Re: [R] 'matplot' for matrix with NAs: broken lines
I just found out that my does this by default statement (by which I was referring to the ability to automatically connect two points with a NA in the middle in a time series) is wrong! Actually, all plotting functions, i.e. plot, matplot and xyplot, don't plot NAs. The solution I came up with is convert the data to long table, remove NAs, and then use xyplot. See example below: set.seed(1234) a=b=matrix(rnorm(9), 3,3) b[2,2]=NA matplot(a, type=b) matplot(b, type=b) ## I want the two 2 connected! matplot(b, type=l) ## Now my data for the second column are missing from the graph ## my solution tmp1 - data.frame(g=rep(1:3,each=3), x=rep(1:3,3), y=c(b)) xyplot(y~x, group=g, data=tmp1, type=b, pch=c(1,2,3)) ## there is still no line connecting two 2s. tmp2 - tmp1[!is.na(tmp1$y),] xyplot(y~x, group=g, data=tmp2, type=b) ## this is what I want, b/c it's easier for me to keep track of both trend and missing values. The original post was really asking whether a simple change of some parameters in matplot can do this. Now, I guess not. ...Tao From: maech...@stat.math.ethz.ch Date: Thu, 6 May 2010 18:34:22 +0200 To: shi...@hotmail.com CC: ggrothendi...@gmail.com; r-help@r-project.org Subject: Re: [R] 'matplot' for matrix with NAs: broken lines TS == Tao Shi on Wed, 5 May 2010 20:11:26 + writes: TS Thanks, Gabor! So, there is no way I can change some graphic parameters in 'matplot' to get this? TS I forgot to mention that I purposely use type=b, so I know where the missing data are. With imputed data, either using b or l, there is no way to keep track of NAs. Plus, in my real data sometimes there is only one non-missing value in a particular column and na.approx can't work (well I could selectively impute the NAs ... ) TS So far, my best solution to this is to use xyplot. It does this by default, but of course I need some data manipulation first. does this by default meaning what? I don't think it does impute missing, does it? Can you elaborate, using your example (below)? I found Gabor's answer appropriate, I really cannot see why matplot() should behave differently here... Martin Maechler TS From: ggrothendi...@gmail.com Date: Wed, 5 May 2010 15:45:44 -0400 Subject: Re: [R] 'matplot' for matrix with NAs: broken lines To: shi...@hotmail.com CC: r-help@r-project.org Try this: library(zoo) matplot(na.approx(b), type = l) On Wed, May 5, 2010 at 2:30 PM, Tao Shi wrote: Hi list, I know that points involving NAs are not plotted in 'matplot', but when I plot them as lines, I still want the lines to connect all the points (i.e. not broken where there are NAs). Please see the example below. How can I achieve this in 'matplot'? If I can't, any good alternatives so I don't have to use 'plot' + 'lines' and loop through all the columns. Many thanks! ...Tao set.seed(1234) a=b=matrix(rnorm(9), 3,3) b[2,2]=NA matplot(a, type=b) TS [[elided Hotmail spam]] matplot(b, type=l) ## Now my data for the second column are missing from the graph _ Hotmail is redefining busy with tools for the New Busy. Get more from your inbox. N:WL:en-US:WM_HMP:042010_2 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. TS _ TS Hotmail has tools for the New Busy. Search, chat and e-mail from your inbox. TS N:WL:en-US:WM_HMP:042010_1 TS __ TS R-help@r-project.org mailing list TS https://stat.ethz.ch/mailman/listinfo/r-help TS PLEASE do read the posting guide http://www.R-project.org/posting-guide.html TS and provide commented, minimal, self-contained, reproducible code. _ Hotmail has tools for the New Busy. Search, chat and e-mail from your inbox. N:WL:en-US:WM_HMP:042010_1 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] 'matplot' for matrix with NAs: broken lines
Thanks for the suggestion! Date: Thu, 6 May 2010 13:40:04 -0700 Subject: Re: [R] 'matplot' for matrix with NAs: broken lines From: djmu...@gmail.com To: shi...@hotmail.com CC: maech...@stat.math.ethz.ch; r-help@r-project.org Hi: If you intend to use your preferred solution, then I would suggest that you increase the size of the plotted points relative to the thickness of the adjoining lines; in your last line of code, something like xyplot(y~x, group=g, data=tmp2, type=b, cex = 2, pch = 16) This way, it will be easier to spot where data values are missing. HTH, Dennis On Thu, May 6, 2010 at 10:44 AM, Tao Shi wrote: I just found out that my does this by default statement (by which I was referring to the ability to automatically connect two points with a NA in the middle in a time series) is wrong! Actually, all plotting functions, i.e. plot, matplot and xyplot, don't plot NAs. The solution I came up with is convert the data to long table, remove NAs, and then use xyplot. See example below: set.seed(1234) a=b=matrix(rnorm(9), 3,3) b[2,2]=NA matplot(a, type=b) [[elided Hotmail spam]] matplot(b, type=l) ## Now my data for the second column are missing from the graph ## my solution tmp1 - data.frame(g=rep(1:3,each=3), x=rep(1:3,3), y=c(b)) xyplot(y~x, group=g, data=tmp1, type=b, pch=c(1,2,3)) ## there is still no line connecting two 2s. tmp2 - tmp1[!is.na(tmp1$y),] xyplot(y~x, group=g, data=tmp2, type=b) ## this is what I want, b/c it's easier for me to keep track of both trend and missing values. The original post was really asking whether a simple change of some parameters in matplot can do this. Now, I guess not. ...Tao From: maech...@stat.math.ethz.ch Date: Thu, 6 May 2010 18:34:22 +0200 To: shi...@hotmail.com CC: ggrothendi...@gmail.com; r-help@r-project.org Subject: Re: [R] 'matplot' for matrix with NAs: broken lines TS == Tao Shi on Wed, 5 May 2010 20:11:26 + writes: TS Thanks, Gabor! So, there is no way I can change some graphic parameters in 'matplot' to get this? TS I forgot to mention that I purposely use type=b, so I know where the missing data are. With imputed data, either using b or l, there is no way to keep track of NAs. Plus, in my real data sometimes there is only one non-missing value in a particular column and na.approx can't work (well I could selectively impute the NAs ... ) TS So far, my best solution to this is to use xyplot. It does this by default, but of course I need some data manipulation first. does this by default meaning what? I don't think it does impute missing, does it? Can you elaborate, using your example (below)? I found Gabor's answer appropriate, I really cannot see why matplot() should behave differently here... Martin Maechler TS From: ggrothendi...@gmail.com Date: Wed, 5 May 2010 15:45:44 -0400 Subject: Re: [R] 'matplot' for matrix with NAs: broken lines To: shi...@hotmail.com CC: r-help@r-project.org Try this: library(zoo) matplot(na.approx(b), type = l) On Wed, May 5, 2010 at 2:30 PM, Tao Shi wrote: Hi list, I know that points involving NAs are not plotted in 'matplot', but when I plot them as lines, I still want the lines to connect all the points (i.e. not broken where there are NAs). Please see the example below. How can I achieve this in 'matplot'? If I can't, any good alternatives so I don't have to use 'plot' + 'lines' and loop through all the columns. Many thanks! ...Tao set.seed(1234) a=b=matrix(rnorm(9), 3,3) b[2,2]=NA matplot(a, type=b) TS [[elided Hotmail spam]] matplot(b, type=l) ## Now my data for the second column are missing from the graph _ Hotmail is redefining busy with tools for the New Busy. Get more from your inbox. N:WL:en-US:WM_HMP:042010_2 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. TS _ TS Hotmail has tools for the New Busy. Search, chat and e-mail from your inbox. TS N:WL:en-US:WM_HMP:042010_1 TS __ TS R-help@r-project.org mailing list TS https://stat.ethz.ch/mailman/listinfo/r-help TS PLEASE do read the posting guide http://www.R-project.org/posting-guide.html TS and provide commented, minimal, self-contained, reproducible code. _ Hotmail has tools for the New Busy. Search
[R] 'matplot' for matrix with NAs: broken lines
Hi list, I know that points involving NAs are not plotted in 'matplot', but when I plot them as lines, I still want the lines to connect all the points (i.e. not broken where there are NAs). Please see the example below. How can I achieve this in 'matplot'? If I can't, any good alternatives so I don't have to use 'plot' + 'lines' and loop through all the columns. Many thanks! ...Tao set.seed(1234) a=b=matrix(rnorm(9), 3,3) b[2,2]=NA matplot(a, type=b) matplot(b, type=b) ## I want the two 2 connected! matplot(b, type=l) ## Now my data for the second column are missing from the graph _ Hotmail is redefining busy with tools for the New Busy. Get more from your inbox. N:WL:en-US:WM_HMP:042010_2 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Read data from .csv file as a matrix
Vincent, The root of this problem seems to be that you don't fully understand the differences between matrix and data.frame. Read up on them and you'll know how to solve this problem. For now: as.matrix(temp[,-1]) or temp = read.csv(Weather.csv, sep=,, row.names=1) temp1 - as.matrix(temp) should work. ...Tao I have a csv file that contains weather observation (rows) by days (in columns). I open using: temp = read.csv(Weather.csv, sep=,) and read: X X1.Jan X2.Jan X3.Jan X4.Jan 1 Min 2 3 4 1 2 Max 6 10 8 6 3 Forecast Min 3 1 1 3 4 Forecast Max 8 7 4 9 If I type mean(temp[2,2:3]) I get X1.Jan X2.Jan 6 10 The same command on y = matrix(1:21, ncol=7) mean(y[2,2:3]) [1] 6.5 Works because the data is in a matrix. I believe R stores the data from the csv file as a data.frame with these annoying headers. So how do I convert the data from my csv file into a matrix? I tried as.matrix but it did not help. _ The New Busy is not the old busy. Search, chat and e-mail from your inbox. N:WL:en-US:WM_HMP:042010_3 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] What is the best way to have R output tables in an MS Word format?
