Re: [R] colouring a table, data.frame or matrix in an interactive R session
On Sun, Jan 8, 2012 at 9:52 AM, Vincent Zoonekynd zoo...@gmail.com wrote: On 7 January 2012 19:48, drflxms drfl...@googlemail.com wrote: as I am dealing with complex confusion matrices, I wonder whether there might be a way to colour text/tabular data in R. I.e. imagine highlighting the true positive values or certain classes in a table. The colorout package does part of what you want: colouring the output, in a terminal. But some more work may be needed if you want to change the colours depending on the values of your matrix. With the next version of the colorout package users will be able to choose a different color for negative numbers. I'll release it soon but anyone wanting to try it immediately may write directly to me. -- Jakson Alves de Aquino Federal University of Ceará Social Sciences Department www.lepem.ufc.br/aquino.php __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Making outregs in R
On Fri, Dec 9, 2011 at 7:22 AM, David . loove...@hotmail.com wrote: I am interesting in making an equivalent command like outreg in stata where I get all my 8 regressions in one table. Does R have an easy command to that? The function of mtable() of memisc package may be what you want. There is also a script called outreg-worked.R written by Paul Johnson that you can find on the web. -- Jakson __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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-pkgs] New package 'colorout' to colorize R output on terminal emulators
Dear R Community, I'm pleased to announce the availability of 'colorout' on CRAN. The package colorizes R output when it is running on a terminal emulator. Screenshot: http://www.lepem.ufc.br/jaa/R_color_output.png You can use either 16 colors (8 colors * 2 degrees of intensity) or 256 colors to highlight normal text, numbers, strings, warnings, errors and the keywords TRUE, FALSE, NA, NaN and Inf. The package is not available for Windows, and there is no support for Graphical User Interfaces, such as RStudio, RKward, JGR, Rcmdr and other interfaces which have their own engine to display R output. The colorization of output only works if R is compiled for Unix systems and it is running interactively in a terminal emulator (like when using RGedit or Vim-R-plugin). The terminal must support Select Graphic Rendition (SGR, also known as ANSI escape codes or sequences), otherwise you may see garbage like this: rnorm(5) [32m[ [33m1 [32m] [0m [32m [33m0.07574585 [32m [0m [32m [33m0.88167822 [32m [0m [32m [33m0.60788656 [32m [0m [32m [33m1.13590951 [32m [0m [32m [33m1.07758879 [32m [0m [32m [0m Notes for Emacs/ESS users: 1. Emacs terminal does not support 256 colors. 2. When the colorizing of R output is enabled, the ESS autocompletion of R object names and function arguments stops working on the R buffer. Functions available in the package: ColorOut: Colorize R output in terminal emulator noColorOut: Stop colorizing R output setOutputColors:Set the colors to be used on R output setOutputColors256: Set the colors to be used on R output show256Colors: Create and show a table with 256 colors Any feedback will be appreciated. Sincerely, -- Jakson Alves de Aquino Federal University of Ceará Social Sciences Department www.lepem.ufc.br/aquino.php jalvesaq at gmail.com ___ R-packages mailing list r-packa...@r-project.org https://stat.ethz.ch/mailman/listinfo/r-packages __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Boxplot
On Sun, Nov 27, 2011 at 2:15 AM, Jeffrey Joh johjeff...@hotmail.com wrote: I'm trying to do the second case among Jim's suggestions. I used Bert's suggestion and it works great. I would also like to ask if anyone is familiar with a package for making box-plots. I would like to bin my datapoints at defined X intervals and display a boxplot for each bin on the same chart. In Stata, there is a tool for making these, and it varies the width of the boxplot based on the number of points in each plot. I am hoping there is a similar tool for R. You can do it if you pass suitable values for the 'width' argument of boxplot(). -- Jakson Alves de Aquino Federal University of Ceará Social Sciences Department www.lepem.ufc.br/aquino.php __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] On-demand importing of a package
On Fri, Nov 25, 2011 at 1:21 PM, Gabor Grothendieck ggrothendi...@gmail.com wrote: [...] I was framing this in terms of the Matrix example, but perhaps its easier to understand with the actual example which motivated this for me. That is, the feature is that whenever sqldf is installed then RSQLite is installed too without having RSQLite automatically load when sqldf loads. [...] I think that the following procedure has the result that you want: Put in the DESCRIPTION file: Imports: RSQLite And in the R code write something like: RSQLite::AnRSQLiteFunction() -- Jakson Alves de Aquino Federal University of Ceará Social Sciences Department www.lepem.ufc.br/aquino.php __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] On-demand importing of a package
