Re: [R] Is 'history' recorded in Rscript?
You should be looking for .Rhistory Some OSes make that task difficult. savehistory is not the file name but rather the name of the function that performs that operation. Try savehistory(file=text.Rhistory) and see if the history file is easier to find. Should be in your working directory. Rscript is a program, not a record of the prior session. -- David. On Sep 4, 2009, at 11:03 PM, Peng Yu wrote: Hi, I run the following command and try to save the commands that have been run in the script. But it seems that no history is recorded. Is it because that the history is not recorded in Rscript? Regards, Peng $ Rscript savehistory.R f=tempfile() f [1] /tmp/Rtmp7WBjGG/file327b23c6 history() Error in savehistory(file) : no history available to save Calls: history - savehistory Execution halted __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. David Winsemius, MD Heritage Laboratories West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] R2WinBUGS question from beginner
Hi R Users, I have--what I think--is a very basic question. I'm trying to use R2WinBUGS and am having difficulty setting up the data properly for repeated measures data in a hierarchical model. First, I know that it is me...not the package, as I sucessfully used R2WinBUGS to run a basic regression. Second, I know that it's not my hierarchical model as I've run it successfully in WinBUGS by using data in rectangular format. Despite this, I would like to figure out how to use R2WinBUGS so that I could examine the data more thoroughly subsequent to the WinBUGS run. 1) Is there literally a step-by-step guide somewhere online that shows how to do this? Some claim to be step by step (Gelman Hill's book, for instance) but gloss over this part of the process. 2) If no online resource, is there a trick that I'm missing to appropriately structure the data. Here are the specific details: I have 100 repeated measures on 655 people. The dataset is initially in long format. From my perusal of online examples/WinBUGS website, I believe data must be in wide format. I have copied the R2WinBUGS code from Gelman and Hill's book website, have tried using dput, have tried using matrix, structure, and dim commands to get things structured correctly. Having tried all these things, each time the data looks good in R, but is rejected by R2WinBUGS usually with the error message expected collection operator c. Despite this, when I look at the datafile in WinBUGS there is a c right there! I've been slowly going crazy trying to figure this out for the last week. Anyway, I'm sure that I am doing something goofy here. Was just hoping for some advice. Sorry, I can't share the data as it is proprietary. Thanks in advance, Mike __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 Boxplot
Hi Petr, Thanks for these comments. I'm sorry that my post was not clear. I was referring to the questions in my original post/code/file uploads, but I had forgotten to include an updated file (now attached http://www.nabble.com/file/p25304663/Post%2Btrial%2Bdata.csv Post+trial+data.csv ) to work with the new code: testdata- c(C:\\Files\\R\\Sample R code\\Post trial data.csv) new_data- read.table(testdata, skip = 0, sep = ,, na.strings = na,header = TRUE) x11(width=16, height=7, pointsize=14) boxplot(new_data,outline = FALSE, col = c(lightblue, salmon), las =1, boxwex = 0.5) legend(top, c(Label for blue boxes,Label for red boxes), cex=1.5, lty=1:2, fill=c(lightblue, salmon), bty=n); title(main=Chart title text, cex.main = 1.8) grid() I'm still not clear how I can get the number format showing #,###. E.g. with this code and attached file, the scale shows as 2000, 1 etc. I don't know how to show 2,000. 10,000 etc. I have looked through sprintf (thanks for suggesting that - I'd spent hours looking without finding it) and it seems incredibly flexible, but the formats shown are more scientific in focus. I still haven't been able to find a way of getting a comma style. Thanks again Guy Petr Pikal wrote: Hi it is rather difficult to understand what you mean by your questions/answers without real reproducible code. r-help-boun...@r-project.org napsal dne 03.09.2009 13:41:11: I'd be interested if anyone has a quick way to get percentages and additionally, how do I get numbers in the 0,000 format along the x or y-axis? In the meantime, I can live with this. plot(1:10,1:10, axes=F) axis(2, at=c(2,3,7,9), labels=c(1.2, 2.38, 13.54, 16.8)) the same applies with boxplot. by bbb- boxplot() you obtain an object which is used by bxp. See help page for boxplot, section See also ... See also par for graphic options, format and or sprintf for formating numbers Regards Petr -- View this message in context: http://www.nabble.com/Problems-with-Boxplot-tp25256461p25304663.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] Problem with xtabs(), exclude=NULL, and counting NA's
xtabs(~wkhp, x, exclude=NULL, na.action=na.pass) wkhp 20 30 40 45 60 NA 1 1 10 1 3 4 Thanks! I must say that this is slightly odd behavior to require both na.action= AND exclude=. Does anyone know of a justification? Shouldn't it be changed? vent Ah well, if R were internally consistent or corresponded to typical programming Unix practices, it just wouldn't feel the same ... /vent Cheers! -- David Winsemius, MD Heritage Laboratories West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Running R on read-only file system, without temporary directory
Thanks for all the answers. I have made some quick and dirty modifications to make it start without a temporary directory and so far it runs OK. Obviously, I cannot do help(), example(), install.packages() and Rprof() and maybe many more, but this is not an interactive machine, but an Rserve server, so these are OK. I will check the tempfile() and tempdir() calls to see what to expect. Gabor On Sat, Sep 5, 2009 at 2:40 AM, William Dunlapwdun...@tibco.com wrote: -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Duncan Murdoch Sent: Friday, September 04, 2009 5:05 PM To: Gábor Csárdi Cc: R mailing list Subject: Re: [R] Running R on read-only file system,without temporary directory On 04/09/2009 3:42 PM, Gábor Csárdi wrote: Dear All, I would like to do run R without having write permissions to any directory on the system. It seems that I need to modify the R source code for this, to make R start without creating a temporary directory. So far, so good. But should I expect any more complications? Does R really need the temporary directory that much? Many R functions create temporary files in it. (There are around 20 calls to tempfile() and another 20 to tempdir() in the base R sources, if my quick grep was right. I've no idea how many calls there are from contributed packages.) Would R work if these all failed? I don't know, but I'd guess it wouldn't work very well. Duncan Murdoch On Linux R can do quite a bit without using R_SESSION_TMPDIR (which is where its temp files get made). You can see if it can do enough for your needs by doing Sys.chmod(Sys.getenv(R_SESSION_TMPDIR), ) right after starting up. E.g., Sys.chmod(Sys.getenv(R_SESSION_TMPDIR), ) 1:10 [1] 1 2 3 4 5 6 7 8 9 10 names(cars) [1] speed dist lm(dist~speed, data=cars) Call: lm(formula = dist ~ speed, data = cars) Coefficients: (Intercept) speed -17.579 3.932 plot(.Last.value) Hit Return to see next plot: Hit Return to see next plot: Hit Return to see next plot: Hit Return to see next plot: help(plot) Error in file(out, wt) : cannot open the connection In addition: Warning message: In file(out, wt) : cannot open file '/tmp/RtmpPxKrY4/Rtxt327b23c6': Permission denied example(lm) Error in file(out, wt) : cannot open the connection In addition: Warning message: In file(out, wt) : cannot open file '/tmp/RtmpPxKrY4/Rex643c9869': Permission denied install.packages(ggplot2) --- Please select a CRAN mirror for use in this session --- Loading Tcl/Tk interface ... done Error in install.packages(ggplot2) : unable to create temporary directory '/tmp/RtmpPxKrY4/downloaded_packages' In addition: Warning message: In dir.create(tmpd) : cannot create dir '/tmp/RtmpPxKrY4/downloaded_packages', reason 'Permission denied' Of couse, that doesn't catch things done during startup or temp files created outside of the R-standard directory. Bill Dunlap TIBCO Software Inc - Spotfire Division wdunlap tibco.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. -- Gabor Csardi gabor.csa...@unil.ch 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] Problem with xtabs(), exclude=NULL, and counting NA's
I must say that this is slightly odd behavior to require both na.action= AND exclude=. Does anyone know of a justification? Not strange at all. ?options na.action, sub head Options set in package stats. You need to override the default setting. ws-7 wrote: xtabs(~wkhp, x, exclude=NULL, na.action=na.pass) wkhp 20 30 40 45 60 NA 1 1 10 1 3 4 Thanks! I must say that this is slightly odd behavior to require both na.action= AND exclude=. Does anyone know of a justification? Shouldn't it be changed? vent Ah well, if R were internally consistent or corresponded to typical programming Unix practices, it just wouldn't feel the same ... /vent Cheers! -- David Winsemius, MD Heritage Laboratories West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- View this message in context: http://www.nabble.com/Problem-with-xtabs%28%29%2C-exclude%3DNULL%2C-and-counting-NA%27s-tp25304142p25305878.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] What is the difference between read.delim and read.delim2?
In some countries a decimal comma is the norm. On Fri, Sep 4, 2009 at 6:16 PM, David Winsemiusdwinsem...@comcast.net wrote: It's pretty subtle, I will admit, but look more carefully at the dec= parameter in the help page. Kind of like the historical battles between between the Liebnizians and the Newtonians. On Sep 4, 2009, at 5:58 PM, Peng Yu wrote: Hi, I don't see what the difference between read.delim and read.delim2 after reading the help. Can somebody let me know what it is? Regards, Peng David Winsemius, MD Heritage Laboratories West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 can I appoint a small part of the whole data
Dear Petr, your suggestion is useful many thanks for your help ! best, Yichih 2009/9/3 Petr PIKAL petr.pi...@precheza.cz Hi use any of suitable selection ways that are in R. E.g. data[data$gender==1, ] selects only female values data$wage[(data$gender==1) (data$race=1)] selects black female wages. and see also ?subset Regards Petr r-help-boun...@r-project.org napsal dne 03.09.2009 10:51:59: Dear all, I have 1980~1990 eleven datas, every year have three variables, wage gender(1=female, 2=male) race(1=black, 2=white) My original commands is: fig2b-reldist(y=mu1990$wage,yo=mu1980$wage,...) I have three questions: 1. If I want to appoint y=women's wage in 1990 yo=women's wage in 1980 2. If I want to appoint y=women's wage in 1990 yo=men's wage in 1990 3. If I want to appoint y=black women's wage in 1990 yo=white women's wage in 1990 How can I modify the commands? All help highly appreciated. Best, Yichih -- Yichih Hsieh e-mail : yichih.hs...@gmail.com [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.htmlhttp://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Yichih Hsieh e-mail : yichih.hs...@gmail.com [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Problem accessing functions in package 'roxygen'
Robert A LaBudde wrote:
Thanks, Uwe. Unfortunately, that doesn't work either:
library('roxygen')
Warning message:
package 'roxygen' was built under R version 2.9.1
roxygen::trim(' 1234 ')
You need three colons as indicated in my previous answer!
