Re: [R] paste adjacent elements matching string
thanks so much, this did the trick! Jill Gabor Grothendieck wrote: Try this which assumes that comma does not appear in any of the strings. You can substitute a different non-appearing character if a comma does appear in any of the strings: strsplit(gsub(string,, string, paste(vec, collapse = ,)), ,)[[1]] It first runs all the strings together into a single comma-separate string using paste and then replaces each occurrence of string, with string using gsub. Finally it breaks the long string back up into individual strings using strsplit. On Fri, Dec 4, 2009 at 8:42 PM, Jill Hollenbach jil...@sbcglobal.netwrote: Hi all, I would like to combine elements of a vector: vec - c(astring, b, cstring, d, e) vec [1] astring b cstring d e such that for every element that contains string at the end, it is combined with the next element, so that I get this: res [1] astringb cstringd e Any help is much appreciated, still learning. Many thanks, Jill Jill Hollenbach, PhD, MPH Associate Staff Scientist Center for Genetics Children's Hospital Oakland Research Institute jhollenb...@chori.org skype: jillah11 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- View this message in context: http://n4.nabble.com/paste-adjacent-elements-matching-string-tp949036p949111.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] categorical vs numerical
Thanks, however the group sizes are really big (each a,b,c.. category has 60,000 observations). Its hard to see whats going on withe the jittered stripchart, i just get big black blobs. Any other suggestions? Peter Ehlers wrote: If your group sizes are not too large, I would use jittered stripcharts. They're more informative than boxplots and much less subject to misinterpretation. One warning, I'm not fond of the default pch=0. -Peter Ehlers DispersionMap wrote: What ways are there to plot categorical vs numerical data in R. I have two columns: one with categorical data in 5 categories a,b,c,d,e, and a numerical column with integers between 1 and 100. I have used a boxplot with a,b,c,d,e on the x-axis and an increasing numerical scale on the y-axis. This look fine but im looking for other ways to present the data. What other ways can i do this??? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- View this message in context: http://n4.nabble.com/categorical-vs-numerical-tp948817p949117.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] categorical vs numerical
You could try density plots: If dat is your dataframe, y is your numerical vector and g is your factor, library(lattice) trellis.device(height=9, width=7) densityplot(~g|y, data=dat, plot.points=FALSE, layout=c(1,4)) See ?densityplot, ?panel.densityplot -Peter Ehlers DispersionMap wrote: Thanks, however the group sizes are really big (each a,b,c.. category has 60,000 observations). Its hard to see whats going on withe the jittered stripchart, i just get big black blobs. Any other suggestions? Peter Ehlers wrote: If your group sizes are not too large, I would use jittered stripcharts. They're more informative than boxplots and much less subject to misinterpretation. One warning, I'm not fond of the default pch=0. -Peter Ehlers DispersionMap wrote: What ways are there to plot categorical vs numerical data in R. I have two columns: one with categorical data in 5 categories a,b,c,d,e, and a numerical column with integers between 1 and 100. I have used a boxplot with a,b,c,d,e on the x-axis and an increasing numerical scale on the y-axis. This look fine but im looking for other ways to present the data. What other ways can i do this??? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 boxplot for time class
hi again I will try this time to explain my problem clearly I have the following data from the file skiing.csv (3 first rows) protokollid datestart end 14 2/23/2009 8:50:10 15:17:30 24 2/24/2009 9:47:00 13:52:25 35 3/22/2009 8:51:25 12:00:05 I have the following script library(chron) skiers=read.csv(skiing.csv) strptime(08:50:10,%H:%M:%S) start=times(skiers[,3]) strptime(start,%H:%M:%S) end=times(skiers[,4]) strptime(end,%H:%M:%S) #calc lenght of the route length.route=end-start #calc medians median(start) median(length.route) Then I want to do a box plot of the staring time when I use: boxplot(start) this error appears: Warning message: In is.na(x) : is.na() applied to non-(list or vector) of type 'NULL' when I try to convert start as POSIXct start=as.POSIXct(start) Error in as.POSIXct.default(start) : do not know how to convert 'start' to class POSIXlt and when I try to convert skiers[,3] as POSIXct skiers[,3]=as.POSIXct(skiers[,3]) Error in as.POSIXlt.character(as.character(x)) : character string is not in a standard unambiguous format start is of times class and skiers[,3] of factor class I want to do a boxplot of the starting time of my data, which reflect the median 08:36:45, and all O get in the y axis are decimal numbers :( Help please Best regards Maria Stauss -- View this message in context: http://n4.nabble.com/HELP-boxplot-for-time-class-tp949154p949154.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] categorical vs numerical
Whoops, that should be densityplot(~y|g, data=dat, plot.points=FALSE, layout=c(1,4)) -Peter Ehlers Peter Ehlers wrote: You could try density plots: If dat is your dataframe, y is your numerical vector and g is your factor, library(lattice) trellis.device(height=9, width=7) densityplot(~g|y, data=dat, plot.points=FALSE, layout=c(1,4)) See ?densityplot, ?panel.densityplot -Peter Ehlers DispersionMap wrote: Thanks, however the group sizes are really big (each a,b,c.. category has 60,000 observations). Its hard to see whats going on withe the jittered stripchart, i just get big black blobs. Any other suggestions? Peter Ehlers wrote: If your group sizes are not too large, I would use jittered stripcharts. They're more informative than boxplots and much less subject to misinterpretation. One warning, I'm not fond of the default pch=0. -Peter Ehlers DispersionMap wrote: What ways are there to plot categorical vs numerical data in R. I have two columns: one with categorical data in 5 categories a,b,c,d,e, and a numerical column with integers between 1 and 100. I have used a boxplot with a,b,c,d,e on the x-axis and an increasing numerical scale on the y-axis. This look fine but im looking for other ways to present the data. What other ways can i do this??? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Peter Ehlers University of Calgary 403.202.3936 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Using rgl to put a graphic beneath a plot
I've written a very simple bit of code to plot a trajectory using rgl: x - (c(0,-5.947,-11.496,-16.665,-21.474,-25.947,-30.116,-34.017,-37.684,-41.148,-44.435,-47.568,-50.567,-53.448,-56.223,-58.906)) y - (c(0,33.729,65.198,94.514,121.784,147.151,170.797,192.920,213.717,233.360,252.003,269.774,286.781,303.117,318.858,334.071)) z - (c(3,11.914,19.629,26.066,31.167,34.902,37.262,38.257,37.903,36.221,33.233,28.964,23.442,16.696,8.761,-0.325)) plot3d(x,y,z, type='l',axes=FALSE, box=FALSE) I have a PNG file that I want to place the plot on top of. I've arranged the image so that the point at x=282 px and y=52 px should correspond with the origin of the graph. Thanks in advance for your help, --CW _ id=1media=aero-shake-7secondlistid=1stop=1ocid=PID24727::T:WLMTAGL:ON:WL:en-US:WWL_WIN_7secdemo:122009 [[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] Using rgl to put a graphic beneath a plot
On 05/12/2009 3:07 AM, Colin Wyers wrote: I've written a very simple bit of code to plot a trajectory using rgl: x - (c(0,-5.947,-11.496,-16.665,-21.474,-25.947,-30.116,-34.017,-37.684,-41.148,-44.435,-47.568,-50.567,-53.448,-56.223,-58.906)) y - (c(0,33.729,65.198,94.514,121.784,147.151,170.797,192.920,213.717,233.360,252.003,269.774,286.781,303.117,318.858,334.071)) z - (c(3,11.914,19.629,26.066,31.167,34.902,37.262,38.257,37.903,36.221,33.233,28.964,23.442,16.696,8.761,-0.325)) plot3d(x,y,z, type='l',axes=FALSE, box=FALSE) I have a PNG file that I want to place the plot on top of. I've arranged the image so that the point at x=282 px and y=52 px should correspond with the origin of the graph. One way is to use the PNG file as a texture on a rectangle behind the line. demo(flag) does a fairly elaborate example of this. See ?rgl.surface for the description of how to do it. Another way is to use the image on the background sphere; example(bg3d) and demo(envmap) do this. 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] categorical vs numerical
Thanks, ill give them whirl...when i was installing the lattice package i got
the error in bold below...why does it say permission denied and what effect
does this have?
utils:::menuInstallLocal()
package 'lattice' successfully unpacked and MD5 sums checked
updating HTML package descriptions
Warning message:
In file.create(f.tg) :
cannot create file 'C:\PROGRA~1\R\R-29~1.2/doc/html/packages.html', reason
'Permission denied'
local({pkg - select.list(sort(.packages(all.available = TRUE)))
+ if(nchar(pkg)) library(pkg, character.only=TRUE)})
Warning message:
package 'lattice' was built under R version 2.10.0
I have it loaded
Peter Ehlers wrote:
Whoops, that should be
densityplot(~y|g, data=dat, plot.points=FALSE, layout=c(1,4))
-Peter Ehlers
Peter Ehlers wrote:
You could try density plots:
If dat is your dataframe, y is your numerical vector and
g is your factor,
library(lattice)
trellis.device(height=9, width=7)
densityplot(~g|y, data=dat, plot.points=FALSE, layout=c(1,4))
See ?densityplot, ?panel.densityplot
-Peter Ehlers
DispersionMap wrote:
Thanks, however the group sizes are really big (each a,b,c.. category
has
60,000 observations). Its hard to see whats going on withe the jittered
stripchart, i just get big black blobs.
Any other suggestions?
Peter Ehlers wrote:
If your group sizes are not too large, I would use jittered
stripcharts.
They're more informative than boxplots and much less subject to
misinterpretation. One warning, I'm not fond of the default pch=0.
-Peter Ehlers
DispersionMap wrote:
What ways are there to plot categorical vs numerical data in R.
I have two columns: one with categorical data in 5 categories
a,b,c,d,e,
and
a numerical column with integers between 1 and 100.
I have used a boxplot with a,b,c,d,e on the x-axis and an increasing
numerical scale on the y-axis. This look fine but im looking for other
ways
to present the data.
What other ways can i do this???
__
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PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
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https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Peter Ehlers
University of Calgary
403.202.3936
__
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PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
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--
View this message in context:
http://n4.nabble.com/categorical-vs-numerical-tp948817p949178.html
Sent from the R help mailing list archive at Nabble.com.
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Re: [R] HELP boxplot for time class
Try this: Lines - protokollid datestart end 4 2/23/2009 8:50:10 15:17:30 4 2/24/2009 9:47:00 13:52:25 5 3/22/2009 8:51:25 12:00:05 library(chron) skiers - read.table(textConnection(Lines), header = TRUE, as.is = TRUE) skiers - transform(skiers, date = dates(date), start = times(start), end = times(end)) bp - boxplot(as.numeric(skiers$start), yaxt = n) axis(2, bp$stats, times(bp$stats), las = 2, cex.axis = 0.5) On Sat, Dec 5, 2009 at 6:52 AM, uvilla maruchave...@hotmail.com wrote: hi again I will try this time to explain my problem clearly I have the following data from the file skiing.csv (3 first rows) protokollid datestart end 14 2/23/2009 8:50:10 15:17:30 24 2/24/2009 9:47:00 13:52:25 35 3/22/2009 8:51:25 12:00:05 I have the following script library(chron) skiers=read.csv(skiing.csv) strptime(08:50:10,%H:%M:%S) start=times(skiers[,3]) strptime(start,%H:%M:%S) end=times(skiers[,4]) strptime(end,%H:%M:%S) #calc lenght of the route length.route=end-start #calc medians median(start) median(length.route) Then I want to do a box plot of the staring time when I use: boxplot(start) this error appears: Warning message: In is.na(x) : is.na() applied to non-(list or vector) of type 'NULL' when I try to convert start as POSIXct start=as.POSIXct(start) Error in as.POSIXct.default(start) : do not know how to convert 'start' to class POSIXlt and when I try to convert skiers[,3] as POSIXct skiers[,3]=as.POSIXct(skiers[,3]) Error in as.POSIXlt.character(as.character(x)) : character string is not in a standard unambiguous format start is of times class and skiers[,3] of factor class I want to do a boxplot of the starting time of my data, which reflect the median 08:36:45, and all O get in the y axis are decimal numbers :( Help please Best regards Maria Stauss -- View this message in context: http://n4.nabble.com/HELP-boxplot-for-time-class-tp949154p949154.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. [[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] paste adjacent elements matching string
A different approach than those other people listed would be to change the vector into a matrix (by setting its dimension, if you don't need to keep the original vector) and then applying paste along one of the dimensions. Obviously, you'd need to pad the end of the vector with NAs or empty strings. Since you have a working solution, I won't write code... but this approach might be a little easier to scale if, for example, you need to concatenate every three elements of the vector. Best, Gray On Fri, Dec 4, 2009 at 5:42 PM, Jill Hollenbach jil...@sbcglobal.net wrote: Hi all, I would like to combine elements of a vector: vec - c(astring, b, cstring, d, e) vec [1] astring b cstring d e such that for every element that contains string at the end, it is combined with the next element, so that I get this: res [1] astringb cstringd e Any help is much appreciated, still learning. Many thanks, Jill Jill Hollenbach, PhD, MPH Associate Staff Scientist Center for Genetics Children's Hospital Oakland Research Institute jhollenb...@chori.org skype: jillah11 [[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. -- Gray Calhoun Assistant Professor of Economics Iowa State University __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] paste adjacent elements matching string
Try this also: sapply(grep(string$, vec), function(idx)paste(vec[idx + 0:1], collapse = )) On Fri, Dec 4, 2009 at 11:42 PM, Jill Hollenbach jil...@sbcglobal.net wrote: Hi all, I would like to combine elements of a vector: vec - c(astring, b, cstring, d, e) vec [1] astring b cstring d e such that for every element that contains string at the end, it is combined with the next element, so that I get this: res [1] astringb cstringd e Any help is much appreciated, still learning. Many thanks, Jill Jill Hollenbach, PhD, MPH Associate Staff Scientist Center for Genetics Children's Hospital Oakland Research Institute jhollenb...@chori.org skype: jillah11 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] R CMD BATCH continue after an error in the script
Hi, I have a problem with R CMD BATCH, because I created a .bat file to run a script: C:\R\R-2.9.2\bin\R CMD BATCH C:\Scrip_test.R It work perfectly but after 3 lines of script there is a line with a nls() function that cannot be fitted and this end in an error message. I'm not bother by the error message, I just want that the script continue. If I use the R windows GUI the script show the error message but it continue till the very end. I want that the script continue to run also in BATCH mode, How can I do that? Many thanks in advance, Fabio Fabio Veronesi Ph.D Student Cranfield University School of Applied Sciences Building 37 Cranfield, Bedforshire MK43 0AL tel. +4407984049316 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R CMD BATCH continue after an error in the script
Fabio, If you're not using the nls() function's result, then why don't you comment it out from the script? That way, there will be no error and the script will work fine. Please post your script if you need further help. Veronesi, Fabio wrote: Hi, I have a problem with R CMD BATCH, because I created a .bat file to run a script: C:\R\R-2.9.2\bin\R CMD BATCH C:\Scrip_test.R It work perfectly but after 3 lines of script there is a line with a nls() function that cannot be fitted and this end in an error message. I'm not bother by the error message, I just want that the script continue. If I use the R windows GUI the script show the error message but it continue till the very end. I want that the script continue to run also in BATCH mode, How can I do that? Many thanks in advance, Fabio Fabio Veronesi Ph.D Student Cranfield University School of Applied Sciences Building 37 Cranfield, Bedforshire MK43 0AL tel. +4407984049316 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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://n4.nabble.com/R-CMD-BATCH-continue-after-an-error-in-the-script-tp949199p949207.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] R CMD BATCH continue after an error in the script
