Re: [R] searching R-help within a function
Olivia Lau wrote:
Hi,
I am working on a package which requires separate documentation
(tutorial documentation, really, with a lot of beautifully
latexed equations), and does not use R-help. I am trying to
make it so that my help function will automatically search
R-help if the help topic isn't found in my documentation.
The function looks something like this:
help.pkg - function(topic) {# where the topic is a
character string
url - NULL
if(is.character(topic)) {
. # assignments for the URL given the topic
}
if (is.null(url)) {
topic - as.name(topic)
help(topic)
}
}
In the last line, help(topic) returns that there is no help for
topic. I have also tried various permutations of
substitute(help(topic)) and eval() to no avail.
do.call(help, list(topic))
Uwe Ligges
Any suggestions are greatly appreciated. Thanks,
Olivia Lau.
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Re: [R] Managing a list with a list
[EMAIL PROTECTED] wrote: OK. Another amateur question. I have a list with attributes on pine trees, like the stem's location, a logical value set to T if it's alive, some parameters for growth, diameter, etc. The tree list has another list in it which is a new data type for me. I want to make a new list that retains all the live trees. That is where Living == T. Here's the summary of the list: summary(tf) Length Class Mode id 10 -none- numeric x 10 -none- numeric y 10 -none- numeric A 10 -none- numeric NegB 10 -none- numeric K 10 -none- numeric Age10 -none- numeric DBH10 -none- numeric Living 10 -none- logical pSeed 10 -none- list TCI10 -none- numeric STA10 -none- numeric Here are the living trees. tf$Living [1] FALSE TRUE TRUE TRUE TRUE TRUE TRUE FALSE TRUE TRUE So, here are the ids of the trees I want to retain. tf$id[tf$Living == T] lapply(tf, [, tf$Living) selects (by indexing with []) those elements from each element of tf, where tf$Living is TRUE. Uwe Ligges [1] 2 3 4 5 6 7 9 10 Same with the easting coordinates. tf$x[tf$Living == T] #tf[[2]][tf$Living == T] [1] 28 35 18 34 36 92 3 47 But when I try to keep the whole list minus the dead trees it returns a list with all the trees living and dead (as I'm sure it is supposed to): tf[tf$Living == T] What am I doing wrong? I'm happy to RTFM, but if the manual in question is section 3.4 of R-lang then I'm still going to need help. I can break it all apart and then concatonate a new list but that seems heavy handed. Thanks, Andy __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] R Production Performance
Zitan Broth wrote: Greetings All, Been playing with R and it is very easy to get going with the UI or infile batch commands :-) What I am wondering is how scalable and fast R is for running as part of a web service. I believe R is written in C which is a great start, but what are peoples general thoughts on this? Thanks greatly, Z. I use R in such a way. R is called by dynamic pages written in PHP, performs a calculation and writes results in a XML file. Results are then read by other pages. Performances still could be better but I haven't tried every solution yet (RSOAP seems very interesting). MySQL database access is made thanks to RMySQL. Anyway, R is not incompatible with such projects. __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
[R] Plotting of the lm
Hi, I would like to enquire if by typing plot (lm(y~x)) would this show me the plot of the fitted line? I tried this function previously but I was only able to get the last 4 plots starting with Residuals vs fitted. Thank You. Melissa JLT Risk Solutions Ltd 6 Crutched Friars, London EC3N 2PH. Co Reg No 1536540 Tel: (44) (0)20 7528 4000 Fax: (44) (0)20 7528 4500 http://www.jltgroup.com Lloyd's Broker. Regulated by the General Insurance Standards Council The content of this e-mail (including any attachments) as received may not be the same as sent. If you consider that the content is material to the formation or performance of a contract or you are otherwise relying upon its accuracy, you should consider requesting a copy be sent by facsimile or normal mail. The information in this e-mail is confidential and may be legally privileged. If you are not the intended recipient, please notify the sender immediately and then delete this e-mail entirely - you must not retain, copy, distribute or use this e-mail for any purpose or disclose any of its content to others. Opinions, conclusions and other information in this e-mail that do not relate to the official business of JLT Risk Solutions Ltd shall be understood as neither given nor endorsed by it. Please note we intercept and monitor incoming / outgoing e-mail and therefore you should neither expect nor intend any e-mail to be private in nature. We have checked this e-mail for viruses and other harmful components and believe but not guarantee it virus-free prior to leaving our computer system. However, you should satisfy yourself that it is free from harmful components, as we do not accept responsibility for any loss or damage it may cause to your computer systems. __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
[R] filled.contour without box
Dear all, I would like to make a filled contour plot without the box R is generating by default around the plotting area, i.e. I'm looking for an option in filled.contour similar to 'axes=F' in 'contour' or in 'plot'. I couldn't find any option to get rid of the box, any help is welcome. Thanks, Jan:-) __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] Plotting of the lm
[EMAIL PROTECTED] wrote: Hi, I would like to enquire if by typing plot (lm(y~x)) would this show me the plot of the fitted line? I tried this function previously but I was only able to get the last 4 plots starting with Residuals vs fitted. No, it shows plots for analyses of the residuals. Try plot(x, y) abline(lm(y~x)) in order to see the fitted line. Uwe Ligges Thank You. Melissa JLT Risk Solutions Ltd 6 Crutched Friars, London EC3N 2PH. Co Reg No 1536540 Tel: (44) (0)20 7528 4000 Fax: (44) (0)20 7528 4500 http://www.jltgroup.com Lloyd's Broker. Regulated by the General Insurance Standards Council The content of this e-mail (including any attachments) as received may not be the same as sent. If you consider that the content is material to the formation or performance of a contract or you are otherwise relying upon its accuracy, you should consider requesting a copy be sent by facsimile or normal mail. The information in this e-mail is confidential and may be legally privileged. If you are not the intended recipient, please notify the sender immediately and then delete this e-mail entirely - you must not retain, copy, distribute or use this e-mail for any purpose or disclose any of its content to others. Opinions, conclusions and other information in this e-mail that do not relate to the official business of JLT Risk Solutions Ltd shall be understood as neither given nor endorsed by it. Please note we intercept and monitor incoming / outgoing e-mail and therefore you should neither expect nor intend any e-mail to be private in nature. We have checked this e-mail for viruses and other harmful components and believe but not guarantee it virus-free prior to leaving our computer system. However, you should satisfy yourself that it is free from harmful components, as we do not accept responsibility for any loss or damage it may cause to your computer systems. __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] Very small estimated random effect variance (lme)
Remko Duursma [EMAIL PROTECTED] writes: Dear R-helpers, i get some strange results using a linear mixed-effects model (lme), of the type: lme1 - lme(y ~ x, random=~x|group, ...) For some datasets, i obtain very small standard deviations of the random effects. I compared these to standard deviations of the slope and intercept using a lmList approach. Of course, the SD from the lme is always smaller (shrinkage estimator), but in some cases (the problem cases) the SD from the lme seems way too small. E.g.: SD of intercept = 0.14, SD of slope = 0.0004, SD residual=0.11. An lmList gives a slope SD of 0.07. I have about n=6 observations per group, and about 20-100 groups depending on the dataset. thank you for any suggestions, It's not a shrinkage estimator it is a subtraction estimator, measuring the excess variance of the empirical slopes over what would be expected from their s.e. if all (true) slopes were identical. This can even be negative, although the parametrizations in lme() will enforce a zero or very small variance in that case. (There are occasional cases where a negative variance can be interpreted, e.g. plants competing for the same growth medium, but you're generally in trouble if the design is unbalanced.) -- O__ Peter Dalgaard Blegdamsvej 3 c/ /'_ --- Dept. of Biostatistics 2200 Cph. N (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] filled.contour without box
Jan Kleinn wrote: Dear all, I would like to make a filled contour plot without the box R is generating by default around the plotting area, i.e. I'm looking for an option in filled.contour similar to 'axes=F' in 'contour' or in 'plot'. I couldn't find any option to get rid of the box, any help is welcome. Thanks, Jan:-) Easy to add a corresponding feature: fix(filled.contour) Now, remove the two lines including box(). Or even better, add an argument to turn plotting of the box on or off. Uwe Ligges __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] Plotting of the lm