Uwe
Error: 'trim' is not an exported object from 'namespace:roxygen'
I ended up using
trim - function(x) gsub(^[[:space:]]+|[[:space:]]+$, , x)
instead.
At 01:42 PM 9/3/2009, Uwe Ligges wrote:
Robert A. LaBudde wrote:
I have Vista Home with R-2.9.0, and installed and tried to test the
package 'roxygen':
utils:::menuInstallPkgs()
trying URL
'http://lib.stat.cmu.edu/R/CRAN/bin/windows/contrib/2.9/roxygen_0.1.zip'
Content type 'application/zip' length 699474 bytes (683 Kb)
opened URL
downloaded 683 Kb
package 'roxygen' successfully unpacked and MD5 sums checked
The downloaded packages are in
C:\Users\RAL\AppData\Local\Temp\RtmpZPlILq\downloaded_packages
updating HTML package descriptions
Warning message:
In file.create(f.tg) :
cannot create file 'C:\PROGRA~1\R\R-29~1.0/doc/html/packages.html',
reason 'Permission denied'
library('roxygen')
Warning message:
package 'roxygen' was built under R version 2.9.1
trim( 1234)
Error: could not find function trim
I have a similar problem with trim.right(), trim.left() and other
functions I've tried.
Any ideas?
Probably it is not intende to call trim and friends like that, because
they are not exported from roxygen's namespace, hence you could use
roxygen:::trim( 1234)
Uwe Ligges
Robert A. LaBudde, PhD, PAS, Dpl. ACAFS e-mail: r...@lcfltd.com
Least Cost Formulations, Ltd.URL: http://lcfltd.com/
824 Timberlake Drive Tel: 757-467-0954
Virginia Beach, VA 23464-3239Fax: 757-467-2947
Vere scire est per causas scire
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PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Robert A. LaBudde, PhD, PAS, Dpl. ACAFS e-mail: r...@lcfltd.com
Least Cost Formulations, Ltd.URL: http://lcfltd.com/
824 Timberlake Drive Tel: 757-467-0954
Virginia Beach, VA 23464-3239Fax: 757-467-2947
Vere scire est per causas scire
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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[R] Color index in image function
Dear All, I was looking for the color index in image function, such as from topo.colors(n) and etc. but still never found it. For instance, from the help menu. ### # Volcano data visualized as matrix. Need to transpose and flip # matrix horizontally. image(t(volcano)[ncol(volcano):1,]) # A prettier display of the volcano x - 10*(1:nrow(volcano)) y - 10*(1:ncol(volcano)) image(x, y, volcano, col = terrain.colors(100), axes = FALSE) contour(x, y, volcano, levels = seq(90, 200, by = 5), add = TRUE, col = peru) axis(1, at = seq(100, 800, by = 100)) axis(2, at = seq(100, 600, by = 100)) box() title(main = Maunga Whau Volcano, font.main = 4) # From the script above, it yields a beautiful image of volcano with variety of colors but i have to list down the color index that could show the meaning of each color in my thesis. Could someone please help me to extract this color index? Thank you Fir __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Color index in image function
Dear All, I was looking for the color index in image function, such as from topo.colors(n) and etc. but still never found it. For instance, from the help menu. ### # Volcano data visualized as matrix. Need to transpose and flip # matrix horizontally. image(t(volcano)[ncol(volcano):1,]) # A prettier display of the volcano x - 10*(1:nrow(volcano)) y - 10*(1:ncol(volcano)) image(x, y, volcano, col = terrain.colors(100), axes = FALSE) contour(x, y, volcano, levels = seq(90, 200, by = 5), add = TRUE, col = peru) axis(1, at = seq(100, 800, by = 100)) axis(2, at = seq(100, 600, by = 100)) box() title(main = Maunga Whau Volcano, font.main = 4) # From the script above, it yields a beautiful image of volcano with variety of colors but i have to list down the color index that could show the meaning of each color in my thesis. Could someone please help me to extract this color index? Thank you Fir __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] several questions about R graphic properties
I have a several questions about R graphic properties. I use a barplot2 function for creating plots with error bars. My data include species' names in first column, and I need make plots for each species. I know how to select species for each plot: D-read.table(FD_R.txt, h=T) Dens-D[D[,1]==Sit.eur,] but I want to make a cycle which will automatically change the species' name and save each plot in jpg file. How can I do it? Also, my data include results of two-year work, and I want to make two plots for each year one above another in the same box. Is it possible? And the last question: are there any functions in R which will allow to get data from Access? I know about getfromaccess function from vegan packcage, but it works only with environmental data with very restricted structure. I would be very much obliged for your answers. A. A. Morkovin, PhD student. -- __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] several questions about R graphic properties
SOmething like this should work where you 'split' you data frame by
the contents of the first column and then plot the data:
Dens - split(D, D[,1])
for (i in Dens){ # process each species
jpeg(paste(i[1,1], '.jpg', sep='') # create file with species name
plot(., main=i[1,1])
dev.off()
}
On Sat, Sep 5, 2009 at 7:52 AM, Антон Морковинa-morko...@yandex.ru wrote:
I have a several questions about R graphic properties.
I use a barplot2 function for creating plots with error bars. My data
include species' names in first column, and I need make plots for each
species. I know how to select species for each plot:
D-read.table(FD_R.txt, h=T)
Dens-D[D[,1]==Sit.eur,]
but I want to make a cycle which will automatically change the species' name
and save each plot in jpg file. How can I do it?
Also, my data include results of two-year work, and I want to make two plots
for each year one above another in the same box. Is it possible?
And the last question: are there any functions in R which will allow to get
data from Access? I know about getfromaccess function from vegan packcage,
but it works only with environmental data with very restricted structure.
I would be very much obliged for your answers.
A. A. Morkovin, PhD student.
--
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Jim Holtman
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+1 513 646 9390
What is the problem that you are trying to solve?
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Re: [R] How can I appoint a small part of the whole data
Dear all, I got another problem: if education have five levels edu=1 edu=2 edu=3 edu=4 edu=5 If I want to appoint y=edu2~4 in 1990 which programs is correct? I tried this two programs, they both work, but two results is different. 1. fig2b-reldist(y=mu1990$wage[mu1990$edu==2|3|4],..) 2. fig2b-reldist(y=mu1990$wage[mu1990$edu%in%2:4],..) which one is correct? and why they have different results? All help high appreciated. best, Yichih 2009/9/5 Yichih Hsieh yichih.hs...@gmail.com Dear Petr, your suggestion is useful many thanks for your help ! best, Yichih 2009/9/3 Petr PIKAL petr.pi...@precheza.cz Hi use any of suitable selection ways that are in R. E.g. data[data$gender==1, ] selects only female values data$wage[(data$gender==1) (data$race=1)] selects black female wages. and see also ?subset Regards Petr r-help-boun...@r-project.org napsal dne 03.09.2009 10:51:59: Dear all, I have 1980~1990 eleven datas, every year have three variables, wage gender(1=female, 2=male) race(1=black, 2=white) My original commands is: fig2b-reldist(y=mu1990$wage,yo=mu1980$wage,...) I have three questions: 1. If I want to appoint y=women's wage in 1990 yo=women's wage in 1980 2. If I want to appoint y=women's wage in 1990 yo=men's wage in 1990 3. If I want to appoint y=black women's wage in 1990 yo=white women's wage in 1990 How can I modify the commands? All help highly appreciated. Best, Yichih -- Yichih Hsieh e-mail : yichih.hs...@gmail.com [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.htmlhttp://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Yichih Hsieh e-mail : yichih.hs...@gmail.com -- Yichih Hsieh e-mail : yichih.hs...@gmail.com [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How can I appoint a small part of the whole data
Hi, you have two problems in your first scenario, 1- Wrong operator precedence. For example, 1 == 2 | 3 [1] TRUE where 1==2 is tested as FALSE, but 1 is not tested against 3 for equality as it would be using, 1 == 2 | 1 == 3 [1] FALSE or using %in% 2:3 Instead, R evaluates FALSE | 3, and 2- it so happens that non-zero integers are treated as TRUE, according to ?| as.logical(1) [1] TRUE as.logical(0) [1] FALSE HTH, baptiste 2009/9/5 Yichih Hsieh yichih.hs...@gmail.com Dear all, I got another problem: if education have five levels edu=1 edu=2 edu=3 edu=4 edu=5 If I want to appoint y=edu2~4 in 1990 which programs is correct? I tried this two programs, they both work, but two results is different. 1. fig2b-reldist(y=mu1990$wage[mu1990$edu==2|3|4],..) 2. fig2b-reldist(y=mu1990$wage[mu1990$edu%in%2:4],..) which one is correct? and why they have different results? All help high appreciated. best, Yichih 2009/9/5 Yichih Hsieh yichih.hs...@gmail.com Dear Petr, your suggestion is useful many thanks for your help ! best, Yichih 2009/9/3 Petr PIKAL petr.pi...@precheza.cz Hi use any of suitable selection ways that are in R. E.g. data[data$gender==1, ] selects only female values data$wage[(data$gender==1) (data$race=1)] selects black female wages. and see also ?subset Regards Petr r-help-boun...@r-project.org napsal dne 03.09.2009 10:51:59: Dear all, I have 1980~1990 eleven datas, every year have three variables, wage gender(1=female, 2=male) race(1=black, 2=white) My original commands is: fig2b-reldist(y=mu1990$wage,yo=mu1980$wage,...) I have three questions: 1. If I want to appoint y=women's wage in 1990 yo=women's wage in 1980 2. If I want to appoint y=women's wage in 1990 yo=men's wage in 1990 3. If I want to appoint y=black women's wage in 1990 yo=white women's wage in 1990 How can I modify the commands? All help highly appreciated. Best, Yichih -- Yichih Hsieh e-mail : yichih.hs...@gmail.com [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html http://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Yichih Hsieh e-mail : yichih.hs...@gmail.com -- Yichih Hsieh e-mail : yichih.hs...@gmail.com [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- _ Baptiste Auguié School of Physics University of Exeter Stocker Road, Exeter, Devon, EX4 4QL, UK http://newton.ex.ac.uk/research/emag __ [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How can I appoint a small part of the whole data