On Dec 5, 2009, at 9:21 AM, Veronesi, Fabio wrote: Hi, I have a problem with R CMD BATCH, because I created a .bat file to run a script: C:\R\R-2.9.2\bin\R CMD BATCH C:\Scrip_test.R It work perfectly but after 3 lines of script there is a line with a nls() function that cannot be fitted and this end in an error message. I'm not bother by the error message, I just want that the script continue. The try function will provide a mechaism for gracefully stepping around coding potholes. ?try If I use the R windows GUI the script show the error message but it continue till the very end. I want that the script continue to run also in BATCH mode, How can I do that? Many thanks in advance, Fabio Fabio Veronesi Ph.D Student Cranfield University School of Applied Sciences 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] Partial correlations and p-values
Your R code looks correct. Because this is a straightforward calculation, I would be surprised if there were any differences with SPSS. It may be worthwhile to check if SPSS gives partial correlations or semipartial correlations. For example, if you take the correlation between py - resid(lm(y ~ z1 + z2,data=mydat2)) and x where mydat2 has missing values removed, you get 0.47. On Tue, Dec 1, 2009 at 8:24 PM, dadrivr dadr...@gmail.com wrote: I am trying to calculate a partial correlation and p-values. Unfortunately, the results in R are different than what SPSS gives. Here is an example in R (calculating the partial correlation of x and y, controlling for z1 and z2): x - c(1,20,14,30,9,4,8) y - c(5,6,7,9,NA,10,6) z1 - c(13,8,16,14,26,13,20) z2 - c(12,NA,2,5,8,16,13) fmx - lm(x ~ z1 + z2, na.action = na.exclude) fmy - lm(y ~ z1 + z2, na.action = na.exclude) yres - resid(fmy) xres - resid(fmx) cor(xres, yres, use = p) ct - cor.test(xres, yres) ct$estimate ct$p.value R give me: r = .65, p = .23 However, SPSS calculates: r = .46, p = .70 I think something may be different with R's handling of missing data, as when I replace the NA's with values, R and SPSS give the same r-values, albeit different p-values still. I am doing pairwise case exclusion in both R and SPSS. Any ideas why I'm getting different values? Is something wrong with my formula in R? Any help would be greatly appreciated. Thanks! __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Referencing variable names rather than column numbers
I apologize for how basic a question this is. I am a Stata user who has begun using R, and the syntax differences still trip me up. The most basic questions, involving as they do general terms, can be the hardest to find solutions for through search. Assume for the moment that I have a dataset that contains seven variables: Pollution, Temp, Industry, Population, Wind, Rain and Wet.days. (This actual dataset is taken from Michael Crawley's Statistics: An Introduction Using R and is available as pollute.txt in http://www.bio.ic.ac.uk/research/crawley/statistics/data/zipped.zip.) Assume I have attached pollute. Then cor(pollute) will give me the correlation table for these seven variables. If I would prefer only to see the correlations between, say, Pollution, Temp and Industry, I can get that with cor(pollute[,1:3]) or with cor(pollute[1:3]) Similarly, I can see the correlations between Temp, Population and Rain with cor(pollute[,c(2,4,6)]) or with cor(pollute[c(2,4,6)]) This is fine for a seven-variable dataset. When I have 250 variables, though, I start to pale at looking up column indexes over and over. I know from reading the list archives that I can extract the column index of Industry, for example, by typing which(Industry==names(pollute)) but doing that before each command seems dire. Trained to using Stata as I am, I am inclined to check the correlation of the first three or the second, fourth and sixth columns by substituting the column names for the column indexes--something like the following: cor(pollute[Pollution:Industry]) cor(pollute[c(Temp,Population,Rain)]) These however throw errors. I know that many commands in R are perfectly happy to take variable names--the regression models, for example--but that some do not. And so I ask you two general questions: 1. Is there a syntax for referring to variable names rather than column indexes in situations like these? 2. Is there something that I should look for in a command's help file that often indicates whether it can take column names rather than indexes? Again, apologies for asking something that has likely been asked before. I would appreciate any suggestions that you have. Best, John-Paul Ferguson Assistant Professor of Organizational Behavior Stanford University Graduate School of Business 518 Memorial Way, K313 Stanford, CA 94305 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Referencing variable names rather than column numbers
Hi, Try this, cor(pollute[ ,c(Pollution,Temp,Industry)]) and ?[ in particular, Character vectors will be matched to the names of the object HTH, baptiste 2009/12/5 John-Paul Ferguson ferguson_john-p...@gsb.stanford.edu: I apologize for how basic a question this is. I am a Stata user who has begun using R, and the syntax differences still trip me up. The most basic questions, involving as they do general terms, can be the hardest to find solutions for through search. Assume for the moment that I have a dataset that contains seven variables: Pollution, Temp, Industry, Population, Wind, Rain and Wet.days. (This actual dataset is taken from Michael Crawley's Statistics: An Introduction Using R and is available as pollute.txt in http://www.bio.ic.ac.uk/research/crawley/statistics/data/zipped.zip.) Assume I have attached pollute. Then cor(pollute) will give me the correlation table for these seven variables. If I would prefer only to see the correlations between, say, Pollution, Temp and Industry, I can get that with cor(pollute[,1:3]) or with cor(pollute[1:3]) Similarly, I can see the correlations between Temp, Population and Rain with cor(pollute[,c(2,4,6)]) or with cor(pollute[c(2,4,6)]) This is fine for a seven-variable dataset. When I have 250 variables, though, I start to pale at looking up column indexes over and over. I know from reading the list archives that I can extract the column index of Industry, for example, by typing which(Industry==names(pollute)) but doing that before each command seems dire. Trained to using Stata as I am, I am inclined to check the correlation of the first three or the second, fourth and sixth columns by substituting the column names for the column indexes--something like the following: cor(pollute[Pollution:Industry]) cor(pollute[c(Temp,Population,Rain)]) These however throw errors. I know that many commands in R are perfectly happy to take variable names--the regression models, for example--but that some do not. And so I ask you two general questions: 1. Is there a syntax for referring to variable names rather than column indexes in situations like these? 2. Is there something that I should look for in a command's help file that often indicates whether it can take column names rather than indexes? Again, apologies for asking something that has likely been asked before. I would appreciate any suggestions that you have. Best, John-Paul Ferguson Assistant Professor of Organizational Behavior Stanford University Graduate School of Business 518 Memorial Way, K313 Stanford, CA 94305 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] categorical vs numerical
pkg:lattice is installed as part of the base R distribution.
You don't need to install it.
DispersionMap wrote:
Thanks, ill give them whirl...when i was installing the lattice package i got
the error in bold below...why does it say permission denied and what effect
does this have?
I guess that you're on Vista and don't have write permission
for that directory.
-Peter Ehlers
utils:::menuInstallLocal()
package 'lattice' successfully unpacked and MD5 sums checked
updating HTML package descriptions
Warning message:
In file.create(f.tg) :
cannot create file 'C:\PROGRA~1\R\R-29~1.2/doc/html/packages.html', reason
'Permission denied'
local({pkg - select.list(sort(.packages(all.available = TRUE)))
+ if(nchar(pkg)) library(pkg, character.only=TRUE)})
Warning message:
package 'lattice' was built under R version 2.10.0
I have it loaded
Peter Ehlers wrote:
Whoops, that should be
densityplot(~y|g, data=dat, plot.points=FALSE, layout=c(1,4))
-Peter Ehlers
Peter Ehlers wrote:
You could try density plots:
If dat is your dataframe, y is your numerical vector and
g is your factor,
library(lattice)
trellis.device(height=9, width=7)
densityplot(~g|y, data=dat, plot.points=FALSE, layout=c(1,4))
See ?densityplot, ?panel.densityplot
-Peter Ehlers
DispersionMap wrote:
Thanks, however the group sizes are really big (each a,b,c.. category
has
60,000 observations). Its hard to see whats going on withe the jittered
stripchart, i just get big black blobs.
Any other suggestions?
Peter Ehlers wrote:
If your group sizes are not too large, I would use jittered
stripcharts.
They're more informative than boxplots and much less subject to
misinterpretation. One warning, I'm not fond of the default pch=0.
-Peter Ehlers
DispersionMap wrote:
What ways are there to plot categorical vs numerical data in R.
I have two columns: one with categorical data in 5 categories
a,b,c,d,e,
and
a numerical column with integers between 1 and 100.
I have used a boxplot with a,b,c,d,e on the x-axis and an increasing
numerical scale on the y-axis. This look fine but im looking for other
ways
to present the data.
What other ways can i do this???
__
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Peter Ehlers
University of Calgary
403.202.3936
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Peter Ehlers
University of Calgary
403.202.3936
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Re: [R] Referencing variable names rather than column numbers
As baptiste noted, you can do cor(pollute[ ,c(Pollution,Temp,Industry)]). But cor(pollute[,Pollution:Industry]) will not work. For that you can do cor(pollute[ ,which(names(pollute)==Pollution):which(names(pollute)==Industry)]) -Ista On Sat, Dec 5, 2009 at 11:22 AM, John-Paul Ferguson ferguson_john-p...@gsb.stanford.edu wrote: I apologize for how basic a question this is. I am a Stata user who has begun using R, and the syntax differences still trip me up. The most basic questions, involving as they do general terms, can be the hardest to find solutions for through search. Assume for the moment that I have a dataset that contains seven variables: Pollution, Temp, Industry, Population, Wind, Rain and Wet.days. (This actual dataset is taken from Michael Crawley's Statistics: An Introduction Using R and is available as pollute.txt in http://www.bio.ic.ac.uk/research/crawley/statistics/data/zipped.zip.) Assume I have attached pollute. Then cor(pollute) will give me the correlation table for these seven variables. If I would prefer only to see the correlations between, say, Pollution, Temp and Industry, I can get that with cor(pollute[,1:3]) or with cor(pollute[1:3]) Similarly, I can see the correlations between Temp, Population and Rain with cor(pollute[,c(2,4,6)]) or with cor(pollute[c(2,4,6)]) This is fine for a seven-variable dataset. When I have 250 variables, though, I start to pale at looking up column indexes over and over. I know from reading the list archives that I can extract the column index of Industry, for example, by typing which(Industry==names(pollute)) but doing that before each command seems dire. Trained to using Stata as I am, I am inclined to check the correlation of the first three or the second, fourth and sixth columns by substituting the column names for the column indexes--something like the following: cor(pollute[Pollution:Industry]) cor(pollute[c(Temp,Population,Rain)]) These however throw errors. I know that many commands in R are perfectly happy to take variable names--the regression models, for example--but that some do not. And so I ask you two general questions: 1. Is there a syntax for referring to variable names rather than column indexes in situations like these? 2. Is there something that I should look for in a command's help file that often indicates whether it can take column names rather than indexes? Again, apologies for asking something that has likely been asked before. I would appreciate any suggestions that you have. Best, John-Paul Ferguson Assistant Professor of Organizational Behavior Stanford University Graduate School of Business 518 Memorial Way, K313 Stanford, CA 94305 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Ista Zahn Graduate student University of Rochester Department of Clinical and Social Psychology http://yourpsyche.org __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Referencing variable names rather than column numbers
Dear John-Paul, Take a look at https://stat.ethz.ch/pipermail/r-help/2009-July/204027.html It contains different ways to do (in part) what you want. HTH, Jorge On Sat, Dec 5, 2009 at 11:22 AM, John-Paul Ferguson wrote: I apologize for how basic a question this is. I am a Stata user who has begun using R, and the syntax differences still trip me up. The most basic questions, involving as they do general terms, can be the hardest to find solutions for through search. Assume for the moment that I have a dataset that contains seven variables: Pollution, Temp, Industry, Population, Wind, Rain and Wet.days. (This actual dataset is taken from Michael Crawley's Statistics: An Introduction Using R and is available as pollute.txt in http://www.bio.ic.ac.uk/research/crawley/statistics/data/zipped.zip.) Assume I have attached pollute. Then cor(pollute) will give me the correlation table for these seven variables. If I would prefer only to see the correlations between, say, Pollution, Temp and Industry, I can get that with cor(pollute[,1:3]) or with cor(pollute[1:3]) Similarly, I can see the correlations between Temp, Population and Rain with cor(pollute[,c(2,4,6)]) or with cor(pollute[c(2,4,6)]) This is fine for a seven-variable dataset. When I have 250 variables, though, I start to pale at looking up column indexes over and over. I know from reading the list archives that I can extract the column index of Industry, for example, by typing which(Industry==names(pollute)) but doing that before each command seems dire. Trained to using Stata as I am, I am inclined to check the correlation of the first three or the second, fourth and sixth columns by substituting the column names for the column indexes--something like the following: cor(pollute[Pollution:Industry]) cor(pollute[c(Temp,Population,Rain)]) These however throw errors. I know that many commands in R are perfectly happy to take variable names--the regression models, for example--but that some do not. And so I ask you two general questions: 1. Is there a syntax for referring to variable names rather than column indexes in situations like these? 2. Is there something that I should look for in a command's help file that often indicates whether it can take column names rather than indexes? Again, apologies for asking something that has likely been asked before. I would appreciate any suggestions that you have. Best, John-Paul Ferguson Assistant Professor of Organizational Behavior Stanford University Graduate School of Business 518 Memorial Way, K313 Stanford, CA 94305 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Referencing variable names rather than column numbers