Try this: plot(x, y) abline(lm(y ~ x)) #plots the fitted line or this if you need the model results elsewhere: mod.lm - lm(y ~ x) # store the model plot(x, y)# plot the data abline(mod.lm)# plot the fitted line see ?plot.lm and ?abline HTH Gav [EMAIL PROTECTED] wrote: Hi, I would like to enquire if by typing plot (lm(y~x)) would this show me the plot of the fitted line? I tried this function previously but I was only able to get the last 4 plots starting with Residuals vs fitted. Thank You. Melissa JLT Risk Solutions Ltd 6 Crutched Friars, London EC3N 2PH. Co Reg No 1536540 Tel: (44) (0)20 7528 4000 Fax: (44) (0)20 7528 4500 http://www.jltgroup.com Lloyd's Broker. Regulated by the General Insurance Standards Council The content of this e-mail (including any attachments) as received may not be the same as sent. If you consider that the content is material to the formation or performance of a contract or you are otherwise relying upon its accuracy, you should consider requesting a copy be sent by facsimile or normal mail. The information in this e-mail is confidential and may be legally privileged. If you are not the intended recipient, please notify the sender immediately and then delete this e-mail entirely - you must not retain, copy, distribute or use this e-mail for any purpose or disclose any of its content to others. Opinions, conclusions and other information in this e-mail that do not relate to the official business of JLT Risk Solutions Ltd shall be understood as neither given nor endorsed by it. Please note we intercept and monitor incoming / outgoing e-mail and therefore you should neither expect nor intend any e-mail to be private in nature. We have checked this e-mail for viruses and other harmful components and believe but not guarantee it virus-free prior to leaving our computer system. However, you should satisfy yourself that it is free from harmful components, as we do not accept responsibility for any loss or damage it may cause to your computer systems. __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Gavin Simpson [T] +44 (0)20 7679 5522 ENSIS Research Fellow [F] +44 (0)20 7679 7565 ENSIS Ltd. ECRC [E] [EMAIL PROTECTED] UCL Department of Geography [W] http://www.ucl.ac.uk/~ucfagls/cv/ 26 Bedford Way[W] http://www.ucl.ac.uk/~ucfagls/ London. WC1H 0AP. %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
[R] problems installing Design and Hmisc libs
Dear All, when I try to: install.packages(Design); install.packages(Hmisc) I get the following error messages: * Installing *source* package 'Design' ... ** libs g77 -mieee-fp -O2 -fomit-frame-pointer -pipe -march=i586 -mcpu=pentiumpro -O2 -fomit-frame-pointer -pipe -march=i586 -mcpu=pentiumpro -c lrmfit.f -o lrmfit.o make: g77: Command not found make: *** [lrmfit.o] Error 127 ERROR: compilation failed for package 'Design' * Installing *source* package 'Hmisc' ... ** libs g77 -mieee-fp -O2 -fomit-frame-pointer -pipe -march=i586 -mcpu=pentiumpro -O2 -fomit-frame-pointer -pipe -march=i586 -mcpu=pentiumpro -c cidxcn.f -o cidxcn.o make: g77: Command not found make: *** [cidxcn.o] Error 127 ERROR: compilation failed for package 'Hmisc' The connection to CRAN and the download are fine though. I am using R 1.7.1 under Mandrake Linux 9.1. My C compiler is gcc 3.2.2. Any idea how to install the packages? Regads, Federico -- = Federico C. F. Calboli Department of Biology University College London Darwin Building Gower Street London WC1E 6BT tel: 020 7679 4395 fax: 020 7679 7096 f.calboli at ucl.ac.uk __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] problems installing Design and Hmisc libs
Federico Calboli wrote: Dear All, when I try to: install.packages(Design); install.packages(Hmisc) I get the following error messages: * Installing *source* package 'Design' ... ** libs g77 -mieee-fp -O2 -fomit-frame-pointer -pipe -march=i586 -mcpu=pentiumpro -O2 -fomit-frame-pointer -pipe -march=i586 -mcpu=pentiumpro -c lrmfit.f -o lrmfit.o make: g77: Command not found make: *** [lrmfit.o] Error 127 ERROR: compilation failed for package 'Design' * Installing *source* package 'Hmisc' ... ** libs g77 -mieee-fp -O2 -fomit-frame-pointer -pipe -march=i586 -mcpu=pentiumpro -O2 -fomit-frame-pointer -pipe -march=i586 -mcpu=pentiumpro -c cidxcn.f -o cidxcn.o make: g77: Command not found make: *** [cidxcn.o] Error 127 ERROR: compilation failed for package 'Hmisc' The connection to CRAN and the download are fine though. I am using R 1.7.1 under Mandrake Linux 9.1. My C compiler is gcc 3.2.2. You need the Fortran compiler (g77) as well (as indicated by the error message). Is it installed? Is it in your path? Uwe Ligges Any idea how to install the packages? Regads, Federico __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
RE: [R] Date on x-axis of xyplot
One thing you could do is to use the 'its' (irregular time-series)
package on CRAN.
e.g. using a trivial dataset
require(its)
its.format(%Y-%m-%d) #defines text format of dates in dimnames
df - data.frame(1:3,(1:3)^2)
dimnames(df) - list(c(2003-01-03,2003-01-06,2003-01-07),letters[1:2])
plot(its(as.matrix(df)),type=p)
or more simply
mat -
structure(1:6,dim=c(3,2),dimnames=list(c(2003-01-03,2003-01-06,2003-01-
07),letters[1:2]))
plot(its(mat),type=p)
Clearly plot does not provide the same functionality as the
beautifully crafted xyplot of lattice, but dates do get handled
as an abcissa. Incidentally the implementation of 'its' uses the
POSIXct class, but this is largely encapsulated.
Giles
-Original Message-
From: Charles H. Franklin [mailto:[EMAIL PROTECTED]
Sent: 17 September 2003 04:00
To: [EMAIL PROTECTED]
Subject: [R] Date on x-axis of xyplot
xyplot doesn't seem to want to label my x-axis with dates but
instead puts
the day-number for each date.
begdate is the number of days since January 1, 1960 and was initially
created by
library(date)
...
polls$begdate-mdy.date(begmm,begdd,begyy)
I create a new dataframe (pollstack) which includes begdate.
In the process
begdate seems to lose its date attribute so I redo it as:
pollstack$begdate-as.date(pollstack$begdate)
after which
attach(pollstack)
summary(pollstack)
begdate pct names
First :15Nov2002 Min. : 0.000 Clark : 54
Last :10Sep2003 1st Qu.: 2.000 Dean: 54
Median : 5.000 Edwards : 54
Mean : 6.991 Gephardt: 54
3rd Qu.:12.000 Graham : 54
Max. :29.000 Kerry : 54
(Other) :216
And all seems well.
But xyplot continues to use day number on the x-axis. My
plots are created
by
print(xyplot(pct ~ begdate | names, pch=2, cex=.2,
prepanel = function(x, y) prepanel.loess(x, y, span = 1),
main=2004 Democratic Primary Race,
xlab = Date of Survey,
ylab = Percent Support,
panel = function(x, y) {
panel.grid(h=-1, v= -1)
panel.xyplot(x, y, pch=1,col=2,cex=.7)
panel.loess(x,y, span=.65, lwd=2,col=4)
}, ) )
What am I missing?
Thanks!
Charles
/**
** Charles H. Franklin
** Professor, Political Science
** University of Wisconsin, Madison
** 1050 Bascom Mall
** Madison, WI 53706
** 608-263-2022 Office
** 608-265-2663 Fax
** mailto:[EMAIL PROTECTED] (best)
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** http://www.polisci.wisc.edu/~franklin
**/
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Re: [R] problems installing Design and Hmisc libs
You need the Fortran compiler (g77) as well (as indicated by the error message). Is it installed? Is it in your path? Uwe Ligges It was not installed. Now everything works. Cheers, Federico -- = Federico C. F. Calboli Department of Biology University College London Darwin Building Gower Street London WC1E 6BT tel: 020 7679 4395 fax: 020 7679 7096 f.calboli at ucl.ac.uk __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
[R] Rank and extract data from a series
I would like to rank a time-series of data, extract the top ten data items from this series, determine the corresponding row numbers for each value in the sample, and take a mean of these *row numbers* (not the data). I would like to do this in R, rather than pre-process the data on the UNIX command line if possible, as I need to calculate other statistics for the series. I understand that I can use 'sort' to order the data, but I am not aware of a function in R that would allow me to extract a given number of these data and then determine their positions within the original time series. e.g. Time series: 1.0 (row 1) 4.5 (row 2) 2.3 (row 3) 1.0 (row 4) 7.3 (row 5) Sort would give me: 1.0 1.0 2.3 4.5 7.3 I would then like to extract the top two data items: 4.5 7.3 and determine their positions within the original (unsorted) time series: 4.5 = row 2 7.3 = row 5 then take a mean: 2 and 5 = 3.5 Thanks in advance. James Brown ___ James Brown Cambridge Coastal Research Unit (CCRU) Department of Geography University of Cambridge Downing Place Cambridge CB2 3EN, UK Telephone: +44 (0)1223 339776 Mobile: 07929 817546 Fax: +44 (0)1223 355674 E-mail: [EMAIL PROTECTED] E-mail: [EMAIL PROTECTED] http://www.geog.cam.ac.uk/ccru/CCRU.html ___ On Wed, 10 Sep 2003, Jerome Asselin wrote: On September 10, 2003 04:03 pm, Kevin S. Van Horn wrote: Your method looks like a naive reimplementation of integration, and won't work so well for distributions that have the great majority of the probability mass concentrated in a small fraction of the sample space. I was hoping for something that would retain the adaptability of integrate(). Yesterday, I've suggested to use approxfun(). Did you consider my suggestion? Below is an example. N - 500 x - rexp(N) y - rank(x)/(N+1) empCDF - approxfun(x,y) xvals - seq(0,4,.01) plot(xvals,empCDF(xvals),type=l, xlab=Quantile,ylab=Cumulative Distribution Function) lines(xvals,pexp(xvals),lty=2) legend(2,.4,c(Empirical CDF,Exact CDF),lty=1:2) It's possible to tune in some parameters in approxfun() to better match your personal preferences. Have a look at help(approxfun) for details. HTH, Jerome Asselin __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
RE: [R] R-project [.com?] [.net?]