Hi Max, It looks like most of answers were towards to the statisticians you work with (i.e. R - Word). For yourself, if you just worry about converting the PDF reports from your statisticians to Word, here is another link with a more comprehensive review besides the two online apps Prof. Harrell's mentioned on his webpage. http://www.freewaregenius.com/2010/03/06/how-to-convert-pdf-to-word-doc-for-free-a-comparative-test/ Also, Adobe Acrobat 9.0 can do PDF-Word, but I haven't tried it personally. ...Tao On Fri, Apr 30, 2010 at 5:13 PM, Max Gunther max.gunt...@vanderbilt.eduwrote: Dear R list, Our statisticians usually give us results back in a PDF format. I would like to be able to copy and past tables from R output directly into a Microsoft Word table since this will save us tons of time, be more accurate to minimize human copying errors and help us update data in our papers more easily. Do people have suggestions for the best way to do this? I am a novice to R but I do work with a couple of very knowledgeable statisticians who do most of the heavy statistical lifting for our research group. Many thanks, Max Max Gunther, PhD Vanderbilt University - Radiology Institute of Imaging Sciences - VUIIS Center for Health Services Research Nashville, TN www.ICUdelirium.org _ Hotmail has tools for the New Busy. Search, chat and e-mail from your inbox. N:WL:en-US:WM_HMP:042010_1 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] 'matplot' for matrix with NAs: broken lines
Thanks, Gabor! So, there is no way I can change some graphic parameters in 'matplot' to get this? I forgot to mention that I purposely use type=b, so I know where the missing data are. With imputed data, either using b or l, there is no way to keep track of NAs. Plus, in my real data sometimes there is only one non-missing value in a particular column and na.approx can't work (well I could selectively impute the NAs ... ) So far, my best solution to this is to use xyplot. It does this by default, but of course I need some data manipulation first. ...Tao From: ggrothendi...@gmail.com Date: Wed, 5 May 2010 15:45:44 -0400 Subject: Re: [R] 'matplot' for matrix with NAs: broken lines To: shi...@hotmail.com CC: r-help@r-project.org Try this: library(zoo) matplot(na.approx(b), type = l) On Wed, May 5, 2010 at 2:30 PM, Tao Shi wrote: Hi list, I know that points involving NAs are not plotted in 'matplot', but when I plot them as lines, I still want the lines to connect all the points (i.e. not broken where there are NAs). Please see the example below. How can I achieve this in 'matplot'? If I can't, any good alternatives so I don't have to use 'plot' + 'lines' and loop through all the columns. Many thanks! ...Tao set.seed(1234) a=b=matrix(rnorm(9), 3,3) b[2,2]=NA matplot(a, type=b) [[elided Hotmail spam]] matplot(b, type=l) ## Now my data for the second column are missing from the graph _ Hotmail is redefining busy with tools for the New Busy. Get more from your inbox. N:WL:en-US:WM_HMP:042010_2 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. _ Hotmail has tools for the New Busy. Search, chat and e-mail from your inbox. N:WL:en-US:WM_HMP:042010_1 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Can't load doSMP from REvolutionR in regular R2.11.0
Hi David, Thank you for the reply! Do you know where I can find the source code for these packages? I can give it a try. ...Tao From: da...@revolution-computing.com Date: Thu, 29 Apr 2010 08:59:08 -0700 Subject: Re: [R] Can't load doSMP from REvolutionR in regular R2.11.0 To: shi...@hotmail.com CC: r-help@r-project.org We haven't tested doSMP with the mingw compiler (hence why we haven't yet submitted it to CRAN). We compiled it under R 2.10 using the same Intel compilers we use for REvolution R. It is open source (GPL) so you're welcome to try compiling it under mingw yourself, but we can't offer support for that configuration. # David Smith On Wed, Apr 28, 2010 at 5:10 PM, Tao Shi wrote: I was testing out the doSMP package from REvolutionR in my regular R2.11.0 installation and I got the following error message. Well, one obvious thing is that R2.11.0 was built using i386-pc-mingw32 which is different from what revoIPC used. I could just use REvolutionR, but all my R peripherals were set up to work with the regular R2.11.0. So, I really want to make this work. Anyideas? -- David M Smith VP of Marketing, REvolution Computing http://blog.revolution-computing.com Tel: +1 (650) 330-0553 x205 (Palo Alto, CA, USA) Download REvolution R free: www.revolution-computing.com/downloads/revolution-r.php _ Hotmail is redefining busy with tools for the New Busy. Get more from your inbox. N:WL:en-US:WM_HMP:042010_2 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Can't load doSMP from REvolutionR in regular R2.11.0
Thanks, David! I forgot to check that email... I have built the revoIPC using R2.11.0 and it seemed there were no error messages. I can load doSMP now, but haven't tested it yet. Tal, I'll send you the file offline, so you can also test it. best! ...Tao From: da...@revolution-computing.com Date: Thu, 29 Apr 2010 13:15:43 -0700 Subject: Re: [R] Can't load doSMP from REvolutionR in regular R2.11.0 To: shi...@hotmail.com CC: r-help@r-project.org; tal.gal...@gmail.com Did you download the source bundle when you downloaded REvolution R? You'll find them there. There's a link in the same email that gives instructions for downloading the binaries. # David Smith On Thu, Apr 29, 2010 at 12:48 PM, Tao Shi wrote: Hi David, Thank you for the reply! Do you know where I can find the source code for these packages? I can give it a try. ...Tao From: da...@revolution-computing.com Date: Thu, 29 Apr 2010 08:59:08 -0700 Subject: Re: [R] Can't load doSMP from REvolutionR in regular R2.11.0 To: shi...