Alternatively, you can use subset(), which supports the : operator for the 'select' argument: cor(subset(iris, select = Sepal.Length:Petal.Length)) Sepal.Length Sepal.Width Petal.Length Sepal.Length1.000 -0.11756980.8717538 Sepal.Width-0.1175698 1.000 -0.4284401 Petal.Length0.8717538 -0.42844011.000 which is equivalent to: cor(iris[, 1:3]) Sepal.Length Sepal.Width Petal.Length Sepal.Length1.000 -0.11756980.8717538 Sepal.Width-0.1175698 1.000 -0.4284401 Petal.Length0.8717538 -0.42844011.000 So for the pollute data: cor(subset(pollute, select = Pollution:Industry)) should work. Note also that the 'select' argument to subset can take non-contiguous column names: # Skip 'Sepal.Width' cor(subset(iris, select = c(Sepal.Length, Petal.Length:Petal.Width))) Sepal.Length Petal.Length Petal.Width Sepal.Length1.0000.8717538 0.8179411 Petal.Length0.87175381.000 0.9628654 Petal.Width 0.81794110.9628654 1.000 So you have the option of specifying, by name, multiple series of contiguous and non-contiguous column names. See ?subset HTH, Marc Schwartz On Dec 5, 2009, at 10:43 AM, Ista Zahn wrote: As baptiste noted, you can do cor(pollute[ ,c(Pollution,Temp,Industry)]). But cor(pollute[,Pollution:Industry]) will not work. For that you can do cor (pollute [ ,which (names(pollute)==Pollution):which(names(pollute)==Industry)]) -Ista On Sat, Dec 5, 2009 at 11:22 AM, John-Paul Ferguson ferguson_john-p...@gsb.stanford.edu wrote: I apologize for how basic a question this is. I am a Stata user who has begun using R, and the syntax differences still trip me up. The most basic questions, involving as they do general terms, can be the hardest to find solutions for through search. Assume for the moment that I have a dataset that contains seven variables: Pollution, Temp, Industry, Population, Wind, Rain and Wet.days. (This actual dataset is taken from Michael Crawley's Statistics: An Introduction Using R and is available as pollute.txt in http://www.bio.ic.ac.uk/research/crawley/statistics/data/zipped.zip.) Assume I have attached pollute. Then cor(pollute) will give me the correlation table for these seven variables. If I would prefer only to see the correlations between, say, Pollution, Temp and Industry, I can get that with cor(pollute[,1:3]) or with cor(pollute[1:3]) Similarly, I can see the correlations between Temp, Population and Rain with cor(pollute[,c(2,4,6)]) or with cor(pollute[c(2,4,6)]) This is fine for a seven-variable dataset. When I have 250 variables, though, I start to pale at looking up column indexes over and over. I know from reading the list archives that I can extract the column index of Industry, for example, by typing which(Industry==names(pollute)) but doing that before each command seems dire. Trained to using Stata as I am, I am inclined to check the correlation of the first three or the second, fourth and sixth columns by substituting the column names for the column indexes--something like the following: cor(pollute[Pollution:Industry]) cor(pollute[c(Temp,Population,Rain)]) These however throw errors. I know that many commands in R are perfectly happy to take variable names--the regression models, for example--but that some do not. And so I ask you two general questions: 1. Is there a syntax for referring to variable names rather than column indexes in situations like these? 2. Is there something that I should look for in a command's help file that often indicates whether it can take column names rather than indexes? Again, apologies for asking something that has likely been asked before. I would appreciate any suggestions that you have. Best, John-Paul Ferguson Assistant Professor of Organizational Behavior Stanford University Graduate School of Business 518 Memorial Way, K313 Stanford, CA 94305 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Ista Zahn Graduate student University of Rochester Department of Clinical and Social Psychology http://yourpsyche.org __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Referencing variable names rather than column numbers
On Dec 5, 2009, at 11:30 AM, baptiste auguie wrote: Hi, Try this, cor(pollute[ ,c(Pollution,Temp,Industry)]) and ?[ in particular, Character vectors will be matched to the names of the object John-Paul; In the time it took me to compose this, I see that others have already pointed out all of what I had written so it only remains to offer yet- another-R-method for ranges of column names. You could have defined a targets vector of names if you know the starting and ending position: ?Extract # or equivalently ?[ targets - names(pollute)[1:3]# colnames is an equivalent function for dataframe objects targets pollute[ , targets] -- Best; David. HTH, baptiste 2009/12/5 John-Paul Ferguson ferguson_john-p...@gsb.stanford.edu: I apologize for how basic a question this is. I am a Stata user who has begun using R, and the syntax differences still trip me up. The most basic questions, involving as they do general terms, can be the hardest to find solutions for through search. Assume for the moment that I have a dataset that contains seven variables: Pollution, Temp, Industry, Population, Wind, Rain and Wet.days. (This actual dataset is taken from Michael Crawley's Statistics: An Introduction Using R and is available as pollute.txt in http://www.bio.ic.ac.uk/research/crawley/statistics/data/zipped.zip.) Assume I have attached pollute. Then cor(pollute) will give me the correlation table for these seven variables. If I would prefer only to see the correlations between, say, Pollution, Temp and Industry, I can get that with cor(pollute[,1:3]) or with cor(pollute[1:3]) Similarly, I can see the correlations between Temp, Population and Rain with cor(pollute[,c(2,4,6)]) or with cor(pollute[c(2,4,6)]) This is fine for a seven-variable dataset. When I have 250 variables, though, I start to pale at looking up column indexes over and over. I know from reading the list archives that I can extract the column index of Industry, for example, by typing which(Industry==names(pollute)) but doing that before each command seems dire. Trained to using Stata as I am, I am inclined to check the correlation of the first three or the second, fourth and sixth columns by substituting the column names for the column indexes--something like the following: cor(pollute[Pollution:Industry]) cor(pollute[c(Temp,Population,Rain)]) These however throw errors. I know that many commands in R are perfectly happy to take variable names--the regression models, for example--but that some do not. And so I ask you two general questions: 1. Is there a syntax for referring to variable names rather than column indexes in situations like these? 2. Is there something that I should look for in a command's help file that often indicates whether it can take column names rather than indexes? Again, apologies for asking something that has likely been asked before. I would appreciate any suggestions that you have. Best, John-Paul Ferguson Assistant Professor of Organizational Behavior Stanford University Graduate School of Business 518 Memorial Way, K313 Stanford, CA 94305 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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. 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] Referencing variable names rather than column numbers
Holy Cats, those were four quick responses! And the question, basically, is answered: 1. When in doubt, try quoting column names where you would try using unquoted column indexes. 2. Subset() seems, overall, the most flexible analog to Stata's variable-referencing syntax. I appreciate the help. I'm encouraging several of my PhD students to pick up R, given the research that they are doing, but it seems wrong to make them do that without learning it myself. Humbling to be back at this level of basic interface interaction, but very good to know that a resource like this list exists. Best, John-Paul 2009/12/5 Marc Schwartz marc_schwa...@me.com: Alternatively, you can use subset(), which supports the : operator for the 'select' argument: cor(subset(iris, select = Sepal.Length:Petal.Length)) Sepal.Length Sepal.Width Petal.Length Sepal.Length 1.000 -0.1175698 0.8717538 Sepal.Width -0.1175698 1.000 -0.4284401 Petal.Length 0.8717538 -0.4284401 1.000 which is equivalent to: cor(iris[, 1:3]) Sepal.Length Sepal.Width Petal.Length Sepal.Length 1.000 -0.1175698 0.8717538 Sepal.Width -0.1175698 1.000 -0.4284401 Petal.Length 0.8717538 -0.4284401 1.000 So for the pollute data: cor(subset(pollute, select = Pollution:Industry)) should work. Note also that the 'select' argument to subset can take non-contiguous column names: # Skip 'Sepal.Width' cor(subset(iris, select = c(Sepal.Length, Petal.Length:Petal.Width))) Sepal.Length Petal.Length Petal.Width Sepal.Length 1.000 0.8717538 0.8179411 Petal.Length 0.8717538 1.000 0.9628654 Petal.Width 0.8179411 0.9628654 1.000 So you have the option of specifying, by name, multiple series of contiguous and non-contiguous column names. See ?subset HTH, Marc Schwartz On Dec 5, 2009, at 10:43 AM, Ista Zahn wrote: As baptiste noted, you can do cor(pollute[ ,c(Pollution,Temp,Industry)]). But cor(pollute[,Pollution:Industry]) will not work. For that you can do cor (pollute [ ,which (names(pollute)==Pollution):which(names(pollute)==Industry)]) -Ista On Sat, Dec 5, 2009 at 11:22 AM, John-Paul Ferguson ferguson_john-p...@gsb.stanford.edu wrote: I apologize for how basic a question this is. I am a Stata user who has begun using R, and the syntax differences still trip me up. The most basic questions, involving as they do general terms, can be the hardest to find solutions for through search. Assume for the moment that I have a dataset that contains seven variables: Pollution, Temp, Industry, Population, Wind, Rain and Wet.days. (This actual dataset is taken from Michael Crawley's Statistics: An Introduction Using R and is available as pollute.txt in http://www.bio.ic.ac.uk/research/crawley/statistics/data/zipped.zip.) Assume I have attached pollute. Then cor(pollute) will give me the correlation table for these seven variables. If I would prefer only to see the correlations between, say, Pollution, Temp and Industry, I can get that with cor(pollute[,1:3]) or with cor(pollute[1:3]) Similarly, I can see the correlations between Temp, Population and Rain with cor(pollute[,c(2,4,6)]) or with cor(pollute[c(2,4,6)]) This is fine for a seven-variable dataset. When I have 250 variables, though, I start to pale at looking up column indexes over and over. I know from reading the list archives that I can extract the column index of Industry, for example, by typing which(Industry==names(pollute)) but doing that before each command seems dire. Trained to using Stata as I am, I am inclined to check the correlation of the first three or the second, fourth and sixth columns by substituting the column names for the column indexes--something like the following: cor(pollute[Pollution:Industry]) cor(pollute[c(Temp,Population,Rain)]) These however throw errors. I know that many commands in R are perfectly happy to take variable names--the regression models, for example--but that some do not. And so I ask you two general questions: 1. Is there a syntax for referring to variable names rather than column indexes in situations like these? 2. Is there something that I should look for in a command's help file that often indicates whether it can take column names rather than indexes? Again, apologies for asking something that has likely been asked before. I would appreciate any suggestions that you have. Best, John-Paul Ferguson Assistant Professor of Organizational Behavior Stanford University Graduate School of Business 518 Memorial Way, K313 Stanford, CA 94305 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] three plots as one JEPG?
Dear List, i have a question concerning these device-related function (i.e. pdf(),jpeg(), etc.). Currently, I plot three graphs, one below the other into a /single/ window by using par(). I would like to save this figure now as JPEG or PNG. By now, code looks as follows: jepg(...) par(...) plot(...) par(...) plot(...) par(...) plot(...) dev.off() Unfortunaltely, I just get the last plot saved, the rest is dismissed. Does anyone have a solution for this problem? Cheers Alex __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Refresh with default x11() cairo
Greetings R community: Since R 2.9.0+ I have noticed that when I use the default cairo x11() device, if I obscure a device window (or switch virtual desktops), the window does not refresh. I need to move it or resize it to make it redraw. This behavior did not happen before 2.9.0. It also does not occur currently when using the Xlib type in x11. Now, I should make clear that I am not running on a machine under my administrative control, so it is entirely possible that something changed in the default X Window System configuration that prevents Cairo from refreshing. I would like to ask if anyone has seen this behavior before and if so, have you found the cause and/or solution? Thank you. Possibly useful info: Linux sunfire47 2.6.18-164.6.1.el5 #1 SMP Tue Oct 27 11:28:30 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux R version 2.10.0 (2009-10-26) Name: cairoRelocations: (not relocatable) Version : 1.2.4 Vendor: Red Hat, Inc. Release : 5.el5 Build Date: Fri 18 Jan 2008 04:55:11 PM EST Regards, Marc __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] categorical vs numerical
im using w7 ultimate
Peter Ehlers wrote:
pkg:lattice is installed as part of the base R distribution.
You don't need to install it.
DispersionMap wrote:
Thanks, ill give them whirl...when i was installing the lattice package i
got
the error in bold below...why does it say permission denied and what
effect
does this have?
I guess that you're on Vista and don't have write permission
for that directory.
-Peter Ehlers
utils:::menuInstallLocal()
package 'lattice' successfully unpacked and MD5 sums checked
updating HTML package descriptions
Warning message:
In file.create(f.tg) :
cannot create file 'C:\PROGRA~1\R\R-29~1.2/doc/html/packages.html',
reason
'Permission denied'
local({pkg - select.list(sort(.packages(all.available = TRUE)))
+ if(nchar(pkg)) library(pkg, character.only=TRUE)})
Warning message:
package 'lattice' was built under R version 2.10.0
I have it loaded
Peter Ehlers wrote:
Whoops, that should be
densityplot(~y|g, data=dat, plot.points=FALSE, layout=c(1,4))
-Peter Ehlers
Peter Ehlers wrote:
You could try density plots:
If dat is your dataframe, y is your numerical vector and
g is your factor,
library(lattice)
trellis.device(height=9, width=7)
densityplot(~g|y, data=dat, plot.points=FALSE, layout=c(1,4))
See ?densityplot, ?panel.densityplot
-Peter Ehlers
DispersionMap wrote:
Thanks, however the group sizes are really big (each a,b,c.. category
has
60,000 observations). Its hard to see whats going on withe the
jittered
stripchart, i just get big black blobs.
Any other suggestions?
Peter Ehlers wrote:
If your group sizes are not too large, I would use jittered
stripcharts.
They're more informative than boxplots and much less subject to
misinterpretation. One warning, I'm not fond of the default pch=0.
-Peter Ehlers
DispersionMap wrote:
What ways are there to plot categorical vs numerical data in R.
I have two columns: one with categorical data in 5 categories
a,b,c,d,e,
and
a numerical column with integers between 1 and 100.
I have used a boxplot with a,b,c,d,e on the x-axis and an increasing
numerical scale on the y-axis. This look fine but im looking for
other
ways
to present the data.
What other ways can i do this???
__
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__
R-help@r-project.org mailing list
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http://www.R-project.org/posting-guide.html
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--
Peter Ehlers
University of Calgary
403.202.3936
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--
Peter Ehlers
University of Calgary
403.202.3936
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Re: [R] three plots as one JEPG?
On Dec 5, 2009, at 11:21 AM, Walther, Alexander wrote: Dear List, i have a question concerning these device-related function (i.e. pdf(),jpeg(), etc.). Currently, I plot three graphs, one below the other into a /single/ window by using par(). I would like to save this figure now as JPEG or PNG. By now, code looks as follows: jepg(...) par(...) plot(...) par(...) plot(...) par(...) plot(...) dev.off() Unfortunaltely, I just get the last plot saved, the rest is dismissed. Does anyone have a solution for this problem? Cheers Alex In the sequence you have above, each time you call plot(), you are erasing the prior plot. What you want is: jpeg(...) par(mfrow = (3, 1)) plot(...) plot(...) plot(...) dev.off() That will create a plot matrix of 3 rows and 1 column, which will be saved to the jpeg file. Each new plot will be below the prior one. A good way of going about this is to start by just plotting to the normal display device and then output to an external file. For the most part, the output should be similar, as long as you don't re-size the display device (eg. dragging a corner, etc.). With the code you have above, you would see right away that each new plot was clearing the prior one, thus knowing that this behavior was not unique to jpeg(). You can then tweak the plot as may be needed for the jpeg device. You can also use ?layout to play around with creating differing arrangements of plots within a single device instance. HTH, Marc Schwartz __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] three plots as one JEPG?
On 05/12/2009 12:21 PM, Walther, Alexander wrote: Dear List, i have a question concerning these device-related function (i.e. pdf(),jpeg(), etc.). Currently, I plot three graphs, one below the other into a /single/ window by using par(). I would like to save this figure now as JPEG or PNG. By now, code looks as follows: jepg(...) par(...) plot(...) par(...) plot(...) par(...) plot(...) dev.off() Unfortunaltely, I just get the last plot saved, the rest is dismissed. Does anyone have a solution for this problem? Sure, just do it like this: jpeg(...) par(mfrow=c(3,1)) plot(...) plot(...) plot(...) dev.off() There's also the layout() function, and more elaborate layout possibilities in the grid package. But the basic idea is that you want the code to generate just one image on screen if you use a screen device rather than jpeg(), then jpeg() will generate something very similar. 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] three plots as one JEPG?