From: Murray Jorgensen [mailto:[EMAIL PROTECTED] I got a shock a few days ago when I accidentally visited www.r-project.com . I thought that the r-project site had been hacked This one seems to be about some sort of city revival projects in Japan. (The introduction starts with Recycle, Redesign, Rethink, Refine, Restore, Recreation I can't read Japanese, but just guessing from the Chinese characters that were sprinkled in the text. until I realised my mistake. There is also a site www.r-project.net. No indication what this is about. Seems to say the site is still under construction. Andy Both of these sites appear to be Japanese. Does anyone know anything about them? I suppose that it is not unusual for names close to those of popular sites to be used. It is good that they use a different language or there might well be confusion. Murray -- Dr Murray Jorgensen http://www.stats.waikato.ac.nz/Staff/maj.html Department of Statistics, University of Waikato, Hamilton, New Zealand Email: [EMAIL PROTECTED]Fax 7 838 4155 Phone +64 7 838 4773 wk+64 7 849 6486 homeMobile 021 1395 862 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo /r-help __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
RE: [R] Rank and extract data from a series
Here's one way. Suppose your time series is in a vector called x. top10 - sort(x, decreasing=TRUE)[1:10] mean.index - mean(which(x %in% top10)) HTH, Andy -Original Message- From: James Brown [mailto:[EMAIL PROTECTED] Sent: Tuesday, September 23, 2003 7:51 AM To: [EMAIL PROTECTED] Subject: [R] Rank and extract data from a series I would like to rank a time-series of data, extract the top ten data items from this series, determine the corresponding row numbers for each value in the sample, and take a mean of these *row numbers* (not the data). I would like to do this in R, rather than pre-process the data on the UNIX command line if possible, as I need to calculate other statistics for the series. I understand that I can use 'sort' to order the data, but I am not aware of a function in R that would allow me to extract a given number of these data and then determine their positions within the original time series. e.g. Time series: 1.0 (row 1) 4.5 (row 2) 2.3 (row 3) 1.0 (row 4) 7.3 (row 5) Sort would give me: 1.0 1.0 2.3 4.5 7.3 I would then like to extract the top two data items: 4.5 7.3 and determine their positions within the original (unsorted) time series: 4.5 = row 2 7.3 = row 5 then take a mean: 2 and 5 = 3.5 Thanks in advance. James Brown ___ James Brown Cambridge Coastal Research Unit (CCRU) Department of Geography University of Cambridge Downing Place Cambridge CB2 3EN, UK Telephone: +44 (0)1223 339776 Mobile: 07929 817546 Fax: +44 (0)1223 355674 E-mail: [EMAIL PROTECTED] E-mail: [EMAIL PROTECTED] http://www.geog.cam.ac.uk/ccru/CCRU.html ___ On Wed, 10 Sep 2003, Jerome Asselin wrote: On September 10, 2003 04:03 pm, Kevin S. Van Horn wrote: Your method looks like a naive reimplementation of integration, and won't work so well for distributions that have the great majority of the probability mass concentrated in a small fraction of the sample space. I was hoping for something that would retain the adaptability of integrate(). Yesterday, I've suggested to use approxfun(). Did you consider my suggestion? Below is an example. N - 500 x - rexp(N) y - rank(x)/(N+1) empCDF - approxfun(x,y) xvals - seq(0,4,.01) plot(xvals,empCDF(xvals),type=l, xlab=Quantile,ylab=Cumulative Distribution Function) lines(xvals,pexp(xvals),lty=2) legend(2,.4,c(Empirical CDF,Exact CDF),lty=1:2) It's possible to tune in some parameters in approxfun() to better match your personal preferences. Have a look at help(approxfun) for details. HTH, Jerome Asselin __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo /r-help __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
AW: [R] Rank and extract data from a series
Hi, I would like to rank a time-series of data, extract the top ten data items from this series, determine the corresponding row numbers for each value in the sample, and take a mean of these *row numbers* (not the data). I would like to do this in R, rather than pre-process the data on the UNIX command line if possible, as I need to calculate other statistics for the series. I understand that I can use 'sort' to order the data, but I am not aware of a function in R that would allow me to extract a given number of these data and then determine their positions within the original time series. e.g. Time series: 1.0 (row 1) 4.5 (row 2) 2.3 (row 3) 1.0 (row 4) 7.3 (row 5) Sort would give me: 1.0 1.0 2.3 4.5 7.3 I would then like to extract the top two data items: 4.5 7.3 and determine their positions within the original (unsorted) time series: 4.5 = row 2 7.3 = row 5 then take a mean: 2 and 5 = 3.5 Thanks in advance. James Brown X - c(1, 4.5, 2.3, 1, 7.3) X1 - sort(X, decreasing=TRUE)[1:2] X2 - match(X1, X) mean(X2) Hope this helps Thomas ___ James Brown Cambridge Coastal Research Unit (CCRU) Department of Geography University of Cambridge Downing Place Cambridge CB2 3EN, UK Telephone: +44 (0)1223 339776 Mobile: 07929 817546 Fax: +44 (0)1223 355674 E-mail: [EMAIL PROTECTED] E-mail: [EMAIL PROTECTED] http://www.geog.cam.ac.uk/ccru/CCRU.html ___ On Wed, 10 Sep 2003, Jerome Asselin wrote: On September 10, 2003 04:03 pm, Kevin S. Van Horn wrote: Your method looks like a naive reimplementation of integration, and won't work so well for distributions that have the great majority of the probability mass concentrated in a small fraction of the sample space. I was hoping for something that would retain the adaptability of integrate(). Yesterday, I've suggested to use approxfun(). Did you consider my suggestion? Below is an example. N - 500 x - rexp(N) y - rank(x)/(N+1) empCDF - approxfun(x,y) xvals - seq(0,4,.01) plot(xvals,empCDF(xvals),type=l, xlab=Quantile,ylab=Cumulative Distribution Function) lines(xvals,pexp(xvals),lty=2) legend(2,.4,c(Empirical CDF,Exact CDF),lty=1:2) It's possible to tune in some parameters in approxfun() to better match your personal preferences. Have a look at help(approxfun) for details. HTH, Jerome Asselin __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
[R] Marginal Means with the lme()
I need help computing model-predicted estimated marginal means of the dependent variable in the cells defined by the fixed factors, including interactions. By estimated marginal means, I just mean cell means collapsed over all other factors and adjusted for the mean values of other covariates in the model. Basically, I need an lme() analog of the model.tables() function for an aov() object. model.tables() does not work for lme() fits. Does anyone know if there is a equivalent model.tables() for lme? Thank you, Scott - [[alternative HTML version deleted]] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] filled.contour without box
If you just want to get rid of the axes, you can do
filled.contour(x, plot.axes = { })
-roger
Uwe Ligges wrote:
Jan Kleinn wrote:
Dear all,
I would like to make a filled contour plot without the box R is
generating by default around the plotting area, i.e. I'm looking for
an option in filled.contour similar to 'axes=F' in 'contour' or in
'plot'. I couldn't find any option to get rid of the box, any help is
welcome.
Thanks, Jan:-)
Easy to add a corresponding feature:
fix(filled.contour)
Now, remove the two lines including box().
Or even better, add an argument to turn plotting of the box on or off.
Uwe Ligges
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Re: [R] what does the sum of square of Gaussian RVs with different variance obey?