On Fri, Nov 25, 2011 at 2:40 PM, Gabor Grothendieck ggrothendi...@gmail.com wrote: I think that the following procedure has the result that you want: Put in the DESCRIPTION file: Imports: RSQLite And in the R code write something like: RSQLite::AnRSQLiteFunction() I had been thinking of using Imports in DESCRIPTION but was concerned that that would put RSQLite objects ahead of everything else on sqldf's search path even when not wanted but I gather you are intending that Imports be used in DESCRIPTION: but _not_ in the NAMESPACE file. I think that that would likely work. I will test it out to be sure. What I would probably want to do is to require() RSQLite in case the user wants to mix sqldf and RSQLite calls and I will check whether the check procedure allows that if the package is only named in Imports but, if not, it might be sufficient to put RSQLite in both Imports and Suggests. Thanks. I have done this with the 'descr' package. It wasn't necessary to put the imported packages in two places, only in the Imports field. This was enough to make R install all dependencies but not load then along with 'descr'. -- Jakson Alves de Aquino Federal University of Ceará Social Sciences Department www.lepem.ufc.br/aquino.php __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] new package: colorout (Colorize R output on terminal emulator)
Hello, Two days ago I posted a patch to R source code to colorize its output when running it in a terminal emulator (Linux or other Unix with support to ANSI escape codes). I converted the patch into an R package, and people interested in testing it should do the following: 1) Download and install: wget http://www.lepem.ufc.br/jaa/colorout_0.1.tar.gz R CMD INSTALL colorout_0.1.tar.gz 2) Run R and load the package: library(colorout) Best regards, -- Jakson Aquino Federal University of Ceará - Brazil www.lepem.ufc.br/aquino.php __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Colored output in terminal emulator
Hi, I wrote a small patch to make it possible to get colored output from R running in a Linux terminal emulator. It's a dirty patch. I hope that someone with better knowledge of R source code and C programming will improve it. To force the use of Rstd_WriteConsoleEx function (src/unix/sys-std.c) I edited the file src/unix/system.c and I copied four lines from an AQUA #ifdef preprocessor directive and pasted them outside the condition. Then I edited the Rstd_WriteConsoleEx function to change the colors of the output: errors and warnings are red, normal output is green and numbers are yellow. If anyone is interested in trying the patch, here how to do it: 1) Copy the file rcolor.patch to R-2.14.0/src/unix/ directory. 2) Go to the R-2.14.0/src/unix directory and do the following command: patch -p3 rcolor.patch 3) Compile R. 4) Put in your ~/.Rprofile: options(color.output = TRUE) The patch is attached and a screenshot is available at http://www.lepem.ufc.br/jaa/R_color_output.png -- Jakson Aquino __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Need some help in R : value more than equals to a row.
suparna mitra wrote: Hallo, I was trying some code, but couldn't make one step of the code properly. Can anybody please help me? I have one matrix like this values [,1] [,2] [,3] [,4] [,5] [1,] 0.778 0.3611 0. 0.139 0.000 [2,] 1.000 0. 0.53846154 0.000 0.5384615 [3,] 0.520 0.4800 0.6400 0.000 0.880 [4,] 0.8928571 1. 0. 0.8928571 0.1071429 And I want to get some matrix like: values.new [,1] [,2] [,3] [,4] [,5] [1,] 0.2 0.4 0.6 0.8 1.0 [2,] 0.2 1.0 0.6 1.0 0.6 [3,] 0.6 0.8 0.4 1.0 0.2 [4,] 0.6 0.2 1.0 0.6 0.8 This table should be computed by taking proportion of values in the row that are larger or equals to the value being considered with the total no of objects in the row. I think the code below do what you want, but I would like to know how to do it with one of the *apply functions: m - read.table(stdin(), header=F) 0.778 0.3611 0. 0.139 0.000 1.000 0. 0.53846154 0.000 0.5384615 0.520 0.4800 0.6400 0.000 0.880 0.8928571 1. 0. 0.8928571 0.1071429 m - as.matrix(m) bdim - dim(m) m2 - m for(i in 1:bdim[1]) for(j in 1:bdim[2]) m2[i,j] - sum(m[i,j] = m[i,]) / bdim[2] m2 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Journal Articles that Have Used R
Jason Rupert wrote: Is there a way to get a reference list of journal articles that have used R? I am just looking for some examples of R graphs and presentation of results where R was used to generate the results. Did you try Google Scholar: http://scholar.google.com.br/scholar?q=R%3A+A+Language+and+Environment+for+Statistical+Computing It has cited by links. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Bug in gmodels CrossTable()?