On Dec 5, 2009, at 11:34 AM, Marc Schwartz wrote: On Dec 5, 2009, at 11:21 AM, Walther, Alexander wrote: Dear List, i have a question concerning these device-related function (i.e. pdf(),jpeg(), etc.). Currently, I plot three graphs, one below the other into a /single/ window by using par(). I would like to save this figure now as JPEG or PNG. By now, code looks as follows: jepg(...) par(...) plot(...) par(...) plot(...) par(...) plot(...) dev.off() Unfortunaltely, I just get the last plot saved, the rest is dismissed. Does anyone have a solution for this problem? Cheers Alex In the sequence you have above, each time you call plot(), you are erasing the prior plot. What you want is: jpeg(...) par(mfrow = (3, 1)) Sorry, typo on that line. It should be: par(mfrow = c(3, 1)) Marc __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 boxplot for time class
Thanks a lot Gabor, now I could finally plot the as time data. I just have one more question, and I hope it is the last. In the script of the boxplot, bp - boxplot(as.numeric(skiers$start), yaxt = n) axis(2, bp$stats, times(bp$stats), las = 2, cex.axis = 0.5) I have been trying to add a main tittle and xlab, ylab with no succes. Where I am supposed to type: main=skiing starting tour and so on Thanks a lot!! Maria Gabor Grothendieck wrote: Try this: Lines - protokollid datestart end 4 2/23/2009 8:50:10 15:17:30 4 2/24/2009 9:47:00 13:52:25 5 3/22/2009 8:51:25 12:00:05 library(chron) skiers - read.table(textConnection(Lines), header = TRUE, as.is = TRUE) skiers - transform(skiers, date = dates(date), start = times(start), end = times(end)) bp - boxplot(as.numeric(skiers$start), yaxt = n) axis(2, bp$stats, times(bp$stats), las = 2, cex.axis = 0.5) On Sat, Dec 5, 2009 at 6:52 AM, uvilla maruchave...@hotmail.com wrote: hi again I will try this time to explain my problem clearly I have the following data from the file skiing.csv (3 first rows) protokollid datestart end 14 2/23/2009 8:50:10 15:17:30 24 2/24/2009 9:47:00 13:52:25 35 3/22/2009 8:51:25 12:00:05 I have the following script library(chron) skiers=read.csv(skiing.csv) strptime(08:50:10,%H:%M:%S) start=times(skiers[,3]) strptime(start,%H:%M:%S) end=times(skiers[,4]) strptime(end,%H:%M:%S) #calc lenght of the route length.route=end-start #calc medians median(start) median(length.route) Then I want to do a box plot of the staring time when I use: boxplot(start) this error appears: Warning message: In is.na(x) : is.na() applied to non-(list or vector) of type 'NULL' when I try to convert start as POSIXct start=as.POSIXct(start) Error in as.POSIXct.default(start) : do not know how to convert 'start' to class POSIXlt and when I try to convert skiers[,3] as POSIXct skiers[,3]=as.POSIXct(skiers[,3]) Error in as.POSIXlt.character(as.character(x)) : character string is not in a standard unambiguous format start is of times class and skiers[,3] of factor class I want to do a boxplot of the starting time of my data, which reflect the median 08:36:45, and all O get in the y axis are decimal numbers :( Help please Best regards Maria Stauss -- View this message in context: http://n4.nabble.com/HELP-boxplot-for-time-class-tp949154p949154.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. [[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://n4.nabble.com/HELP-boxplot-for-time-class-tp949154p949270.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] Partial correlations and p-values
On Sat, 5 Dec 2009, Juliet Hannah wrote: Your R code looks correct. There are a couple of hiccups. First the degrees of freedom for the partial correlation would be wrong even if there was no missing data. Because this is a straightforward calculation, I would be surprised if there were any differences with SPSS. There are differences. SPSS seems to use the correlation matrix computed with a pairwise present method and compute partial correlations from that. Following http://wiki.r-project.org/rwiki/doku.php?id=tips:data-matrices:part_corr R.pp - cor(cbind(x,y,z1,z2),use='pair') R.comp - cor(cbind(x,y,z1,z2),use='complete') Rinv - solve(R.pp) D - diag(1 / sqrt(diag(Rinv))) P - -D %*% Rinv %*% D P[1,2] [1] 0.4596122 Rinv - solve(R.comp) D - diag(1 / sqrt(diag(Rinv))) P - -D %*% Rinv %*% D P[1,2] [1] 0.657214 The pairwise present value seems to be what SPSS is reporting. The complete cases values is nearly (but not the same as) what you got. A real issue here is how to usefully compute and test partial correlations in the presence of missing data. If you want to persue that, I would suggest opening a new thread with a subject line like 'partial correlations with missing observations' HTH, Chuck It may be worthwhile to check if SPSS gives partial correlations or semipartial correlations. For example, if you take the correlation between py - resid(lm(y ~ z1 + z2,data=mydat2)) and x where mydat2 has missing values removed, you get 0.47. On Tue, Dec 1, 2009 at 8:24 PM, dadrivr dadr...@gmail.com wrote: I am trying to calculate a partial correlation and p-values. Unfortunately, the results in R are different than what SPSS gives. Here is an example in R (calculating the partial correlation of x and y, controlling for z1 and z2): x - c(1,20,14,30,9,4,8) y - c(5,6,7,9,NA,10,6) z1 - c(13,8,16,14,26,13,20) z2 - c(12,NA,2,5,8,16,13) fmx - lm(x ~ z1 + z2, na.action = na.exclude) fmy - lm(y ~ z1 + z2, na.action = na.exclude) yres - resid(fmy) xres - resid(fmx) cor(xres, yres, use = p) ct - cor.test(xres, yres) ct$estimate ct$p.value R give me: r = .65, p = .23 However, SPSS calculates: r = .46, p = .70 I think something may be different with R's handling of missing data, as when I replace the NA's with values, R and SPSS give the same r-values, albeit different p-values still. I am doing pairwise case exclusion in both R and SPSS. Any ideas why I'm getting different values? Is something wrong with my formula in R? Any help would be greatly appreciated. Thanks! __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Charles C. Berry(858) 534-2098 Dept of Family/Preventive Medicine E mailto:cbe...@tajo.ucsd.edu UC San Diego http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego 92093-0901 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Partial correlations and p-values
you might look at partial.r in the psych package dadrivr wrote: I'm trying to write code to calculate partial correlations (along with p-values). I'm new to R, and I don't know how to do this. I have searched and come across different functions, but I haven't been able to get any of them to work (for example, pcor and pcor.test from the ggm package). In the following example, I am trying to compute the correlation between x and y, while controlling for z (partial correlation): x - c(1,20,14,7,9) y - c(5,6,7,9,10) z - c(13,27,16,5,4) What function can I append to this to find this partial correlation? Many thanks! -- View this message in context: http://n4.nabble.com/Partial-correlations-and-p-values-tp908641p949283.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] regression tests still fail for R version 2.10.0
Hello, on Mon Nov 9 17:57:04 CET 2009 I've sent an e-mail to the R mailing list (see below), about a failing regression test. Yet nobody replied, while (obviously) the situation didn't change (installation still fails, and might continue to do so in the future). I wonder whether somebody has to say something here? Shall a bug report be submitted? Or will R 2.10.1 have fixed the bug? Oliver -- Hello, I have installed R version 2.9.2, and everything works fine, but when attempting to install version 2.10.0 I get: running code in 'datasets.R' ... OK comparing 'datasets.Rout' to './datasets.Rout.save' ... OK make[4]: Leaving directory `/home/csoliver/SAT-Algorithmen/OKplatform/ExternalSources/builds/R/R-2.10.0/tests' make[3]: Leaving directory `/home/csoliver/SAT-Algorithmen/OKplatform/ExternalSources/builds/R/R-2.10.0/tests' make[3]: Entering directory `/home/csoliver/SAT-Algorithmen/OKplatform/ExternalSources/builds/R/R-2.10.0/tests' running regression tests ... make[4]: Entering directory `/home/csoliver/SAT-Algorithmen/OKplatform/ExternalSources/builds/R/R-2.10.0/tests' running code in 'reg-tests-1.R' ...make[4]: *** [reg-tests-1.Rout] Error 1 make[4]: Leaving directory `/home/csoliver/SAT-Algorithmen/OKplatform/ExternalSources/builds/R/R-2.10.0/tests' make[3]: *** [test-Reg] Error 2 make[3]: Leaving directory `/home/csoliver/SAT-Algorithmen/OKplatform/ExternalSources/builds/R/R-2.10.0/tests' make[2]: *** [test-all-basics] Error 1 make[2]: Leaving directory `/home/csoliver/SAT-Algorithmen/OKplatform/ExternalSources/builds/R/R-2.10.0/tests' make[1]: *** [check] Error 2 make[1]: Leaving directory `/home/csoliver/SAT-Algorithmen/OKplatform/ExternalSources/builds/R/R-2.10.0' make: *** [R_base] Error 1 Before that the build seems alright. Oliver -- Dr. Oliver Kullmann Computer Science Department Swansea University Faraday Building, Singleton Park Swansea SA2 8PP, UK http://cs.swan.ac.uk/~csoliver/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] regression tests still fail for R version 2.10.0
The question lacks so many specifics that would be needed to address problem that I suspect persons with sufficient knowledge to address it (and I am probably not among that group) simply passed it over and waited for you to get sufficiently motivated to actually read the Posting Guide. Among the missing items are OS specifics, why you need to install from sources, which version of the source bundle, (perhaps) which mirror, etc, etc. (I surely would not report a bug with so much missing information.) -- David. On Dec 5, 2009, at 1:25 PM, Oliver Kullmann wrote: Hello, on Mon Nov 9 17:57:04 CET 2009 I've sent an e-mail to the R mailing list (see below), about a failing regression test. Yet nobody replied, while (obviously) the situation didn't change (installation still fails, and might continue to do so in the future). I wonder whether somebody has to say something here? Shall a bug report be submitted? Or will R 2.10.1 have fixed the bug? Oliver -- Hello, I have installed R version 2.9.2, and everything works fine, but when attempting to install version 2.10.0 I get: running code in 'datasets.R' ... OK comparing 'datasets.Rout' to './datasets.Rout.save' ... OK make[4]: Leaving directory `/home/csoliver/SAT-Algorithmen/ OKplatform/ExternalSources/builds/R/R-2.10.0/tests' make[3]: Leaving directory `/home/csoliver/SAT-Algorithmen/ OKplatform/ExternalSources/builds/R/R-2.10.0/tests' make[3]: Entering directory `/home/csoliver/SAT-Algorithmen/ OKplatform/ExternalSources/builds/R/R-2.10.0/tests' running regression tests ... make[4]: Entering directory `/home/csoliver/SAT-Algorithmen/ OKplatform/ExternalSources/builds/R/R-2.10.0/tests' running code in 'reg-tests-1.R' ...make[4]: *** [reg-tests-1.Rout] Error 1 make[4]: Leaving directory `/home/csoliver/SAT-Algorithmen/ OKplatform/ExternalSources/builds/R/R-2.10.0/tests' make[3]: *** [test-Reg] Error 2 make[3]: Leaving directory `/home/csoliver/SAT-Algorithmen/ OKplatform/ExternalSources/builds/R/R-2.10.0/tests' make[2]: *** [test-all-basics] Error 1 make[2]: Leaving directory `/home/csoliver/SAT-Algorithmen/ OKplatform/ExternalSources/builds/R/R-2.10.0/tests' make[1]: *** [check] Error 2 make[1]: Leaving directory `/home/csoliver/SAT-Algorithmen/ OKplatform/ExternalSources/builds/R/R-2.10.0' make: *** [R_base] Error 1 Before that the build seems alright. Oliver -- Dr. Oliver Kullmann Computer Science Department Swansea University Faraday Building, Singleton Park Swansea SA2 8PP, UK http://cs.swan.ac.uk/~csoliver/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Installing RandomForest on SuSe Linux - warnings
If the package passes the checks (R CMD check) on your macine, it should be fine. Some compiler warnings are expected. Best wishes, Uwe Ligges NCS wrote: I installed RF on Linux OpenSuSe 11.1 and while it did install and did run a model I had created on Windows correctly, it gave me a lot of uninitialized warnings. I don't know if these are significant and so am a little concerned even though my model ran. Any thoughts? Thanks R version 2.10.0 (2009-10-26) Copyright (C) 2009 The R Foundation for Statistical Computing ISBN 3-900051-07-0 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. install.packages(randomForest) --- Please select a CRAN mirror for use in this session --- CRAN mirror 1: Argentina (Buenos Aires) 2: Australia 3: Austria4: Belarus 5: Belgium6: Brazil (PR) 7: Brazil (RJ)8: Brazil (SP 1) 9: Brazil (SP 2) 10: Canada (BC) 11: Canada (ON) 12: Canada (QC) 13: Chile 14: China (Beijing 1) 15: China (Beijing 2) 16: China (Hong Kong) 17: Colombia 18: Denmark 19: France (Toulouse) 20: France (Lyon) 21: France (Paris)22: Germany (Berlin) 23: Germany (Goettingen) 24: Germany (Hannover) 25: Germany (Muenchen)26: Germany (Wiesbaden) 27: Iran 28: Ireland 29: Italy (Milano)30: Italy (Padua) 31: Italy (Palermo) 32: Japan (Aizu) 33: Japan (Hyogo) 34: Japan (Tokyo) 35: Japan (Tsukuba) 36: Korea 37: Netherlands 38: New Zealand 39: Norway40: Poland (Oswiecim) 41: Poland (Wroclaw) 42: Portugal 43: Russia44: Singapore 1 45: Singapore 2 46: Slovakia 47: South Africa 48: Spain (Madrid) 49: Sweden50: Switzerland 51: Taiwan (Taichung) 52: Taiwan (Taipeh) 53: Thailand 54: UK (Bristol) 55: UK (London) 56: USA (AZ) 57: USA (CA 1)58: USA (CA 2) 59: USA (IA) 60: USA (MA) 61: USA (MD) 62: USA (MI) 63: USA (MO) 64: USA (NC) 65: USA (OH) 66: USA (PA 1) 67: USA (PA 2)68: USA (TN) 69: USA (TX 1)70: USA (TX 3) 71: USA (WA) Selection: 57 trying URL 'http://cran.cnr.Berkeley.edu/src/contrib/randomForest_4.5-33.tar.gz' Content type 'application/x-gzip' length 71745 bytes (70 Kb) opened URL == downloaded 70 Kb * installing *source* package ârandomForestâ ... ** libs gcc -std=gnu99 -I/usr/lib64/R/include -I/usr/local/include-fpic -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -c classTree.c -o classTree.o classTree.c: In function âpredictClassTreeâ: classTree.c:414: warning: âcbestsplitâ may be used uninitialized in this function gcc -std=gnu99 -I/usr/lib64/R/include -I/usr/local/include-fpic -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -c regTree.c -o regTree.o regTree.c: In function âpredictRegTreeâ: regTree.c:294: warning: âcbestsplitâ may be used uninitialized in this function gcc -std=gnu99 -I/usr/lib64/R/include -I/usr/local/include-fpic -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -c regrf.c -o regrf.o regrf.c: In function âregRFâ: regrf.c:61: warning: ânodextsâ may be used uninitialized in this function regrf.c:55: warning: âytreeâ may be used uninitialized in this function gcc -std=gnu99 -I/usr/lib64/R/include -I/usr/local/include-fpic -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -c rf.c -o rf.o rf.c: In function âclassRFâ: rf.c:97: warning: âoobpairâ may be used uninitialized in this function rf.c:98: warning: âstrata_sizeâ may be used uninitialized in this function rf.c:98: warning: âstrata_idxâ may be used uninitialized in this function rf.c:97: warning: ânindâ may be used uninitialized in this function rf.c:89: warning: ânstrataâ may be used uninitialized in this function rf.c:92: warning: âncltsâ may be used uninitialized in this function gfortran -fpic -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -c rfsub.f -o rfsub.o
Re: [R] Rounding a Measurement to be Consistent with its Uncertainty
Tom La Bone wrote: I have a measurement of 8165.666 and an uncertainty of 338.9741 (the units of both are unimportant). I can easily round the uncertainty to two significant digits with signif(338.9741,2), which gives 340. Is there a function in R that will take 8165.666 and round it to be consistent with its uncertainty, i.e., 8170? That's not consistent, you have 3 significant digits here, but 2 for the uncertainty (whatever that is) ... Uwe Ligges Tom __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to draw a big heatmap?