On Tue, 23 Sep 2003, Jean Sun wrote: From basic statistics principle,we know,given several i.i.d Gaussian RVs with zero or nonzero mean,the sum of square of them is a central or noncentral Chi-distributed RV.However if these Gaussian RVs have different variances,what does the sum of square of them obey? Nothing very useful. It's a mixture of chisquare(1) variables. One standard approach is to approximate it by a multiple of a chisquared distribution that has the correct mean and variance. -thomas __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] problems installing Design and Hmisc libs
On Tue, 23 Sep 2003, Federico Calboli wrote: Dear All, when I try to: install.packages(Design); install.packages(Hmisc) I get the following error messages: * Installing *source* package 'Design' ... ** libs g77 -mieee-fp -O2 -fomit-frame-pointer -pipe -march=i586 -mcpu=pentiumpro -O2 -fomit-frame-pointer -pipe -march=i586 -mcpu=pentiumpro -c lrmfit.f -o lrmfit.o make: g77: Command not found make: *** [lrmfit.o] Error 127 ERROR: compilation failed for package 'Design' * Installing *source* package 'Hmisc' ... ** libs g77 -mieee-fp -O2 -fomit-frame-pointer -pipe -march=i586 -mcpu=pentiumpro -O2 -fomit-frame-pointer -pipe -march=i586 -mcpu=pentiumpro -c cidxcn.f -o cidxcn.o make: g77: Command not found make: *** [cidxcn.o] Error 127 ERROR: compilation failed for package 'Hmisc' The connection to CRAN and the download are fine though. I am using R 1.7.1 under Mandrake Linux 9.1. My C compiler is gcc 3.2.2. Any idea how to install the packages? You need a Fortran compiler, such as g77. If you have g77 then it looks like it has moved since you compiled R. If you don't, then you presumably installed R binaries, and you need g77. -thomas __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
[R] discretization method
Hi R users I need to apply discretization to my continuous data. Is there a method in R to do this? Thanks in advance, Jaime __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
[R] (Fwd) Re: goodfit macro
Dear R-Help: As you can see, Prof. Friendly refers me to your site for an executable version of vcd. I don't mean to be obtuse, but 15 minutes spent exploring your site failed to locate a downloadable version of the vcd package to which he referred. I know plainly what this application can do. What I need to know is how to obtain the application itself. My thanks in advance for any help you can provide. MS --- Forwarded message follows --- Date sent: Tue, 23 Sep 2003 09:14:28 -0400 From: Michael Friendly [EMAIL PROTECTED] Subject:Re: goodfit macro To: [EMAIL PROTECTED] Send reply to: [EMAIL PROTECTED] Organization: York University You can also carry out goodness of fit tests using the function goodfit in the vcd package for R (a free version of S/Splus), http://www.r-project.org -Michael Michael Shott wrote: Dear Michael: Recently I searched the web for guidance in gauging the goodness-of- fit of frequency data to statistical models. Your website came up in virtually every combination of keywords searched in Google. The site describes the goodfit.sas macro, which seems to do exactly what I'd like. But it seems to be available only as a .sas file. Do you have some application file that can be downloaded and used? I ask because I'd like to analyze some archaeological data. They are frequency distributions of the number of a particular artifact type by site. That is, x sites may have 1 occurrence, y sites may have 2 occurrences, z sites 3 occurrences and so on. Your goodfit macro seems to do the job, but I can't execute it from the .sas version that appears on your website's ftp link. Thanks for any help that you can provide. Best, Mike Shott Michael J. Shott Professor Dept. of Sociology, Anthropology Criminology University of Northern Iowa Cedar Falls, IA 50614-0513 319/273-7337 -- Michael Friendly Email: [EMAIL PROTECTED] Professor, Psychology Dept. York University Voice: 416 736-5115 x66249 Fax: 416 736-5814 4700 Keele Streethttp://www.math.yorku.ca/SCS/friendly.html Toronto, ONT M3J 1P3 CANADA --- End of forwarded message --- Michael J. Shott Professor Dept. of Sociology, Anthropology Criminology University of Northern Iowa Cedar Falls, IA 50614-0513 319/273-7337 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] discretization method
On Tue, 23 Sep 2003, Jaime Lopez Carvajal wrote: I need to apply discretization to my continuous data. Is there a method in R to do this? See help(cut). - tom blackwell - u michigan medical school - ann arbor - __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] discretization method
Consider: ?cut ?round With more detail we might be able to help more ... On Tue, 23 Sep 2003, Jaime Lopez Carvajal wrote: Hi R users I need to apply discretization to my continuous data. Is there a method in R to do this? Thanks in advance, Jaime -- 620B Bartram Hall[EMAIL PROTECTED] Zoology Department, University of Floridahttp://www.zoo.ufl.edu/bolker Box 118525 (ph) 352-392-5697 Gainesville, FL 32611-8525 (fax) 352-392-3704 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
[R] loops in Sweave
Dear all, I was wondering whether there is a way to make loops in Sweave, i.e. for example to: 1) calculate a parameter, say, a=length(b) 2) according to that, add #a# chapters to the document, each including some repetitive analysis, each time done on a particular subset of the data indexed by the elements of 1:a. This would be of great help for repeating exploratory data analyses on, say, questionaries when the number of questions changes without having to change the Sweave .snw file. Many thanx for your answers Giovanni Millo RD Dept. Assicurazioni Generali SpA Trieste, Italy Ai sensi della Legge 675/96 si precisa che le informazioni contenute in questo messaggio sono riservate ed a uso esclusivo del destinatario. Qualora il messaggio in parola Le fosse pervenuto per errore, la preghiamo di eliminarlo senza copiarlo e di non inoltrarlo a terzi, dandocene gentilmente comunicazione. Grazie.BRBRThis message, for the law 675/96, may contain confidential and/or privileged information. If you are not the addressee or authorized to receive this for the addressee, you must not use, copy, disclose or take any action based on this message or any information herein. If you have received this message in error, please advise the sender immediately by reply e-mail and delete this message. Thank you for your cooperation. [[alternative HTML version deleted]] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] (Fwd) Re: goodfit macro
Michael Shott wrote: Dear R-Help: As you can see, Prof. Friendly refers me to your site for an executable version of vcd. I don't mean to be obtuse, but 15 minutes spent exploring your site failed to locate a downloadable version of the vcd package to which he referred. I know plainly what this application can do. What I need to know is how to obtain the application itself. My thanks in advance for any help you can provide. MS Well, vcd is a contributed package, not a stand-alone executable. At first, you need to intstall R, after that, just type install.packages(vcd) if you are connected to the internet, and the package will be installed. Then, you can use the function: library(vcd) goodfit(.) But you will need to learn some basics of R at first, e.g. from An Introduction to R (a manual that comes with R), in order to import your data etc. Uwe Ligges --- Forwarded message follows --- Date sent: Tue, 23 Sep 2003 09:14:28 -0400 From: Michael Friendly [EMAIL PROTECTED] Subject:Re: goodfit macro To: [EMAIL PROTECTED] Send reply to: [EMAIL PROTECTED] Organization: York University You can also carry out goodness of fit tests using the function goodfit in the vcd package for R (a free version of S/Splus), http://www.r-project.org -Michael Michael Shott wrote: Dear Michael: Recently I searched the web for guidance in gauging the goodness-of- fit of frequency data to statistical models. Your website came up in virtually every combination of keywords searched in Google. The site describes the goodfit.sas macro, which seems to do exactly what I'd like. But it seems to be available only as a .sas file. Do you have some application file that can be downloaded and used? I ask because I'd like to analyze some archaeological data. They are frequency distributions of the number of a particular artifact type by site. That is, x sites may have 1 occurrence, y sites may have 2 occurrences, z sites 3 occurrences and so on. Your goodfit macro seems to do the job, but I can't execute it from the .sas version that appears on your website's ftp link. Thanks for any help that you can provide. Best, Mike Shott Michael J. Shott Professor Dept. of Sociology, Anthropology Criminology University of Northern Iowa Cedar Falls, IA 50614-0513 319/273-7337 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
AW: [R] weighted standard deviation
Thank you all for the reply, the Hmisc library is exactly what i was looking for. Johannes __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
RE: [R] what does the sum of square of Gaussian RVs with differen t variance obey?
This is a relatively recent article that is somewhat accessible. Jensen, D. R., and Solomon, Herbert (1994), Approximations to joint distributions of definite quadratic forms, Journal of the American Statistical Association, 89 , 480-486 It has references to previous work. I also have an old paper that is so old I can't tell what journal it came out of:( Grad, Arthur and Solomon, Herbert Distribution of Quadratic Forms and Some Applications probably published in 55 or 56 but I can't tell. The paper by Grad and Solomon uses the moment generating function to give the exact distribution and various approximations to produce a table for a sum of 2 or 3 variates. Usual disclaimers ... Bob -Original Message- From: Thomas Lumley [mailto:[EMAIL PROTECTED] Sent: Tuesday, September 23, 2003 10:07 AM To: Jean Sun Cc: [EMAIL PROTECTED] Subject: Re: [R] what does the sum of square of Gaussian RVs with different variance obey? On Tue, 23 Sep 2003, Jean Sun wrote: From basic statistics principle,we know,given several i.i.d Gaussian RVs with zero or nonzero mean,the sum of square of them is a central or noncentral Chi-distributed RV.However if these Gaussian RVs have different variances,what does the sum of square of them obey? Nothing very useful. It's a mixture of chisquare(1) variables. One standard approach is to approximate it by a multiple of a chisquared distribution that has the correct mean and variance. -thomas __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help [[alternative HTML version deleted]] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] (Fwd) Re: goodfit macro
On Tuesday 23 September 2003 16:38, Michael Shott wrote: Dear R-Help: As you can see, Prof. Friendly refers me to your site for an executable version of vcd. I don't mean to be obtuse, but 15 minutes spent exploring your site failed to locate a downloadable version of the vcd package to which he referred. I know plainly what this application can do. What I need to know is how to obtain the application itself. Michael, you need to install the R system first and then the add-on package vcd. If you look at http://www.R-project.org/ there are some manuals and the FAQ which will tell you how to obtain and install R on your operating system. Having done that you can install the package vcd which is also covered in the documentation I mentioned above. Both R itself and the vcd package can be downloaded from http://CRAN.R-project.org/ HTH, Z My thanks in advance for any help you can provide. MS --- Forwarded message follows --- Date sent:Tue, 23 Sep 2003 09:14:28 -0400 From: Michael Friendly [EMAIL PROTECTED] Subject: Re: goodfit macro To: [EMAIL PROTECTED] Send reply to:[EMAIL PROTECTED] Organization: York University You can also carry out goodness of fit tests using the function goodfit in the vcd package for R (a free version of S/Splus), http://www.r-project.org -Michael Michael Shott wrote: Dear Michael: Recently I searched the web for guidance in gauging the goodness-of- fit of frequency data to statistical models. Your website came up in virtually every combination of keywords searched in Google. The site describes the goodfit.sas macro, which seems to do exactly what I'd like. But it seems to be available only as a .sas file. Do you have some application file that can be downloaded and used? I ask because I'd like to analyze some archaeological data. They are frequency distributions of the number of a particular artifact type by site. That is, x sites may have 1 occurrence, y sites may have 2 occurrences, z sites 3 occurrences and so on. Your goodfit macro seems to do the job, but I can't execute it from the .sas version that appears on your website's ftp link. Thanks for any help that you can provide. Best, Mike Shott Michael J. Shott Professor Dept. of Sociology, Anthropology Criminology University of Northern Iowa Cedar Falls, IA 50614-0513 319/273-7337 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] filled.contour without box
UweL == Uwe Ligges [EMAIL PROTECTED]
on Tue, 23 Sep 2003 11:30:02 +0200 writes:
UweL Jan Kleinn wrote:
Dear all,
I would like to make a filled contour plot without the
box R is generating by default around the plotting area,
i.e. I'm looking for an option in filled.contour similar
to 'axes=F' in 'contour' or in 'plot'. I couldn't find
any option to get rid of the box, any help is welcome.
