Has the viewport been popped? I had a quick look at the functions involved (eg ggplot_plot) but there is no obvious problem there. library(ggplot2) qplot(1:10, 1:10) current.viewport() viewport[ROOT] downViewport(panel_1_1) Error in downViewport.vpPath(vpPathDirect(name), strict, recording = recording) : Viewport 'panel_1_1' was not found current.vpTree() viewport[ROOT]-(viewport[GRID.VP.1]) grid.ls(viewports=T, grob=F) ROOT GRID.VP.2 1 GRID.VP.3 layout strip_h_1_1 1 strip_v_1_1 1 axis_h_1_1 1 axis_v_1_1 1 panel_1_1 2 layout panel_1_1 2 layout axis_v_1_1 left_axis labels 1 ticks 2 left_axis ticks 2 left_axis labels 2 2 layout axis_h_1_1 bottom_axis labels 1 ticks 2 bottom_axis ticks 2 bottom_axis labels 2 2 layout panel_1_1 2 layout panel_1_1 2 layout panel_1_1 2 1 GRID.VP.4 1 GRID.VP.5 1 GRID.VP.6 1 sessionInfo() R version 2.6.1 (2007-11-26) i386-pc-mingw32 locale: LC_COLLATE=English_Australia.1252;LC_CTYPE=English_Australia.1252;LC_MONETARY=English_Australia.1252;LC_NUMERIC=C;LC_TIME=English_Australia.1252 attached base packages: [1] splines grid stats graphics grDevices utils datasets [8] methods base other attached packages: [1] ggplot2_0.5.7 colorspace_0.95RColorBrewer_1.0-2 MASS_7.2-38 [5] proto_0.3-8reshape_0.8.0 loaded via a namespace (and not attached): [1] tools_2.6.1 -- Felix Andrews / 安福立 PhD candidate Integrated Catchment Assessment and Management Centre The Fenner School of Environment and Society The Australian National University (Building 48A), ACT 0200 Beijing Bag, Locked Bag 40, Kingston ACT 2604 http://www.neurofractal.org/felix/ 3358 543D AAC6 22C2 D336 80D9 360B 72DD 3E4C F5D8 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] how to go to a line in R
Hi, List When I was writing R code, I notice that there is no number indicating how many lines of codes you are writing. Is there a way to go to a line with defined number? say I want to go to the 20th line. Thanks, Jack [[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] unload reload a (new version of a) package
On 14/01/2008, hadley wickham [EMAIL PROTECTED] wrote: On Jan 14, 2008 5:48 PM, Harte, Thomas P [EMAIL PROTECTED] wrote: i'm putting the final touches on a package that i'm developing and i noticed that if i detach the package, and then re-build re-install it (using R CMD) then I can't get the newer version of the package to load in the existing R session (i have to close it out and start a new session, then the newer version of the package is loaded). looking through the source of 'detach' i see : .Call(R_lazyLoadDBflush, paste(libpath, /R/, pkgname, .rdb, sep = ), PACKAGE = base) is there some absolute way similar to the above to flush the package db and ensure that a newer version of the package can be loaded into the existing R session? detach calls .Last.lib and seems to go through the motions of purging the loaded package; why, then, is the package still lurking around in the existing R session? For testing, I usually just resource all of my code: lapply(dir(~/documents/ggplot/ggplot/R, full.name=T), source) obviously it's no good for testing data, namespaces or compiled code, but 95% of the time it's good enough for me. In R.utils, there is sourceDirectory(), which in turn calls sourceTo() on each file, and it (actually the latter) takes an argument 'modifiedOnly' that allows you to only source those files modified since last time you source them, e.g. sourceDirectory(~/documents/ggplot/ggplot/R, modifiedOnly=TRUE) /Henrik 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. __ 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] Retrieve results from chisq.test programmatically
Hi, Coyne chisq.test(x)$p.value can retrieve the p-value of the test. chisq.test(x)$statistic will give you the x-squared result, if you only want the number chisq.test(x)$statistic[[1]] can retrieve the numeric value. So you can simply write a loop to do the test and save the results in some matrix. I hope it helps Jingru Dai My Coyne wrote: Hello, I would like to run a series of chisq.test() and store results (x-square, df, p-value) in a matrix for further analysis, but don't know how to do such. Currently I run the command line for each set of data at a time and it is time consuming. Thank you for your help. --My Coyne [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Retrieve results from chisq.test programmatically