@hotmail.com CC: r-help@r-project.org We haven't tested doSMP with the mingw compiler (hence why we haven't yet submitted it to CRAN). We compiled it under R 2.10 using the same Intel compilers we use for REvolution R. It is open source (GPL) so you're welcome to try compiling it under mingw yourself, but we can't offer support for that configuration. # David Smith On Wed, Apr 28, 2010 at 5:10 PM, Tao Shi wrote: I was testing out the doSMP package from REvolutionR in my regular R2.11.0 installation and I got the following error message. Well, one obvious thing is that R2.11.0 was built using i386-pc-mingw32 which is different from what revoIPC used. I could just use REvolutionR, but all my R peripherals were set up to work with the regular R2.11.0. So, I really want to make this work. Anyideas? -- David M Smith VP of Marketing, REvolution Computing http://blog.revolution-computing.com Tel: +1 (650) 330-0553 x205 (Palo Alto, CA, USA) Download REvolution R free: www.revolution-computing.com/downloads/revolution-r.php _ Hotmail is redefining busy with tools for the New Busy. Get more from your inbox. http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_2 -- David M Smith VP of Marketing, REvolution Computing http://blog.revolution-computing.com Tel: +1 (650) 330-0553 x205 (Palo Alto, CA, USA) Download REvolution R free: www.revolution-computing.com/downloads/revolution-r.php _ Hotmail has tools for the New Busy. Search, chat and e-mail from your inbox. N:WL:en-US:WM_HMP:042010_1 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] apply vs. foreach vs. foreach with doSMP (multi cores)
Hi David and list, I'm a little puzzled to see these results below. Since, apply is basically a for loop, I was expecting foreach uses about same amount of time as apply, whereas foreach after registering 2-cores runs much faster. However, the results show apply is the fastest. Also could you please explain the error message (i.e. Error in ipcTaskSetEnvironment(taskq, envir) : ...) in the second run? The results were recorded on REvolution R 3.2 and I observed the same on regular R2.11.0. Many thanks! ...Tao library(doSMP) Loading required package: foreach Loading required package: iterators Loading required package: codetools foreach: simple, scalable parallel programming from REvolution Computing Use REvolution R for scalability, fault tolerance and more. http://www.revolution-computing.com Loading required package: revoIPC m - matrix(rnorm(10), 1, 10) system.time(tmp - t(apply(m, 1, function(x) x/mean(x user system elapsed 0.21 0.00 0.21 system.time(tmp1 - foreach(i=1:nrow(m), .combine=rbind) %dopar% (m[i,] / mean(m[i,]))) user system elapsed 5.50 0.00 5.53 Warning message: executing %dopar% sequentially: no parallel backend registered w - startWorkers(2) Warning messages: 1: In startWorkers(2) : there is an existing doSMP session using doSMP1 2: In startWorkers(2) : there is an existing doSMP session using doSMP2 registerDoSMP(w) system.time(tmp1 - foreach(i=1:nrow(m), .combine=rbind) %dopar% (m[i,] / mean(m[i,]))) user system elapsed 6.02 0.03 7.84 stopWorkers(w) ## second run system.time(tmp - t(apply(m, 1, function(x) x/mean(x user system elapsed 0.22 0.02 0.23 system.time(tmp1 - foreach(i=1:nrow(m), .combine=rbind) %dopar% (m[i,] / mean(m[i,]))) Error in ipcTaskSetEnvironment(taskq, envir) : The task queue has been freed. Timing stopped at: 0.03 0.02 0.04 w - startWorkers(2) Warning messages: 1: In startWorkers(2) : there is an existing doSMP session using doSMP1 2: In startWorkers(2) : there is an existing doSMP session using doSMP2 registerDoSMP(w) system.time(tmp1 - foreach(i=1:nrow(m), .combine=rbind) %dopar% (m[i,] / mean(m[i,]))) user system elapsed 6.11 0.01 7.62 stopWorkers(w) dim(m) [1] 1 10 sessionInfo() R version 2.10.1 (2009-12-14) i386-pc-intel32 locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] doSMP_1.0-1 revoIPC_1.0-2 foreach_1.3.0 codetools_0.2-2 iterators_1.0.3 Revobase_3.2.0 _ The New Busy is not the old busy. Search, chat and e-mail from your inbox. N:WL:en-US:WM_HMP:042010_3 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Can't load doSMP from REvolutionR in regular R2.11.0
Hi list, I was testing out the doSMP package from REvolutionR in my regular R2.11.0 installation and I got the following error message. Well, one obvious thing is that R2.11.0 was built using i386-pc-mingw32 which is different from what revoIPC used. I could just use REvolutionR, but all my R peripherals were set up to work with the regular R2.11.0. So, I really want to make this work. Anyideas? Many thanks in advance! ...Tao library(doSMP) Loading required package: foreach Loading required package: iterators Loading required package: codetools foreach: simple, scalable parallel programming from REvolution Computing Use REvolution R for scalability, fault tolerance and more. http://www.revolution-computing.com Loading required package: revoIPC Error: package 'revoIPC' was built for i386-pc-intel32 sessionInfo() R version 2.11.0 (2010-04-22) i386-pc-mingw32 locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C LC_TIME=English_United States.1252 attached base packages: [1] grDevices datasets splines graphics stats tcltk utils methods base other attached packages: [1] foreach_1.3.0 codetools_0.2-2 iterators_1.0.3 svSocket_0.9-48 TinnR_1.0.3 R2HTML_2.0.0 Hmisc_3.7-0 survival_2.35-8 loaded via a namespace (and not attached): [1] cluster_1.12.3 grid_2.11.0 lattice_0.18-5 svMisc_0.9-57 tools_2.11.0 _ The New Busy is not the too busy. Combine all your e-mail accounts with Hotmail. ID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_4 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] a warning message from heatmap.2
Hi List, I want to show the heatmap of a correlation matrix using heatmap.2, however always get this warning message (see below) and the column dendrogram is not showing. It's not really a big deal, but curious how to suppress it and still let R show what I want to show (i.e. a symmetrical heatmap with dendrogram for both rows and columns). I'm using gplots 2.7.4 and R2.10.1 on Win XP. Thanks! heatmap.2(cor(matrix(rnorm(100),10,10)), symm=T, symbreaks=T, trace=none, density.info=none) Warning message: In heatmap.2(cor(matrix(rnorm(100), 10, 10)), symm = T, symbreaks = T, : Discrepancy: Colv is FALSE, while dendrogram is `row'. Omitting column dendogram. _ The New Busy think 9 to 5 is a cute idea. Combine multiple calendars with Hotmail. PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_5 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] lineplot.CI in sciplot: option ci.fun can't be changed?