Ning Ma wrote: Hi everyone. How can I draw a big heatmaps? png(foo.png,1,1) heatmap(x) dev.off() where x is a big matrix, say 200*200. The code above generates a small heatmap in the middle of the png file and leaves big margins. I expect it to take up more space so that the labels are not overlapping. Without having looked in detail - I cannot even allocate enough space for a 1x1 and you certainly do not want to produce some 300Mb file, do you? Anway, to proceed, decrease the size of the margins, see ?par. Uwe Ligges Thanks in advance. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Problem with date x-axis
PtitBleu wrote: Hello, I have a friday problem. I'm trying to plot the number of measures by day with this command between the 2008-07-31 and the 2009-11-13 (it works) : plot(unique(as.Date(strptime(data$date, format=%Y-%m-%d %H:%M:%S))), measuresbyday) then I would like to plot vertical lines for each month. But it doesn't work because par()$usr gives 14071.16 14579.84 -7.16 213.16 and as.numeric(as.POSIXct(unique(as.Date(strptime(data$date, format=%Y-%m-%d %H:%M:%S)))[1])) corresponding to 2008-08-01 gives 1217376000 I think the last value is ok but I don't understand why the par()$usr values are so low. Any idea ? Seems to be unanswered so far - not a big surprise given we do not see a small reproducible example (we do neither have measuresbyday nor data) that would be easy and quick to adapt to your needs. Best wishes, Uwe Ligges Thanks in advance and have a nice week-end, Ptit Bleu. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Announcing a new R news site: R-bloggers.com
Hello everyone. After some good time of work, I am proud to present: www.r-bloggers.com What is R-Bloggers.com? R-Bloggers.com hopes to serve the R community by presenting (in one place) all the new articles (posts) written (in English) about R in the R blogosphere. How does R-Bloggers operate? This site aggregates feeds (only with permission!) from participating R blogs. The beginnings of each participating blogs posts will automatically be displayed on the main page with links to the original posts; inside every post there is a link to the original blog and links to other related articles. All participating blogs will have links in the Contributors section of our sidebar What does R-Bloggers offer the community? - Discover: If every blogger will add itself, we will all be able to find new R blogs (which is hard to find on the web, if you ever tried). The site also allows to search in the content of the bloggers (although for searches of older content - you better go to the blogs themselves or wait for the customized google search box I will add in the future) - Follow: Enter your e-mail and subscribe to receive a daily digest with teasers of new posts from participating blogs. You will more easily get a sense of hot topics in the R blogosphere. - Connect: Click on Fan this site to become a fan of R Bloggers. You can friend other people and share thoughts on our wall. Or just by leaving comments on the blog. - Participate: Add your R blog to get increased visibility (for readers and search engines) with permanent links on our Contributors sidebar. Your blog will also gain visibility via our e-mail digest and through your presence on the main page with posts. How do I become a participating blog in R Bloggers? To add your blog, simply click on Add your blog!http://www.r-bloggers.com/add-your-blog/ and enter the required information. I will review your link and approve it in a timely fashion. How can I help? We share readers to gain readers! If you are interested and havent already, please submit your blog http://www.r-bloggers.com/add-your-blog/. Also please consider putting *a link from your blog* to R-Bloggers from your sidebar (we do the same for you); you can even put up a post about us - if each blogger will do so - all of us will gain from it. Who started R-Bloggers (and way)? R Bloggers was started by Tal Galili http://talgalili.com/. After searching for numerous R blogs, Tal (well, me) decided that there must be more R blogs our there then he knows about, and maybe the best way for finding them is to make them find him. You can reach Tal via the Contacthttp://www.r-bloggers.com/contact-us/ page (or just e-mail him: tal.gal...@gmail.com). Extra thanks and a deceleration of good intentions I would like to thank John, Yihui, Jaanus and Taiyun for being the first bloggers to allow me to enlist their blogs to the project. There are more R bloggers out there that I know of, and didn't get to ask for permission. I apologies to you for not contacting you personally, still If you are one such blogger, and you want to join the site, please feel welcome to submit your blog http://www.r-bloggers.com/add-your-blog/. I hope this e-mail was not an abuse of the R mailing list. Since I intended this project for the good of the R community I allowed myself to publish the site here, so I hope it wouldn't upset anyone. Best wishes to all, Tal Contact Details:--- Contact me: tal.gal...@gmail.com | 972-52-7275845 Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) | www.r-statistics.com/ (English) -- [[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] Announcing a new R news site: R-bloggers.com
On 5 December 2009 at 21:38, Tal Galili wrote: | R-Bloggers.com hopes to serve the R community by presenting (in one place) | all the new articles (posts) written (in English) about R in the R | blogosphere. But how is that different from http://PlanetR.stderr.org which has been doing the same quite admirably for years? Dirk -- Three out of two people have difficulties with fractions. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 boxplot for time class
Use the title function: title(My main, xlab = My X, ylab = My Y) On Sat, Dec 5, 2009 at 12:38 PM, uvilla maruchave...@hotmail.com wrote: Thanks a lot Gabor, now I could finally plot the as time data. I just have one more question, and I hope it is the last. In the script of the boxplot, bp - boxplot(as.numeric(skiers$start), yaxt = n) axis(2, bp$stats, times(bp$stats), las = 2, cex.axis = 0.5) I have been trying to add a main tittle and xlab, ylab with no succes. Where I am supposed to type: main=skiing starting tour and so on Thanks a lot!! Maria Gabor Grothendieck wrote: Try this: Lines - protokollid datestart end 4 2/23/2009 8:50:10 15:17:30 4 2/24/2009 9:47:00 13:52:25 5 3/22/2009 8:51:25 12:00:05 library(chron) skiers - read.table(textConnection(Lines), header = TRUE, as.is = TRUE) skiers - transform(skiers, date = dates(date), start = times(start), end = times(end)) bp - boxplot(as.numeric(skiers$start), yaxt = n) axis(2, bp$stats, times(bp$stats), las = 2, cex.axis = 0.5) On Sat, Dec 5, 2009 at 6:52 AM, uvilla maruchave...@hotmail.com wrote: hi again I will try this time to explain my problem clearly I have the following data from the file skiing.csv (3 first rows) protokollid datestart end 14 2/23/2009 8:50:10 15:17:30 24 2/24/2009 9:47:00 13:52:25 35 3/22/2009 8:51:25 12:00:05 I have the following script library(chron) skiers=read.csv(skiing.csv) strptime(08:50:10,%H:%M:%S) start=times(skiers[,3]) strptime(start,%H:%M:%S) end=times(skiers[,4]) strptime(end,%H:%M:%S) #calc lenght of the route length.route=end-start #calc medians median(start) median(length.route) Then I want to do a box plot of the staring time when I use: boxplot(start) this error appears: Warning message: In is.na(x) : is.na() applied to non-(list or vector) of type 'NULL' when I try to convert start as POSIXct start=as.POSIXct(start) Error in as.POSIXct.default(start) : do not know how to convert 'start' to class POSIXlt and when I try to convert skiers[,3] as POSIXct skiers[,3]=as.POSIXct(skiers[,3]) Error in as.POSIXlt.character(as.character(x)) : character string is not in a standard unambiguous format start is of times class and skiers[,3] of factor class I want to do a boxplot of the starting time of my data, which reflect the median 08:36:45, and all O get in the y axis are decimal numbers :( Help please Best regards Maria Stauss -- View this message in context: http://n4.nabble.com/HELP-boxplot-for-time-class-tp949154p949154.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. [[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://n4.nabble.com/HELP-boxplot-for-time-class-tp949154p949270.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. [[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] Announcing a new R news site: R-bloggers.com
Hi Dirk, I wish to emphasis that I came across PlanetR over a year ago, but completely forgot it existed when working on R-bloggers. Also, when I contacted the bloggers about this idea, non of them actually wrote to me about it (which makes me feel better about not remembering it). I apologies if setting up R-bloggers seems like trying to compete with PlanetR, this at all wasn't my intention. Yet, now that my website is up, I hope it will be of use and here are several ways in which (at hindsight) I can say it has something to offer: 1) Planet R is limited (for years) to 26 feeds only, and I don't remember seeing it evolve to include (or allow inclusion) of new R blogs that came around. 2) The feeds are of blogs and non blogs (such as wiki or cran updates). That makes finding reading material inside it very difficult, since the site is cluttered with a lot of updates from cranbarries and the wiki. 3) In PlanetR, one can only view (about) 5 days back and no more (R-bloggers allows viewing of much more then 5 days back). 4) R-bloggers allows searching inside the content, PlanetR doesn't. 5) R-bloggers allow one to get e-mail updates, PlanetR doesn't. 6) R-bloggers offers related articles, PlanetR doesn't. I see R-bloggers http://www.r-bloggers.com/ as a news site based on the R bloggers, and I can't say the same about PlanetR for the reasons I gave above. With much respect to you Dirk, Tal Contact Details:--- Contact me: tal.gal...@gmail.com | 972-52-7275845 Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) | www.r-statistics.com/ (English) -- On Sat, Dec 5, 2009 at 9:59 PM, Dirk Eddelbuettel e...@debian.org wrote: On 5 December 2009 at 21:38, Tal Galili wrote: | R-Bloggers.com hopes to serve the R community by presenting (in one place) | all the new articles (posts) written (in English) about R in the R | blogosphere. But how is that different from http://PlanetR.stderr.org which has been doing the same quite admirably for years? Dirk -- Three out of two people have difficulties with fractions. [[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] Announcing a new R news site: R-bloggers.com
-Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Tal Galili Sent: Saturday, December 05, 2009 11:38 AM To: r-help@r-project.org Subject: [R] Announcing a new R news site: R-bloggers.com Hello everyone. After some good time of work, I am proud to present: www.r-bloggers.com What is R-Bloggers.com? R-Bloggers.com hopes to serve the R community by presenting (in one place) all the new articles (posts) written (in English) about R in the R blogosphere. How does R-Bloggers operate? This site aggregates feeds (only with permission!) from participating R blogs. The beginnings of each participating blogs posts will automatically be displayed on the main page with links to the original posts; inside every post there is a link to the original blog and links to other related articles. All participating blogs will have links in the Contributors section of our sidebar What does R-Bloggers offer the community? - Discover: If every blogger will add itself, we will all be able to find new R blogs (which is hard to find on the web, if you ever tried). The site also allows to search in the content of the bloggers (although for searches of older content - you better go to the blogs themselves or wait for the customized google search box I will add in the future) - Follow: Enter your e-mail and subscribe to receive a daily digest with teasers of new posts from participating blogs. You will more easily get a sense of hot topics in the R blogosphere. - Connect: Click on Fan this site to become a fan of R Bloggers. You can friend other people and share thoughts on our wall. Or just by leaving comments on the blog. - Participate: Add your R blog to get increased visibility (for readers and search engines) with permanent links on our Contributors sidebar. Your blog will also gain visibility via our e-mail digest and through your presence on the main page with posts. How do I become a participating blog in R Bloggers? To add your blog, simply click on Add your blog!http://www.r-bloggers.com/add-your-blog/ and enter the required information. I will review your link and approve it in a timely fashion. How can I help? We share readers to gain readers! If you are interested and havent already, please submit your blog http://www.r-bloggers.com/add-your- blog/. Also please consider putting *a link from your blog* to R-Bloggers from your sidebar (we do the same for you); you can even put up a post about us - if each blogger will do so - all of us will gain from it. Who started R-Bloggers (and way)? R Bloggers was started by Tal Galili http://talgalili.com/. After searching for numerous R blogs, Tal (well, me) decided that there must be more R blogs our there then he knows about, and maybe the best way for finding them is to make them find him. You can reach Tal via the Contacthttp://www.r-bloggers.com/contact-us/ page (or just e-mail him: tal.gal...@gmail.com). Extra thanks and a deceleration of good intentions I would like to thank John, Yihui, Jaanus and Taiyun for being the first bloggers to allow me to enlist their blogs to the project. There are more R bloggers out there that I know of, and didn't get to ask for permission. I apologies to you for not contacting you personally, still If you are one such blogger, and you want to join the site, please feel welcome to submit your blog http://www.r-bloggers.com/add-your-blog/. I hope this e-mail was not an abuse of the R mailing list. Since I intended this project for the good of the R community I allowed myself to publish the site here, so I hope it wouldn't upset anyone. Best wishes to all, Tal I went to the site listed above and ZoneAlarm on my computer reported the site as suspicious (I can count on one hand the number of times I have received that warning). My question: do you know what your site is doing that might be considered suspicious? Dan Daniel Nordlund Bothell, WA USA __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Announcing a new R news site: R-bloggers.com
Hi Daniel. In short: no. In more words: 1) I have zone alarm also on my computer and it gives me no warnings. 2) The only two external scripts the site has are of woopra and google analytics, both are known external statistics services. 3) It could be (although not likely) that the site is hacked and was injected with something, but services like this one: http://www.unmaskparasites.com/security-report/ claims that my site is clean. If you have anymore suggestions - I would love to know them. Thanks for reporting, what do you think of the site itself BTW? Best, Tal Contact Details:--- Contact me: tal.gal...@gmail.com | 972-52-7275845 Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) | www.r-statistics.com/ (English) -- On Sat, Dec 5, 2009 at 11:04 PM, Daniel Nordlund djnordl...@verizon.netwrote: -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Tal Galili Sent: Saturday, December 05, 2009 11:38 AM To: r-help@r-project.org Subject: [R] Announcing a new R news site: R-bloggers.com Hello everyone. After some good time of work, I am proud to present: www.r-bloggers.com What is R-Bloggers.com? R-Bloggers.com hopes to serve the R community by presenting (in one place) all the new articles (posts) written (in English) about R in the R blogosphere. How does R-Bloggers operate? This site aggregates feeds (only with permission!) from participating R blogs. The beginnings of each participating blog s posts will automatically be displayed on the main page with links to the original posts; inside every post there is a link to the original blog and links to other related articles. All participating blogs will have links in the Contributors section of our sidebar What does R-Bloggers offer the community? - Discover: If every blogger will add itself, we will all be able to find new R blogs (which is hard to find on the web, if you ever tried). The site also allows to search in the content of the bloggers (although for searches of older content - you better go to the blogs themselves or wait for the customized google search box I will add in the future) - Follow: Enter your e-mail and subscribe to receive a daily digest with teasers of new posts from participating blogs. You will more easily get a sense of hot topics in the R blogosphere. - Connect: Click on Fan this site to become a fan of R Bloggers. You can friend other people and share thoughts on our wall. Or just by leaving comments on the blog. - Participate: Add your R blog to get increased visibility (for readers and search engines) with permanent links on our Contributors sidebar. Your blog will also gain visibility via our e-mail digest and through your presence on the main page with posts. How do I become a participating blog in R Bloggers? To add your blog, simply click on Add your blog!http://www.r-bloggers.com/add-your-blog/ and enter the required information. I will review your link and approve it in a timely fashion. How can I help? We share readers to gain readers! If you are interested and haven t already, please submit your blog http://www.r-bloggers.com/add-your- blog/. Also please consider putting *a link from your blog* to R-Bloggers from your sidebar (we do the same for you); you can even put up a post about us - if each blogger will do so - all of us will gain from it. Who started R-Bloggers (and way)? R Bloggers was started by Tal Galili http://talgalili.com/. After searching for numerous R blogs, Tal (well, me) decided that there must be more R blogs our there then he knows about, and maybe the best way for finding them is to make them find him. You can reach Tal via the Contacthttp://www.r-bloggers.com/contact-us/ page (or just e-mail him: tal.gal...@gmail.com). Extra thanks and a deceleration of good intentions I would like to thank John, Yihui, Jaanus and Taiyun for being the first bloggers to allow me to enlist their blogs to the project. There are more R bloggers out there that I know of, and didn't get to ask for permission. I apologies to you for not contacting you personally, still If you are one such blogger, and you want to join the site, please feel welcome to submit your blog http://www.r-bloggers.com/add-your-blog/. I hope this e-mail was not an abuse of the R mailing list. Since I intended this project for the good of the R community I allowed myself to publish the site here, so I hope it wouldn't upset anyone. Best wishes to all, Tal I went to the site listed above and ZoneAlarm on my computer reported the site as suspicious (I
Re: [R] Rounding a Measurement to be Consistent with its Uncertainty