Is the code below showing a bug in Crosstable()? My expectation was that the values produced by xtabs were rounded instead of truncated: library(gmodels) abc - c(a, a, b, b, c, c) def - c(d, e, f, f, d, e) wgt - c(0.8, 0.6, 0.4, 0.5, 1.4, 1.3) xtabs(wgt ~ abc + def) CrossTable(xtabs(wgt ~ abc + def), prop.r = F, prop.c = F, prop.t = F, prop.chisq = F) -- Jakson Aquino Professor of Political Science Federal University of Ceara, Brazil __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Bug in gmodels CrossTable()?
Dear Marc Schwartz, You are correct: there is no bug in CrossTable(). To get what I want I should have done: CrossTable(round(xtabs(wgt ~ abc + def)), prop.r = F, prop.c = F, prop.t = F, prop.chisq = F) Thank you for the explanation! Jakson Marc Schwartz wrote: On May 31, 2009, at 7:51 AM, Jakson Alves de Aquino wrote: Is the code below showing a bug in Crosstable()? My expectation was that the values produced by xtabs were rounded instead of truncated: library(gmodels) abc - c(a, a, b, b, c, c) def - c(d, e, f, f, d, e) wgt - c(0.8, 0.6, 0.4, 0.5, 1.4, 1.3) xtabs(wgt ~ abc + def) CrossTable(xtabs(wgt ~ abc + def), prop.r = F, prop.c = F, prop.t = F, prop.chisq = F) CrossTable() is designed to take one or two vectors, which are then [cross-]tabulated to yield integer counts, OR a matrix of integer counts, not fractional values. In the latter case, it is presumed that the matrix is the result of an 'a priori' cross-tabulation operation such as the use of table(). The output of xtabs() above is: xtabs(wgt ~ abc + def) def abc d e f a 0.8 0.6 0.0 b 0.0 0.0 0.9 c 1.4 1.3 0.0 The relevant output of CrossTable() in your example above shows: | def abc | d | e | f | Row Total | -|---|---|---|---| a | 0 | 0 | 0 | 1 | -|---|---|---|---| b | 0 | 0 | 0 | 0 | -|---|---|---|---| c | 1 | 1 | 0 | 2 | -|---|---|---|---| Column Total | 2 | 1 | 0 | 5 | -|---|---|---|---| The internal table object that would be generated here is effectively: addmargins(xtabs(wgt ~ abc + def)) def abc d e f Sum a 0.8 0.6 0.0 1.4 b 0.0 0.0 0.9 0.9 c 1.4 1.3 0.0 2.7 Sum 2.2 1.9 0.9 5.0 The textual output of CrossTable() is internally formatted using formatC(..., format = d), which is an integer based format: formatC(addmargins(xtabs(wgt ~ abc + def)), format = d) def abc d e f Sum a 0 0 0 1 b 0 0 0 0 c 1 1 0 2 Sum 2 1 0 5 In other words, you are getting the integer coerced values of the individual cells and then the same for the column, row and table totals: matrix(as.integer(addmargins(xtabs(wgt ~ abc + def))), 4, 4) [,1] [,2] [,3] [,4] [1,]0001 [2,]0000 [3,]1102 [4,]2105 If you review ?as.integer, you will note the following in the 'Value' section: Non-integral numeric values are truncated towards zero (i.e., as.integer(x) equals trunc(x) there) The output is correct, if confusing, but you are really using the function in a fashion that is not intended. 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] Cream Text Editor
JiHO wrote: On 2009-May-23 , at 20:16 , Jakson Alves de Aquino wrote: Just a note: there is no need of Esc before F9. Almost all key bindings work in insert, normal and visual modes. Well, without switching to the non-insert mode, I find that pressing F9 prints the commands in the file instead of executing them. Maybe that's specific to Cream. I installed and tested cream here, and F9 in insert mode works for me, but in few minutes I've found other problems. The customization of key bindings in .vimrc is ignored by cream and omni completion doesn't work correctly: cream inserts a spurious '.x:call Cream - redo(i)' in addition to the correct completion. It seems that cream is unable to work properly in expert mode. Instead of using cream in expert mode it might be easier to use gvim. Alternatively, if you prefer to use cream, it might be easier to copy and paste commands in a regular R session running directly in a terminal emulator because you will benefit from R's built-in tab-completion. -- Jakson __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Cream Text Editor