Thanks, Jan:-)
[ filled.contour() does have an `axes = FALSE' option but that
eliminates axes both on the image _and_ on the key/legend.
As Roger Peng has just noted you can get rid of the axes of
the image alone, using `plot.axes = {}',
however as you say, it's the box, not the axes you want to get
rid of
]
UweL Easy to add a corresponding feature:
UweL fix(filled.contour)
UweL Now, remove the two lines including box(). Or even
UweL better, add an argument to turn plotting of the box on
UweL or off.
R-1.8.0 will also have an argument 'frame.plot'
which can be set to FALSE to eliminate the box around the plot.
Note that it does not eliminate the box around the legend.
Since I think this is hardly desired this is still not an option
of the future filled.contour().
Martin Maechler [EMAIL PROTECTED] http://stat.ethz.ch/~maechler/
Seminar fuer Statistik, ETH-Zentrum LEO C16Leonhardstr. 27
ETH (Federal Inst. Technology) 8092 Zurich SWITZERLAND
phone: x-41-1-632-3408 fax: ...-1228
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[R] How to extract data from Excel
Hi,
I would like to know how to extract the data from Excel Spreadsheet.
Thank you very much.
Melissa
JLT Risk Solutions Ltd
6 Crutched Friars, London EC3N 2PH. Co Reg No 1536540
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Re: [R] How to extract data from Excel
[EMAIL PROTECTED] wrote: Hi, I would like to know how to extract the data from Excel Spreadsheet. I would like to know whether you have read the manual R Data Import/Export before having posted the question. It tells about you more than one way. Uwe Ligges Thank you very much. Melissa __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] discretization method
there are plenty of discretization methods, which one are you looking for? (In Spanish hay bastantes metodos de discretizacion cual de ellos estas busacando? Regards (saludos) Edgar Acuna On Tue, 23 Sep 2003, Jaime Lopez Carvajal wrote: Hi R users I need to apply discretization to my continuous data. Is there a method in R to do this? Thanks in advance, Jaime __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: AW: [R] Rank and extract data from a series
Using Thomas Unternährer's handy example, one could also do: X - c(1, 4.5, 2.3, 1, 7.3) mean(order(X, decreasing=TRUE)[1:2]) [1] 3.5 I think this will give the same results as Thomas Unternährer's suggested code in almost all cases, but it is perhaps more concise and direct (provided that you don't actually need the values of the top items). (of course you have to change the 1:2 to 1:10 for your needs). Note that this question gets tricky if there are ties such that there is no unique set of row numbers that identify N top items. For example, consider the following data: X - c(1,3,2,3,4) Taking top two, should the answer be 3.5 (avg of row numbers 2 and 5), 4.5 (avg of row numbers 4 and 5), or 3.67 (avg of row numbers 2,4 and 5)? mean(order(X, decreasing=TRUE)[1:2]) [1] 3.5 order(X, decreasing=TRUE)[1:2] [1] 5 2 # Andy Liaw's suggestion: mean(which(X %in% sort(X, decreasing=TRUE)[1:2])) [1] 3.67 which(X %in% sort(X, decreasing=TRUE)[1:2]) [1] 2 4 5 # Thomas Unternährer's suggestion: mean(match(sort(X, decreasing=TRUE)[1:2], X)) [1] 3.5 match(sort(X, decreasing=TRUE)[1:2], X) [1] 5 2 hope this helps, Tony Plate At Tuesday 02:23 PM 9/23/2003 +0200, Unternährer Thomas, uth wrote: Hi, I would like to rank a time-series of data, extract the top ten data items from this series, determine the corresponding row numbers for each value in the sample, and take a mean of these *row numbers* (not the data). I would like to do this in R, rather than pre-process the data on the UNIX command line if possible, as I need to calculate other statistics for the series. I understand that I can use 'sort' to order the data, but I am not aware of a function in R that would allow me to extract a given number of these data and then determine their positions within the original time series. e.g. Time series: 1.0 (row 1) 4.5 (row 2) 2.3 (row 3) 1.0 (row 4) 7.3 (row 5) Sort would give me: 1.0 1.0 2.3 4.5 7.3 I would then like to extract the top two data items: 4.5 7.3 and determine their positions within the original (unsorted) time series: 4.5 = row 2 7.3 = row 5 then take a mean: 2 and 5 = 3.5 Thanks in advance. James Brown X - c(1, 4.5, 2.3, 1, 7.3) X1 - sort(X, decreasing=TRUE)[1:2] X2 - match(X1, X) mean(X2) Hope this helps Thomas ___ James Brown Cambridge Coastal Research Unit (CCRU) Department of Geography University of Cambridge Downing Place Cambridge CB2 3EN, UK Telephone: +44 (0)1223 339776 Mobile: 07929 817546 Fax: +44 (0)1223 355674 E-mail: [EMAIL PROTECTED] E-mail: [EMAIL PROTECTED] http://www.geog.cam.ac.uk/ccru/CCRU.html ___ On Wed, 10 Sep 2003, Jerome Asselin wrote: On September 10, 2003 04:03 pm, Kevin S. Van Horn wrote: Your method looks like a naive reimplementation of integration, and won't work so well for distributions that have the great majority of the probability mass concentrated in a small fraction of the sample space. I was hoping for something that would retain the adaptability of integrate(). Yesterday, I've suggested to use approxfun(). Did you consider my suggestion? Below is an example. N - 500 x - rexp(N) y - rank(x)/(N+1) empCDF - approxfun(x,y) xvals - seq(0,4,.01) plot(xvals,empCDF(xvals),type=l, xlab=Quantile,ylab=Cumulative Distribution Function) lines(xvals,pexp(xvals),lty=2) legend(2,.4,c(Empirical CDF,Exact CDF),lty=1:2) It's possible to tune in some parameters in approxfun() to better match your personal preferences. Have a look at help(approxfun) for details. HTH, Jerome Asselin __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help Tony Plate [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] How to extract data from Excel
Your best bet is saving as a comma-separated value file (.csv) and using
read.csv to get the data into R.
Ben
On Tue, 23 Sep 2003 [EMAIL PROTECTED] wrote:
Hi,
I would like to know how to extract the data from Excel Spreadsheet.
Thank you very much.
Melissa
JLT Risk Solutions Ltd
6 Crutched Friars, London EC3N 2PH. Co Reg No 1536540
Tel: (44) (0)20 7528 4000 Fax: (44) (0)20 7528 4500
http://www.jltgroup.com
Lloyd's Broker. Regulated by the General Insurance
Standards Council
The content of this e-mail (including any attachments) as\ r...{{dropped}}
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620B Bartram Hall[EMAIL PROTECTED]
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Box 118525 (ph) 352-392-5697
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[R] Plotting multiple lines
Hi, I have a data set with 7 years worth of data, and 2 different values (a real value and a model value) of interest in each year for different lengths. I would like a plot with the year on the y axis and an animal length along the x axis. For each year I would like to see two lines, one representing real data and one representing model data. I would like either the model or real line to be red. I have no idea how to start this. Can anybody help me?? If I didn't explain it well enough, I can try to explain it better... Thank you, Kay __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] Plotting multiple lines
On 09/23/03 15:49, K Skanes wrote: Hi, I have a data set with 7 years worth of data, and 2 different values (a real value and a model value) of interest in each year for different lengths. I would like a plot with the year on the y axis and an animal length along the x axis. For each year I would like to see two lines, one representing real data and one representing model data. I would like either the model or real line to be red. One way to do it is with barplot. You would put your data in a matrix m1 in which the columns were animals and the rows were real/model. (I might have it backward about rows/columns). The something like barplot(m1,beside=T) and lots of other options for labels, colors, line thickness, line spacing, etc., although red just might turn out to be the default. Look at the help for barplot. -- Jonathan Baron, Professor of Psychology, University of Pennsylvania Home page:http://www.sas.upenn.edu/~baron R page: http://finzi.psych.upenn.edu/ __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
[R] bug in stack?
I am posting it here because I am not sure if the behavior described below
is actually a bug.
If I do something like this:
x1 - 1:3
x2 - 5:9
x3 - 21:27
ll - list(x1, x2, x3)
stack(x1,x2,x3)
I get the following error:
Error in rep.int(names(x), lapply(x, length)) :
invalid number of copies in rep
The problem seems to be that the generic list ll is lacking the names
attribute.
The stack.default function (in frametools.R) looks like this:
stack.default
function (x, ...)
{
x - as.list(x)
x - x[unlist(lapply(x, is.vector))]
data.frame(values = unlist(unname(x)), ind = factor(rep.int(names(x),
lapply(x, length
}
and the last statement generates an error if names(x) evaluates to NULL.
If we add the following line of code before the last statement
if(is.null(names(x))) names(x) - seq(along=x)
the stack function will work fine even for nameless lists.