Yichih, Answer 2 is correct, because your indexing specification for 1 is wrong. You also seem to have left out a comma. ## mu1990$wage[mu1990$edu==2|mu1990$edu==3|mu1990$edu==4, ] ## like this mu1990$wage[mu1990$edu%in%2:4, ] You really could have worked this out for yourself by looking at the results of your subsetting/indexing operation. Mark. Yichih Hsieh wrote: Dear all, I got another problem: if education have five levels edu=1 edu=2 edu=3 edu=4 edu=5 If I want to appoint y=edu2~4 in 1990 which programs is correct? I tried this two programs, they both work, but two results is different. 1. fig2b-reldist(y=mu1990$wage[mu1990$edu==2|3|4],..) 2. fig2b-reldist(y=mu1990$wage[mu1990$edu%in%2:4],..) which one is correct? and why they have different results? All help high appreciated. best, Yichih 2009/9/5 Yichih Hsieh yichih.hs...@gmail.com Dear Petr, your suggestion is useful many thanks for your help ! best, Yichih 2009/9/3 Petr PIKAL petr.pi...@precheza.cz Hi use any of suitable selection ways that are in R. E.g. data[data$gender==1, ] selects only female values data$wage[(data$gender==1) (data$race=1)] selects black female wages. and see also ?subset Regards Petr r-help-boun...@r-project.org napsal dne 03.09.2009 10:51:59: Dear all, I have 1980~1990 eleven datas, every year have three variables, wage gender(1=female, 2=male) race(1=black, 2=white) My original commands is: fig2b-reldist(y=mu1990$wage,yo=mu1980$wage,...) I have three questions: 1. If I want to appoint y=women's wage in 1990 yo=women's wage in 1980 2. If I want to appoint y=women's wage in 1990 yo=men's wage in 1990 3. If I want to appoint y=black women's wage in 1990 yo=white women's wage in 1990 How can I modify the commands? All help highly appreciated. Best, Yichih -- Yichih Hsieh e-mail : yichih.hs...@gmail.com [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.htmlhttp://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Yichih Hsieh e-mail : yichih.hs...@gmail.com -- Yichih Hsieh e-mail : yichih.hs...@gmail.com [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- View this message in context: http://www.nabble.com/How-can-I-appoint-a-small-part-of-the-whole-data-tp25272209p25308714.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] help with functions
Thanks Baptiste
On Fri, Sep 4, 2009 at 5:13 PM, baptiste auguie
baptiste.aug...@googlemail.com wrote:
Hi,
I think you've got a problem with environments,
testA-function(input=1)
{
dat - data.frame(A=seq(input,5), B=seq(6,10))
vec.names- c(a, b)
env - new.env()
for(i in 1:ncol(dat))
{
tab- dat[,i]-1
assign(vec.names[i], tab, env=env)
}
do.call(rbind, lapply(vec.names, get, env=env))
}
testA()
But more generally, I doubt your construct using assign and get is the most
natural way to reach your goal in R.
HTH,
baptiste
2009/9/4 jonas garcia garcia.jona...@googlemail.com
Hi all,
I have got 2 function (see bellow) which are simplifications of what I
need
to do. These functions are precisely the same, except for the last line.
My question is, why doesn't function testA work in the same way as
function
testB.
Both functions produce two objects, a and b that must merged with
rbind.
The difference is that in testA, I specify the name of the objects while
in
testA I am stating which objects I want to bind from a character vector.
What's more, if I just run the code without a function (example given
below
as well), they both work...
Why is this?
Thanks in advance
Jonas
testA-function(input)
{
dat- data.frame(A=seq(input,5), B=seq(6,10))
vec.names- c(a, b)
for(i in 1:ncol(dat))
{
tab- dat[,i]-1
assign(vec.names[i], tab)
}
do.call(rbind, lapply(vec.names, get))
}
testB-function(input)
{
dat- data.frame(A=seq(input,5), B=seq(6,10))
vec.names- c(a, b)
for(i in 1:ncol(dat))
{
tab- dat[,i]-1
assign(vec.names[i], tab)
}
rbind(a,b)
}
testA(1)
Error in FUN(c(a, b)[[1L]], ...) : object 'a' not found
testB(1)
[,1] [,2] [,3] [,4] [,5]
a01234
b56789
###
dat- data.frame(A=seq(1,5), B=seq(6,10))
vec.names- c(a, b)
for(i in 1:ncol(dat))
{
tab- dat[,i]-1
assign(vec.names[i], tab)
}
do.call(rbind, lapply(vec.names, get))
[,1] [,2] [,3] [,4] [,5]
[1,]01234
[2,]56789
dat- data.frame(A=seq(1,5), B=seq(6,10))
vec.names- c(a, b)
for(i in 1:ncol(dat))
{
tab- dat[,i]-1
assign(vec.names[i], tab)
}
rbind(a,b)
[,1] [,2] [,3] [,4] [,5]
a01234
b56789
[[alternative HTML version deleted]]
__
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PLEASE do read the posting guide
http://www.R-project.org/posting-guide.htmlhttp://www.r-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
_
Baptiste Auguié
School of Physics
University of Exeter
Stocker Road,
Exeter, Devon,
EX4 4QL, UK
http://newton.ex.ac.uk/research/emag
__
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Re: [R] 0 x 0 matrix
On 04-Sep-09 10:45:27, Markku Karhunen wrote: True. Should have read ?diag. However, this provokes a more general question: Is there some way I can declare some scalar and _all its functions_ as matrices? For instance, I would like to A = as.matrix(0.98) B = function(A) C = diag(sqrt(B)) so that all scalars are explicitly [1,1] matrices. BR, Markku Hmmm, it might be a good idea to explain why you want to do this. For instance: M - matrix(c(1,2,3,4),nrow=2) c - matrix(2,nrow=1) c%*%M # Error in c %*% M : non-conformable arguments c*M # Error in c * M : non-conformable arrays c+M # Error in c + M : non-conformable arrays So what would you want to use the [1,1]-matrix scalars for, that cannot be done just using them as numbers? Ted. Broadly speaking, I would like to use the same code for multivariate and univariate cases. For instance, I use the inverse Wishart densities of MCMCpack. If I take diwish(x) of a scalar x, the programme crashes, because diwish() by default checks ncol(x)==nrow(x). However, I would like to have an inverse gamma density. Best, Markku __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Running two R instances at the same time
Dear R experts, please excuse me for writing to the mailing list without subscribing. I have a somewhat urgent problem that relates to R. I have to process large amounts of data with R - I'm in an international collaboration and the data processing protocol is fixed, that is a specific set of R commands has to be used. I wrote a perl program that manages creation of data subsets from my database and feeds these subsets to an R process via pipes. This worked all right, however, I wanted to speed things up by exploiting the fact that I have a dual-core machine. So I rewrote my perl driver program to use two threads, each starting its own R instance, getting data off a queue and feeding it to its R process. This also worked, except that I noticed something very peculiar: the processing time was almost exactly the same for both cases. I did some tests to look at this, and it seems that R needs twice the time to do the exact same thing if there are two instances of it running. I don't understand how is this possible. Maybe there is an issue of thread-safety with the R backend, meaning that the two R *interpreter* instances are talking to the same backend that's capable of processing only one thing at a time? Technical details: OS was Ubuntu 9.04 running on a Core2Dou E7300, and the R version used was the default one from the Ubuntu repository. Please see http://www.perlmonks.org/?node_id=792460 for an extended discussion of the problem, and especially http://www.perlmonks.org/?node_id=793506 for excerpts of output and actual code. Thanks for your answers in advance: Péter Juhász __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 'history' recorded in Rscript?
Hi, I got the following error. Does it mean that the files in the save session will not be saved in history in Rscript? $ Rscript savehistory.R f=tempfile() f [1] /tmp/RtmpMEGKVq/file327b23c6 savehistory(f) Error in savehistory(file) : no history available to save Execution halted Regards, Peng On Sat, Sep 5, 2009 at 1:04 AM, David Winsemiusdwinsem...@comcast.net wrote: You should be looking for .Rhistory Some OSes make that task difficult. savehistory is not the file name but rather the name of the function that performs that operation. Try savehistory(file=text.Rhistory) and see if the history file is easier to find. Should be in your working directory. Rscript is a program, not a record of the prior session. -- David. On Sep 4, 2009, at 11:03 PM, Peng Yu wrote: Hi, I run the following command and try to save the commands that have been run in the script. But it seems that no history is recorded. Is it because that the history is not recorded in Rscript? Regards, Peng $ Rscript savehistory.R f=tempfile() f [1] /tmp/Rtmp7WBjGG/file327b23c6 history() Error in savehistory(file) : no history available to save Calls: history - savehistory Execution halted __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. David Winsemius, MD Heritage Laboratories West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Is 'history' recorded in Rscript?
You did not make it clear (to me anyway) what computing environment the Rscript command was issued from. I assumed probably incorrectly that you were doing this from inside an R session and did not understand that Rscript was an external program. If I was wrong about that, then you are going to need to provide more details about your operating system and how you have set up your R installation. I also do not know what you mean by a save session. Did you at some time in the past execute a savehistory(file=savehistory,R) command at the end of a session and it's now in the directory that Rscript look for? That would be the only way that a savehistory.R file would exist. So what OS? What did you do before this failed effort? And what are you really trying to do? Then perhaps someone familiar with your OS can answer. -- David . On Sep 5, 2009, at 10:52 AM, Peng Yu wrote: Hi, I got the following error. Does it mean that the files in the save session will not be saved in history in Rscript? $ Rscript savehistory.R f=tempfile() f [1] /tmp/RtmpMEGKVq/file327b23c6 savehistory(f) Error in savehistory(file) : no history available to save Execution halted Regards, Peng On Sat, Sep 5, 2009 at 1:04 AM, David Winsemiusdwinsem...@comcast.net wrote: You should be looking for .Rhistory Some OSes make that task difficult. savehistory is not the file name but rather the name of the function that performs that operation. Try savehistory(file=text.Rhistory) and see if the history file is easier to find. Should be in your working directory. Rscript is a program, not a record of the prior session. -- David. On Sep 4, 2009, at 11:03 PM, Peng Yu wrote: Hi, I run the following command and try to save the commands that have been run in the script. But it seems that no history is recorded. Is it because that the history is not recorded in Rscript? Regards, Peng $ Rscript savehistory.R f=tempfile() f [1] /tmp/Rtmp7WBjGG/file327b23c6 history() Error in savehistory(file) : no history available to save Calls: history - savehistory Execution halted David Winsemius, MD Heritage Laboratories West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] How to 'apply' on multiple arguments?
