Re: [R] Help with scatterplots in R
Hi r-help-boun...@r-project.org napsal dne 29.07.2010 18:13:57: Hi John, yes, you are right. Here is what I have done: plot(DateJonEnd1, End1Jon, main=Weekly Training at Endurance 1, xlim=c(13700,14750), xlab=Date, ylim=c(0,350), ylab=Volume at Endurance 1, type=b, las=1) Where DateJonEnd1 is the date of weekly Training, classified as date and in the format 2010-07-28. I have the data from 2007-05-01 to 2010-03-31. End1Jon is a numerical value, as an indicator of the volume of a particular type of training per week. When I plot a years worth of data, R automatically plots the months on the x-axis, however, as soon as the data spans more than a year R only gives me the years on the x-axis. However to compare the graphs, I would prefer to have the months on the x-axis, as well as the year. I have attached one of the graphs as an example. Make your plot without axes by plot(, axes=FALSE, ...) or plot(, xaxt=n, ...) and than see ?axis.POSIXct how to fine tune date axis with format option Regards Petr Hope this makes it a bit clearer. Sarah From: John Kane [jrkrid...@yahoo.ca] Sent: 28 July 2010 12:48 To: r-help@r-project.org; Sarah Chisholm Subject: Re: [R] Help with scatterplots in R I think that we need an example of what you are doing before anyone can really answer that question. At the moment we don't even know how you are plotting the scatterplot. --- On Wed, 7/28/10, Sarah Chisholm sarah.chisholm...@ucl.ac.uk wrote: From: Sarah Chisholm sarah.chisholm...@ucl.ac.uk Subject: [R] Help with scatterplots in R To: r-help@r-project.org r-help@r-project.org Received: Wednesday, July 28, 2010, 6:57 AM Hi, When I plot a scatter plot, R automatically only gives the years on the x-axis. How can I make R also show the months on the x-axis? Thank you very much! [[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. __ 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 Equivalent of SAS Datastep Line-Hold (@@) Specifier?
This gets you to a matrix, though it is messy and you would still have to convert some of the columns from character to numeric, but maybe it will give you an idea. matrix(data = unlist(strsplit(x = readLines(textConnection( A 1 101 M 55 5 A 1 104 F 27 0 A 1 106 M 31 35 A 1 107 F 44 21 A 1 109 M 47 15 A 1 111 F 69 70 A 1 112 F 31 10 A 1 114 F 50 0 A 1 116 M 32 20 A 1 118 F 39 25 A 1 119 F 54 0 A 1 121 M 70 38 A 1 123 F 57 55 A 1 124 M 37 18 A 1 126 F 41 0 A 1 128 F 48 8 A 1 131 F 35 0 A 1 134 F 28 0 A 1 135 M 27 40 A 1 138 F 42 12 A 2 202 M 58 68 A 2 203 M 42 22 A 2 206 M 26 30 A 2 207 F 36 0 A 2 210 F 35 25 A 2 211 M 51 0 A 2 214 M 51 60 A 2 216 F 42 15 A 2 217 F 50 50 A 2 219 F 41 35 A 2 222 F 59 0 A 2 223 F 38 10 A 2 225 F 32 0 A 2 226 F 28 16 A 2 229 M 42 48 A 2 231 F 51 45 A 2 234 F 26 90 A 2 235 M 42 0 A 3 301 M 38 28 A 3 302 M 41 20 A 3 304 M 65 75 A 3 306 F 64 0 A 3 307 F 30 30 A 3 309 F 64 5 A 3 311 M 39 80 A 3 314 F 57 85 A 3 315 M 61 12 A 3 318 F 45 95 A 3 319 F 34 26 A 3 321 M 39 10 A 3 324 M 27 0 A 3 325 F 56 35 B 1 102 M 19 68 B 1 103 F 51 10 B 1 105 M 45 20 B 1 108 