Paul Heinrich Dietrich wrote: Thank you much for the help, I will work on this over the weekend. Is there a way in Windows to connect R and Cream? Perhaps, although I can't help... It would be necessary to write another plugin: https://stat.ethz.ch/pipermail/r-help/2009-May/197794.html __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Cream Text Editor
As pointed by JiHO the biggest disadvantage of using the plugin is that R is running through a pipe and consequently it is less interactive. Just a note: there is no need of Esc before F9. Almost all key bindings work in insert, normal and visual modes. The last version of the plugin allows the user to set the terminal emulator in the vimrc and now all key bindings are customizable. The details are in the plugin's documentation. Please write, to me if you find bugs in the plugin. Jakson JiHO wrote: On 2009-May-23 , at 17:40 , Paul Heinrich Dietrich wrote: I'm interested in easing my way into learning VIM by first using the Cream text editor, liking the idea that it will work on both my Linux and Windows computers. I've installed Cream on my Linux machine, but can't figure out how to make Cream talk to R? Does anybody know? I'm using Ubuntu if it makes a difference. Thanks. You should install the R Vim Plugin and its dependencies: http://www.vim.org/scripts/script.php?script_id=2628 This creates commands and icons dedicated to the interaction between Vim and R. Then switch cream Settings Preferences Expert Mode. This will allow you to work in Cream and have all the simple keyboard shortcuts (Control-C, Control-V etc.) but still be able to switch between modes as in vim. By default you are in insert mode. You need to switch to normal mode (by pressing ESC) to be able to use the commands of the R-Vim plugin. The workflow is therefore: - open a R file - edit stuff - press ESC (to switch to non-edit mode) - start R in a terminal (click the icon or press F2) - send lines/selection (F9) or document (F5) - press ESC (to switch back to insert mode) - edit 2 lines - ESC - F9 - F9 - ESC - edit again etc... The terminal opened this way does not work completely as a regular one and there are some caveats when reading help and using general command line editing shortcuts (Ctrl-R for backward search for example). I haven't found a way around them so I usually open a second terminal to read the help in, or set R to display the help as HTML files in a browser window. I must say that those caveats can be quite serious and I often find myself just using copy-paste from gedit in a terminal: - set your desktop to focus follow mouse - select text in your editor - move the mouse to the terminal - click middle mouse button - move the mouse back to the editor etc... More cumbersome but reliable. Final note: since you are on ubuntu, you may want to change the terminal from the default X-term to gnome-terminal. You have to edit the file .vim/ftplugin/r.vim. There is a line commented with the gnome-terminal command instead of xterm. Uncomment this one and comment the xterm one. JiHO --- http://jo.irisson.free.fr/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 do a pretty panel plot?