Hi,
I am wonder if there is a function similar 'apply' but it could accept
multiple arguments?
For example, I have the following matrix.
x=matrix(1:6,nr=2)
y=matrix(1:6,nr=2)
I want to find a function that can be used to compute the linear
regression for each pair of rows in the two matrices?
multiple_apply(x,y,1,function(u,v){lm(u ~ v)}
That is, I wound like something like the above to compute the
following. Can somebody let me know if there is such an command in R?
lm(x[1,]~y[1,])
lm(x[2,]~y[2,])
Regards,
Peng
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Re: [R] Is 'history' recorded in Rscript?
Hi, I run Rscript from the command line (bash). My OS is the following $ cat /etc/redhat-release CentOS release 5 (Final) $ uname -a Linux selenium.cluster 2.6.18-53.1.13.el5 #1 SMP Tue Feb 12 13:02:30 EST 2008 x86_64 GNU/Linux $ dmesg | grep gcc Linux version 2.6.18-53.1.13.el5 (mockbu...@builder6.centos.org) (gcc version 4.1.2 20070626 (Red Hat 4.1.2-14)) #1 SMP Tue Feb 12 13:02:30 EST 2008 I can use savehistory in an R session (that is after the R prompt ''). My file 'savehistory.R' only have the following three lines. f=tempfile() f savehistory(f) I run the command 'Rscript savehistory.R' from the bash command line, which gave me the error I showed in my previous email. Can somebody try if he/she receives the save error? Regards, Peng On Sat, Sep 5, 2009 at 10:16 AM, David Winsemiusdwinsem...@comcast.net wrote: You did not make it clear (to me anyway) what computing environment the Rscript command was issued from. I assumed probably incorrectly that you were doing this from inside an R session and did not understand that Rscript was an external program. If I was wrong about that, then you are going to need to provide more details about your operating system and how you have set up your R installation. I also do not know what you mean by a save session. Did you at some time in the past execute a savehistory(file=savehistory,R) command at the end of a session and it's now in the directory that Rscript look for? That would be the only way that a savehistory.R file would exist. So what OS? What did you do before this failed effort? And what are you really trying to do? Then perhaps someone familiar with your OS can answer. -- David . On Sep 5, 2009, at 10:52 AM, Peng Yu wrote: Hi, I got the following error. Does it mean that the files in the save session will not be saved in history in Rscript? $ Rscript savehistory.R f=tempfile() f [1] /tmp/RtmpMEGKVq/file327b23c6 savehistory(f) Error in savehistory(file) : no history available to save Execution halted Regards, Peng On Sat, Sep 5, 2009 at 1:04 AM, David Winsemiusdwinsem...@comcast.net wrote: You should be looking for .Rhistory Some OSes make that task difficult. savehistory is not the file name but rather the name of the function that performs that operation. Try savehistory(file=text.Rhistory) and see if the history file is easier to find. Should be in your working directory. Rscript is a program, not a record of the prior session. -- David. On Sep 4, 2009, at 11:03 PM, Peng Yu wrote: Hi, I run the following command and try to save the commands that have been run in the script. But it seems that no history is recorded. Is it because that the history is not recorded in Rscript? Regards, Peng $ Rscript savehistory.R f=tempfile() f [1] /tmp/Rtmp7WBjGG/file327b23c6 history() Error in savehistory(file) : no history available to save Calls: history - savehistory Execution halted David Winsemius, MD Heritage Laboratories West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Running two R instances at the same time
if I look at your output, the single thread is using almost 100% of the two cpus (3:49 real, 5:49 user or something close to that). for the two thread case it is close to the same with the user now something like 6:15. I would like to see what the contribution of each of the processes are. put some proc. time calls in the R script to see what it is using. Sent from my iPhone On Sep 5, 2009, at 7:21, Peter Juhasz peter.juhas...@gmail.com wrote: Dear R experts, please excuse me for writing to the mailing list without subscribing. I have a somewhat urgent problem that relates to R. I have to process large amounts of data with R - I'm in an international collaboration and the data processing protocol is fixed, that is a specific set of R commands has to be used. I wrote a perl program that manages creation of data subsets from my database and feeds these subsets to an R process via pipes. This worked all right, however, I wanted to speed things up by exploiting the fact that I have a dual-core machine. So I rewrote my perl driver program to use two threads, each starting its own R instance, getting data off a queue and feeding it to its R process. This also worked, except that I noticed something very peculiar: the processing time was almost exactly the same for both cases. I did some tests to look at this, and it seems that R needs twice the time to do the exact same thing if there are two instances of it running. I don't understand how is this possible. Maybe there is an issue of thread-safety with the R backend, meaning that the two R *interpreter* instances are talking to the same backend that's capable of processing only one thing at a time? Technical details: OS was Ubuntu 9.04 running on a Core2Dou E7300, and the R version used was the default one from the Ubuntu repository. Please see http://www.perlmonks.org/?node_id=792460 for an extended discussion of the problem, and especially http://www.perlmonks.org/?node_id=793506 for excerpts of output and actual code. Thanks for your answers in advance: Péter Juhász __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] linear regression between two lists of vectors?
Hi, I am not familiar enough with statistics yet. Please excuse me if my question is wrong. In the simplest form of linear regression, the data points are two list of scalars x_1, ..., x_n and y_1, ..., y_n. I am wondering if there is a linear regression for two lists of vectors X_1, ..., X_n and Y_1, ..., Y_n. 'lm' on two vectors, which works. But it seems that 'lm' does not work on two matrices. Is there a way to do a linear regression on two lists of vectors? Regards, Peng __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Running two R instances at the same time
Why instead you don't explore packages 'multicore' or 'snow+showfall (using sockets)'? Ciao! mario Peter Juhasz wrote: Dear R experts, please excuse me for writing to the mailing list without subscribing. I have a somewhat urgent problem that relates to R. I have to process large amounts of data with R - I'm in an international collaboration and the data processing protocol is fixed, that is a specific set of R commands has to be used. I wrote a perl program that manages creation of data subsets from my database and feeds these subsets to an R process via pipes. This worked all right, however, I wanted to speed things up by exploiting the fact that I have a dual-core machine. So I rewrote my perl driver program to use two threads, each starting its own R instance, getting data off a queue and feeding it to its R process. This also worked, except that I noticed something very peculiar: the processing time was almost exactly the same for both cases. I did some tests to look at this, and it seems that R needs twice the time to do the exact same thing if there are two instances of it running. I don't understand how is this possible. Maybe there is an issue of thread-safety with the R backend, meaning that the two R *interpreter* instances are talking to the same backend that's capable of processing only one thing at a time? Technical details: OS was Ubuntu 9.04 running on a Core2Dou E7300, and the R version used was the default one from the Ubuntu repository. Please see http://www.perlmonks.org/?node_id=792460 for an extended discussion of the problem, and especially http://www.perlmonks.org/?node_id=793506 for excerpts of output and actual code. Thanks for your answers in advance: Péter Juhász __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Ing. Mario Valle Data Analysis and Visualization Group| http://www.cscs.ch/~mvalle Swiss National Supercomputing Centre (CSCS) | Tel: +41 (91) 610.82.60 v. Cantonale Galleria 2, 6928 Manno, Switzerland | Fax: +41 (91) 610.82.82 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Selecting biological data
Hello all, I am new to R but have some experience with MATLAB and am trying to make the switch. I generally find the two languages easy to adapt but there are a few routine tasks which I would like to run smoother in R and I am having trouble finding a help resource. Could someone suggest a guide to filtering, selecting, sorting, and processing biological matrix data? Here is a rudimentary example of what I'm after [ocean research cruise- data.frame-example]: Cruise, dec yr, station, cast, depth, data1 1, 2007.65, 9, 29, 1, 105.04 1, 2007.65, 9, 29, 10, 104.91 1, 2007.65, 9, 29, 20, 101.43 1, 2007.65, 9, 29, 50, 100.68 1, 2007.65, 9, 29, 100, 100.09 1, 2007.69, 11, 33, 1, 107.32 1, 2007.69, 11, 33, 10, 105.94 1, 2007.69, 11, 33, 20, 102.19 1, 2007.69, 11, 33, 50, 101.27 1, 2007.69, 11, 33, 100, 100.15 Let's say I would like to select data1 from cast 33 at 1, 20, and 100m depth... how would I go about this? Thanks in advance for helping out a greenhorn! John _ Facebook. :ON:WL:en-US:SI_SB_facebook:082009 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to 'apply' on multiple arguments?
Yes, see mapply.
On Sat, Sep 5, 2009 at 12:18 PM, Peng Yu pengyu...@gmail.com wrote:
Hi,
I am wonder if there is a function similar 'apply' but it could accept
multiple arguments?