hi List and Manuel, I have encounter the following problem with the function lineplot.CI. I'm running R 2.10.1, sciplot 1.0-7 on Win XP. It seems like it's a scoping issue, but I couldn't figure it out. Thanks! ...Tao lineplot.CI(x.factor = dose, response = len, data = ToothGrowth) ## fine lineplot.CI(x.factor = dose, response = len, data = ToothGrowth, fun=median) ## fine lineplot.CI(x.factor = dose, response = len, data = ToothGrowth, fun=mean) ## fine lineplot.CI(x.factor = dose, response = len, data = ToothGrowth, ci.fun= function(x) c(fun(x)-2*se(x), fun(x)+2*se(x))) ## failed! Error in FUN(X[[1L]], ...) : could not find function fun debug(lineplot.CI) lineplot.CI(x.factor = dose, response = len, data = ToothGrowth, ci.fun= function(x) c(fun(x)-2*se(x), fun(x)+2*se(x))) Browse[2] debug: mn.data - tapply(response, groups, fun) Browse[2] debug: CI.data - tapply(response, groups, ci.fun) Browse[2] fun function (x) mean(x, na.rm = TRUE) environment: 0x07178640 Browse[2] ci.fun function(x) c(fun(x)-2*se(x), fun(x)+2*se(x)) Browse[2] debug(ci.fun) Browse[2] fun function (x) mean(x, na.rm = TRUE) environment: 0x07178640 Browse[2] debugging in: FUN(X[[1L]], ...) debug: c(fun(x) - 2 * se(x), fun(x) + 2 * se(x)) Browse[3] Error in FUN(X[[1L]], ...) : could not find function fun undebug(lineplot.CI) lineplot.CI(x.factor = dose, response = len, data = ToothGrowth, ci.fun= function(x) c(fun(x)-se(x), fun(x)+se(x))) Error in FUN(X[[1L]], ...) : could not find function fun lineplot.CI(x.factor = dose, response = len, data = ToothGrowth, fun = function(x) mean(x, na.rm=TRUE),ci.fun= function(x) c(fun(x)-se(x), fun(x)+se(x))) Error in FUN(X[[1L]], ...) : could not find function fun lineplot.CI(x.factor = dose, response = len, data = ToothGrowth, fun = function(x) median(x, na.rm=TRUE),ci.fun= function(x) c(fun(x)-se(x), fun(x)+se(x))) Error in FUN(X[[1L]], ...) : could not find function fun _ Hotmail has tools for the New Busy. Search, chat and e-mail from your inbox. N:WL:en-US:WM_HMP:042010_1 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] lineplot.CI in sciplot: option ci.fun can't be changed?
Thanks, Manuel!
Subject: Re: lineplot.CI in sciplot: option ci.fun can't be changed?
From: manuel.a.mora...@williams.edu
To: shi...@hotmail.com
CC: r-help@r-project.org; mmora...@williams.edu
Date: Fri, 2 Apr 2010 14:22:33 -0400
For now, just change fun(x) to median(x) (or whatever) in your ci.fun()
below.
E.g.
lineplot.CI(x.factor = dose, response = len, data = ToothGrowth, ci.fun=
function(x) c(mean(x)-2*se(x), mean(x)+2*se(x)))
Otherwise, maybe the list members could help with a solution. An example
that illustrates the problem:
ex.fn - function(x,
fun = mean,
fun2 = function(x) fun(x)+sd(x)) {
list(fun=fun(x), fun2=fun2(x))
}
data - rnorm(10)
ex.fn(data) #works
ex.fn(data, fun=median) #works
ex.fn(data, fun2=function(x) fun(x)+3) #error with fun(x) not found
On Fri, 2010-04-02 at 17:36 +, Tao Shi wrote:
hi List and Manuel,
I have encounter the following problem with the function lineplot.CI. I'm
running R 2.10.1, sciplot 1.0-7 on Win XP. It seems like it's a scoping
issue, but I couldn't figure it out.
Thanks!
...Tao
lineplot.CI(x.factor = dose, response = len, data = ToothGrowth) ## fine
lineplot.CI(x.factor = dose, response = len, data = ToothGrowth,
fun=median) ## fine
lineplot.CI(x.factor = dose, response = len, data = ToothGrowth, fun=mean)
## fine
lineplot.CI(x.factor = dose, response = len, data = ToothGrow[[elided
Hotmail spam]]
Error in FUN(X[[1L]], ...) : could not find function fun
debug(lineplot.CI)
lineplot.CI(x.factor = dose, response = len, data = ToothGrowth, ci.fun=
function(x) c(fun(x)-2*se(x), fun(x)+2*se(x)))
Browse[2]
debug: mn.data - tapply(response, groups, fun)
Browse[2]
debug: CI.data - tapply(response, groups, ci.fun)
Browse[2] fun
function (x)
mean(x, na.rm = TRUE)
Browse[2] ci.fun
function(x) c(fun(x)-2*se(x), fun(x)+2*se(x))
Browse[2] debug(ci.fun)
Browse[2] fun
function (x)
mean(x, na.rm = TRUE)
Browse[2]
debugging in: FUN(X[[1L]], ...)
debug: c(fun(x) - 2 * se(x), fun(x) + 2 * se(x))
Browse[3]
Error in FUN(X[[1L]], ...) : could not find function fun
undebug(lineplot.CI)
lineplot.CI(x.factor = dose, response = len, data = ToothGrowth, ci.fun=
function(x) c(fun(x)-se(x), fun(x)+se(x)))
Error in FUN(X[[1L]], ...) : could not find function fun
lineplot.CI(x.factor = dose, response = len, data = ToothGrowth, fun =
function(x) mean(x, na.rm=TRUE),ci.fun= function(x) c(fun(x)-se(x),
fun(x)+se(x)))
Error in FUN(X[[1L]], ...) : could not find function fun
lineplot.CI(x.factor = dose, response = len, data = ToothGrowth, fun =
function(x) median(x, na.rm=TRUE),ci.fun= function(x) c(fun(x)-se(x),
fun(x)+se(x)))
Error in FUN(X[[1L]], ...) : could not find function fun
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Re: [R] wrap long lines in table using latex in Hmisc
Thank you guys for the wonderful suggestions!
Charlie,
You obviously foresaw my problem! It took me a while to figure out that the
\raggedright and other justification commands should be applied to each cell.
It didn't work for me when applied to the headings. See this nice document
here:
http://nepsweb.co.uk/docs/tableTricks.pdf
Thanks again.
...Tao
Subject: Re: [R] wrap long lines in table using latex in Hmisc
From: marc_schwa...@me.com
Date: Fri, 26 Feb 2010 18:03:33 -0600
CC: r-help@r-project.org; shi...@hotmail.com
To: ch...@sharpsteen.net
On Feb 26, 2010, at 5:18 PM, Sharpie wrote:
Ista Zahn wrote:
Hi Tao,
Just set the appropriate *.just argument, e.g.:
Dat - data.frame(x1 = rep(this value consists of a long string of
text, 5), x2 = rep(this value consists of an even longer string of
text, 5))
library(Hmisc)
latex(Dat, col.just = rep(p{1in}, 2))
You can also set justification for column headings, column group
headings etc. See ?latex for details.
Best,
Ista
As Ista said, you can use the p{}, m{} and b{} LaTeX column specifications
to create a table column that enforces a line wrap on it's contents. See:
http://en.wikibooks.org/wiki/LaTeX/Tables#The_tabular_environment
for full details.
However, one problem with using say, p{2in}, is that the text is set *fully
justified*. This means that the inter-word spacing in each line is expanded
so that the line fully occupies the allotted 2 inches of space. For some
tables the results are a typographical travesty.
The solution is to prepend a {justificationCommand} to your column
specification, such as:
{\centering}p{2in}
The justification commands you can use are :
\centering - Centers wrapped text
\raggedright - *left* aligns wrapped text
\raggedleft - *right* aligns wrapped text
Remember to double the backslash if you are passing this command as an
argument in R.
This trick will cause a LaTeX compilation error if used to specify the
right-most column in a table, unless the hmisc latex() command produces
tables that use \tabularnewline to invoke table row breaks instead of
\\.
Hope this helps.
-Charlie
One other option that you can use is to create a \newcommand that wraps text
in a tabular, which you can then actually use within an existing table cell.
This enables multiple lines of text within the cell, with line breaks that
you specify. So you in effect end up with nested tables. Of course, the
entire row height is adjusted accordingly, but this way, you don't need to
specify a fixed column width.