Uwe Ligges-3 wrote: Tom La Bone wrote: I have a measurement of 8165.666 and an uncertainty of 338.9741 (the units of both are unimportant). I can easily round the uncertainty to two significant digits with signif(338.9741,2), which gives 340. Is there a function in R that will take 8165.666 and round it to be consistent with its uncertainty, i.e., 8170? That's not consistent, you have 3 significant digits here, but 2 for the uncertainty (whatever that is) ... Uwe Ligges Tom In metrology, what I did is indeed consistent (provided that I have correctly interpreted the guidance given in the ISO Guide to the Expression of Uncertainty in Measurement). The uncertainty is basically a way of specifying in which digits I begin to doubt my result. So, I while I will usually have two digits in my uncertainty, I can have 10 significant digits in my result. Some folks have given me some ideas off-line on how to write a function that will round a number in this fashion, but I always prefer to use an existing R function if it already exists rather than write my own. And, with the tens of thousands of R functions in existence, it is always a good idea to ask the forum if they know of one. Tom __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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://n4.nabble.com/Rounding-a-Measurement-to-be-Consistent-with-its-Uncertainty-tp948151p949395.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] R packages and assess to data in packages
Hi Everyone, I have two very basic questions and would appreciate your help. 1. I would like to see/access the data that comes with a given R package by using a function like read.table(). For example, I just installed car package from CRAN. I know that somewhere within the package, there is Duncan.txt file. I would not only like to look at it from file browser (or using ls command in shell) but also to access it as: Duncan - read.table(path/to/data/Duncan.txt, header = T) I can certainly use: data(Duncan) and attach(Duncan) after loading the package car. However, I would like to see all the data that come with a package as separate files. Where are these files located? I installed the car package under Mac OSX under the user level (if this detail is important). However, I do use R under Ubuntu linux also and general solution to this problem will be great. I even downloaded the car binaries and unpacked the zipped file on desktop but I just see .rda files within the data folder; there are no .txt files anywhere. I do see Duncan.rda file (I believe this contains the Duncan.txt data). How can I access the data files from such package, say using a text editor?? 2. What is the safest/preferred place to install an R package that I want to delete/remove once I do not need it. Sometimes, I just need to install a package from a book's website so that I can work on the exercises etc but do not need the package permanently hanging around. Removing such a package and all the associated files etc would be nice. I would appreciate any help and comments on my questions. Regards, Tariq [[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] Announcing a new R news site: R-bloggers.com
On 12/05/2009 09:32 PM, Tal Galili wrote: Hi Dirk, I wish to emphasis that I came across PlanetR over a year ago, but completely forgot it existed when working on R-bloggers. Also, when I contacted the bloggers about this idea, non of them actually wrote to me about it (which makes me feel better about not remembering it). I apologies if setting up R-bloggers seems like trying to compete with PlanetR, this at all wasn't my intention. Yet, now that my website is up, I hope it will be of use and here are several ways in which (at hindsight) I can say it has something to offer: 1) Planet R is limited (for years) to 26 feeds only, and I don't remember seeing it evolve to include (or allow inclusion) of new R blogs that came around. That's not quite true. If you send an email to the maintainer of planet R, he will add your feed (both my blog and r graph gallery was added this year for example). 2) The feeds are of blogs and non blogs (such as wiki or cran updates). That makes finding reading material inside it very difficult, since the site is cluttered with a lot of updates from cranbarries and the wiki. I see this as a good thing. In the program i use to read planet R (thunderbird) you can filter out things you are not interested about. I have requested to be added to yours anyway, might be good for my pagerank. 3) In PlanetR, one can only view (about) 5 days back and no more (R-bloggers allows viewing of much more then 5 days back). 4) R-bloggers allows searching inside the content, PlanetR doesn't. 5) R-bloggers allow one to get e-mail updates, PlanetR doesn't. 6) R-bloggers offers related articles, PlanetR doesn't. I see R-bloggershttp://www.r-bloggers.com/ as a news site based on the R bloggers, and I can't say the same about PlanetR for the reasons I gave above. With much respect to you Dirk, Tal Contact Details:--- Contact me: tal.gal...@gmail.com | 972-52-7275845 Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) | www.r-statistics.com/ (English) -- On Sat, Dec 5, 2009 at 9:59 PM, Dirk Eddelbuettele...@debian.org wrote: On 5 December 2009 at 21:38, Tal Galili wrote: | R-Bloggers.com hopes to serve the R community by presenting (in one place) | all the new articles (posts) written (in English) about R in the R | blogosphere. But how is that different from http://PlanetR.stderr.org which has been doing the same quite admirably for years? Dirk -- Three out of two people have difficulties with fractions. -- Romain Francois Professional R Enthusiast +33(0) 6 28 91 30 30 http://romainfrancois.blog.free.fr |- http://tr.im/Gq7i : ohloh |- http://tr.im/FtUu : new package : highlight `- http://tr.im/EAD5 : LondonR slides __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Incorrect number of dimensions
I am trying to fit a linear model with seasonal effects but keep getting 'Incorrect number of dimensions'. I have no idea what this means or how to fix it. I am following instructions received from an instructor and it worked for him, so I assume it has something to do with my data. Here is my code: sed-ts(data2[,-c(1,2)],start=c(1967,10),end=c(2007,9),freq=12) ym-time(sed) month-as.factor(sed[,Period]) Error in `[.default`(sed, , Period) : incorrect number of dimensions So I am getting the error when I try to designate month as a factor. Help! -- View this message in context: http://n4.nabble.com/Incorrect-number-of-dimensions-tp949301p949301.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] R example for ancova
Hi list, does anybody know a easy to understand example in R which shows how to perfom an ANCOVA? I already tried to understand the example which you get when you type ?aov, but I did not really understand the output. Best, syrvn -- View this message in context: http://n4.nabble.com/R-example-for-ancova-tp949324p949324.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] integrate function
Hello,
I have some trouble in terms of using integrate function in R.
f1 is a function of p and x where x is supposed to be a vector. (See the
code).
Then I want to write function f2 which is a function of the vector
x after I integrate out p.
Can some one give me some help? Many thanks!
Hannah
f1 - function (p,x)
+ {
+y - p*x+(1-p)*x^{2}
+ prod(y)
+ }
f2 - function(x)
+ {
+ integrate(f1, 0,1, x)
+ }
f2(x=c(1,2))
Error in integrate(f1, 0, 1, x) :
evaluation of function gave a result of wrong length
In addition: Warning messages:
1: In p * x :
longer object length is not a multiple of shorter object length
2: In (1 - p) * x^{ :
longer object length is not a multiple of shorter object length
[[alternative HTML version deleted]]
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https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] integrate function
On Dec 5, 2009, at 4:59 PM, li li wrote:
Hello,
I have some trouble in terms of using integrate function in R.
f1 is a function of p and x where x is supposed to be a vector. (See
the
code).
Then I want to write function f2 which is a function of the vector
x after I integrate out p.
Can some one give me some help? Many thanks!
Hannah
f1 - function (p,x)
+ {
+y - p*x+(1-p)*x^{2}
+ prod(y)
+ }
f2 - function(x)
+ {
+ integrate(f1, 0,1, x)
Just looking at the help page for integrate makes me wonder what you
are doing. There are 3 named arguments before the dots, so 0 and 1
will become lower and upper, while x is not among the named
arguemnts, so I suppose x will go to f1 as p. But f1 takes two
arguments, so where will it get the second argument? Maybe if you
would tell us a bit more about why you made those functions the way
you did, it would help. I am guessing it's classwork but perhaps not.
+ }
f2(x=c(1,2))
Error in integrate(f1, 0, 1, x) :
evaluation of function gave a result of wrong length
In addition: Warning messages:
1: In p * x :
longer object length is not a multiple of shorter object length
2: In (1 - p) * x^{ :
longer object length is not a multiple of shorter object length
[[alternative HTML version deleted]]
--
David Winsemius, MD
Heritage Laboratories
West Hartford, CT
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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] Announcing a new R news site: R-bloggers.com
I donât have comments as yet, because I didnât stay around the site too long. I will go back and look at it using a spare Ubuntu box and let you know what I think. Dan Daniel Nordlund Bothell, WA USA _ From: Tal Galili [mailto:tal.gal...@gmail.com] Sent: Saturday, December 05, 2009 1:24 PM To: Daniel Nordlund Cc: r-help@r-project.org Subject: Re: [R] Announcing a new R news site: R-bloggers.com Hi Daniel. In short: no. In more words: 1) I have zone alarm also on my computer and it gives me no warnings. 2) The only two external scripts the site has are of woopra and google analytics, both are known external statistics services. 3) It could be (although not likely) that the site is hacked and was injected with something, but services like this one: http://www.unmaskparasites.com/security-report/ claims that my site is clean. If you have anymore suggestions - I would love to know them. Thanks for reporting, what do you think of the site itself BTW? Best, Tal Contact Details:--- Contact me: tal.gal...@gmail.com | 972-52-7275845 Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) | www.r-statistics.com/ (English) -- On Sat, Dec 5, 2009 at 11:04 PM, Daniel Nordlund djnordl...@verizon.net wrote: -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Tal Galili Sent: Saturday, December 05, 2009 11:38 AM To: r-help@r-project.org Subject: [R] Announcing a new R news site: R-bloggers.com Hello everyone. After some good time of work, I am proud to present: www.r-bloggers.com What is R-Bloggers.com? R-Bloggers.com hopes to serve the R community by presenting (in one place) all the new articles (posts) written (in English) about R in the R blogosphere. How does R-Bloggers operate? This site aggregates feeds (only with permission!) from participating R blogs. The beginnings of each participating blog s posts will automatically be displayed on the main page with links to the original posts; inside every post there is a link to the original blog and links to other related articles. All participating blogs will have links in the Contributors section of our sidebar What does R-Bloggers offer the community? - Discover: If every blogger will add itself, we will all be able to find new R blogs (which is hard to find on the web, if you ever tried). The site also allows to search in the content of the bloggers (although for searches of older content - you better go to the blogs themselves or wait for the customized google search box I will add in the future) - Follow: Enter your e-mail and subscribe to receive a daily digest with teasers of new posts from participating blogs. You will more easily get a sense of hot topics in the R blogosphere. - Connect: Click on Fan this site to become a fan of R Bloggers. You can friend other people and share thoughts on our wall. Or just by leaving comments on the blog. - Participate: Add your R blog to get increased visibility (for readers and search engines) with permanent links on our Contributors sidebar. Your blog will also gain visibility via our e-mail digest and through your presence on the main page with posts. How do I become a participating blog in R Bloggers? To add your blog, simply click on Add your blog!http://www.r-bloggers.com/add-your-blog/ and enter the required information. I will review your link and approve it in a timely fashion. How can I help? We share readers to gain readers! If you are interested and haven t already, please submit your blog http://www.r-bloggers.com/add-your- blog/. Also please consider putting *a link from your blog* to R-Bloggers from your sidebar (we do the same for you); you can even put up a post about us - if each blogger will do so - all of us will gain from it. Who started R-Bloggers (and way)? R Bloggers was started by Tal Galili http://talgalili.com/. After searching for numerous R blogs, Tal (well, me) decided that there must be more R blogs our there then he knows about, and maybe the best way for finding them is to make them find him. You can reach Tal via the Contacthttp://www.r-bloggers.com/contact-us/ page (or just e-mail him: tal.gal...@gmail.com). Extra thanks and a deceleration of good intentions I would like to thank John, Yihui, Jaanus and Taiyun for being the first bloggers to allow me to enlist their blogs to the project. There are more R bloggers out there that I know of, and didn't get to ask for permission. I apologies to you for not contacting you personally, still If you are one such blogger, and you want to join the site, please feel welcome to submit your
Re: [R] Announcing a new R news site: R-bloggers.com
Hi Romain, First - I'd like to say that you where one of the bloggers I wanted to e-mail and didn't get to it. I still remember our short session in useR 2009 where you showed me your plans for an R editor - I am still waiting to see it once it comes out. Regarding the rest of what you wrote, I'll reply to you in each section: On Sun, Dec 6, 2009 at 3:22 AM, Romain Francois romain.franc...@dbmail.com wrote: On 12/05/2009 09:32 PM, Tal Galili wrote: 1) Planet R is limited (for years) to 26 feeds only, and I don't remember seeing it evolve to include (or allow inclusion) of new R blogs that came around. R: that's not quite true. If you send an email to the maintainer of planet R, he will add your feed (both my blog and r graph gallery was added this year for example). T:Thanks for the correction. Yet let's put this in context - I can't see on the planetR website (http://planetr.stderr.org/) any e-mail or link to contact. So for me, for example, I don't know how to add my own blog (What IS the e-mail of the maintainer ?) 2) The feeds are of blogs and non blogs (such as wiki or cran updates). That makes finding reading material inside it very difficult, since the site is cluttered with a lot of updates from cranbarries and the wiki. R: I see this as a good thing. In the program i use to read planet R (thunderbird) you can filter out things you are not interested about. T: But Romain, both planetR and R-bloggers are not meant for you, except as a source for feeds. What you are saying is that you don't use the interface either website offers, which is exactly my point. R: I have requested to be added to yours anyway, might be good for my pagerank. T: Cool, I just added you. [[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] plot data from tapply
i have three data, x coordinate, y coordinate and signal strength i use tapply() function to get the average ss in the give x,y location x=c(1,2,3,1) y=c(1,2,3,1) ss=c(55,NA,55,88) ss_byxy_test=tapply( ss, list( x, y), mean) and I get this table 1 2 3 1 71.5 NA NA 2 NA NA NA 3 NA NA 55 but i don't know how to plot different the ss with the xy location, can anyone help me -- View this message in context: http://n4.nabble.com/plot-data-from-tapply-tp949436p949436.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] R packages and assess to data in packages
Tariq Perwez wrote: Hi Everyone, I have two very basic questions and would appreciate your help. 1. I would like to see/access the data that comes with a given R package by using a function like read.table(). For example, I just installed car package from CRAN. I know that somewhere within the package, there is Duncan.txt file. This is not necessarily true. Most packages distribute data sets in the .rda format. Text files are usually only distributed if the package implements some method of parsing them, such as the example .xml files in the XML package. Tariq Perwez wrote: I would not only like to look at it from file browser (or using ls command in shell) but also to access it as: Duncan - read.table(path/to/data/Duncan.txt, header = T) I can certainly use: data(Duncan) and attach(Duncan) after loading the package car. However, I would like to see all the data that come with a package as separate files. Where are these files located? I installed the car package under Mac OSX under the user level (if this detail is important). However, I do use R under Ubuntu linux also and general solution to this problem will be great. The system.file() command provides a platform-independent method for recovering the path to files distributed in packages. For example, to list all files in the data folder of the car package: system.file( 'data', package = 'car' ) To get the path to the .rda file containing all the datasets: system.file( 'data', 'Rdata.rda', package = 'car' ) Tariq Perwez wrote: I even downloaded the car binaries and unpacked the zipped file on desktop but I just see .rda files within the data folder; there are no .txt files anywhere. I do see Duncan.rda file (I believe this contains the Duncan.txt data). How can I access the data files from such package, say using a text editor?? Package datasets are usually only distributed as binary .Rda files. If you want to view them using a text editor you will have to translate them to a plain text format-- something like load() followed by write.csv(). Tariq Perwez wrote: 2. What is the safest/preferred place to install an R package that I want to delete/remove once I do not need it. Sometimes, I just need to install a package from a book's website so that I can work on the exercises etc but do not need the package permanently hanging around. Removing such a package and all the associated files etc would be nice. I would appreciate any help and comments on my questions. Regards, Tariq Just install it normally. You can remove it by running: R CMD REMOVE packageName From the command line. Hope this helps! -Charlie -- View this message in context: http://n4.nabble.com/R-packages-and-assess-to-data-in-packages-tp949415p949439.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] Forest Plot
Hi All,
I want to produce a similar Forest Plot as it is on the following link,
but my data would be having only two columns (one for Estimate and other
for Std. Dev). Can anyone suggest some function() {Package} which can take
such file as an input and give following forest plot:
http://bm2.genes.nig.ac.jp/RGM2/R_current/library/metafor/man/images/big_plot.rma.uni_001.png
Thanks,
Xin
[[alternative HTML version deleted]]
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https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Forest Plot
The figure that you linked to was produced with the metafor package. It can
also be used to produce a forest plot if you have means and corresponding
standard errors of the means. The standard error of a mean is equal to SD /
sqrt(n), so as long as you also know the sample sizes (n), you can convert
those standard deviations to the standard errors.