For example, I have the following matrix.
x=matrix(1:6,nr=2)
y=matrix(1:6,nr=2)
I want to find a function that can be used to compute the linear
regression for each pair of rows in the two matrices?
multiple_apply(x,y,1,function(u,v){lm(u ~ v)}
That is, I wound like something like the above to compute the
following. Can somebody let me know if there is such an command in R?
lm(x[1,]~y[1,])
lm(x[2,]~y[2,])
Regards,
Peng
__
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PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Henrique Dallazuanna
Curitiba-Paraná-Brasil
25° 25' 40 S 49° 16' 22 O
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] Selecting biological data
subset(data1,cast==33(depth %in% c(1,20,100)) Sent from my iPhone On Sep 5, 2009, at 11:58, John Casey johnrca...@hotmail.com wrote: Hello all, I am new to R but have some experience with MATLAB and am trying to make the switch. I generally find the two languages easy to adapt but there are a few routine tasks which I would like to run smoother in R and I am having trouble finding a help resource. Could someone suggest a guide to filtering, selecting, sorting, and processing biological matrix data? Here is a rudimentary example of what I'm after [ocean research cruise- data.frame-example]: Cruise, dec yr, station, cast, depth, data1 1, 2007.65, 9, 29, 1, 105.04 1, 2007.65, 9, 29, 10, 104.91 1, 2007.65, 9, 29, 20, 101.43 1, 2007.65, 9, 29, 50, 100.68 1, 2007.65, 9, 29, 100, 100.09 1, 2007.69, 11, 33, 1, 107.32 1, 2007.69, 11, 33, 10, 105.94 1, 2007.69, 11, 33, 20, 102.19 1, 2007.69, 11, 33, 50, 101.27 1, 2007.69, 11, 33, 100, 100.15 Let's say I would like to select data1 from cast 33 at 1, 20, and 100m depth... how would I go about this? Thanks in advance for helping out a greenhorn! John _ Facebook. :ON:WL:en-US:SI_SB_facebook:082009 [[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] Selecting biological data
On Sep 5, 2009, at 11:58 AM, John Casey wrote: Hello all, I am new to R but have some experience with MATLAB and am trying to make the switch. I generally find the two languages easy to adapt but there are a few routine tasks which I would like to run smoother in R and I am having trouble finding a help resource. Could someone suggest a guide to filtering, selecting, sorting, and processing biological matrix data? Here is a rudimentary example of what I'm after [ocean research cruise- data.frame-example]: Cruise, dec yr, station, cast, depth, data1 1, 2007.65, 9, 29, 1, 105.04 1, 2007.65, 9, 29, 10, 104.91 1, 2007.65, 9, 29, 20, 101.43 1, 2007.65, 9, 29, 50, 100.68 1, 2007.65, 9, 29, 100, 100.09 1, 2007.69, 11, 33, 1, 107.32 1, 2007.69, 11, 33, 10, 105.94 1, 2007.69, 11, 33, 20, 102.19 1, 2007.69, 11, 33, 50, 101.27 1, 2007.69, 11, 33, 100, 100.15 Let's say I would like to select data1 from cast 33 at 1, 20, and 100m depth... how would I go about this? ?subset subset(df1, cast==33 depth %in% c(1,20,100) ) ... or since your specification was vague; subset(df1, cast==33 depth==1 ) subset(df1, cast==33 depth==20 ) subset(df1, cast==33 depth==100 ) Also: ?[ # the first column specification can be a logical vector, as in df1[df1$col1 == 20, ] and will return subsets. But subset function is nicer in that you don't have precede each column name by the dataframe name. And of course: Thanks in advance for helping out a greenhorn! John _ Facebook. :ON:WL:en-US:SI_SB_facebook:082009 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. David Winsemius, MD Heritage Laboratories West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to 'apply' on multiple arguments?
Hi,
I tried the following code. For example, I want to add the
corresponding rows of x and y. I expect that the result be a matrix of
the same size. But the actual result is different from what I expect.
Would you please let me know what the correct command should be?
Regards,
Peng
x=matrix(1:6,nr=2)
y=matrix(1:6,nr=2)
mapply(function(u,v){u + v},x,y)
[1] 2 4 6 8 10 12
On Sat, Sep 5, 2009 at 10:59 AM, Henrique Dallazuannawww...@gmail.com wrote:
Yes, see mapply.
On Sat, Sep 5, 2009 at 12:18 PM, Peng Yu pengyu...@gmail.com wrote:
Hi,
I am wonder if there is a function similar 'apply' but it could accept
multiple arguments?
For example, I have the following matrix.
x=matrix(1:6,nr=2)
y=matrix(1:6,nr=2)
I want to find a function that can be used to compute the linear
regression for each pair of rows in the two matrices?
multiple_apply(x,y,1,function(u,v){lm(u ~ v)}
That is, I wound like something like the above to compute the
following. Can somebody let me know if there is such an command in R?
lm(x[1,]~y[1,])
lm(x[2,]~y[2,])
Regards,
Peng
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/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] Convert dataframe to array of records
I would like to convert a dataframe to an array of lists, one for every record. A natural choide is apply as.list to the rows. However, as it seems, as.list() automatically converts all list elements to the same datatype. Eg: myData - data.frame(a=foo,b=as.logical(rbinom(10,1,.5))); apply(myData,1,as.list); In this output, all boolean values have been converted to character strings. I don't understand why this happens; a list does not require that every element is of the same datatype. Is there an easy way (ie avoid for-loops etc) to convert the dataframe to an array of records, while keeping the datatypes for every field? - Jeroen Ooms * Dept. of Methodology and Statistics * Utrecht University Visit http://www.jeroenooms.com www.jeroenooms.com to explore some of my current projects. -- View this message in context: http://www.nabble.com/Convert-dataframe-to-array-of-records-tp25310023p25310023.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] Selecting biological data
On Sep 5, 2009, at 12:13 PM, David Winsemius wrote: On Sep 5, 2009, at 11:58 AM, John Casey wrote: Hello all, I am new to R but have some experience with MATLAB and am trying to make the switch. snipped specifics And of course: Sorry: got distracted and forgot to append the intended links: http://germain.its.maine.edu/~hiebeler/comp/matlabR.pdf http://cran.r-project.org/doc/contrib/R-and-octave.txt Thanks in advance for helping out a greenhorn! John _ Facebook. :ON:WL:en-US:SI_SB_facebook:082009 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. David Winsemius, MD Heritage Laboratories West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. David Winsemius, MD Heritage Laboratories West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to 'apply' on multiple arguments?
Hi Peng,
Here is a suugestion using lapply():
res - lapply(1:2, function(i) lm( x[i, ] ~ y[i, ]) )
names(res) - c('row1','row2')
res
# The summaries for each regression
lapply(res, summary)
# for the coefficients only
lapply(res, coef)
# ANOVAs
lapply(res, anova)
HTH,
Jorge
On Sat, Sep 5, 2009 at 11:18 AM, Peng Yu pengyu...@gmail.com wrote:
Hi,
I am wonder if there is a function similar 'apply' but it could accept
multiple arguments?
For example, I have the following matrix.
x=matrix(1:6,nr=2)
y=matrix(1:6,nr=2)
I want to find a function that can be used to compute the linear
regression for each pair of rows in the two matrices?
multiple_apply(x,y,1,function(u,v){lm(u ~ v)}
That is, I wound like something like the above to compute the
following. Can somebody let me know if there is such an command in R?
lm(x[1,]~y[1,])
lm(x[2,]~y[2,])
Regards,
Peng
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/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
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to 'apply' on multiple arguments?
HI,
Try this:
mapply(`+`, as.data.frame(x), as.data.frame(y))
You are using matrices, which are vectors with dim attributes, then you need
convert to data.frame
On Sat, Sep 5, 2009 at 1:16 PM, Peng Yu pengyu...@gmail.com wrote:
Hi,
I tried the following code. For example, I want to add the
corresponding rows of x and y. I expect that the result be a matrix of
the same size. But the actual result is different from what I expect.
Would you please let me know what the correct command should be?
Regards,
Peng
x=matrix(1:6,nr=2)
y=matrix(1:6,nr=2)
mapply(function(u,v){u + v},x,y)
[1] 2 4 6 8 10 12
On Sat, Sep 5, 2009 at 10:59 AM, Henrique Dallazuannawww...@gmail.com
wrote:
Yes, see mapply.
On Sat, Sep 5, 2009 at 12:18 PM, Peng Yu pengyu...@gmail.com wrote:
Hi,
I am wonder if there is a function similar 'apply' but it could accept
multiple arguments?
For example, I have the following matrix.
x=matrix(1:6,nr=2)
y=matrix(1:6,nr=2)
I want to find a function that can be used to compute the linear
regression for each pair of rows in the two matrices?
multiple_apply(x,y,1,function(u,v){lm(u ~ v)}
That is, I wound like something like the above to compute the
following. Can somebody let me know if there is such an command in R?
lm(x[1,]~y[1,])
lm(x[2,]~y[2,])
Regards,
Peng
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/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.
--
Henrique Dallazuanna
Curitiba-Paraná-Brasil
25° 25' 40 S 49° 16' 22 O
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Calling R from a Perl script: much slower?
you might also look at the output of 'ps' to see how much time each process is using. also instrument your R script to collect the cpu time. Sent from my iPhone On Sep 4, 2009, at 11:34, j.delashe...@ed.ac.uk wrote: Ah! sorted! it was NOT running the same code. We're making a GUI using Perl (Tcl/Tkx) to facilitate a number of analyses in our lab to other people who don't necessarily want to know about R (their loss ;-) I provided the R code to my colleague and he assured me he used it without changes... but when I've looked into it, there were a number of changes... (?) I restored the code to what I knew to work and from the Tcl/Tkx GUI it's *almost* as fast as when I run it from a clean session from the R console. So that was the problem. In case I'm still not doing things teh best way, we're invoking R from Perl like this: invoking the script from Perl: @output = qx($R.exe --vanilla --args $list of arguments...) should I use Rterm.exe or Rcmd.exe instead of R.exe? Jose Quoting jim holtman jholt...@gmail.com: What operating system are you running under? You should take a look at the R process and see how much time it is using to see if there is a difference in the CPU time. Are you paging? Exactly how are you invoking the R script? Why are you using the GUI instead of Rterm? You might try to run Rprof on the code to see if there are differences. Are you sure you are running exactly the same data in both cases? On Thu, Sep 3, 2009 at 11:42 AM, j.delashe...@ed.ac.uk wrote: Hello list, I use R for microarray analysis. One procedure I use takes a large matrix, and loops through it looking for specific rows, does an operation with them, and outputs a result (single row) as a row of another matrix. The loop goes on about 25000 times. When I run the loop directly from the R console itself, it takes about 3 minutes in my computer. I'm ok with that. Now, when that same code is ran from within a GUI we created using Perl (Tcl/Tkx) it's taking 25-30 minutes to run. Within the R code I inserted a line so that it writes a little file every 1000th iteration of the loop, so that I can follow the progress. I don't understand why it takes 10x longer when ran from Perl. I am not new to R, but I am new to using it within Perl or any other language. Is there a way to improve performance? What is the reason for the slower speed? I'll happily provide the code if somebody wants it. thank you. Jose -- Dr. Jose I. de las Heras Email: j.delashe...@ed.ac.uk The Wellcome Trust Centre for Cell BiologyPhone: +44 (0)131 6513374 Institute for Cell Molecular BiologyFax: +44 (0)131 6507360 Swann Building, Mayfield Road University of Edinburgh Edinburgh EH9 3JR UK * NEW EMAIL from July'09: nach.mcn...@gmail.com * -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem that you are trying to solve? -- Dr. Jose I. de las Heras Email: j.delashe...@ed.ac.uk The Wellcome Trust Centre for Cell BiologyPhone: +44 (0)131 6513374 Institute for Cell Molecular BiologyFax: +44 (0)131 6507360 Swann Building, Mayfield Road University of Edinburgh Edinburgh EH9 3JR UK * NEW EMAIL from July'09: nach.mcn...@gmail.com * -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Convert dataframe to array of records
-Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Jeroen Ooms Sent: Saturday, September 05, 2009 9:20 AM To: r-help@r-project.org Subject: [R] Convert dataframe to array of records I would like to convert a dataframe to an array of lists, one for every record. A natural choide is apply as.list to the rows. However, as it seems, as.list() automatically converts all list elements to the same datatype. No, apply itself converts the whole data.frame to a matrix, forcing the columns to one data type. I think that apply() is rarely a good tool for working with data.frames. You will have to do something like rowsOfDataFrame - function(dataframe) lapply(seq_len(nrow(dataframe)), function(i)dataframe[i,]) or perhaps as.list(dataframe[i,]) if you really want to get rid of the data.frame-ness. Bill Dunlap TIBCO Software Inc - Spotfire Division wdunlap tibco.com Eg: myData - data.frame(a=foo,b=as.logical(rbinom(10,1,.5))); apply(myData,1,as.list); In this output, all boolean values have been converted to character strings. I don't understand why this happens; a list does not require that every element is of the same datatype. Is there an easy way (ie avoid for-loops etc) to convert the dataframe to an array of records, while keeping the datatypes for every field? - Jeroen Ooms * Dept. of Methodology and Statistics * Utrecht University Visit http://www.jeroenooms.com www.jeroenooms.com to explore some of my current projects. -- View this message in context: http://www.nabble.com/Convert-dataframe-to-array-of-records-tp 25310023p25310023.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.