For example, put the following in your .tex file (or .Rnw file) after the
\begin{document} directive:
\newcommand{\multiliner}[1]{\begin{tabular}[...@{}r@{}}#1\end{tabular}}
\newcommand{\multilinel}[1]{\begin{tabular}[...@{}l@{}}#1\end{tabular}}
\newcommand{\multilinec}[1]{\begin{tabular}[...@{}c@{}}#1\end{tabular}}
Each of the above provides for Right, Left and Centered justification,
respectively, within the table cell.
Then, you can create a cell entry that results in the following TeX markup:
\multilineC{Line 1 \\ Line 2 \\ ...}
If you are cat()ing the output from R, you need to double the backslashes, so
that you begin with something like:
\\multilineC{Line 1 Line 2 ...}
I typically do this with headers for tables that would otherwise be too wide
for the column.
So you would start with a long line of text:
LongLine - This is a really long line that needs to wrap in a table row
Break it into chunks around 15 characters in length using strwrap():
strwrap(LongLine, 15)
[1] This is a really long line that needs to wrap
[5] in a table row
Use paste() to begin to create the proper LaTeX markup for \multilineC:
TMP1 - paste(strwrap(LongLine, 15), collapse = )
TMP1
[1] This is areally longline thatneeds to wrapin a table row
Now create the full line:
TMP2 - paste(\\multiLine{, TMP1, })
TMP2
[1] \\multiLine{ This is areally longline thatneeds to
wrapin a table row }
When you cat() the output, you get:
cat(TMP2)
\multiLine{ This is a\\really long\\line that\\needs to wrap\\in a table row }
TMP2 can now be used in place of the original long line of text and when
processed by 'latex', will be rendered properly.
Of course, rather than using strwrap(), you can hard code the line breaks
into your character vector as you may otherwise require.
HTH,
Marc Schwartz
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[R] wrap long lines in table using latex in Hmisc
Hi list, Is there a way to control long-line wrapping in a table using latex function in Hmisc or any other functions? It seems I can't find any examples. Thank you very much! ...Tao _ Hotmail: Trusted email with Microsoft’s powerful SPAM protection. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] text editors
If you do everything in Windows, Tinn-R is one of the best and also the one I use. I also tried WinEdt. It's very good, but it is not free. If you want a cross-platform editor, Emacs+ESS is the one. Like others said, the learning curve is steep, but worth it. ...Tao === Dear all, Do you use a text editor ? What would you recommend for Windows users ? What about Tinn-R ? Thank you very much, Dwayne _ Hotmail: Free, trusted and rich email service. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] wrap long lines in table using latex in Hmisc
Hi Ista,
Thanks! I missed that.
...Tao
From: istaz...@gmail.com
Date: Fri, 26 Feb 2010 17:48:32 -0500
Subject: Re: [R] wrap long lines in table using latex in Hmisc
To: shi...@hotmail.com
CC: r-help@r-project.org
Hi Tao,
Just set the appropriate *.just argument, e.g.:
Dat - data.frame(x1 = rep(this value consists of a long string of
text, 5), x2 = rep(this value consists of an even longer string of
text, 5))
library(Hmisc)
latex(Dat, col.just = rep(p{1in}, 2))
You can also set justification for column headings, column group
headings etc. See ?latex for details.
Best,
Ista
On Fri, Feb 26, 2010 at 3:37 PM, Tao Shi wrote:
Hi list,
Is there a way to control long-line wrapping in a table using latex
function in Hmisc or any other functions? It seems I can't find any
examples.
[[elided Hotmail spam]]
...Tao
_
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and provide commented, minimal, self-contained, reproducible code.
--
Ista Zahn
Graduate student
University of Rochester
Department of Clinical and Social Psychology
http://yourpsyche.org
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[R] a minor bug in venn from gplots?
Hi list,
I found this one when I was trying to output the Venn diagram to a .pdf file.
When there are 4 sets of groups to draw, the .pdf file automatically has 3
pages and the figure only appears on the 3rd page in the .pdf file with the
first 2 pages being blank. Try the following: (I'm using R-2.9.0 on WinXP,
gplots 2.7.1). gplots 2.7.3 has the same problem.
###==
pdf(test.pdf)
A- 1:20
B- 1:20
C- 2:20
D- 3:21
input-list(A,B,C,D)
venn(input)
dev.off()
###==
By looking at the code of drawVennDiagram, I think the problem comes from the
fact there are one grid.newpage() call and two plot function calls when
numCircles==4 (see below). I wonder the grid.newpage() and the second plot
call are necessary?
Thanks a lot.
...Tao
##=
else if (4 = numCircles numCircles = 5 !simplify) {
grid.newpage()
===
relocate_elp - function(e, alpha, x, y) {
phi = (alpha/180) * pi
xr = e[, 1] * cos(phi) + e[, 2] * sin(phi)
yr = -e[, 1] * sin(phi) + e[, 2] * cos(phi)
xr = x + xr
yr = y + yr
return(cbind(xr, yr))
}
lab - function(identifier, data, showLabel = showSetLogicLabel) {
r - data[identifier, 1]
if (showLabel) {
return(paste(identifier, r, sep = \n))
}
else {
return(r)
}
}
plot(c(0, 400), c(0, 400), type = n, axes = F, ylab = ,
xlab = )
if (4 == numCircles) {
elps = cbind(162 * cos(seq(0, 2 * pi, len = 1000)),
108 * sin(seq(0, 2 * pi, len = 1000)))
plot(c(0, 400), c(0, 400), type = n, axes = F,
===
ylab = , xlab = )
polygon(relocate_elp(elps, 45, 130, 170))
polygon(relocate_elp(elps, 45, 200, 200))
...
###===
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[R] SVM cross validation in e1071
Hi list,
Could someone help me to explain why the leave-one-out cross validation results
I got from svm using the internal option cross are different from those I got
manually? It seems using cross to do cross validation, the results are
always better. Please see the code below. I also include lda as a comparison.
I'm using WinXP, R-2.9.0, and e1071_1.5-19.
Many thanks!
...Tao
##==
## manual
##
##
set.seed(1234)
dat - data.frame( rbind(matrix(rnorm(1000),ncol = 10), matrix(rnorm(1000,
mean=0.6),ncol = 10)))
cl - as.factor(rep(1:2, each=100))
y.lda - rep(NA, nrow(dat))
y.svm - rep(NA, nrow(dat))
for (i in 1:nrow(dat)){
+ testset - dat[i, ]
+ trainset - dat[-i, ]
+ model.lda - lda(cl[-i]~., data=trainset)
+ model.svm - svm(cl[-i]~., data=trainset)
+ y.lda[i] - as.character(predict(model.lda, testset)$class)
+ y.svm[i] - as.character(predict(model.svm, testset))
+ }
table(y.lda, cl)
cl
y.lda 1 2
1 84 10
2 16 90
table(y.svm, cl)
cl
y.svm 1 2
1 83 8
2 17 92
##==
## using internal CV options
##
z2 - lda(cl~., data=dat, CV=T)
table(z2$class, cl)
cl
1 2
1 84 10
2 16 90
z - svm(cl~., data=dat, cross=200)
table(z$fitted, cl)
cl
1 2
1 93 4
2 7 96
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Re: [R] SVM cross validation in e1071
Hi Steve, Thanks for the pointer! After checking the source code myself, it's indeed the case. And of course, the training error is always better than the CV error. And this can be also checked if you vary the fold number in cross, the fitted result is not changing. I wonder if the default value for fitted should be set to FALSE to avoid the confusion: i.e. I thought the fitted field in the returning object is the CV results. ...Tao CC: r-help@r-project.org From: mailinglist.honey...@gmail.com To: shi...@hotmail.com Subject: Re: [R] SVM cross validation in e1071 Date: Tue, 7 Jul 2009 21:43:49 -0400 Hi Tao, On Jul 7, 2009, at 8:33 PM, Tao Shi wrote: Hi list, Could someone help me to explain why the leave-one-out cross validation results I got from svm using the internal option cross are different from those I got manually? It seems using cross to do cross validation, the results are always better. Please see the code below. I also include lda as a comparison. Looking at the C code in Rsvm.c, it looks like the model that is returned is one that is trained on *all* of the data that is originally passed in. After the model is built, and the value for cross is 1, the `do_cross_validation` function is called, in which your data is then split into folds for cross validation. This is only done to report accuracy or MSE (depending on classification vs. regression). The models from this CV do not effect the model that is returned back to R. So ... that's why. If you train your svm without holding out any data (and do no cross validation), you should essentially get back the same model that you're getting back no when you set cross 1. Does that make sense? -steve -- Steve Lianoglou Graduate Student: Physiology, Biophysics and Systems Biology Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos _ Lauren found her dream laptop. Find the PC that’s right for you. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] silhouette: clustering labels have to be consecutive integers starting
Thanks, Martin!