F 44 65 B 1 110 M 32 25 B 1 113 M 61 75 B 1 115 M 45 83 B 1 117 F 21 0 B 1 120 F 19 55 B 1 122 F 38 0 B 1 125 M 37 72 B 1 127 F 53 40 B 1 129 M 48 0 B 1 130 F 36 80 B 1 132 M 49 20 B 1 133 F 28 0 B 1 136 F 34 45 B 1 137 F 57 95 B 1 139 F 47 40 B 1 140 M 29 0 B 2 201 F 63 10 B 2 204 M 36 49 B 2 205 M 36 16 B 2 208 F 48 12 B 2 209 F 42 40 B 2 212 F 32 0 B 2 213 M 24 88 B 2 215 M 40 59 B 2 218 M 31 24 B 2 220 F 45 72 B 2 221 F 27 55 B 2 224 M 56 70 B 2 227 F 41 0 B 2 228 F 24 65 B 2 230 M 44 30 B 2 232 M 37 32 B 2 233 F 33 0 B 3 303 M 40 26 B 3 305 M 46 15 B 3 308 M 59 82 B 3 310 F 62 38 B 3 312 M 52 40 B 3 313 F 33 40 B 3 316 M 62 87 B 3 317 M 52 60 B 3 320 F 32 2 B 3 322 F 43 0 B 3 323 F 51 35 )), [[:space:]]+)), byrow = TRUE, ncol =6) closeAllConnections() On Thu, Jul 29, 2010 at 3:54 PM, Paul Miller pjmiller...@yahoo.com wrote: Hello Everyone, Below is some SAS code that uses a line hold specifier to read multiple observations from each of several input lines of data. There are 3 patients per line in the in-stream data. Is there a way in R to read this kind of data? I've looked in my books and online but haven't found anything Thanks, Paul DATA EXAMP.TRIAL; INPUT TRT $ CENTER PAT SEX $ AGE SCORE @@; DATALINES; A 1 101 M 55 5 A 1 104 F 27 0 A 1 106 M 31 35 A 1 107 F 44 21 A 1 109 M 47 15 A 1 111 F 69 70 A 1 112 F 31 10 A 1 114 F 50 0 A 1 116 M 32 20 A 1 118 F 39 25 A 1 119 F 54 0 A 1 121 M 70 38 A 1 123 F 57 55 A 1 124 M 37 18 A 1 126 F 41 0 A 1 128 F 48 8 A 1 131 F 35 0 A 1 134 F 28 0 A 1 135 M 27 40 A 1 138 F 42 12 A 2 202 M 58 68 A 2 203 M 42 22 A 2 206 M 26 30 A 2 207 F 36 0 A 2 210 F 35 25 A 2 211 M 51 0 A 2 214 M 51 60 A 2 216 F 42 15 A 2 217 F 50 50 A 2 219 F 41 35 A 2 222 F 59 0 A 2 223 F 38 10 A 2 225 F 32 0 A 2 226 F 28 16 A 2 229 M 42 48 A 2 231 F 51 45 A 2 234 F 26 90 A 2 235 M 42 0 A 3 301 M 38 28 A 3 302 M 41 20 A 3 304 M 65 75 A 3 306 F 64 0 A 3 307 F 30 30 A 3 309 F 64 5 A 3 311 M 39 80 A 3 314 F 57 85 A 3 315 M 61 12 A 3 318 F 45 95 A 3 319 F 34 26 A 3 321 M 39 10 A 3 324 M 27 0 A 3 325 F 56 35 B 1 102 M 19 68 B 1 103 F 51 10 B 1 105 M 45 20 B 1 108 F 44 65 B 1 110 M 32 25 B 1 113 M 61 75 B 1 115 M 45 83 B 1 117 F 21 0 B 1 120 F 19 55 B 1 122 F 38 0 B 1 125 M 37 72 B 1 127 F 53 40 B 1 129 M 48 0 B 1 130 F 36 80 B 1 132 M 49 20 B 1 133 F 28 0 B 1 136 F 34 45 B 1 137 F 57 95 B 1 139 F 47 40 B 1 140 M 29 0 B 2 201 F 63 10 B 2 204 M 36 49 B 2 205 M 36 16 B 2 208 F 48 12 B 2 209 F 42 40 B 2 212 F 32 0 B 2 213 M 24 88 B 2 215 M 40 59 B 2 218 M 31 24 B 2 220 F 45 72 B 2 221 F 27 55 B 2 224 M 56 70 B 2 227 F 41 0 B 2 228 F 24 65 B 2 230 M 44 30 B 2 232 M 37 32 B 2 233 F 33 0 B 3 303 M 40 26 B 3 305 M 46 15 B 3 308 M 59 82 B 3 310 F 62 38 B 3 312 M 52 40 B 3 313 F 33 40 B 3 316 M 62 87 B 3 317 M 52 60 B 3 320 F 32 2 B 3 322 F 43 0 B 3 323 F 51 35 ; [[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. -- Joshua Wiley Ph.D. Student, Health Psychology University of California, Los Angeles http://www.joshuawiley.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 Equivalent of SAS Datastep Line-Hold (@@) Specifier?