Re: [R] extract and replace columns of matrices stored in a list
Try this: my.array - replicate(10, data.frame(matrix(sample(9), 3)), simplify = FALSE) #2 lapply(my.array, replace, list = 3, values = newThirdColumn) The solution was for matrices, the above works with data.frames. On Thu, Sep 3, 2009 at 5:03 PM, Carlos Hernandez carlos.u...@gmail.comwrote: On Thu, Sep 3, 2009 at 4:34 PM, Henrique Dallazuanna www...@gmail.comwrote: Try this: #1 lapply(my.array, '[', , 3) this works! thank you a lot! #2 newThirdColumn - sample(3) lapply(my.array, replace, list = 7:9, values = newThirdColumn) i did not understand this last line, so far i couldn't make it work. would it be easier to replace the values (the third column of each matrix in my.array) using an array like in #1? thank you for your reply! On Thu, Sep 3, 2009 at 11:16 AM, Carlos Hernandez carlos.u...@gmail.comwrote: Dear All, I created a list (of length Z) in the following way: my.array - vector(list, Z) then i assigned a matrix (of T rows by N columns) in each of the elements of the list my.array in the following way: my.array[[i]] - matrix.data ##( matrix.data has dimensions TxN, and i repeated this command for i from 1 to Z, the matrix.data contains only numeric data) and 1. i would like to extract all the third columns of each of the Z matrices stored in my.array (such that i get a new list only with the 3rd columns of each matrix in the elements of a new list) 2. i would like to know how could i replace all the 3rd columns of each matrix in my.array if i have a second matrix (size ZxT) with these columns. is there a simple way to do these tasks? i appreciate any hints or advice. Carlos [[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 -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Is 'history' recorded in Rscript?
On 05/09/2009 2:21 PM, David Winsemius wrote: I get the same error in a bash session on a Mac. My assumption at this point is is that the authors of Rscript decided that you should already know what is in the input file and so left out that feature of the console program. Mavbe if you explained why you wanted what would generally be a straight copy of the input file, someone can offer a work-around strategy. In interactive use the GUIs (or Rterm) have their own mechanisms to maintain history. As the man page for savehistory says, in batch use there is no history maintained. Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Is 'history' recorded in Rscript?
I get the same error in a bash session on a Mac. My assumption at this point is is that the authors of Rscript decided that you should already know what is in the input file and so left out that feature of the console program. Mavbe if you explained why you wanted what would generally be a straight copy of the input file, someone can offer a work-around strategy. -- David On Sep 5, 2009, at 11:26 AM, Peng Yu wrote: Hi, I run Rscript from the command line (bash). My OS is the following $ cat /etc/redhat-release CentOS release 5 (Final) $ uname -a Linux selenium.cluster 2.6.18-53.1.13.el5 #1 SMP Tue Feb 12 13:02:30 EST 2008 x86_64 GNU/Linux $ dmesg | grep gcc Linux version 2.6.18-53.1.13.el5 (mockbu...@builder6.centos.org) (gcc version 4.1.2 20070626 (Red Hat 4.1.2-14)) #1 SMP Tue Feb 12 13:02:30 EST 2008 I can use savehistory in an R session (that is after the R prompt ''). My file 'savehistory.R' only have the following three lines. f=tempfile() f savehistory(f) I run the command 'Rscript savehistory.R' from the bash command line, which gave me the error I showed in my previous email. Can somebody try if he/she receives the save error? Regards, Peng On Sat, Sep 5, 2009 at 10:16 AM, David Winsemiusdwinsem...@comcast.net wrote: You did not make it clear (to me anyway) what computing environment the Rscript command was issued from. I assumed probably incorrectly that you were doing this from inside an R session and did not understand that Rscript was an external program. If I was wrong about that, then you are going to need to provide more details about your operating system and how you have set up your R installation. I also do not know what you mean by a save session. Did you at some time in the past execute a savehistory(file=savehistory,R) command at the end of a session and it's now in the directory that Rscript look for? That would be the only way that a savehistory.R file would exist. So what OS? What did you do before this failed effort? And what are you really trying to do? Then perhaps someone familiar with your OS can answer. -- David . On Sep 5, 2009, at 10:52 AM, Peng Yu wrote: Hi, I got the following error. Does it mean that the files in the save session will not be saved in history in Rscript? $ Rscript savehistory.R f=tempfile() f [1] /tmp/RtmpMEGKVq/file327b23c6 savehistory(f) Error in savehistory(file) : no history available to save Execution halted Regards, Peng On Sat, Sep 5, 2009 at 1:04 AM, David Winsemiusdwinsem...@comcast.net wrote: You should be looking for .Rhistory Some OSes make that task difficult. savehistory is not the file name but rather the name of the function that performs that operation. Try savehistory(file=text.Rhistory) and see if the history file is easier to find. Should be in your working directory. Rscript is a program, not a record of the prior session. -- David. On Sep 4, 2009, at 11:03 PM, Peng Yu wrote: Hi, I run the following command and try to save the commands that have been run in the script. But it seems that no history is recorded. Is it because that the history is not recorded in Rscript? Regards, Peng $ Rscript savehistory.R f=tempfile() f [1] /tmp/Rtmp7WBjGG/file327b23c6 history() Error in savehistory(file) : no history available to save Calls: history - savehistory Execution halted David Winsemius, MD Heritage Laboratories West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. David Winsemius, MD Heritage Laboratories West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] help with functions
Try this variation; might have something to do with scope:
testA-function(input)
{
dat- data.frame(A=seq(input,5), B=seq(6,10))
vec.names- c(a, b)
for(i in 1:ncol(dat))
{
tab- dat[,i]-1
assign(vec.names[i], tab)
}
do.call(rbind, lapply(vec.names, function(x) get(x)))
}
Just changed the way 'get' was done in the lapply
On Fri, Sep 4, 2009 at 10:00 AM, jonas
garciagarcia.jona...@googlemail.com wrote:
Hi all,
I have got 2 function (see bellow) which are simplifications of what I need
to do. These functions are precisely the same, except for the last line.
My question is, why doesn't function testA work in the same way as function
testB.
Both functions produce two objects, a and b that must merged with rbind.
The difference is that in testA, I specify the name of the objects while in
testA I am stating which objects I want to bind from a character vector.
What's more, if I just run the code without a function (example given below
as well), they both work...
Why is this?
Thanks in advance
Jonas
testA-function(input)
{
dat- data.frame(A=seq(input,5), B=seq(6,10))
vec.names- c(a, b)
for(i in 1:ncol(dat))
{
tab- dat[,i]-1
assign(vec.names[i], tab)
}
do.call(rbind, lapply(vec.names, get))
}
testB-function(input)
{
dat- data.frame(A=seq(input,5), B=seq(6,10))
vec.names- c(a, b)
for(i in 1:ncol(dat))
{
tab- dat[,i]-1
assign(vec.names[i], tab)
}
rbind(a,b)
}
testA(1)
Error in FUN(c(a, b)[[1L]], ...) : object 'a' not found
testB(1)
[,1] [,2] [,3] [,4] [,5]
a 0 1 2 3 4
b 5 6 7 8 9
###
dat- data.frame(A=seq(1,5), B=seq(6,10))
vec.names- c(a, b)
for(i in 1:ncol(dat))
{
tab- dat[,i]-1
assign(vec.names[i], tab)
}
do.call(rbind, lapply(vec.names, get))
[,1] [,2] [,3] [,4] [,5]
[1,] 0 1 2 3 4
[2,] 5 6 7 8 9
dat- data.frame(A=seq(1,5), B=seq(6,10))
vec.names- c(a, b)
for(i in 1:ncol(dat))
{
tab- dat[,i]-1
assign(vec.names[i], tab)
}
rbind(a,b)
[,1] [,2] [,3] [,4] [,5]
a 0 1 2 3 4
b 5 6 7 8 9
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[R] save image from R to database server in binary format
Hello, I would appreciate help regarding converting an image (jpeg, bmp) in R and saving it to a postgresql database server. Does the writeBin function provide any support for image to binary conversion? Once converted, how can I use the packages DBI and RPostgreSQL to send such data into the server. I am running R 2.9.0 on WinXP and running postgresql 8.3 Thank you Harsh Singhal [[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] Anova over a list of models
I have a list object, in which I have stored n lme4-models. For example: library(lme4); myModels - list(); myModels[1] - lmer(Reaction ~ Days + (Days|Subject), sleepstudy) myModels[2] - lmer(Reaction ~ Days + (1|Subject) + (0+Days|Subject), sleepstudy) Now I would like to perform an anova over all models in the list. However, the anova function requires that every model is inserted as a seperate argument, i.e. anova(model1,model2). I run into two problems: 1) anova(myModels[1],myModels[2]) returns an error. 2) if n, the number of models, is unknown, how do I add all models as a seperate argument? - Jeroen Ooms * Dept. of Methodology and Statistics * Utrecht University Visit http://www.jeroenooms.com www.jeroenooms.com to explore some of my current projects. -- View this message in context: http://www.nabble.com/Anova-over-a-list-of-models-tp25311985p25311985.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] 0 x 0 matrix
On 05-Sep-09 10:00:26, Markku Karhunen wrote:
On 04-Sep-09 10:45:27, Markku Karhunen wrote:
True. Should have read ?diag.