...Tao
From: maech...@stat.math.ethz.ch
Date: Wed, 13 May 2009 14:13:48 +0200
To: shi...@hotmail.com
CC: rip...@stats.ox.ac.uk; bcarv...@jhsph.edu; r-help@r-project.org;
maech...@stat.math.ethz.ch
Subject: Re: [R] silhouette: clustering labels have to be consecutive
integers starting
TS == Tao Shi shi...@hotmail.com
on Wed, 10 Oct 2007 06:15:53 + writes:
TS Thank you very much, Benilton and Prof. Ripley, for the
TS speedy replies!
TS Looking forward to the fix!
TS Tao
I have finally re-stumbled onto this e-mail thread,
and indeed found fixed the problem.
Version 1.12.0 of 'cluster' should become visible within a few days,
and will allow to call
silhoutte(g, dis)
on a grouping vector of k different integer values which need
*not* necessarily be in 1:k.
Martin Maechler,
ETH Zurich
From: Prof Brian Ripley rip...@stats.ox.ac.uk
To: Benilton Carvalho bcarv...@jhsph.edu
CC: Tao Shi shi...@hotmail.com, maech...@stat.math.ethz.ch,
r-help@r-project.org
Subject: Re: [R] silhouette: clustering labels have to be consecutive
intergers starting from 1?
Date: Wed, 10 Oct 2007 05:33:03 +0100 (BST)
It is a C-level problem in package cluster: valgrind gives
==11377== Invalid write of size 8
==11377==at 0xA4015D3: sildist (sildist.c:35)
==11377==by 0x4706D8: do_dotCode (dotcode.c:1750)
This is a matter for the package maintainer (Cc:ed here), not R-help.
On Tue, 9 Oct 2007, Benilton Carvalho wrote:
that happened to me with R-2.4.0 (alpha) and was fixed on R-2.4.0
(final)...
http://tolstoy.newcastle.edu.au/R/e2/help/06/11/5061.html
then i stopped using... now, the problem seems to be back. The same
examples still apply.
This fails:
require(cluster)
set.seed(1)
x - rnorm(100)
g - sample(2:4, 100, rep=T)
for (i in 1:100){
print(i)
tmp - silhouette(g, dist(x))
}
and this works:
require(cluster)
set.seed(1)
x - rnorm(100)
g - sample(2:4, 100, rep=T)
for (i in 1:100){
print(i)
tmp - silhouette(as.integer(factor(g)), dist(x))
}
and here's the sessionInfo():
sessionInfo()
R version 2.6.0 (2007-10-03)
x86_64-unknown-linux-gnu
locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.U
TF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-
8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_ID
ENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] cluster_1.11.9
(Red Hat EL 2.6.9-42 smp - AMD opteron 848)
b
On Oct 9, 2007, at 8:35 PM, Tao Shi wrote:
Hi list,
When I was using 'silhouette' from the 'cluster' package to
calculate clustering performances, R crashed. I traced the problem
to the fact that my clustering labels only have 2's and 3's. when
I replaced them with 1's and 2's, the problem was solved. Is the
function purposely written in this way so when I have clustering
labels, 2 and 3, for example, the function somehow takes the
'missing' cluster 2 into account when it calculates silhouette
widths?
Thanks,
Tao
##
## sorry about the long attachment
R.Version()
$platform
[1] i386-pc-mingw32
$arch
[1] i386
$os
[1] mingw32
$system
[1] i386, mingw32
$status
[1]
$major
[1] 2
$minor
[1] 5.1
$year
[1] 2007
$month
[1] 06
$day
[1] 27
$`svn rev`
[1] 42083
$language
[1] R
$version.string
[1] R version 2.5.1 (2007-06-27)
library(cluster)
cl1 ## clustering labels
[1] 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 2 2 2 2 2 2 2 2 2
[30] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
[59] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
[88] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
[117] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
[146] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
[175] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
[204] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
x1 ## 1-d input vector
[1] 1.5707963 1.5707963 1.5707963 1.5707963 1.5707963
[6] 1.5707963 1.5707963 1.5707963
[R] why two diff. se in nlsList?
Hi list, In the object returned by summary.nlsList, what's the difference between coefficients and parameters? The have the same Estimate, different se (therefore t value), but same p values. R.2.8.0 on winxp with nlme_3.1-89 Thanks, ...Tao + library(nlme) fm1 - nlsList(uptake ~ SSasympOff(conc, Asym, lrc, c0), data = CO2, start = c(Asym = 30, lrc = -4.5, c0 = 52)) summary(fm1)$para[,,1] Estimate Std. Error t value Pr(|t|) Qn1 38.13977 0.9911148 38.48169 1.991990e-06 Qn2 42.87169 1.0932089 39.21638 2.583953e-06 Qn3 44.22800 1.0241029 43.18706 1.809264e-07 Qc1 36.42874 1.1941594 30.50576 1.140085e-05 Qc3 40.68373 1.2480923 32.59673 1.424635e-04 Qc2 39.81950 1.0167249 39.16447 2.692304e-06 Mn3 28.48286 1.0624246 26.80930 1.066434e-06 Mn2 32.12827 1.0174826 31.57624 3.488786e-06 Mn1 34.08482 1.3400596 25.43530 4.199333e-06 Mc2 13.55519 1.0506404 12.90184 4.385886e-06 Mc3 18.53506 0.8363371 22.16219 1.461563e-06 Mc1 21.78723 1.4113318 15.43735 5.756870e-06 summary(fm1)$coef[,,1] Estimate Std. Error t value Pr(|t|) Qn1 38.13977 0.9163882 41.61967 1.991990e-06 Qn2 42.87169 1.0994599 38.99341 2.583953e-06 Qn3 44.22800 0.5829894 75.86415 1.809264e-07 Qc1 36.42874 1.3556273 26.87224 1.140085e-05 Qc3 40.68373 2.8632576 14.20890 1.424635e-04 Qc2 39.81950 1.0317496 38.59415 2.692304e-06 Mn3 28.48286 0.5852408 48.66861 1.066434e-06 Mn2 32.12827 0.8883225 36.16735 3.488786e-06 Mn1 34.08482 0.9872439 34.52522 4.199333e-06 Mc2 13.55519 0.3969189 34.15104 4.385886e-06 Mc3 18.53506 0.4121147 44.97549 1.461563e-06 Mc1 21.78723 0.6830001 31.89930 5.756870e-06 _ ore_012009 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] latex in Hmisc: cell formating
Hi Dieter,
Thank you for pointing out the website. From the website it seems the bug has
been fixed early 2008 (see
http://biostat.mc.vanderbilt.edu/trac/Hmisc/changeset/582 ).