There is a much simpler way. con - textConnection( A 1 101 M 55 5 A 1 104 F 27 0 A 1 106 M 31 35 A 1 107 F 44 21 A 1 109 M 47 15 A 1 111 F 69 70 A 1 112 F 31 10 A 1 114 F 50 0 A 1 116 M 32 20 A 1 118 F 39 25 A 1 119 F 54 0 A 1 121 M 70 38 A 1 123 F 57 55 A 1 124 M 37 18 A 1 126 F 41 0 A 1 128 F 48 8 A 1 131 F 35 0 A 1 134 F 28 0 A 1 135 M 27 40 A 1 138 F 42 12 A 2 202 M 58 68 A 2 203 M 42 22 A 2 206 M 26 30 A 2 207 F 36 0 A 2 210 F 35 25 A 2 211 M 51 0 A 2 214 M 51 60 A 2 216 F 42 15 A 2 217 F 50 50 A 2 219 F 41 35 A 2 222 F 59 0 A 2 223 F 38 10 A 2 225 F 32 0 A 2 226 F 28 16 A 2 229 M 42 48 A 2 231 F 51 45 A 2 234 F 26 90 A 2 235 M 42 0 A 3 301 M 38 28 A 3 302 M 41 20 A 3 304 M 65 75 A 3 306 F 64 0 A 3 307 F 30 30 A 3 309 F 64 5 A 3 311 M 39 80 A 3 314 F 57 85 A 3 315 M 61 12 A 3 318 F 45 95 A 3 319 F 34 26 A 3 321 M 39 10 A 3 324 M 27 0 A 3 325 F 56 35 B 1 102 M 19 68 B 1 103 F 51 10 B 1 105 M 45 20 B 1 108 F 44 65 B 1 110 M 32 25 B 1 113 M 61 75 B 1 115 M 45 83 B 1 117 F 21 0 B 1 120 F 19 55 B 1 122 F 38 0 B 1 125 M 37 72 B 1 127 F 53 40 B 1 129 M 48 0 B 1 130 F 36 80 B 1 132 M 49 20 B 1 133 F 28 0 B 1 136 F 34 45 B 1 137 F 57 95 B 1 139 F 47 40 B 1 140 M 29 0 B 2 201 F 63 10 B 2 204 M 36 49 B 2 205 M 36 16 B 2 208 F 48 12 B 2 209 F 42 40 B 2 212 F 32 0 B 2 213 M 24 88 B 2 215 M 40 59 B 2 218 M 31 24 B 2 220 F 45 72 B 2 221 F 27 55 B 2 224 M 56 70 B 2 227 F 41 0 B 2 228 F 24 65 B 2 230 M 44 30 B 2 232 M 37 32 B 2 233 F 33 0 B 3 303 M 40 26 B 3 305 M 46 15 B 3 308 M 59 82 B 3 310 F 62 38 B 3 312 M 52 40 B 3 313 F 33 40 B 3 316 M 62 87 B 3 317 M 52 60 B 3 320 F 32 2 B 3 322 F 43 0 B 3 323 F 51 35 ) Example_Trial - data.frame(scan(con, list(Trt = , Centre = 0, Patient = 0, Sex = , Age = 0, Score = 0))) ## head(Example_Trial) Trt Centre Patient Sex Age Score 1 A 1 101 M 55 5 2 A 1 104 F 27 0 3 A 1 106 M 3135 4 A 1 107 F 4421 5 A 1 109 M 4715 6 A 1 111 F 6970 Rather than use a textConnection, you would probably just use a file. -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Joshua Wiley Sent: Friday, 30 July 2010 4:59 PM To: Paul Miller Cc: r-help@r-project.org Subject: Re: [R] R Equivalent of SAS Datastep Line-Hold (@@) Specifier? This gets you to a matrix, though it is messy and you would still have to convert some of the columns from character to numeric, but maybe it will give you an idea. matrix(data = unlist(strsplit(x = readLines(textConnection( A 1 101 M 55 5 A 1 104 F 27 0 A 1 106 M 31 35 A 1 107 F 44 21 A 1 109 M 47 15 A 1 111 F 69 70 A 1 112 F 31 10 A 1 114 F 50 0 A 1 116 M 32 20 A 1 118 F 39 25 A 1 119 F 54 0 A 1 121 M 70 38 A 1 123 F 57 55 A 1 124 M 37 18 A 1 126 F 41 0 A 1 128 F 48 8 A 1 131 F 35 0 A 1 134 F 28 0 A 1 135 M 27 40 A 1 138 F 42 12 A 2 202 M 58 68 A 2 203 M 42 22 A 2 206 M 26 30 A 2 207 F 36 0 A 2 210 F 35 25 A 2 211 M 51 0 A 2 214 M 51 60 A 2 216 F 42 15 A 2 217 F 50 50 A 2 219 F 41 35 A 2 222 F 59 0 A 2 223 F 38 10 A 2 225 F 32 0 A 2 226 F 28 16 A 2 229 M 42 48 A 2 231 F 51 45 A 2 234 F 26 90 A 2 235 M 42 0 A 3 301 M 38 28 A 3 302 M 41 20 A 3 304 M 65 75 A 3 306 F 64 0 A 3 307 F 30 30 A 3 309 F 64 5 A 3 311 M 39 80 A 3 314 F 57 85 A 3 315 M 61 12 A 3 318 F 45 95 A 3 319 F 34 26 