Thanks a bunch. -Original Message- From: Jingru Dai [mailto:[EMAIL PROTECTED] Sent: Monday, January 14, 2008 10:25 PM To: [EMAIL PROTECTED]; r-help@r-project.org Subject: Re: [R] Retrieve results from chisq.test programmatically Hi, Coyne chisq.test(x)$p.value can retrieve the p-value of the test. chisq.test(x)$statistic will give you the x-squared result, if you only want the number chisq.test(x)$statistic[[1]] can retrieve the numeric value. So you can simply write a loop to do the test and save the results in some matrix. I hope it helps Jingru Dai My Coyne wrote: Hello, I would like to run a series of chisq.test() and store results (x-square, df, p-value) in a matrix for further analysis, but don't know how to do such. Currently I run the command line for each set of data at a time and it is time consuming. Thank you for your help. --My Coyne [[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] EMACS and ESS
Fedora Linux 8
R 2.6.1
Intel CPU
I am trying to get started with R under Linux. It has been suggested to me that
I run R under EMACS. I have looked at the CRAN website, and several other
places to try to find an RPM for EMACS and, if I need it for ESS. I have not
succeeded in finding one. Can someone tell me where to go to get the RPMs? If
anyone would have a suggestion for an editor other than EMACS to use with R, I
would appreciate any suggestions.
Thanks,
John
John Sorkin M.D., Ph.D.
Chief, Biostatistics and Informatics
University of Maryland School of Medicine Division of Gerontology
Baltimore VA Medical Center
10 North Greene Street
GRECC (BT/18/GR)
Baltimore, MD 21201-1524
(Phone) 410-605-7119
(Fax) 410-605-7913 (Please call phone number above prior to faxing)
Confidentiality Statement:
This email message, including any attachments, is for th...{{dropped:6}}
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[R] In chisq.test(x) : Chi-squared approximation may be incorrect
Hello, I received the following warning when running chi-square; n Is there a way to catch the 'error' code of 'warning' after run chisq.test(x)? n What does this error mean? Thank you for your help. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Help with the generic function [
Hello Everyone:
I'm hoping to get some suggestions on this problem i'm having with
subsetting on an R object i've created. I would really appreciate any advice.
I've created this simple S3 class:
str(ans)
Class 'myObj' atomic [1:45000] 0.0428 0.0423 0.0554 0.0338 0.0345 ...
..- attr(*, Size)= int 10
..- attr(*, Region)= chr EXON
I create instances of this class by doing something like this:
ans - structure(x,class=myObj, Size=length(i), Region=attr(x,UTR))
where x is a vector of reals.
When I subset it via ans[c(2,3,4),c(2,4,8)] I get the result I want (my
subsetting works as if its a two dimensional object for reasons I'll omit
since I don't think its pertinent to the problem).
I've written my subsetting code in C, so my R function is basically just a
wrapper function to a .Call.
[.myObj - function(x, i=NA, j=NA, ...){
.. do some parameter checking...
.. then pass the data on to my C routine...
ans - .Call(foo,as.numeric(x),as.integer(i),as.integer(j))
ans - structure(ans,class=myObj, Size=length(i), Region=attr(x,UTR))
return(ans)
}
One of my main goals is to do this subsetting quickly (which is why i do
the subsetting in C) However, when I look at my results returned from
summaryRprof I see these 3 lines that are troubling:
$by.total
total.time total.pct self.time self.pct
[41.54 50.3 0.22 0.3
[.myObj 41.32 50.0 0.32 0.4
as.numeric 38.58 46.7 38.58 46.7
these times are much much longer than they should be. I'm not sure why [
is called twice.
I'm guessing that its being called once for the myObj class, and once for
the underlying atomic structure of a vector of reals.
I've been looking at this issue for a while and trying to mimic other
subsetting packages but with no luck. I think the solution involves
understanding NextMethod([) but then again I'm not so sure.
Again, I really appreciate any comments or advice!
Thanks a bunch,
Greg W.
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