Best,
--
Wolfgang Viechtbauerhttp://www.wvbauer.com/
Department of Methodology and StatisticsTel: +31 (0)43 388-2277
School for Public Health and Primary Care Office Location:
Maastricht University, P.O. Box 616 Room B2.01 (second floor)
6200 MD Maastricht, The Netherlands Debyeplein 1 (Randwyck)
From: r-help-boun...@r-project.org [r-help-boun...@r-project.org] On Behalf Of
Xin Ge [xingemaill...@gmail.com]
Sent: Sunday, December 06, 2009 12:11 AM
To: r-help@r-project.org
Subject: [R] Forest Plot
Hi All,
I want to produce a similar Forest Plot as it is on the following link,
but my data would be having only two columns (one for Estimate and other
for Std. Dev). Can anyone suggest some function() {Package} which can take
such file as an input and give following forest plot:
http://bm2.genes.nig.ac.jp/RGM2/R_current/library/metafor/man/images/big_plot.rma.uni_001.png
Thanks,
Xin
[[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] Forest Plot
Thanks for your reply. Which function I should explore in metafor package
for this kind of plot.
Also I have to do a forest plot for regressions estimates (betas) and
corresponding sqrt(var). I hope in this case there is no difference
between std. error and std. deviation? So, a 95% confidence interval would
be [estimate +/- 1.96*sqrt(variance of estimate)]. Am I correct in saying
this?
Thanks again,
Xin
On Sat, Dec 5, 2009 at 6:21 PM, Viechtbauer Wolfgang (STAT)
wolfgang.viechtba...@stat.unimaas.nl wrote:
The figure that you linked to was produced with the metafor package. It
can also be used to produce a forest plot if you have means and
corresponding standard errors of the means. The standard error of a mean is
equal to SD / sqrt(n), so as long as you also know the sample sizes (n), you
can convert those standard deviations to the standard errors.
Best,
--
Wolfgang Viechtbauerhttp://www.wvbauer.com/
Department of Methodology and StatisticsTel: +31 (0)43 388-2277
School for Public Health and Primary Care Office Location:
Maastricht University, P.O. Box 616 Room B2.01 (second floor)
6200 MD Maastricht, The Netherlands Debyeplein 1 (Randwyck)
From: r-help-boun...@r-project.org [r-help-boun...@r-project.org] On
Behalf Of Xin Ge [xingemaill...@gmail.com]
Sent: Sunday, December 06, 2009 12:11 AM
To: r-help@r-project.org
Subject: [R] Forest Plot
Hi All,
I want to produce a similar Forest Plot as it is on the following link,
but my data would be having only two columns (one for Estimate and other
for Std. Dev). Can anyone suggest some function() {Package} which can
take
such file as an input and give following forest plot:
http://bm2.genes.nig.ac.jp/RGM2/R_current/library/metafor/man/images/big_plot.rma.uni_001.png
Thanks,
Xin
[[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.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.htmlhttp://www.r-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[[alternative HTML version deleted]]
__
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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] integrate function
Thank you very much for your reply!
It is not an assignment.
What I want to do is what we often do. If we have a bivariate function of x
and p,
I first fix x and integrate out p. Then the resultant function is only in
terms of x.
Here f1 is a bivariate function of x and p.
f1 - function (p,x)
+ {
+prod(p*x+(1-p)*x^{2})
}
f2 is a function of x only after integrating out p from f1. Here f1 is the
integrand, x is the additional argument to be
passed to f1. The integration is in terms of p.
f2 - function(x)
+ {
+ integrate(f1, lower=0,upper=1, x)
+ }
There is error output when I evaluate f2 at specific x values. See below:
f2(c(2,3))
Error in integrate(f1, lower = 0, upper = 1, x) :
evaluation of function gave a result of wrong length
In addition: Warning messages:
1: In p * x :
longer object length is not a multiple of shorter object length
2: In (1 - p) * x^{ :
longer object length is not a multiple of shorter object length
Can any one give me some suggestions! Thank you!
2009/12/5 David Winsemius dwinsem...@comcast.net
On Dec 5, 2009, at 4:59 PM, li li wrote:
Hello,
I have some trouble in terms of using integrate function in R.
f1 is a function of p and x where x is supposed to be a vector. (See the
code).
Then I want to write function f2 which is a function of the vector
x after I integrate out p.
Can some one give me some help? Many thanks!
Hannah
f1 - function (p,x)
+ {
+y - p*x+(1-p)*x^{2}
+ prod(y)
+ }
f2 - function(x)
+ {
+ integrate(f1, 0,1, x)
Just looking at the help page for integrate makes me wonder what you are
doing. There are 3 named arguments before the dots, so 0 and 1 will become
lower and upper, while x is not among the named arguemnts, so I suppose
x will go to f1 as p. But f1 takes two arguments, so where will it get the
second argument? Maybe if you would tell us a bit more about why you made
those functions the way you did, it would help. I am guessing it's classwork
but perhaps not.
+ }
f2(x=c(1,2))
Error in integrate(f1, 0, 1, x) :
evaluation of function gave a result of wrong length
In addition: Warning messages:
1: In p * x :
longer object length is not a multiple of shorter object length
2: In (1 - p) * x^{ :
longer object length is not a multiple of shorter object length
[[alternative HTML version deleted]]
--
David Winsemius, MD
Heritage Laboratories
West Hartford, CT
[[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] STATISTICAL ANALYSIS OF TEXT EMAILS Re: Refreshments after SOMS Seminar Friday 3:30-4:30 in HBB 334
Dear Professor Frank Guess, Why did you call me a Curious George? What is a curious george as in American context? Why did you address this email only to Laura and me. Why did you not answer my early query on what is a curious George? Why do you also send me emails saying I and Gandhi are full of compassion? How come University of Tennessee is funded by Federal Bailout Funds AND has a row of churches just behind the HODGES library and so accessible to CHRISTIAN students BUT NO temples or mosques near to Library. We are children of a lesser God But we are also children. Thanks and Have a Happy Holidays and Merry Christmas. * WHY DO YOU SAY you may have one of those emails and better not to use?* AJAY Graduate Student University of Tennessee, Knoxville. Go Vols! Websites- http://decisionstats.com http://dudeofdata.com http://prayers2go.com Linkedin- www.linkedin.com/in/ajayohri Facebook-www.facebook.com/ajayohri Twitter-www.twitter.com/dudeofdata Quote for the Day- Mike Ditka - If God had wanted man to play soccer, he wouldn't have given us arms. - http://www.brainyquote.com/quotes/authors/m/mike_ditka.html On Thu, Sep 24, 2009 at 3:46 PM, Guess, Frank M fgu...@utk.edu wrote: Thanks Laura, great email. Ajay is just a curious George on understanding better. Thanks Ajay, also. We are blessed to have both of you here at UT!! Best to all, Dr. Guess (Ajay, I may have one of these email, best not to use, which is it?) From: Brewster, Laura Sent: Thu 9/24/2009 3:09 PM To: Beal, Dennis Jack; Carty, Dillon M; Cinder, Matthew Robert; Duraisamy, Praveen Raja; Erar, Bahar; Ezell, Ashley Renee; Fajolu, Olufemi Nelson; fjiang6; Harper, Matt (Matt); Huang, Xia; Jarajapu, Neeharika; Jeong, Jaehwan; Kim, Je Guk; Kitchens, Karin Elizabeth; Kodra, Evan Anton; Kuang, Xun; lge; Liu, Nancy; Loghavi, Mina; Lu, Xin (Lucy); Mathias, Blake Dustin; Mcclary, Erica Whitney; Muindi, Pius Matheka; Ohri, Ajay; Pan, Chun; Pannell Jr, T Allen (Allen); Robson, Paul Andrew; Romanova, Anna V; Roth, Wendy; Shah, Reshma; Shipman, Michael Livingston; Turan, Esra; Vepkhvadze, Nana; Wang, Wenfang; Wang, Yingjin; Weese, Maria L; White, Philip Robert; Williams, Maria Annette; Wu, Wei; Xu, Liang; Xu, Qin; Zeng, Yan; Zhang, Shuping; Zhao, Yijia; Moser, Jane; Walker, Rebecca M (Becky); Bichescu, Bogdan Cristian; Edirisinghe, Nalin C P; Bowers, Melissa R; Noon, Charles E; Srinivasan, Mandyam M; js...@arcautomotive.com; Kirby, Kenneth E; Bozdogan, Hamparsum; Cwiek, Charles Mitchell; Gilbert, Kenneth C; Guess, Frank M; Leitnaker, Mary G; Leon, Ramon V; Mee, Robert W; Petrie, Adam George; Zaretzki, Russell Lee; Schmidhammer, James L; Seaver, William L; Younger, Mary Sue Subject: Refreshments after SOMS Seminar Friday 3:30-4:30 in HBB 334 Everyone, Directly after Maria Weeseâs seminar tomorrow, we will meet in HBB 334 for light refreshments and stimulating conversation. I hope youâll join us! Remember, the actual seminar is in HBB 403 from 2:30-3:30. Laura Brewster Administrative Assistant Department of Statistics, Operations and Management Science 344A Stokely Management Center Knoxville, TN 37996-0532 (865) 974-5544 (865) 974-2490 (fax) [[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] barchart() {lattice} help.
Hi, I'm plotting grouped barplot using following code and data. I need help with re-ordering the labels. 1. On x-axis the factor AGE is grouped in order 0--4, 15--18, 5--14; whereas I would like to have it in 0--4, 5--14, 15--18. 2. If I need to re-order RACE variable. How can I do it assuming I need to change it on both the x-axis and legend. Currenlty the order is Black,Other,White; whereas I would like White, Black, Other. Can anyone help please. I'm using following code, which is working fine except above issues. Code: library(lattice) ### assuming data is read in object name dta. attach(dta) barchart(sum ~ age | gender, data = dta, groups = race, stack = FALSE, ylab=Sum of admissions over 10 years (1996-2005), xlab=Age, par.settings=simpleTheme(col = c(green1, yellow1, orange)), key=list(space=right, cex=1, text=list(c(Black,Other,White)), rectangles=list(size=1.7, border=white, col = c(green1, yellow1, orange))), strip = strip.custom(bg=greenyellow) ) detach(dta) Data: age gender race sum 0--4 Female Black 145 0--4 Female Other 53 0--4 Female White 47 0--4 Male Black 286 0--4 Male Other 130 0--4 Male White 94 15--18 Female Black 30 15--18 Female Other 3 15--18 Female White 9 15--18 Male Black 21 15--18 Male Other 2 15--18 Male White 3 5--14 Female Black 138 5--14 Female Other 31 5--14 Female White 23 5--14 Male Black 199 5--14 Male Other 65 5--14 Male White 29 Thanks, Peng [[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] SAS datalines or cards statement equivalent in R?
Hi R Users, Is there a equivalent command in R where I can read in raw data? For example I'm looking for equivalent R code for following SAS code: DATA survey; INPUT id sex $ age inc r1 r2 r3 ; DATALINES; 1 F 35 17 7 2 2 17 M 50 14 5 5 3 33 F 45 6 7 2 7 49 M 24 14 7 5 7 65 F 52 9 4 7 7 81 M 44 11 7 7 7 2 F 34 17 6 5 3 18 M 40 14 7 5 2 34 F 47 6 6 5 6 50 M 35 17 5 7 5 ; Any help would be highly appreciated, Gary [[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] SAS datalines or cards statement equivalent in R?
Dear Gary, Here is a suggestion using read.table() and textConnection(): toread - id sex age inc r1 r2 r3 1 F 35 17 7 2 2 17 M 50 14 5 5 3 33 F 45 6 7 2 7 49 M 24 14 7 5 7 65 F 52 9 4 7 7 81 M 44 11 7 7 7 2 F 34 17 6 5 3 18 M 40 14 7 5 2 34 F 47 6 6 5 6 50 M 35 17 5 7 5 survey - read.table(textConnection(toread), header = TRUE) closeAllConnections() survey See ?read.table and ?textConnection for more information. HTH, Jorge On Sat, Dec 5, 2009 at 8:11 PM, Gary Miller wrote: Hi R Users, Is there a equivalent command in R where I can read in raw data? For example I'm looking for equivalent R code for following SAS code: DATA survey; INPUT id sex $ age inc r1 r2 r3 ; DATALINES; 1 F 35 17 7 2 2 17 M 50 14 5 5 3 33 F 45 6 7 2 7 49 M 24 14 7 5 7 65 F 52 9 4 7 7 81 M 44 11 7 7 7 2 F 34 17 6 5 3 18 M 40 14 7 5 2 34 F 47 6 6 5 6 50 M 35 17 5 7 5 ; Any help would be highly appreciated, Gary [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] integrate function
Here is how you can do it:
f1 - function (p,x) {
sapply(p, function(p) prod( p*x+(1-p)*x^2) ) # the function should be
vectorized for `integrate'
}
f2 - function(x) {
integrate(f1, 0, 1, x)$val # you need to only return the `value' of integration
}
f2(x=1:3)
Hope this helps,
Ravi.
Ravi Varadhan, Ph.D.
Assistant Professor,
Division of Geriatric Medicine and Gerontology
School of Medicine
Johns Hopkins University
Ph. (410) 502-2619
email: rvarad...@jhmi.edu
- Original Message -
From: li li hannah@gmail.com
Date: Saturday, December 5, 2009 7:13 pm
Subject: Re: [R] integrate function
To: David Winsemius dwinsem...@comcast.net
Cc: r-help@r-project.org
Thank you very much for your reply!
It is not an assignment.
What I want to do is what we often do. If we have a bivariate
function of x
and p,
I first fix x and integrate out p. Then the resultant function is
only in
terms of x.
Here f1 is a bivariate function of x and p.
f1 - function (p,x)
+ {
+prod(p*x+(1-p)*x^{2})
}
f2 is a function of x only after integrating out p from f1. Here f1
is the
integrand, x is the additional argument to be
passed to f1. The integration is in terms of p.
f2 - function(x)
+ {
+ integrate(f1, lower=0,upper=1, x)
+ }
There is error output when I evaluate f2 at specific x values. See below:
f2(c(2,3))
Error in integrate(f1, lower = 0, upper = 1, x) :
evaluation of function gave a result of wrong length
In addition: Warning messages:
1: In p * x :
longer object length is not a multiple of shorter object length
2: In (1 - p) * x^{ :
longer object length is not a multiple of shorter object length
Can any one give me some suggestions! Thank you!
2009/12/5 David Winsemius dwinsem...@comcast.net
On Dec 5, 2009, at 4:59 PM, li li wrote:
Hello,
I have some trouble in terms of using integrate function in R.
f1 is a function of p and x where x is supposed to be a vector.
(See the
code).
Then I want to write function f2 which is a function of the vector
x after I integrate out p.
Can some one give me some help? Many thanks!
Hannah
f1 - function (p,x)
+ {
+y - p*x+(1-p)*x^{2}
+ prod(y)
+ }
f2 - function(x)
+ {
+ integrate(f1, 0,1, x)
Just looking at the help page for integrate makes me wonder what
you are
doing. There are 3 named arguments before the dots, so 0 and 1 will
become
lower and upper, while x is not among the named arguemnts, so I
suppose
x will go to f1 as p. But f1 takes two arguments, so where will
it get the
second argument? Maybe if you would tell us a bit more about why
you made
those functions the way you did, it would help. I am guessing it's
classwork
but perhaps not.