Andy
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[R] Typical R installation problem
Dear Peter, I don't know if this is the proper way to ask for help installing R, but if not, I presume you can pass this on to the appropriate place. I'm trying to install the latest binary on Redhat 9, and keep getting the same error message no matter what I try. [EMAIL PROTECTED] mhu]# rpm -i R-1.7.1-1.i386.rpm warning: R-1.7.1-1.i386.rpm: V3 DSA signature: NOKEY, key ID 97d3544e error: Failed dependencies: libtcl8.3.so is needed by R-1.7.1-1 libtk8.3.so is needed by R-1.7.1-1 [EMAIL PROTECTED] mhu]# exit I actually found these two files in an obscure location on my computer, and copied them to /usr/lib/ I also set my path to include the obscure location. SO they are actually available. At least when I enter libtcl8.3.so it is apparently read and a segmentation fault occurs. So, do you have any suggestions about how to get around this problem. I don't know what else to do to make these routines available to the R install. Any help would be greatly appreciated. I had no problem installing R on my MAC OS 10.1.5. Thank you very much, Michael Huston Oak Ridge, Tennessee __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
[R] install problem with R Windows
Dear R People: I'm trying to install R 1.7.1 for Windows from Source. The error that I get is: previous declarion of 'ssize_t' MAKE[2]: ***[internet.o]Error 1 MAKE[1]: ***[all]Error 1 MAKE: *** [rmodules] Error 2 Any ideas on how to proceed, please? thanks in advance! Sincerely, Erin Hodgess mailto: [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] loops in Sweave
On Wed, 2003-09-24 at 03:06, Millo Giovanni wrote:
Dear all,
I was wondering whether there is a way to make loops in Sweave, i.e. for example to:
1) calculate a parameter, say, a=length(b)
2) according to that, add #a# chapters to the document, each including some
repetitive analysis, each time done on a particular subset of the data indexed by
the elements of 1:a.
This would be of great help for repeating exploratory data analyses on, say,
questionaries when the number of questions changes without having to change the
Sweave .snw file.
Two possible ways, off the top of my head:
1) Within LaTeX, use \Sexpr{a} to get the length, then loop within
LaTeX. I believe Lamport includes an example of looping within LaTeX,
but I haven't got the book handy.
2) Within the R chunk, generate the table using xtable() (package
xtable) or Latex (package Hmisc) and print directly within R. I
haven't tried it, but something like
echo=FALSE,results=tex=
## build your table in R
tt - xtable(foo)
print(tt)
@
might do the trick. I'd been meaning to look at this anyway; you
question prompted me ;)
Check the Sweave manual at Herr Dr Leisch's site.
http://www.ci.tuwein.ac.at/~leisch/Sweave
This has the R chunk options required to produce the above, if my
untested example is not correct.
Cheers
Jason
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[R] install R for Windows problem
Here are all of the messages: In file included from internet.c:858: sock.h.27:conflicting types for 'ssize_t' c:/mingw/include/sys/types.h:119: previous declaration of 'ssize_t' MAKE[2]: ***[internet.o] Error 1 MAKE[1]: ***[all] Error 1 MAKE: ***[rmodules] Error 2 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] R Production Performance
Hi James, Thanks for your response :-) - Original Message - It is like anything else that you want to run as part of web services: what do you want it to do? Yes, it is fast in doing computations, but what will you have it do? It is probably as fast as anything else that you will find out there that is fairly general purpose. I just want to use R for mathematical computations, and will call it via PHP from the commandline with infile. We'll need to obviously test this ourselves, but I just thought I'd raise the question :-)) Are you going to be creating a lot of graphics that have to be displayed back on the screen? How is the user going to input data (flat files, XML, Excel worksheets, Oracle database, ...)? Will you be invoking a unique process each time a user calls, or will you be using a 'daemon' that will communicate with DCOM and such? How many people will be trying to access it once and what is the mix of transactions that they will use? Well for sure the rest of the app needs to scale as well and be fast, failsafe etc..., but I am just asking about R. I was imagining using a unique process call each time I access R, which is how the apache/php/*nix environment works best (although keeping processes in memory is achievable as well). My experience to date on integration with C packages deploying to *nix is that this works quite effectively although certain packages require process management that are not multiprocess (to ensure that R for example only executes one computation at a time), but this is no problem. There are ways to call c packages directly with PHP (swig) and I am investigating this at present. You can probably get a real good feel by enclosing the operations that you want to do in a system.time function to see how long it will take. This really depends on what you are trying to do. I can definitely say that it is faster than trying to code the algorithm in PERL or another scripting language. Makes sense because R is written in C, where PERL and PHP are also written in C, so R is a layer deep so to speak :-) Thanks again, Z. Greetings All, Been playing with R and it is very easy to get going with the UI or infile batch commands :-) What I am wondering is how scalable and fast R is for running as part of a web service. I believe R is written in C which is a great start, but what are peoples general thoughts on this? Thanks greatly, Z. [[alternative HTML version deleted]] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help -- NOTICE: The information contained in this electronic mail transmission is intended by Convergys Corporation for the use of the named individual or entity to which it is directed and may contain information that is privileged or otherwise confidential. If you have received this electronic mail transmission in error, please delete it from your system without copying or forwarding it, and notify the sender of the error by reply email or by telephone (collect), so that the sender's address records can be corrected. __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] Typical R installation problem
On Tue, 2003-09-23 at 15:28, [EMAIL PROTECTED] wrote: Dear Peter, I don't know if this is the proper way to ask for help installing R, but if not, I presume you can pass this on to the appropriate place. I'm trying to install the latest binary on Redhat 9, and keep getting the same error message no matter what I try. [EMAIL PROTECTED] mhu]# rpm -i R-1.7.1-1.i386.rpm warning: R-1.7.1-1.i386.rpm: V3 DSA signature: NOKEY, key ID 97d3544e error: Failed dependencies: libtcl8.3.so is needed by R-1.7.1-1 libtk8.3.so is needed by R-1.7.1-1 [EMAIL PROTECTED] mhu]# exit I actually found these two files in an obscure location on my computer, and copied them to /usr/lib/ I also set my path to include the obscure location. SO they are actually available. At least when I enter libtcl8.3.so it is apparently read and a segmentation fault occurs. So, do you have any suggestions about how to get around this problem. I don't know what else to do to make these routines available to the R install. Any help would be greatly appreciated. I had no problem installing R on my MAC OS 10.1.5. Thank you very much, Michael Huston Oak Ridge, Tennessee First, you have posted to r-help, which is an international e-mail list and the primary source of assistance with R. Since I now typically compile from source, I decided to remove my present installation of R and freshly install the RPM that Martyn has created on CRAN. I run RH 9 and have a clean and fully updated installation. The aforementioned tcl/tk files are in /usr/lib on my system. I installed the RPM without problem and then installed John Fox's Rcmdr to test the tcltk functionality. It works without problem. I also tested a tcl/tk function that I wrote and it works fine as well. If your above listed files were not in /usr/lib to start with, that may be (probably is) an indication that something is amiss in your tcl/tk installation. You may need to remove and reinstall tcl/tk. Also, I am unsure as to what you mean by At least when I enter libtcl8.3.so it is apparently read and a segmentation fault occurs. Are you trying to execute it directly from the command line? .so files are shared libraries (akin to .DLLs in Windows). HTH, Marc Schwartz __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
[R] least squares regression line
I can't seem to find the command to find the least squares regression line for my bivariate data set. Can you please help? ~Carmen __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
[R] confusion about what to expect?
In playing around with data.frames (and wanting a simple, cheap way to
use the variable and case names in plots; but I've solved that with
some hacks, yech), I noticed the following behavior with subsetting.
testdata - data.frame(matrix(1:20,nrow=4,ncol=5))
names(testdata) ## expect labels, get them
names(testdata[2,]) ## expect labels, get them
names(testdata[,2]) ## expect labels, but NOT -- STRIPPED OFF??
testdata[,2] ## would have expect a name (X2) in the front? NOT EXPECTED
testdata[2,] ## get what I expect
testdata[2,2] ## just a number, not a sub-data.frame? unexpected
testdata[2,2:3] ## this is a data.frame
testdata[2:3,2:3] ## and this is, too.
version
_
platform i386-pc-linux-gnu
arch i386
os linux-gnu
system i386, linux-gnu
status alpha
major1
minor8.0
year 2003
month09
day 20
language R
I don't have 1.7.1 handy at this location to test, but I would've
expected a data.frame-like object upon subsetting; should I have
expected otherwise? (granted, a data.frame with just a single
variable could be thought of as silly, but it does have some extra
information that might be worthwhile, on occassion?)
I'm not sure that it is a bug, but I was caught by suprise. If it
isn't a bug, and someone has a concise way to think through this, for
my future reference, I'd appreciate hearing about it.
best,
-tony
--
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UW (Tu/Th/F): 206-616-7630 FAX=206-543-3461 | Voicemail is unreliable
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[R] Omitting blank lines with read.table
Say we have a tab delimited file called bug.txt PartRep CageHb pupae 1 1 S 32 1 M 34 L 42 2 S 36 M 28 L 36 read.delim(bug.txt) Part Rep Cage Hb.pupae 11 1S 32 2 NA 1M 34 3 NA NAL 42 4 NA NANA 5 NA NANA 6 NA 2S 36 7 NA NAM 28 8 NA NAL 36 Variations on read.table give the same result. When I first used read.table in Splus, I liked the way it ignored rows that were empty (at least when using sep = \t). A line was considerend empty if it contained only tab characters, so the rows of NAs or s are omitted, so that rows 4 and 5 above would be deleted. R's read.table differs in this respect (and a number of really neat ones). I probably know enough Perl to be able to write a short script that could delete such lines, and it's not difficult to remove the rows from the dataframe afterwards; but maybe there's something simple I've misunderstood in the use of R's read.table. I can't use na.omit since the other NAs in the data can be dealt with so I don't want them removed. Other suggestions welcome. Thanks -- Patrick Connolly HortResearch Mt Albert Auckland New Zealand Ph: +64-9 815 4200 x 7188 ~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~ I have the world`s largest collection of seashells. I keep it on all the beaches of the world ... Perhaps you`ve seen it. ---Steven Wright ~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~ __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
[R] Updating least squares
Paul Meagher [EMAIL PROTECTED] wrote: I am looking at developing a user modelling type app (new data points coming in and wanting to dynamically update regression co-efficients for each user) which could be viewed as a type of control problem. Alan Miller's AS274 (in C, f77 or f90) does this -- see statlib or his home page (there are several similar routines eg AS164). It would be straightforward to write an R interface. David Duffy __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] confusion about what to expect?