A 3 321 M 39 10 A 3 324 M 27 0 A 3 325 F 56 35 B 1 102 M 19 68 B 1 103 F 51 10 B 1 105 M 45 20 B 1 108 F 44 65 B 1 110 M 32 25 B 1 113 M 61 75 B 1 115 M 45 83 B 1 117 F 21 0 B 1 120 F 19 55 B 1 122 F 38 0 B 1 125 M 37 72 B 1 127 F 53 40 B 1 129 M 48 0 B 1 130 F 36 80 B 1 132 M 49 20 B 1 133 F 28 0 B 1 136 F 34 45 B 1 137 F 57 95 B 1 139 F 47 40 B 1 140 M 29 0 B 2 201 F 63 10 B 2 204 M 36 49 B 2 205 M 36 16 B 2 208 F 48 12 B 2 209 F 42 40 B 2 212 F 32 0 B 2 213 M 24 88 B 2 215 M 40 59 B 2 218 M 31 24 B 2 220 F 45 72 B 2 221 F 27 55 B 2 224 M 56 70 B 2 227 F 41 0 B 2 228 F 24 65 B 2 230 M 44 30 B 2 232 M 37 32 B 2 233 F 33 0 B 3 303 M 40 26 B 3 305 M 46 15 B 3 308 M 59 82 B 3 310 F 62 38 B 3 312 M 52 40 B 3 313 F 33 40 B 3 316 M 62 87 B 3 317 M 52 60 B 3 320 F 32 2 B 3 322 F 43 0 B 3 323 F 51 35 )), [[:space:]]+)), byrow = TRUE, ncol =6) closeAllConnections() On Thu, Jul 29, 2010 at 3:54 PM, Paul Miller pjmiller...@yahoo.com wrote: Hello Everyone, Below is some SAS code that uses a line hold specifier to read multiple observations from each of several input lines of data. There are 3 patients per line in the in-stream data. Is there a way in R to read this kind of data? I've looked in my books and online but haven't found anything Thanks, Paul DATA EXAMP.TRIAL;
Re: [R] package xpose4 in Vista - Update
Thanks for your response. How do I install xpose4 package with R.2.11.1? -Santosh 2010/7/29 Uwe Ligges lig...@statistik.tu-dortmund.de The binary package you downloaded is a binary for R 2.11.x. Since it is a package bndle, it cannot work on R-2.11.x anymore: Package bundles are no longer supported. Best, Uwe Ligges On 29.07.2010 02:11, Santosh wrote: Dear R experts, There seems to be a problem (please see the error messages below) with the installation of the latest version of xpose4 (version 4.2.1) with the latest R version.(2.11.1)... I didn't face such installation problems when using version R.2.10.1 Would really appreciate your assistance in debugging installation of xpose 4..2.1 with R.2.11.1 Thanks again.. -Santosh On Wed, Jul 28, 2010 at 12:46 PM, Santoshsantosh2...@gmail.com wrote: Dear R experts... I would really appreciate your suggestions in installing a package in Windows Vista... I am unable to install a package on a windows vista based computer, in spite of running it as an administrator. The package xpose4.2.1 is available from https://sourceforge.net/projects/xpose/files/Xpose4/Xpose_4.2.1/xpose4_4.2.1_win32.zip/download Following is the error message when I try to install the package from the Rgui command line... I get similar errors when I try to install the packages from Rgui (Packages | Install packages from local zip files) menu, but with default lib=C:/Users/santosh/Documents/R/win-library/2.11 .___ install.packages(C:/Users/santosh/Downloads/xpose4_4.2.1_win32.zip,repos=NULL,lib=C:/Program Files/R/R-2.11.1/library) Error in gzfile(file, r) : cannot open the connection In addition: Warning message: In gzfile(file, r) : cannot open compressed file 'xpose4_4.2.1_win32/DESCRIPTION', probable reason 'No such file or directory' However, I see file folder in which the library related folders are installed, and contains different xpose4 related folders.. Thanks again, Santosh [[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] lm.influence on glm objects