So I upgraded my Hmisc package to 3.4-4, which was published on 11/3/2008 and
hoped it would work. However, the problem persisted.
...Tao
Tao Shi hotmail.com writes:
## I'm using R 2.8.0 on WinXP, Hmisc_3.4-3
table1 - matrix(10, 180,7)
cell.format - matrix(, ncol=7, nrow=180)
cell.format[c(seq(3,180,6),seq(4,180,6)),] - color{red}
cell.format[c(seq(5,180,6),seq(6,180,6)),] - color{green}
latex(table1, where='htbp', long=TRUE, lines.page=1000, size=scriptsize,
+ cgroup=c(group1,group2), n.cgroup=c(6,1),
+ rgroup=c(n=1,n=5,n=10,n=20,n=50), n.rgroup=rep(36,5),
+ cellTexCmds=cell.format, numeric.dollar = FALSE)
Error in cat(rcellTexCmds[i, colNum], , cx[i, colNum], file = file, :
subscript out of bounds
## if I remove the column name grouping, it works fine!
##
latex(table1, where='htbp', long=TRUE, lines.page=1000, size=scriptsize,
+ #cgroup=c(group1,group2), n.cgroup=c(6,1),
+ rgroup=c(n=1,n=5,n=10,n=20,n=50), n.rgroup=rep(36,5),
+ cellTexCmds=cell.format, numeric.dollar = FALSE)
The example you posted is good, but it is more helpful to post the code,
not the pasted result, so that trying you example does not require
manual editing.
I had reported a similar case a year ago; see below. Maybe you should
post it at:
http://biostat.mc.vanderbilt.edu/trac/Hmisc/
#
library(Hmisc)
sessionInfo()
x - matrix(1:12, nrow=2, dimnames=list(c('a','p'),
letters[1:6]))
cellTex = matrix(rep(, NROW(x) * NCOL(x)), nrow=NROW(x))
cellTex[1,1] - cellcolor[gray]{0.9}
# works ok
p = latex(x,file=a.tex,
cellTexCmds = cellTex) # ok
# Works ok
p = latex(x,file=a.tex,
cgroup = c(a,b,c),n.cgroup=c(2,2,2)
)
# Fails with a error message subscript out of bounds
p = latex(x, file=a.tex,
cellTexCmds = cellTex,
cgroup = c(a,b,c),n.cgroup=c(2,2,2)
)
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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[R] latex in Hmisc: cell formating
Hi list,
Could you explain the error I see here? Thanks!
## I'm using R 2.8.0 on WinXP, Hmisc_3.4-3
table1 - matrix(10, 180,7)
cell.format - matrix(, ncol=7, nrow=180)
cell.format[c(seq(3,180,6),seq(4,180,6)),] - color{red}
cell.format[c(seq(5,180,6),seq(6,180,6)),] - color{green}
latex(table1, where='htbp', long=TRUE, lines.page=1000, size=scriptsize,
+ cgroup=c(group1,group2), n.cgroup=c(6,1),
+ rgroup=c(n=1,n=5,n=10,n=20,n=50), n.rgroup=rep(36,5),
+ cellTexCmds=cell.format, numeric.dollar = FALSE)
Error in cat(rcellTexCmds[i, colNum], , cx[i, colNum], file = file, :
subscript out of bounds
## if I remove the column name grouping, it works fine!
##
latex(table1, where='htbp', long=TRUE, lines.page=1000, size=scriptsize,
+ #cgroup=c(group1,group2), n.cgroup=c(6,1),
+ rgroup=c(n=1,n=5,n=10,n=20,n=50), n.rgroup=rep(36,5),
+ cellTexCmds=cell.format, numeric.dollar = FALSE)
Thanks!
...Tao
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[R] follow up on [Rd] NAMESPACE methods guidance, please ( http://tolstoy.newcastle.edu.au/R/e4/devel/08/06/1901.html )
This is a follow-up on the discussion originally posted on the R-devel list (
http://tolstoy.newcastle.edu.au/R/e4/devel/08/06/1901.html ), as I have
encountered the exact same issue mentioned in Martin's email. Here is a
simplified version of my problem:
##=
## I created a package, say, tmpA, with a NAMESPACE with Depend: and Imports:
org.Hs.eg.db and in a new session of R
library(tmpA)
foo
function ()
{
require(org.Hs.eg.db)
get(A GO TERM, org.Hs.egGO2ALLEGS)
}
foo()
Error in as.environment(pos) : invalid object for 'as.environment'
##=
I fixed the problem by changing get explicitly to AnnotationDbi::get. I'm
just wondering what was the final decision on the problem and if there are more
elegant ways of handling this.
Thanks,
...Tao
_
50F681DAD532637!5295.entry?ocid=TXT_TAGLM_WL_domore_092008
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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.
[R] a question regarding package building
Hi List, In Windows, if I do R CMD build mypkg, then I'll get 'mypkg_1.0.tar.gz'. Any option in R CMD build lets me to change the version, i.e. gives me 'mypkg_2.0.tar.gz? It seems -version option doesn't do anything for me. Is it OK if I just change the version number in the file name manually? Thanks, ...Tao _ The i’m Talkathon starts 6/24/08. For now, give amongst yourselves. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] a question regarding package building
Got it! Thank you very much! ...Tao Date: Thu, 26 Jun 2008 20:41:29 +0200 From: [EMAIL PROTECTED] To: [EMAIL PROTECTED] CC: r-help@r-project.org Subject: Re: [R] a question regarding package building Tao Shi wrote: Hi List, In Windows, if I do R CMD build mypkg, then I'll get 'mypkg_1.0.tar.gz'. Any option in R CMD build lets me to change the version, i.e. gives me 'mypkg_2.0.tar.gz? It seems -version option doesn't do anything for me. Is it OK if I just change the version number in the file name manually? No, you need to change it in the DESCRIPTION file. Uwe Ligges Thanks, ...Tao _ The i’m Talkathon starts 6/24/08. For now, give amongst yourselves. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. _ [[elided Hotmail spam]] ntrosrchcashback __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] nlme model specification (revisit)
Hi List, While using 'nlme' function, I have encountered the similar problem Dr. Stevens and Dr. Graves observed (please see the posts: https://stat.ethz.ch/pipermail/r-help/2006-May/105832.html ). I have tried Dr. Stevens's original example, the problem is still there, mod.lis - nlsList(circumference ~ SSlogis(age, Asymp, xmid, scal), + data=Orange ) mod - nlme(circumference ~ SSlogis(age, Asymp, xmid, scal), + data=Orange, + fixed = Asymp + xmid + scal ~ 1, + start = fixef(mod.lis) ) mod - nlme(circumference ~ SSlogis(age, Asymp, xmid, scal), + data=Orange, + fixed = list(Asymp ~ 1, xmid ~ 1, scal ~ 1), + start = fixef(mod.lis) ) Error in parse(file, n, text, prompt, srcfile, encoding) : syntax error, unexpected END_OF_INPUT in ~ sessionInfo() R version 2.5.1 (2007-06-27) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: lattice nlme 0.15-11 3.1-86 Just wondering if you guys have any answers for this since I didn't see any for the original posts. Thanks, ...Tao _ GLM_CPC_VideoChat_distantfamily_012008 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] updating a helper function in a R package
Hi list,
Sorry for the vague title, but here is the scenario.