+ }
f2(x=c(1,2))
Error in integrate(f1, 0, 1, x) :
evaluation of function gave a result of wrong length
In addition: Warning messages:
1: In p * x :
longer object length is not a multiple of shorter object length
2: In (1 - p) * x^{ :
longer object length is not a multiple of shorter object length
[[alternative HTML version deleted]]
--
David Winsemius, MD
Heritage Laboratories
West Hartford, CT
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
PLEASE do read the posting guide
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] integrate function
Thank you all very much!
Yes, f2 is the function I wanted to write. I tried to do use Vectorize
function to f1, it did not work.
f2 - function(x)
+ {
+ integrate(Vectorize(f1,vectorize.args =p), lower=0,upper=1, x)
+ }
f2(c(2,3))
Error in Vectorize(f1, vectorize.args = p) :
must specify formal argument names to vectorize
I do not quite understand the logic why we need to vectorize here.
2009/12/5 Ravi Varadhan rvarad...@jhmi.edu
Here is how you can do it:
f1 - function (p,x) {
sapply(p, function(p) prod( p*x+(1-p)*x^2) ) # the function should be
vectorized for `integrate'
}
f2 - function(x) {
integrate(f1, 0, 1, x)$val # you need to only return the `value' of
integration
}
f2(x=1:3)
Hope this helps,
Ravi.
Ravi Varadhan, Ph.D.
Assistant Professor,
Division of Geriatric Medicine and Gerontology
School of Medicine
Johns Hopkins University
Ph. (410) 502-2619
email: rvarad...@jhmi.edu
- Original Message -
From: li li hannah@gmail.com
Date: Saturday, December 5, 2009 7:13 pm
Subject: Re: [R] integrate function
To: David Winsemius dwinsem...@comcast.net
Cc: r-help@r-project.org
Thank you very much for your reply!
It is not an assignment.
What I want to do is what we often do. If we have a bivariate
function of x
and p,
I first fix x and integrate out p. Then the resultant function is
only in
terms of x.
Here f1 is a bivariate function of x and p.
f1 - function (p,x)
+ {
+prod(p*x+(1-p)*x^{2})
}
f2 is a function of x only after integrating out p from f1. Here f1
is the
integrand, x is the additional argument to be
passed to f1. The integration is in terms of p.
f2 - function(x)
+ {
+ integrate(f1, lower=0,upper=1, x)
+ }
There is error output when I evaluate f2 at specific x values. See
below:
f2(c(2,3))
Error in integrate(f1, lower = 0, upper = 1, x) :
evaluation of function gave a result of wrong length
In addition: Warning messages:
1: In p * x :
longer object length is not a multiple of shorter object length
2: In (1 - p) * x^{ :
longer object length is not a multiple of shorter object length
Can any one give me some suggestions! Thank you!
2009/12/5 David Winsemius dwinsem...@comcast.net
On Dec 5, 2009, at 4:59 PM, li li wrote:
Hello,
I have some trouble in terms of using integrate function in R.
f1 is a function of p and x where x is supposed to be a vector.
(See the
code).
Then I want to write function f2 which is a function of the vector
x after I integrate out p.
Can some one give me some help? Many thanks!
Hannah
f1 - function (p,x)
+ {
+y - p*x+(1-p)*x^{2}
+ prod(y)
+ }
f2 - function(x)
+ {
+ integrate(f1, 0,1, x)
Just looking at the help page for integrate makes me wonder what
you are
doing. There are 3 named arguments before the dots, so 0 and 1 will
become
lower and upper, while x is not among the named arguemnts, so I
suppose
x will go to f1 as p. But f1 takes two arguments, so where will
it get the
second argument? Maybe if you would tell us a bit more about why
you made
those functions the way you did, it would help. I am guessing it's
classwork
but perhaps not.
+ }
f2(x=c(1,2))
Error in integrate(f1, 0, 1, x) :
evaluation of function gave a result of wrong length
In addition: Warning messages:
1: In p * x :
longer object length is not a multiple of shorter object length
2: In (1 - p) * x^{ :
longer object length is not a multiple of shorter object length
[[alternative HTML version deleted]]
--
David Winsemius, MD
Heritage Laboratories
West Hartford, CT
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
PLEASE do read the posting guide
and provide commented, minimal, self-contained, reproducible code.
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] integrate function
I did get it to work with Vectorize. My problem was that I don't
know if the answer made sense because I could not tell what
mathematical underpinnings were being studied.
--
David.
On Dec 5, 2009, at 10:05 PM, li li wrote:
Thank you all very much!
Yes, f2 is the function I wanted to write. I tried to do use
Vectorize function to f1, it did not work.
f2 - function(x)
+ {
+ integrate(Vectorize(f1,vectorize.args =p), lower=0,upper=1, x)
+ }
f2(c(2,3))
Error in Vectorize(f1, vectorize.args = p) :
must specify formal argument names to vectorize
I do not quite understand the logic why we need to vectorize here.
2009/12/5 Ravi Varadhan rvarad...@jhmi.edu
Here is how you can do it:
f1 - function (p,x) {
sapply(p, function(p) prod( p*x+(1-p)*x^2) ) # the function should
be vectorized for `integrate'
}
f2 - function(x) {
integrate(f1, 0, 1, x)$val # you need to only return the `value' of
integration
}
f2(x=1:3)
Hope this helps,
Ravi.
Ravi Varadhan, Ph.D.
Assistant Professor,
Division of Geriatric Medicine and Gerontology
School of Medicine
Johns Hopkins University
Ph. (410) 502-2619
email: rvarad...@jhmi.edu
- Original Message -
From: li li hannah@gmail.com
Date: Saturday, December 5, 2009 7:13 pm
Subject: Re: [R] integrate function
To: David Winsemius dwinsem...@comcast.net
Cc: r-help@r-project.org
Thank you very much for your reply!
It is not an assignment.
What I want to do is what we often do. If we have a bivariate
function of x
and p,
I first fix x and integrate out p. Then the resultant function is
only in
terms of x.
Here f1 is a bivariate function of x and p.
f1 - function (p,x)
+ {
+prod(p*x+(1-p)*x^{2})
}
f2 is a function of x only after integrating out p from f1. Here f1
is the
integrand, x is the additional argument to be
passed to f1. The integration is in terms of p.
f2 - function(x)
+ {
+ integrate(f1, lower=0,upper=1, x)
+ }
There is error output when I evaluate f2 at specific x values.
See below:
f2(c(2,3))
Error in integrate(f1, lower = 0, upper = 1, x) :
evaluation of function gave a result of wrong length
In addition: Warning messages:
1: In p * x :
longer object length is not a multiple of shorter object length
2: In (1 - p) * x^{ :
longer object length is not a multiple of shorter object length
Can any one give me some suggestions! Thank you!
2009/12/5 David Winsemius dwinsem...@comcast.net
On Dec 5, 2009, at 4:59 PM, li li wrote:
Hello,
I have some trouble in terms of using integrate function in R.
f1 is a function of p and x where x is supposed to be a vector.
(See the
code).
Then I want to write function f2 which is a function of the
vector
x after I integrate out p.
Can some one give me some help? Many thanks!
Hannah
f1 - function (p,x)
+ {
+y - p*x+(1-p)*x^{2}
+ prod(y)
+ }
f2 - function(x)
+ {
+ integrate(f1, 0,1, x)
Just looking at the help page for integrate makes me wonder what
you are
doing. There are 3 named arguments before the dots, so 0 and 1
will
become
lower and upper, while x is not among the named arguemnts,
so I
suppose
x will go to f1 as p. But f1 takes two arguments, so where will
it get the
second argument? Maybe if you would tell us a bit more about why
you made
those functions the way you did, it would help. I am guessing
it's
classwork
but perhaps not.
+ }
f2(x=c(1,2))
Error in integrate(f1, 0, 1, x) :
evaluation of function gave a result of wrong length
In addition: Warning messages:
1: In p * x :
longer object length is not a multiple of shorter object length
2: In (1 - p) * x^{ :
longer object length is not a multiple of shorter object length
[[alternative HTML version deleted]]
--
David Winsemius, MD
Heritage Laboratories
West Hartford, CT
[[alternative HTML version deleted]]
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David Winsemius, MD
Heritage Laboratories
West Hartford, CT
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[R] Error in eval(expr, envir, enclos) : object 'N' not found
I'm running an LSODA to generate some graphs, but I need to stop at a certain
point and use those values to generate another LSODA output. This is
working fine, but when I try to run the second LSODA, I get the Error in
eval(expr, envir, enclos) : object 'N' not found. Any ideas what can be
causing this? I have no object 'N' anywhere in the script. I made an
identical version of models states, parameters, and everything just by
adding 2 after each one, and I'm still getting this error.
Thanks,
-Hans
::CODE::
require(odesolve);
###Params for running script ##
iniT=1E3; iniN=10; iniM=0; iniC=1E3;
num_days = 30; interval_size = .1; OF_prcnt = .10;
model - function(t, state, pars)
{
with (as.list(c(state, pars)), {
dT=(a*T-a*T*b*T) - (c1*N*T) - (Kt*M*T)
dN=a1 - (f*N) + g * (T/(h+T)) * N - (p * N * T) - (Kn * M * N)
dC=a2 - (beta * C) - (Kc * M * C)
dM= -(gamma) * M + Vm
return(list(c(dT,dN,dC,dM)))
})
}
model2 - function(t, state2, pars2)
{
with (as.list(c(state2, pars2)), {
dT=(a*T-a*T*b*T) - (c1*N*T) - (Kt*M*T)
dN=a1 - (f*N) + g * (T/(h+T)) * N - (p * N * T) - (Kn * M * N)
dC=a2 - (beta * C) - (Kc * M * C)
dM= -(gamma) * M + Vm
return(list(c(dT,dN,dC,dM)))
})
}
### First Half - Tumor growth to 10%
pars - list( Tini=iniT, Nini=iniN, Mini=iniM, Cini=iniC,
a=4.31E-3, b=1.02E-14, c1=3.41E-10, Kt=8E-1,
f=4.12E-2, g=1.5E-2, h=2.02E1, beta=1.20E-2, gamma=9E-1,
Kc=6E-1, Kn=6E-1, p=2E-11, a1=1.2E4, a2=7.5E8, Vm=0 )
tout- seq(0, num_days, by=interval_size)
state - c(T = pars$Tini, N = pars$Nini, C = pars$Cini, M = pars$Mini)
out - lsoda(state, tout, model, pars)
## Finding position at which OF function is reached
final_matrix = out;
loopsize = (num_days / interval_size) + 1
OF_tumor_size = iniT + (OF_prcnt * iniT)
## Sentinel Value to find at which row in the matrix reaches OF_tumor_size
OF_row=-1;
for(i in 1:loopsize) {
if( out[i,2] = OF_tumor_size) {
OF_row=i;
break;
}
}
if(OF_row != -1) {
##Params setup
OF_iniT=out[OF_row,2]; OF_iniN=out[OF_row,3]; OF_iniC=out[OF_row,4];
OF_iniM=out[OF_row,5];
pars2 - list( Tini=OF_iniT, Nini=OF_iniN, Mini=OF_iniM, Cini=OF_iniC,
a=4.31E-3, b=1.02E-14, c1=3.41E-10, Kt=8E-1,
f=4.12E-2, g=1.5E-2, h=2.02E1, beta=1.20E-2, gamma=9E-1,
Kc=6E-1, Kn=6E-1, p=2E-11, a1=1.2E4, a2=7.5E8, Vm=0 )
state2 - c(T = pars2$Tini, N = pars2$Nini, C = pars2$Cini, M =
pars2$Mini)
out2 - lsoda(state2, tout, model2, pars2)
}
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and provide commented, minimal, self-contained, reproducible code.
[R] Error in eval(expr, envir, enclos) : object 'N' not found
I'm running an LSODA to generate some graphs, but I need to stop at a certain
point and use those values to generate another LSODA output. This is
working fine, but when I try to run the second LSODA, I get the Error in
eval(expr, envir, enclos) : object 'N' not found. Any ideas what can be
causing this? I have no object 'N' anywhere in the script. I made an
identical version of models states, parameters, and everything just by
adding 2 after each one, and I'm still getting this error.
Thanks,
-Hans
::CODE::
require(odesolve);
###Params for running script ##
iniT=1E3; iniN=10; iniM=0; iniC=1E3;
num_days = 30; interval_size = .1; OF_prcnt = .10;
model - function(t, state, pars)
{
with (as.list(c(state, pars)), {
dT=(a*T-a*T*b*T) - (c1*N*T) - (Kt*M*T)
dN=a1 - (f*N) + g * (T/(h+T)) * N - (p * N * T) - (Kn * M * N)
dC=a2 - (beta * C) - (Kc * M * C)
dM= -(gamma) * M + Vm
return(list(c(dT,dN,dC,dM)))
})
}
model2 - function(t, state2, pars2)
{
with (as.list(c(state2, pars2)), {
dT=(a*T-a*T*b*T) - (c1*N*T) - (Kt*M*T)
dN=a1 - (f*N) + g * (T/(h+T)) * N - (p * N * T) - (Kn * M * N)
dC=a2 - (beta * C) - (Kc * M * C)
dM= -(gamma) * M + Vm
return(list(c(dT,dN,dC,dM)))
})
}
### First Half - Tumor growth to 10%
pars - list( Tini=iniT, Nini=iniN, Mini=iniM, Cini=iniC,
a=4.31E-3, b=1.02E-14, c1=3.41E-10, Kt=8E-1,
f=4.12E-2, g=1.5E-2, h=2.02E1, beta=1.20E-2, gamma=9E-1,
Kc=6E-1, Kn=6E-1, p=2E-11, a1=1.2E4, a2=7.5E8, Vm=0 )
tout- seq(0, num_days, by=interval_size)
state - c(T = pars$Tini, N = pars$Nini, C = pars$Cini, M = pars$Mini)
out - lsoda(state, tout, model, pars)
## Finding position at which OF function is reached
final_matrix = out;
loopsize = (num_days / interval_size) + 1
OF_tumor_size = iniT + (OF_prcnt * iniT)
## Sentinel Value to find at which row in the matrix reaches OF_tumor_size
OF_row=-1;
for(i in 1:loopsize) {
if( out[i,2] = OF_tumor_size) {
OF_row=i;
break;
}
}
if(OF_row != -1) {
##Params setup
OF_iniT=out[OF_row,2]; OF_iniN=out[OF_row,3]; OF_iniC=out[OF_row,4];
OF_iniM=out[OF_row,5];
pars2 - list( Tini=OF_iniT, Nini=OF_iniN, Mini=OF_iniM, Cini=OF_iniC,
a=4.31E-3, b=1.02E-14, c1=3.41E-10, Kt=8E-1,
f=4.12E-2, g=1.5E-2, h=2.02E1, beta=1.20E-2, gamma=9E-1,
Kc=6E-1, Kn=6E-1, p=2E-11, a1=1.2E4, a2=7.5E8, Vm=0 )
state2 - c(T = pars2$Tini, N = pars2$Nini, C = pars2$Cini, M =
pars2$Mini)
out2 - lsoda(state2, tout, model2, pars2)
}
--
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Re: [R] integrate function
li li-13 wrote:
Yes, f2 is the function I wanted to write. I tried to do use Vectorize
function to f1, it did not work.
f2 - function(x)
+ {
+ integrate(Vectorize(f1,vectorize.args =p), lower=0,upper=1, x)
+ }
f2(c(2,3))
Error in Vectorize(f1, vectorize.args = p) :
must specify formal argument names to vectorize
Use integrate(Vectorize(f1,vectorize.args =c(p)), lower=0,upper=1, x)
vectorize.args is a character vector of arguments according to the
documentation.
Then f2(1:3) will give: 19 with absolute error 2.1e-13
Berend
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