Have you investigated the drop= argument to [? (as in the expression
testdata[,2,drop=F], which will return a dataframe).
[.data.frame has somewhat different behavior from [ on matrices with
respect to the drop argument: If the result would be a dataframe with a
single column, the default behavior of [.data.frame is to return a vector
(return a dataframe always if drop=F), but if the result would be a
dataframe with a single row, the default behavior is to return a dataframe
(return a list if drop=T).
E.g.:
class(data.frame(a=1:3,b=4:6)[,1])
[1] integer
class(data.frame(a=1:3,b=4:6)[,1,drop=F])
[1] data.frame
class(data.frame(a=1:3,b=4:6)[1,])
[1] data.frame
class(data.frame(a=1:3,b=4:6)[1,,drop=T])
[1] list
The default behavior is often what you want, but when it isn't it can be
confusing, especially it's not that easy to find documentation for this (at
least not in a quick look through the FAQ, ?[, and An Introduction to R
-- please excuse me if I overlooked something.)
The thing you have going on with names(testdata[...]) is merely a
consequence of whether or not the result of the subsetting operation is a
dataframe or a vector.
hope this helps,
Tony Plate
At Tuesday 04:08 PM 9/23/2003 -0700, you wrote:
In playing around with data.frames (and wanting a simple, cheap way to
use the variable and case names in plots; but I've solved that with
some hacks, yech), I noticed the following behavior with subsetting.
testdata - data.frame(matrix(1:20,nrow=4,ncol=5))
names(testdata) ## expect labels, get them
names(testdata[2,]) ## expect labels, get them
names(testdata[,2]) ## expect labels, but NOT -- STRIPPED OFF??
testdata[,2] ## would have expect a name (X2) in the front? NOT EXPECTED
testdata[2,] ## get what I expect
testdata[2,2] ## just a number, not a sub-data.frame? unexpected
testdata[2,2:3] ## this is a data.frame
testdata[2:3,2:3] ## and this is, too.
version
_
platform i386-pc-linux-gnu
arch i386
os linux-gnu
system i386, linux-gnu
status alpha
major1
minor8.0
year 2003
month09
day 20
language R
I don't have 1.7.1 handy at this location to test, but I would've
expected a data.frame-like object upon subsetting; should I have
expected otherwise? (granted, a data.frame with just a single
variable could be thought of as silly, but it does have some extra
information that might be worthwhile, on occassion?)
I'm not sure that it is a bug, but I was caught by suprise. If it
isn't a bug, and someone has a concise way to think through this, for
my future reference, I'd appreciate hearing about it.
best,
-tony
--
[EMAIL PROTECTED]http://www.analytics.washington.edu/
Biomedical and Health Informatics University of Washington
Biostatistics, SCHARP/HVTN Fred Hutchinson Cancer Research Center
UW (Tu/Th/F): 206-616-7630 FAX=206-543-3461 | Voicemail is unreliable
FHCRC (M/W): 206-667-7025 FAX=206-667-4812 | use Email
CONFIDENTIALITY NOTICE: This e-mail message and any attachme...{{dropped}}
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Re: [R] confusion about what to expect?
On Tue, 2003-09-23 at 18:08, A.J. Rossini wrote: In playing around with data.frames (and wanting a simple, cheap way to use the variable and case names in plots; but I've solved that with some hacks, yech), I noticed the following behavior with subsetting. testdata - data.frame(matrix(1:20,nrow=4,ncol=5)) names(testdata) ## expect labels, get them names(testdata[2,]) ## expect labels, get them names(testdata[,2]) ## expect labels, but NOT -- STRIPPED OFF?? testdata[,2] ## would have expect a name (X2) in the front? NOT EXPECTED testdata[2,] ## get what I expect testdata[2,2] ## just a number, not a sub-data.frame? unexpected testdata[2,2:3] ## this is a data.frame testdata[2:3,2:3] ## and this is, too. version _ platform i386-pc-linux-gnu arch i386 os linux-gnu system i386, linux-gnu status alpha major1 minor8.0 year 2003 month09 day 20 language R I don't have 1.7.1 handy at this location to test, but I would've expected a data.frame-like object upon subsetting; should I have expected otherwise? (granted, a data.frame with just a single variable could be thought of as silly, but it does have some extra information that might be worthwhile, on occassion?) I'm not sure that it is a bug, but I was caught by suprise. If it isn't a bug, and someone has a concise way to think through this, for my future reference, I'd appreciate hearing about it. best, -tony Tony, A quick review of what is returned when you subset the data.frame testdata: str(testdata[,2]) int [1:4] 5 6 7 8 str(testdata[2,]) `data.frame': 1 obs. of 5 variables: $ X1: int 2 $ X2: int 6 $ X3: int 10 $ X4: int 14 $ X5: int 18 dim(testdata[,2]) NULL dim(testdata[2,]) [1] 1 5 Quoting from ?Extract: When [.data.frame is used for subsetting rows of a data.frame, it returns a data frame with unique (and non-missing)row names, if necessary transforming the names using make.names( * , unique = TRUE) What is unstated, but covered by R FAQ 7.7 (Why do my matrices lose dimensions?), a single column in a data.frame resulting from the subset operation is by default turned into a vector. Hence, no names. HTH, Marc Schwartz __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] least squares regression line
On Wed, 2003-09-24 at 11:04, Carmen Fridell wrote: I can't seem to find the command to find the least squares regression line for my bivariate data set. Can you please help? ~Carmen Any time you're lost in R, you can type help.start(). This will start a web browser, which loads the starting help page. Click on Keyword Search. Once the new page loads, type in some of the words you're looking for. regression is a good place to start. That will lead to a list of potential matches by subject. Hint - you're looking for a function to estimate a *linear* model. Cheers Jason -- Indigo Industrial Controls Ltd. http://www.indigoindustrial.co.nz +64-(0)21-343-545 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] install problem with R Windows
On Tue, 23 Sep 2003 16:16:38 -0500, you wrote: Dear R People: I'm trying to install R 1.7.1 for Windows from Source. The error that I get is: previous declarion of 'ssize_t' MAKE[2]: ***[internet.o]Error 1 MAKE[1]: ***[all]Error 1 MAKE: *** [rmodules] Error 2 Any ideas on how to proceed, please? Can you describe your setup? Have you installed the tools as described in src/gnuwin32/INSTALL, or are you using others? Duncan Murdoch __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] R Production Performance
Hi Zitan,
Below is the test I ran awhile back on invoking R as a system call. It
might be faster if you had a c-extension to R but before I went that route I
would want to know 1) roughly how fast Python and Perl are in returning
results with their c-bindings/embedded stuff/dcom stuff, 2) whether R can be
run as a daemon process so you don't incur start up costs, and 3) whether R
can act as a math server in the sense that it will fork children or threads
as multiple users establish sessions with it. I agree it would be nice to
have a better interface to R than via a system call.
Regards,
Paul Meagher
=
I just timed how long it took to pipe a file containing 2 lines below into R
(via a PHP script executed from my browser):
input.R
--
x = cbind(4,5,3,2,3,4)
x
?php
// timer.php
function getmicrotime(){
list($usec, $sec) = explode( ,microtime());
return ((float)$usec + (float)$sec);
}
$time_start = getmicrotime();
$Input = ./input.R;
$Output = ./output.R;
$RPath = /usr/local/bin/R;
system($RPath --no-save $Input $Output);
$fp = fopen($Output, r);
while (!feof($fp)) {
$line = fgets($fp,4096);
echo $line .br;
}
fclose($fp);
$time_end = getmicrotime();
$time = $time_end - $time_start;
echo pTime To Execute: $time seconds/p;
?
The time to execute this script was 3.1081320047379 seconds (if I execute
the script a few times this around what I get).
I then removed the line that calls R only. There was something in the
output.R file so, in essense, the only difference between the original
script and modified script is the removal of the system call to R.
The time to execute was 0.0010089874267578 seconds
By subtractive logic, this means the call to R incurs an overhead of around
3 seconds on a average web server box using the php-apache module.
- Original Message -
From: Zitan Broth [EMAIL PROTECTED]
To: [EMAIL PROTECTED]
Cc: [EMAIL PROTECTED]
Sent: Wednesday, September 24, 2003 2:46 PM
Subject: Re: [R] R Production Performance
Hi James,
Thanks for your response :-)
- Original Message -
It is like anything else that you want to run as part of web services:
what
do you want it to do? Yes, it is fast in doing computations, but what
will
you have it do? It is probably as fast as anything else that you will
find
out there that is fairly general purpose.