I’m writing an R package, let’s say, ‘pkg1’, which contains 3 functions: f1,
f2, f3. f2 and f3 are helper functions for f1, i.e. f1 calls f2 which in turn
calls f3.
f1 - function(…) {
….
f2()
…
}
f2 - function(…){
…
f3(…)
…
}
f3 - function(...){
}
Then, I wrote a new version of f3 and I want to test it. With the old version
of ‘pkg1’ already loaded into my R session, I tried just copy-and-paste the new
‘f3’ to R console and hope f1 will pick the new ‘f3’ up. It obviously didn’t
work. I know it’s b/c the new f3 and old f3 are in different environments and
when f1 is called, only old f3 is used. Then I tried to change the environment
of new f3 to the same as the old f3's by calling:
environment(f3) - environment(pkg1:::f3)
but it wasn't working either.
So,
1) Could somebody help me to put all these into perspectives?
2) Is there an easier way to update f3 without rebuilding the package? (by
that I mean, writing the new version of f3 in a way that I only need to
copy-and-paste to R console and I’m good to go. I know it’s kind of stupid but
I’m curious to know)
I'm using R-2.5.1, on WinXP.
Many thanks,
…Tao
_
07
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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[R] RMySQL installation problem
Hi List, I'm running R2.5.1 on WinXP. Downloaded RMySQL_0.6-0.zip from http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/2.6/ and the installation seemed fine. However, when I tried to load the package, the error occured: utils:::menuInstallLocal() package 'RMySQL' successfully unpacked and MD5 sums checked updating HTML package descriptions library(RMySQL) Loading required package: DBI Error in dyn.load(x, as.logical(local), as.logical(now)) : unable to load shared library 'C:/PROGRA~1/R/R-25~1.1/library/RMySQL/libs/RMySQL.dll': LoadLibrary failure: The specified module could not be found. Error: package/namespace load failed for 'RMySQL' ## However, I can see the .dll file is there from window's explorer!! There was also a pop windows says: R Console: Rgui.exe-Unable To Locate Component This application has failed to start because LIBMYSQL.dll was not found. Re-installing the application may fix the problem. I tried the re-installation. It didn't work. The DBI package I have is version 0.2-4, just in case. thanks, ...Tao _ Climb to the top of the charts! Play Star Shuffle: the word scramble challenge with star power. t __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] silhouette: clustering labels have to be consecutive intergers starting
Thank you very much, Benilton and Prof. Ripley, for the speedy replies!
Looking forward to the fix!
Tao
From: Prof Brian Ripley [EMAIL PROTECTED]
To: Benilton Carvalho [EMAIL PROTECTED]
CC: Tao Shi [EMAIL PROTECTED], [EMAIL PROTECTED],
r-help@r-project.org
Subject: Re: [R] silhouette: clustering labels have to be consecutive
intergers starting from 1?
Date: Wed, 10 Oct 2007 05:33:03 +0100 (BST)
It is a C-level problem in package cluster: valgrind gives
==11377== Invalid write of size 8
==11377==at 0xA4015D3: sildist (sildist.c:35)
==11377==by 0x4706D8: do_dotCode (dotcode.c:1750)
This is a matter for the package maintainer (Cc:ed here), not R-help.
On Tue, 9 Oct 2007, Benilton Carvalho wrote:
that happened to me with R-2.4.0 (alpha) and was fixed on R-2.4.0
(final)...
http://tolstoy.newcastle.edu.au/R/e2/help/06/11/5061.html
then i stopped using... now, the problem seems to be back. The same
examples still apply.
This fails:
require(cluster)
set.seed(1)
x - rnorm(100)
g - sample(2:4, 100, rep=T)
for (i in 1:100){
print(i)
tmp - silhouette(g, dist(x))
}
and this works:
require(cluster)
set.seed(1)
x - rnorm(100)
g - sample(2:4, 100, rep=T)
for (i in 1:100){
print(i)
tmp - silhouette(as.integer(factor(g)), dist(x))
}
and here's the sessionInfo():
sessionInfo()
R version 2.6.0 (2007-10-03)
x86_64-unknown-linux-gnu
locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.U
TF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-
8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_ID
ENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] cluster_1.11.9
(Red Hat EL 2.6.9-42 smp - AMD opteron 848)
b
On Oct 9, 2007, at 8:35 PM, Tao Shi wrote:
Hi list,
When I was using 'silhouette' from the 'cluster' package to
calculate clustering performances, R crashed. I traced the problem
to the fact that my clustering labels only have 2's and 3's. when
I replaced them with 1's and 2's, the problem was solved. Is the
function purposely written in this way so when I have clustering
labels, 2 and 3, for example, the function somehow takes the
'missing' cluster 2 into account when it calculates silhouette
widths?
Thanks,
Tao
##
## sorry about the long attachment
R.Version()
$platform
[1] i386-pc-mingw32
$arch
[1] i386
$os
[1] mingw32
$system
[1] i386, mingw32
$status
[1]
$major
[1] 2
$minor
[1] 5.1
$year
[1] 2007
$month
[1] 06
$day
[1] 27
$`svn rev`
[1] 42083
$language
[1] R
$version.string
[1] R version 2.5.1 (2007-06-27)
library(cluster)
cl1 ## clustering labels
[1] 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 2 2 2 2 2 2 2 2 2
[30] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
[59] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
[88] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
[117] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
[146] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
[175] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
[204] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
x1 ## 1-d input vector
[1] 1.5707963 1.5707963 1.5707963 1.5707963 1.5707963
[6] 1.5707963 1.5707963 1.5707963 1.5707963 1.5707963
[11] 1.5707963 1.5707963 1.5707963 1.5707963 1.5707963
[16] 1.5707963 1.5707963 1.5707963 1.5707963 1.5707963
[21] 1.0163758 0.7657763 0.7370084 0.6999689 0.7366476
[26] 0.7883921 0.6925395 0.7729240 0.7202391 0.7910149
[31] 0.7397698 0.7958092 0.6978596 0.7350255 0.7294362
[36] 0.6125713 0.7174000 0.7413046 0.7044205 0.7568104
[41] 0.7048469 0.7334515 0.7143170 0.7002311 0.7540981
[46] 0.7627527 0.7712762 0.8193611 0.7801148 0.9061762
[51] 0.8248195 0.7932630 0.7248037 0.7423547 0.6419314
[56] 0.6001092 0.7572272 0.7631742 0.7085384 0.8710853
[61] 0.6589563 0.7464943 0.7487340 0.7751280 0.7946542
[66] 0.7666081 0.8508109 0.8314308 0.7442471 0.8006093
[71] 0.7949156 0.7852447 0.7630048 0.7104764 0.6768218
[76] 0.6806351 0.7255355 0.7431389 0.7523627 0.7670515
[81] 0.8118214 0.7215615 0.8186164 0.6941610 0.8285453
[86] 0.8395170 0.8088044 0.8182706 0.7550723 0.7948639
[91] 0.7204830 0.7109068 0.7756949 0.6837856 0.7055604
[96] 0.612 0.7201964 0.6849890 0.7779753 0.7845284
[101] 0.9370788 0.8242935 0.6908860 0.6446151 0.7660386
[106] 0.8141526 0.8111984 0.8624186 0.7865335 0.8213035
[111] 0.8059171 0.6735751 0.7815353 0.6972508 0.6699396
[116] 0.6293971 0.7475913 0.7700821 0.8258339 0.8096144
[121] 0.7058171 0.7516635 0.7323909 0.7229136 0.8344846
[126] 0.7205433 0.8287774 0.8322097 0.7767547 0.7402277
[131] 0.7939879 0.7797308 0.7112453 0.7091554 0.6417382
[136] 0.6369171 0.7059020 0.7496380 0.7298359 0.8202566
[141] 0.7331830 0.7344492 0.8316894 0.7323979 0.7977615
[146] 0.7841205 0.7587060 0.8056685 0.7895643 0.8140731
[151] 0.7890221 0.8016008 0.7381577 0.6936453 0.7133525
[156