Was this issue resolved? -- View this message in context: http://r.789695.n4.nabble.com/lm-influence-on-glm-objects-tp1574781p2307622.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] CBIND / MERGE two time series objects along time (overlapping indices, redundant data)
Hi there, I need to merge/bind two time series objects (from RPackage: timeSeries) by column. The theory is laid out nicely, even for overlapping indices. In my example, I have overlapping indices (01.01.2001), where in one time series I have one data point and in the other redundant data. Default usage of merge and cbind would lead to the result that the one data point would be replicated (see example below). However, I do not like the replicating feature and would like to have the NA's filled instead. Desired output, would be: TS.1 SS.2 2001-01-01 23.1 23.1 2001-01-01 NA 23.4 Is there a slick way to produce above result? Thank you for your answer - help is really appreciated. Kind regards, Bernhard. --- # R Console example: require(timeSeries) date -timeDate(01.01.2001, format = %d.%m.%Y) test1 - timeSeries(c(23.1), charvec = date) test2 - timeSeries(c(23.1, 23.4), charvec = c(date, date)) colnames(test2) - SS.2 merge(test1, test2) GMT TS.1 SS.2 2001-01-01 23.1 23.1 2001-01-01 23.1 23.4 cbind(test1, test2) Fehler in cbind(deparse.level, ...) : number of rows must match cbind(test2, test1) GMT SS.2 TS.1 2001-01-01 23.1 23.1 2001-01-01 23.4 23.1 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] how to get higher derivatives with deriv
Okay, great. Thanks. Cheers, Marius -- View this message in context: http://r.789695.n4.nabble.com/how-to-get-higher-derivatives-with-deriv-tp2306711p2307709.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] (no subject)
hello,
i am new to R and trying to calculate the beta coefficient for standard linear
regression for a series of randomly generated numbers. I have created this
loop, but it runs really slow, is there a way to improve it?
#number of simulations
n.k-999
#create the matrix for regression coefficients generated from #random data
beta-matrix(0,1,n.k+1)
e-matrix(0,tslength,n.k+1)
for(k in 1:n.k+1)
{
for(i in 1:tslength)
{
beta[1,1]-beta1
e[i,k]-c(rnorm(1,0,var.all))
beta[1,k]-summary(lm(e[1:tslength,k]~t))$coefficient[2]
}
}
thanks
Anastasia Tzortzaki
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[R] Need a help to plot bar for time series Rain data
Hey Guys,
I am quite new to R, am trying to plot a bar plot for my monthly rainfall
data from 1920 to 1990. For every year I have the data from January to
December. I have created this code:
data-read.table(C://R//Data//Rain.txt, header=TRUE)
data-data[,2:13]
Rdata-data[1,]
for(i in 2:79){Rdata-c(Rdata,data[i,])}
times-ts(Rdata,start=1920,frequency=12)
pdf(plot_Rain,width=20,height=5)
barplot(times)
I am getting this error:
Error in barplot.default(times) : 'height' must be a vector or a matrix
Could anyone please tell me how should I specify/write the code to plot the
bars??