I just want to use R for mathematical computations, and will call it via
PHP
from the commandline with infile. We'll need to obviously test this
ourselves, but I just thought I'd raise the question :-))
Are you going to be creating a lot of graphics that have to be displayed
back on the screen? How is the user going to input data (flat files,
XML,
Excel worksheets, Oracle database, ...)? Will you be invoking a unique
process each time a user calls, or will you be using a 'daemon' that
will
communicate with DCOM and such? How many people will be trying to
access
it once and what is the mix of transactions that they will use?
Well for sure the rest of the app needs to scale as well and be fast,
failsafe etc..., but I am just asking about R.
I was imagining using a unique process call each time I access R, which is
how the apache/php/*nix environment works best (although keeping processes
in memory is achievable as well). My experience to date on integration
with
C packages deploying to *nix is that this works quite effectively although
certain packages require process management that are not multiprocess (to
ensure that R for example only executes one computation at a time), but
this
is no problem. There are ways to call c packages directly with PHP (swig)
and I am investigating this at present.
You can probably get a real good feel by enclosing the operations that
you
want to do in a system.time function to see how long it will take.
This
really depends on what you are trying to do. I can definitely say that
it
is faster than trying to code the algorithm in PERL or another scripting
language.
Makes sense because R is written in C, where PERL and PHP are also written
in C, so R is a layer deep so to speak :-)
Thanks again,
Z.
Greetings All,
Been playing with R and it is very easy to get going with the UI or
infile
batch commands :-)
What I am wondering is how scalable and fast R is for running as part of
a
web service. I believe R is written in C which is a great start, but
what
are peoples general thoughts on this?
Thanks greatly,
Z.
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Re: [R] confusion about what to expect?
Marc Schwartz [EMAIL PROTECTED] writes:
On Tue, 2003-09-23 at 18:08, A.J. Rossini wrote:
-- about confusion --
Anyway, the mnemonic to use seems to be to remember that complex data
structures get simplified whenever possible. Thanks to Doug G. and
Patrick C. for that!
I'll plead an excess of Lisp, Python, and C++ recently, but that isn't
a real excuse.
best,
-tony
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[R] weird behaviour when calling c++
I am using 1.7.1 in a PC ( redhat 9, linux ) I created a subroutine in C++, mySubrutine, to be used in R. To debug this subroutine I have a main routine in C++ that calls mySubrutine. The only thing main () does is to provide mySubrutine with its arguments (this is the easiest way for me to debug subroutines written in C++ and intended to be used in R ). I also have a version of the same program in R: an R script that provides mySubrutine with its arguments. When I run the C++ version in gdb I do not have any problem, every time I run it I get the result ( the same result ). The R script calls mySubrutine through .( ) C. Sometimes it gives me the same result I get in the C++ version; sometimes it freezes. This even happens if I execute the script several times in a row ( I use C-c when it freezes ) Any idea? I am using new and delete in mySubrutine, but I guess this should not be any problem. P.S: The first thing the R script executes is rm ( list = ls ( )). To use dyn.unload does not make any difference. Thank you. __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] Omitting blank lines with read.table
On 24 Sep 2003 at 11:32, Patrick Connolly wrote: read.table has an argument blank.lines.skip, which is true by default, at least in read.table. You can try to give that to read.delim? Kjetil Halvorsen Say we have a tab delimited file called bug.txt Part Rep CageHb pupae 1 1 S 32 1 M 34 L 42 2 S 36 M 28 L 36 read.delim(bug.txt) Part Rep Cage Hb.pupae 11 1S 32 2 NA 1M 34 3 NA NAL 42 4 NA NANA 5 NA NANA 6 NA 2S 36 7 NA NAM 28 8 NA NAL 36 Variations on read.table give the same result. When I first used read.table in Splus, I liked the way it ignored rows that were empty (at least when using sep = \t). A line was considerend empty if it contained only tab characters, so the rows of NAs or s are omitted, so that rows 4 and 5 above would be deleted. R's read.table differs in this respect (and a number of really neat ones). I probably know enough Perl to be able to write a short script that could delete such lines, and it's not difficult to remove the rows from the dataframe afterwards; but maybe there's something simple I've misunderstood in the use of R's read.table. I can't use na.omit since the other NAs in the data can be dealt with so I don't want them removed. Other suggestions welcome. Thanks -- Patrick Connolly HortResearch Mt Albert Auckland New Zealand Ph: +64-9 815 4200 x 7188 ~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~ I have the world`s largest collection of seashells. I keep it on all the beaches of the world ... Perhaps you`ve seen it. ---Steven Wright ~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~ __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] R Production Performance
Paul Meagher wrote:
Below is the test I ran awhile back on invoking R as a system call. It
might be faster if you had a c-extension to R but before I went that route I
would want to know 1) roughly how fast Python and Perl are in returning
results with their c-bindings/embedded stuff/dcom stuff, 2) whether R can be
run as a daemon process so you don't incur start up costs, and 3) whether R
can act as a math server in the sense that it will fork children or threads
as multiple users establish sessions with it. I agree it would be nice to
have a better interface to R than via a system call.
I'm doing something similar using PL/R (an R procedural language handler
extension to Postgres that I wrote) with Postgres, R, and PHP. In
Postgres 7.4 (currently at beta3) or with a back-patched copy of 7.3,
you can preload the R interpreter when the Postgres postmaster first
starts. This means that essentially R is running as part of the Postgres
daemon. Whenever a connection is made to the database, the forked
process already has an initialized copy of R running inside it. The
startup savings I see are similar to what you did (2.2 seconds versus
0.009 seconds):
--
Function -- intentionally very simple:
--
create or replace function echo(text) returns text as 'print(arg1)'
language 'plr';
Without preloading (first function call):
-
regression=# explain analyze select echo('hello');
Total runtime: 2195.35 msec
Without preloading (second function call):
-
regression=# explain analyze select echo('hello');
Total runtime: 0.55 msec
With preloading (first function call):
-
regression=# explain analyze select echo('hello');
Total runtime: 9.74 msec
With preloading (second function call):
-
regression=# explain analyze select echo('hello');
Total runtime: 0.59 msec
--
In both cases the second (and subsequent) function calls are even faster
because the PL/R function itself has been precompiled and cached.
I call the PL/R function from PHP to read my data directly from the
database, process it, and generate whatever charts I need. Here's a very
simple example:
The PL/R function:
--
create type histtup as
(
break float8,
count int
);
create or replace function hist(text, text)
returns setof histtup as '
sql - paste(select id_val from sample_numeric_data ,
where ia_id='', arg1, '', sep=)
rs - pg.spi.exec(sql)
if (!is.na(arg2)) {
x11(display=:5)
jpeg(file=arg2, width = 480, height = 480,
pointsize = 12, quality = 75)
par(ask = FALSE, bg = #F8F8F8)
sql - paste(select ia_attname as val from atts ,
where ia_id='', arg1, '', sep=)
attname - pg.spi.exec(sql)
h - hist(rs[,1], col = blue,
main = paste(Histogram of, attname$val),
xlab = attname$val);
dev.off()
system(paste(chmod 666 , arg2, sep=),
intern = FALSE, ignore.stderr = TRUE)
}
else
h - hist(rs[,1], plot = FALSE);
result = data.frame(breaks = h$breaks[1:length(h$breaks)-1],
count = h$counts);
return(result)
' language 'plr';
--
The PHP page:
--
HTMLBODY
?PHP
echo
FORM ACTION='$PHP_SELF' METHOD='post' NAME='proto_form'
TABLE WIDTH='482' CELLSPACING='0' CELLPADDING='1' BORDER='0'
TR
TDData/TD
TDINPUT TYPE='text' NAME='userdata' value='' size='80'/TD
/TR
TR
TD colspan='2'
INPUT TYPE='submit' NAME='submit' value='Submit'
/TD
/TR
/TABLE
/FORM
;
if ($_POST['submit'] == Submit)
{
$tmpfilename = 'charts/hist1.jpg';
$conn = pg_connect(dbname=oscon user=postgres);
$sql = select * from hist(' . $_POST['userdata'] . ',' .
/tmp/ . $tmpfilename . ');
$rs = pg_query($conn,$sql);
echo img src='$tmpfilename' border=0;
}
?
/BODY/HTML
--
Hopefully this gives you some ideas about what is possible. If you're
interested in PL/R, you can grab a copy (along with a patched 7.3.4
source RPM for Postgres) here: http://www.joeconway.com/
HTH,
Joe
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[R] data.frame with duplicated id's
Hi, is there a exstisting function (..i found nothing until now.) what makes it possible transfrom a dataset: ID AGE V.MAI V.JUNE 11 20 100 120 12 30 200 90 into IDAGEV 1120 100 1120 120 1230200 123090 ,or have i to programm ths my self? Thanks for any comment, help and/or starting point. regards,christian [[alternative HTML version deleted]] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
RE: [R] data.frame with duplicated id's
Try ?reshape A -Original Message- From: Christian Schulz [mailto:[EMAIL PROTECTED] Sent: Wednesday, 24 September 2003 3:42 PM To: [EMAIL PROTECTED] Subject: [R] data.frame with duplicated id's Hi, is there a exstisting function (..i found nothing until now.) what makes it possible transfrom a dataset: ID AGE V.MAI V.JUNE 11 20 100 120 12 30 200 90 into IDAGEV 1120 100 1120 120 1230200 123090 ,or have i to programm ths my self? Thanks for any comment, help and/or starting point. regards,christian [[alternative HTML version deleted]] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