Ajay Shah wrote: Here's my best version of your code: ## Data M - structure(list(date = structure(c(13634, 13665, 13695, 13726, 13757, 13787, 13818, 13848, 13879, 13910, 13939, 13970, 14000, 14031, 14061, 14092, 14123, 14153, 14184, 14214, 14245, 14276, 14304, 14335), class = Date), cospi = c(1987.31, 2033.37, 2140.13, 2120.66, 2427.09, 2917.7, 2915.28, 3262.06, 2616.26, 2617.75, 2277.69, 2538.13, 2374.09, 1911.22, 2063.73, 2081.28, 1813.58, 1304.96, 1219.73, 1361.74, 1299.2, 1242.74, 1339.18, 1557.29), cospi.PE = c(19.2, 19.69, 20.13, 24.08, 27.61, 30.9, 30.69, 34.92, 26.95, 27.63, 23.86, 26.14, 23.72, 19.5, 23.43, 23.73, 20.69, 16.4, 16.12, 18.04, 18.46, 18.86, 20.24, 23.53)), .Names = c(date, cospi, cospi.PE), row.names = 209:232, class = data.frame) ## Set up par's to make 2 panel chart par(bty=l); par(ps=10) par(mfrow=c(2,1)) # try to get two plots, one above the other par(mar=c(0,4,0,1)) ## Set par(mar) to eliminate X axis gap par(oma=c(2,2,2,2)) ## Make Plot 1 plot(M$date, M$cospi, type=l, log=y, xaxs=i, yaxs=i, axes=F, lwd=2, ylab=Cospi level) axis(1, col=grey, at=NULL, labels=FALSE) axis(2, col=black, labels=TRUE) axis(3, col=grey, labels=TRUE) grid(col = lightgrey, lty=1) box(col = grey) ## Adjust par(mar) for 2nd plot par(mar=c(2,4,0,1)) ## Second plot plot(M$date, M$cospi.PE, type=l, col=black, log=y, xaxs=i, yaxs=i, axes=F, lwd=2, ylab=Cospi P/E) axis(2, col=black, at=NULL, labels=T) axis(1, col=lightgrey, at=NULL, labels=T) grid(col = lightgrey, lty=1) box(col = grey) I think it's better if the lines are above the grid: ## Data M - structure(list(date = structure(c(13634, 13665, 13695, 13726, 13757, 13787, 13818, 13848, 13879, 13910, 13939, 13970, 14000, 14031, 14061, 14092, 14123, 14153, 14184, 14214, 14245, 14276, 14304, 14335), class = Date), cospi = c(1987.31, 2033.37, 2140.13, 2120.66, 2427.09, 2917.7, 2915.28, 3262.06, 2616.26, 2617.75, 2277.69, 2538.13, 2374.09, 1911.22, 2063.73, 2081.28, 1813.58, 1304.96, 1219.73, 1361.74, 1299.2, 1242.74, 1339.18, 1557.29), cospi.PE = c(19.2, 19.69, 20.13, 24.08, 27.61, 30.9, 30.69, 34.92, 26.95, 27.63, 23.86, 26.14, 23.72, 19.5, 23.43, 23.73, 20.69, 16.4, 16.12, 18.04, 18.46, 18.86, 20.24, 23.53)), .Names = c(date, cospi, cospi.PE), row.names = 209:232, class = data.frame) ## Set up par's to make 2 panel chart par(bty=l) par(ps=10) par(mfrow=c(2,1)) # try to get two plots, one above the other par(mar=c(0,4,0,1)) ## Set par(mar) to eliminate X axis gap par(oma=c(2,2,2,2)) ## Make Plot 1 plot(M$date, M$cospi, type=l, log=y, xaxs=i, yaxs=i, axes=F, lwd=0, ylab=Cospi level) grid(col = lightgrey, lty=1) lines(M$date, M$cospi, type=l, lwd=2) axis(1, col=grey, at=NULL, labels=FALSE) axis(2, col=black, labels=TRUE) axis(3, col=grey, labels=TRUE) box(col = grey) ## Adjust par(mar) for 2nd plot par(mar=c(2,4,0,1)) ## Second plot plot(M$date, M$cospi.PE, type=l, col=black, log=y, xaxs=i, yaxs=i, axes=F, lwd=0, ylab=Cospi P/E) grid(col = lightgrey, lty=1) lines(M$date, M$cospi.PE, col=black, lwd=2) axis(2, col=black, at=NULL, labels=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] Reading large files quickly
Rob Steele wrote: I'm finding that readLines() and read.fwf() take nearly two hours to work through a 3.5 GB file, even when reading in large (100 MB) chunks. The unix command wc by contrast processes the same file in three minutes. Is there a faster way to read files in R? I use statist to convert the fixed width data file into a csv file because read.table() is considerably faster than read.fwf(). For example: system(statist --na-string NA --xcols collist big.txt big.csv) bigdf - read.table(file = big.csv, header=T, as.is=T) The file collist is a text file whose lines contain the following information: variable begin end where variable is the column name, and begin and end are integer numbers indicating where in big.txt the columns begin and end. Statist can be downloaded from: http://statist.wald.intevation.org/ -- Jakson Aquino Social Sciences Department Federal University of Ceará, Brazil __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