Thank you in advance for your time!
Nyanzura
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Re: [R] package xpose4 in Vista - Update
On 30.07.2010 08:56, Santosh wrote: Thanks for your response. How do I install xpose4 package with R.2.11.1? Only by unbundling it manually and installing the separate packages from sources afterwards. I highly suggest to contact the maintainers. Uwe -Santosh 2010/7/29 Uwe Ligges lig...@statistik.tu-dortmund.de mailto:lig...@statistik.tu-dortmund.de The binary package you downloaded is a binary for R 2.11.x. Since it is a package bndle, it cannot work on R-2.11.x anymore: Package bundles are no longer supported. Best, Uwe Ligges On 29.07.2010 02:11, Santosh wrote: Dear R experts, There seems to be a problem (please see the error messages below) with the installation of the latest version of xpose4 (version 4.2.1) with the latest R version.(2.11.1)... I didn't face such installation problems when using version R.2.10.1 Would really appreciate your assistance in debugging installation of xpose 4..2.1 with R.2.11.1 Thanks again.. -Santosh On Wed, Jul 28, 2010 at 12:46 PM, Santoshsantosh2...@gmail.com mailto:santosh2...@gmail.com wrote: Dear R experts... I would really appreciate your suggestions in installing a package in Windows Vista... I am unable to install a package on a windows vista based computer, in spite of running it as an administrator. The package xpose4.2.1 is available from https://sourceforge.net/projects/xpose/files/Xpose4/Xpose_4.2.1/xpose4_4.2.1_win32.zip/download Following is the error message when I try to install the package from the Rgui command line... I get similar errors when I try to install the packages from Rgui (Packages | Install packages from local zip files) menu, but with default lib=C:/Users/santosh/Documents/R/win-library/2.11 .___ install.packages(C:/Users/santosh/Downloads/xpose4_4.2.1_win32.zip,repos=NULL,lib=C:/Program Files/R/R-2.11.1/library) Error in gzfile(file, r) : cannot open the connection In addition: Warning message: In gzfile(file, r) : cannot open compressed file 'xpose4_4.2.1_win32/DESCRIPTION', probable reason 'No such file or directory' However, I see file folder in which the library related folders are installed, and contains different xpose4 related folders.. Thanks again, Santosh [[alternative HTML version deleted]] __ R-help@r-project.org mailto: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] reading dates in Excel into R
Does function ?strptime help you in any way? -- View this message in context: http://r.789695.n4.nabble.com/reading-dates-in-Excel-into-R-tp2306830p2307744.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] Sweave line breaks
Hello, when I print x in Sweave, the lines do not wrap. However, I want them to wrap (perhaps at a specified width). How? Thanks, *S* keep.source=TRUE= x - Lorem ipsum dolor sit amet, consectetur adipisicing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum. print(x) @ __ 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 dates in Excel into R
To read the data into R 1) I format my dates as -MM-DD in Excel (or OpenOffice Calc), 2) (change =na() to NA) 3) Check that required number of significant decimal places are displayed, 4) export as csv and 5) Use readSeries() function from Rmetrics timeSeries package to read the data into R. For what it is worth I have found this approach flexible . Best Regards John On 29 July 2010 22:18, Peter Alspach peter.alsp...@plantandfood.co.nz wrote: Tena koe What do you want to control? You can govern the format used in R using the appropriate R functions. I doubt it would be useful to have dates read from Excel depend on the format set for displaying those dates in Excel. HTH ,,, Peter Alspach -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r- project.org] On Behalf Of Hongying Li Sent: Friday, 30 July 2010 5:33 a.m. To: r-help@r-project.org Subject: [R] reading dates in Excel into R I am reading dates in Excel2007 into R. Here are the functions I used: library(RODBC) channel-odbcConnectExcel2007(myfile.xlsx) tmp-sqlFetch(channel,1,as.is=T) The dates in myfile.xlsx are all in this format: mm/dd/. But when I read it to R, some columns look like -mm-dd 00:00:00, some columns look like -mm-dd, and some columns are numbers. I do not know how I can control this. Any help? Thanks! _ Hotmail is redefining busy with tools for the New Busy. Get more from your inbox. N:WL:en-US:WM_HMP:042010_2 [[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. -- John C Frain Economics Department Trinity College Dublin Dublin 2 Ireland www.tcd.ie/Economics/staff/frainj/home.html mailto:fra...@tcd.ie mailto:fra...@gmail.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] Out-of-sample predictions with boosting model
Hi Travis,
I try to give you some hints that might bring you closer to a solution.