However, this provokes a more general question: Is there some way I
can declare some scalar and _all its functions_ as matrices?
For instance, I would like to
A = as.matrix(0.98)
B = function(A)
C = diag(sqrt(B))
so that all scalars are explicitly [1,1] matrices.
BR, Markku
Hmmm, it might be a good idea to explain why you want to do this.
For instance:
M - matrix(c(1,2,3,4),nrow=2)
c - matrix(2,nrow=1)
c%*%M
# Error in c %*% M : non-conformable arguments
c*M
# Error in c * M : non-conformable arrays
c+M
# Error in c + M : non-conformable arrays
So what would you want to use the [1,1]-matrix scalars for, that
cannot be done just using them as numbers?
Ted.
Broadly speaking, I would like to use the same code for multivariate
and univariate cases. For instance, I use the inverse Wishart
densities of MCMCpack. If I take diwish(x) of a scalar x, the
programme crashes, because diwish() by default checks
ncol(x)==nrow(x). However, I would like to have an inverse gamma
density.
Best,
Markku
I see. In such a case, it might be worth wrapping diwish() inside
a function of your own, which tests for 'x' being a scalar and,
if it is, converting it to a 1x1 matrix within the function.
For example:
diWish - function(x){
if( all.equal(dim(x),c(1,1)) ) {X - x} else
if( (is.vector(x))(length(x)==1) ) X - as.matrix(x)
diwish(X)
}
(This may not be optimal, but it gives the idea).
Hoping this helps,
Ted.
E-Mail: (Ted Harding) ted.hard...@manchester.ac.uk
Fax-to-email: +44 (0)870 094 0861
Date: 05-Sep-09 Time: 21:26:29
-- XFMail --
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Re: [R] Anova over a list of models
Try this: 1) anova(myModels[[1]],myModels[[2]]) 2) do.call(anova, myModels) On Sat, Sep 5, 2009 at 5:18 PM, Jeroen Ooms j.c.l.o...@uu.nl wrote: I have a list object, in which I have stored n lme4-models. For example: library(lme4); myModels - list(); myModels[1] - lmer(Reaction ~ Days + (Days|Subject), sleepstudy) myModels[2] - lmer(Reaction ~ Days + (1|Subject) + (0+Days|Subject), sleepstudy) Now I would like to perform an anova over all models in the list. However, the anova function requires that every model is inserted as a seperate argument, i.e. anova(model1,model2). I run into two problems: 1) anova(myModels[1],myModels[2]) returns an error. 2) if n, the number of models, is unknown, how do I add all models as a seperate argument? - Jeroen Ooms * Dept. of Methodology and Statistics * Utrecht University Visit http://www.jeroenooms.com www.jeroenooms.com to explore some of my current projects. -- View this message in context: http://www.nabble.com/Anova-over-a-list-of-models-tp25311985p25311985.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. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Anova over a list of models
2009/9/5 Henrique Dallazuanna www...@gmail.com Try this: anova(myModels[[1]],myModels[[2]]) do.call(anova, myModels) Does this work for you? Both functions are failing here: anova(myModels[[1]],myModels[[2]]) Error in names(mods) - sapply(as.list(mCall)[c(FALSE, TRUE, modp)], as.character) : 'names' attribute [6] must be the same length as the vector [2] do.call(anova, myModels) Error in as.character.default(X[[1L]], ...) : no method for coercing this S4 class to a vector __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 or or and all the values in a logical vector?
Try this: # Use cummin for 'and' x - c(TRUE, TRUE, FALSE, TRUE) cummin(x) == TRUE# the last element below is the result you want [1] TRUE TRUE FALSE FALSE # Use cummax for 'or' y - c(FALSE, FALSE, TRUE, FALSE) cummax(y) == TRUE# the last element below is the result you want [1] FALSE FALSE TRUE TRUE David Winsemius wrote: On Sep 4, 2009, at 10:37 PM, Peng Yu wrote: Hi, Suppose I have a logical vector x, I want to compute the 'and' ?all and 'or' ?any of all its element (the result should be a single value TRUE or FALSE). I have read the R-intro.pdf logical vector section, but I don't find the answer. I couldn't find them either. Can somebody let me know how to do it? x= rep(TRUE, 3) Regards, Peng -- David Winsemius, MD Heritage Laboratories West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. - Chi Yau http://r-tutor.com http://r-tutor.com -- View this message in context: http://www.nabble.com/How-to-or-or-and-all-the-values-in-a-logical-vector--tp25304562p25312249.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] Easy way to get top 2 items from vector
Tyr this: system.time(sort(x, partial=c(99,100))) user system elapsed 0.120.000.14 On Fri, Sep 4, 2009 at 3:53 AM, ONKELINX, Thierrythierry.onkel...@inbo.be wrote: Using tail() for the selection is more elegant and slightly faster. N- 100 x - runif(N) system.time(x[order(x)[c(N-1,N)]]) user system elapsed 1.08 0.01 1.10 system.time(sort(x)[c(N-1,N)]) user system elapsed 0.36 0.00 0.35 system.time(tail(sort(x), 2)) user system elapsed 0.33 0.00 0.33 HTH, Thierry ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest Cel biometrie, methodologie en kwaliteitszorg / Section biometrics, methodology and quality assurance Gaverstraat 4 9500 Geraardsbergen Belgium tel. + 32 54/436 185 thierry.onkel...@inbo.be www.inbo.be To call in the statistician after the experiment is done may be no more than asking him to perform a post-mortem examination: he may be able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher The plural of anecdote is not data. ~ Roger Brinner The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. ~ John Tukey -Oorspronkelijk bericht- Van: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] Namens andrew Verzonden: vrijdag 4 september 2009 4:24 Aan: r-help@r-project.org Onderwerp: Re: [R] Easy way to get top 2 items from vector it is speedier to use sort than a combination of [] and order: N- 100 x - runif(N) system.time(x[order(x)[c(N-1,N)]]) user system elapsed 1.03 0.00 1.03 system.time(sort(x)[c(N-1,N)]) user system elapsed 0.28 0.00 0.28 On Sep 4, 11:17 am, Noah Silverman n...@smartmediacorp.com wrote: Phil, That's perfect. (For my application, I've never seen a tie. While possible, the likelihood is almost none.) Thanks! -- Noah On 9/3/09 4:29 PM, Phil Spector wrote: Noah - max(x[-which.max(x)] will give you the second largest value, but it doesn't handle ties. x[order(x,decreasing=TRUE)[n]] will give you the nth largest value, with the same caveat regarding ties. For example, x[order(x,decreasing=TRUE)[1:3]] will give you the three largest values. - Phil Spector Statistical Computing Facility Department of Statistics UC Berkeley spec...@stat.berkeley.edu On Thu, 3 Sep 2009, Noah Silverman wrote: Hi, I use the max function often to find the top value from a matrix or column of a data.frame. Now I'm looking to find the top 2 (or three) values from my data. I know that I could sort the list and then access the first two items, but that seems like the long way. Is there some way to access max_2 or similar? Thanks! -- Noah __ r-h...@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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-h...@r-project.org mailing listhttps://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guidehttp://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. Druk dit bericht a.u.b. niet onnodig af. Please do not print this message unnecessarily. Dit bericht en eventuele bijlagen geven enkel de visie van de schrijver weer en binden het INBO onder geen enkel beding, zolang dit bericht niet bevestigd is door een geldig ondertekend document. The views expressed in this message and any annex are purely those of the writer and may not be regarded as stating an official position of INBO, as long as the message is not confirmed by a duly signed document. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem that you are trying to solve? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the
Re: [R] Creating mixed line and point graphs with xyplot
I would use the base plot routine plot(x,c, type='l', ylim=range(a,c)) points(x,a) park(new=TRUE) plot(x,d,type='l', ylim=range(b,d), axes=FALSE,ylab='', xlab='') pints(x,b) axis(4) On Fri, Sep 4, 2009 at 11:28 AM, Paul Sweetingm...@paulsweeting.co.uk wrote: Hi Well, I think the title says it all! I've looked through the documentation but I can't find a way of doing this. The situation is that I have 4 series, say a, b, c and d. Series a and c are plotted on the lh y axis, series b and d are plotted on the rh (secondary) y axis. I've worked out how to do this. However, I need to plot series a and b a points (symbols only, no line), whislt c and d need plotting as lines (with no symbols). What is the easiest way to do this in xyplot? Or should I be using something else? Thanks! Paul __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem that you are trying to solve? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] ggplot2::qplot() -- arbitary transformations of coordinate system?
Hi, Does anyone know how to do a coord_trans() in which the y-axis is tranformed into (for example) -1000/y? Thanks, _ Professor Michael Kubovy University of Virginia Department of Psychology USPS: P.O.Box 400400Charlottesville, VA 22904-4400 Parcels:Room 102Gilmer Hall McCormick RoadCharlottesville, VA 22903 Office:B011+1-434-982-4729 Lab:B019+1-434-982-4751 Fax:+1-434-982-4766 WWW:http://www.people.virginia.edu/~mk9y/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Video Analysis?
What software exists for digitizing video to quantify the motion of specific features in the image? I might be willing to use something that's NOT in R, though I'd prefer something in R (or at least with an R intereface). Thanks, Spencer Graves __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] ggplot2::qplot() -- arbitary transformations of coordinate system?
why not transform the y-data? On Sat, Sep 5, 2009 at 8:03 PM, Michael Kubovykub...@virginia.edu wrote: Hi, Does anyone know how to do a coord_trans() in which the y-axis is tranformed into (for example) -1000/y? Thanks, _ Professor Michael Kubovy University of Virginia Department of Psychology USPS: P.O.Box 400400 Charlottesville, VA 22904-4400 Parcels: Room 102 Gilmer Hall McCormick Road Charlottesville, VA 22903 Office: B011 +1-434-982-4729 Lab: B019 +1-434-982-4751 Fax: +1-434-982-4766 WWW: http://www.people.virginia.edu/~mk9y/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Stephen Sefick Let's not spend our time and resources thinking about things that are so little or so large that all they really do for us is puff us up and make us feel like gods. We are mammals, and have not exhausted the annoying little problems of being mammals. -K. Mullis __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Regarding SVM using R
Hi Abbas, Before I try to give you answers, I just want to mention that you should send R related reqests to the R-help list, and not me personally because (i) there's a greater likelihood that it will get answered in a timely manner, and (ii) people who might have a similar problem down the road might benefit from any answer via searching the list archives ... anyway: On Sep 5, 2009, at 1:41 PM, Abbas R. Ali wrote: Hi Steve I need your kind help on implementing SVM using R. I am previously applied neural network technique on the same data and want to get results from SVM as well. I have 2-D data and want to apply regression on it. After training and prediction I will pass it on my function model_metric(predicted, original, …) to plot the data as I have attached with this email. I want SVM training and prediction source code in R (regression) which can plot my data same as the attached figure. Use the e1071 package and (i) look at the Example section in ?svm and (ii) run it to see it work live. There is an example of running running regression: R library(e1071) R ?svm R example(svm) You'll see several plots pop up that are very similar to what you're trying to do. On thing is that I have to read data directly from SQL server can you please tell me how can I separate target field from rest of the data (any R command which can separate last field of a matrix). Figure out what type of database you need to query and get the appropriate library to do so. Do you mean sql server as Microsoft's SQLServer? Try RODBC, otherwise there's RSQLite, RPostgreSQL, and RMySQL you can try if you're using those databases. You can use those libraries to send a sql query to your database and will be returned a data.frame of your results. You can manipulate that data.frame in the usual way to pick off your target column from. the predictor/feature columns and train your SVM accordingly (or use the entire data.frame along with the formula invocation of SVM). Hope that helps, -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Video Analysis?
On Sep 5, 2009, at 5:07 PM, spencerg wrote: What software exists for digitizing video to quantify the motion of specific features in the image? I might be willing to use something that's NOT in R, though I'd prefer something in R (or at least with an R intereface). A few options that I can think of (2 non-R, 1 R): - If you have access to Matlab, Ty Hedrick (UNC Chapel Hill) has a good digitizing program that can handle 3d digitizing with DLT (but works fine for 2D), automatic point tracking, reads/writes csv. http://www.unc.edu/~thedrick/software1.html - James Rholf's tpsDig (Windows only; http://life.bio.sunysb.edu/ee/rohlf/software.html ) can be used as a general point digitizer. I think you would have to save the videos as image sequences first and reformat the data after. I haven't tried this, but I think it would work. - For one-off, small digitizing projects in R, I have exported videos to jpg sequences, loaded them with read.jpeg(), and used locator() for digitizing. Negatives: (1) lack of flexibility, (2) very hard to go back and fix mistakes, (3) plotting jpeg images is slow unless the image dimensions are reduced. But it's a native R solution. Kevin - Kevin M. Middleton Department of Biology California State University San Bernardino __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Matrix as input to xyplot {lattice} - proper extended formula syntax
Hello R Folks... I have a list with the following structure: str(df) List of 3 $ y: num [1:4, 1:1242] -0.005379 0.029874 -0.023274 0.000655 -0.004537 .. $ x: num [1:1242] 501 503 505 507 509 ... $ names: Factor w/ 4 levels PC Loading 1,..: 1 2 3 4 I want to plot each row of df$y against df$x, and have each plot in it¹s own panel according to the levels of df$names. The following works in the sense that the layout is right, but the y values have clearly been recycled or skipped in some fashion (and an error is thrown for each panel that the length of x and y aren¹t the same): p - xyplot(y ~ x | names, data = df, main = title, layout = c(1, dim(y)[1]) In reviewing the extended formula interface in the Lattice Book, what I want to happen is y1 + y2 + y3 + y4 ~ x | names, outer = TRUE I see two options: figure out a way to create the extended formula on the fly (and the actual number of rows in y may vary), which seems potentially tricky, or create a data frame by stacking each row of y and repeating x and names to match. This seems like a waste of memory. I¹ve looked through the archives and haven¹t come across something quite like this, or at least I don¹t recognize it if I have! Is there a more elegant way to tell xyplot I want to use each row of y repeatedly with the same x, in a loop-like fashion? TIA. Bryan * Bryan Hanson Professor of Chemistry Biochemistry DePauw University, Greencastle IN 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] Matrix as input to xyplot {lattice} - proper extended formula syntax
I'm not exactly sure what structure df has. Here's my effort to duplicate it: df - data.frame(y=matrix(rnorm(24), nrow=6), x=1:6) df y.1y.2y.3y.4 x 1 0.1734636 0.2348417 -1.2375648 -1.3246439 1 2 1.9551669 -1.1027262 -0.7307332 0.3953752 2 3 -0.7645778 1.6297861 0.4743805 -0.4476145 3 4 -0.5308756 -0.5246534 -0.3854609 -1.609 4 5 0.7406525 -0.8691720 -0.8194084 1.6122059 5 6 -0.9625619 -1.0774165 1.0760829 0.3659436 6 And this seems to accomplish the desired task. Presumably you have assigned off-stage the value of title to a meaningful character string? p - xyplot(y.1+y.2+y.3+y.4 ~ x |1:4, data = df, main = title ,layout=c(1,4) ) p On Sep 5, 2009, at 11:52 PM, Bryan Hanson wrote: Hello R Folks... I have a list with the following structure: str(df) List of 3 $ y: num [1:4, 1:1242] -0.005379 0.029874 -0.023274 0.000655 -0.004537 .. $ x: num [1:1242] 501 503 505 507 509 ... $ names: Factor w/ 4 levels PC Loading 1,..: 1 2 3 4 I want to plot each row of df$y against df$x, and have each plot in it’s own panel according to the levels of df$names. The following works in the sense that the layout is right, but the y values have clearly been recycled or skipped in some fashion (and an error is thrown for each panel that the length of x and y aren’t the same): p - xyplot(y ~ x | names, data = df, main = title, layout = c(1, dim(y)[1]) In reviewing the extended formula interface in the Lattice Book, what I want to happen is y1 + y2 + y3 + y4 ~ x | names, outer = TRUE I see two options: figure out a way to create the extended formula on the fly (and the actual number of rows in y may vary), which seems potentially tricky, or create a data frame by stacking each row of y and repeating x and names to match. This seems like a waste of memory. I’ve looked through the archives and haven’t come across something quite like this, or at least I don’t recognize it if I have! Is there a more elegant way to tell xyplot I want to use each row of y repeatedly with the same x, in a loop-like fashion? TIA. Bryan * Bryan Hanson Professor of Chemistry Biochemistry DePauw University, Greencastle IN 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. David Winsemius, MD Heritage Laboratories West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] About BIC
Hello, I am working on getting optimal lags by using BIC, But I don't know how to calculate BIC. Is there any code or useful function for it? Thanks and regards, Dan Zhao __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Matrix as input to xyplot {lattice} - proper extended formula syntax
Thanks David, your way of constructing df is much more compact than what I was using, so I've incorporated it. I also had my rows and columns transposed relative to how xyplot wanted them (though I had tested for that, other problems interfered). In my case, I may have varying numbers of y columns, from y.1 to y.n let's say. Is there an easy way of creating the phrase y.1+y.2+...y.n to pass to xyplot, or even better, some sort of syntax that says take all y.n and plot them against x? Thanks, Bryan On 9/6/09 12:51 AM, David Winsemius dwinsem...@comcast.net wrote: I'm not exactly sure what structure df has. Here's my effort to duplicate it: df - data.frame(y=matrix(rnorm(24), nrow=6), x=1:6) df y.1y.2y.3y.4 x 1 0.1734636 0.2348417 -1.2375648 -1.3246439 1 2 1.9551669 -1.1027262 -0.7307332 0.3953752 2 3 -0.7645778 1.6297861 0.4743805 -0.4476145 3 4 -0.5308756 -0.5246534 -0.3854609 -1.609 4 5 0.7406525 -0.8691720 -0.8194084 1.6122059 5 6 -0.9625619 -1.0774165 1.0760829 0.3659436 6 And this seems to accomplish the desired task. Presumably you have assigned off-stage the value of title to a meaningful character string? p - xyplot(y.1+y.2+y.3+y.4 ~ x |1:4, data = df, main = title ,layout=c(1,4) ) p On Sep 5, 2009, at 11:52 PM, Bryan Hanson wrote: Hello R Folks... I have a list with the following structure: str(df) List of 3 $ y: num [1:4, 1:1242] -0.005379 0.029874 -0.023274 0.000655 -0.004537 .. $ x: num [1:1242] 501 503 505 507 509 ... $ names: Factor w/ 4 levels PC Loading 1,..: 1 2 3 4 I want to plot each row of df$y against df$x, and have each plot in it¹s own panel according to the levels of df$names. The following works in the sense that the layout is right, but the y values have clearly been recycled or skipped in some fashion (and an error is thrown for each panel that the length of x and y aren¹t the same): p - xyplot(y ~ x | names, data = df, main = title, layout = c(1, dim(y)[1]) In reviewing the extended formula interface in the Lattice Book, what I want to happen is y1 + y2 + y3 + y4 ~ x | names, outer = TRUE I see two options: figure out a way to create the extended formula on the fly (and the actual number of rows in y may vary), which seems potentially tricky, or create a data frame by stacking each row of y and repeating x and names to match. This seems like a waste of memory. I¹ve looked through the archives and haven¹t come across something quite like this, or at least I don¹t recognize it if I have! Is there a more elegant way to tell xyplot I want to use each row of y repeatedly with the same x, in a loop-like fashion? TIA. Bryan * Bryan Hanson Professor of Chemistry Biochemistry DePauw University, Greencastle IN 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. David Winsemius, MD Heritage Laboratories West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