The clue to your problem (as far as I understand it) might just be to
appropriately use the predict function of mboost. You can specify a new
data set (e.g. a part of your original data set not used for estimation)
and
predict(model, newdata = newdata)
which gives you a vector of predictions as you wanted. Thus, you could,
for example, specify newdata such that you get your one-step ahead
predictions.
To estimate the model only on a subset of the data you could either use
mboost(y ~ x1 + x2 + x3, data = some_part_of_your_dataset)
or you can apply weights
model - mboost(y ~ x1 + x2 + x3, data = data,
+ weights = c(rep(1, 100), rep(0, nrow(data) - 100)))
predict(model) ## gives you predictions for all observations in data
Now you can extract the subset of out-of-bag predictions, i.e.,
predictions for observations with weight 0.
One further thing to mention:
You term your model blackbox, however you should note that you do NOT
fit a blackbox model but an additive model using P-splines (which is the
default). You can see this if you type, e.g.,
coef(model)
and look at the names.
Another idea for your data problem might be that you fit ONE model with
country as effect modifier specified via the by argument in all
base-learners. A call could look like
mboost(y ~ bbs(x1, by = country) + bbs(x2, by = country)
++ bbs(x3, by = country), data = data)
Or you could use random effects via brandom() base-learners. Oh, and
please note that you need to tune your mstop value (e.g. via cvrisk)!
HTH
Benjamin
Travis Berge travisrh...@gmail.com wrote:
Hi UseRs -
I am new to R, and could use some help making out-of-sample predictions
using a boosting model (the mboost command). The issue is complicated by the
fact that I have panel data (time by country), and am estimating the model
separately for each country. FYI, this is monthly data and I have 1986m1 -
2009m12 for 9 countries.
To give you a flavor of what I am doing, here is a simple example to show
how I make in-sample predictions:
# data has following columns: country year month y x1 x2 x3
dat = read.csv(data.csv)
# Create function that estimates model, produces in-sample predictions
bbox = function(df)
{
blackbox = mboost(y ~ x1 + x2 + x3)
predict(blackbox)
}
# Use lapply to estimate by country
bycountry = lapply(split(dat, dat$country), bbox)
So that in the end I have an object bycountry that contains the in-sample
predictions of the model, estimated for each country separately. What I
would like to do is take this model and estimate it for each country using
some initial data. I.e., estimate Australia with 1986m1-2003m12, make
prediction about 2004m1, roll data forward. Estimate AUS with 1986m2-2004m1,
predict 2004m2, etc for all data points. Now do the same for Canada,
Denmark, etc.
So I guess my problem is twofold. 1) How to make these out-of-sample
predictions, by country, when my data has not been declared as time-series?
(I do not think that mboost can handle time-series data...x1 x2 and x3 have
been lagged appropriately). 2) How to save the one-step ahead predictions
into a vector?
Any thoughts would be greatly appreciated. Many thanks!
-Travis
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Re: [R] adding new devices and plots
On 07/30/2010 04:15 AM, Erin Hodgess wrote:
Dear R People:
I have the following function:
eplot
function (x)
{
plot(x)
z- locator(2)
dev.new()
plot(window(x, start = min(z$x), end = max(z$x)))
}
I want to generate a new plot from a subset of the original, but I
want to keep the original plot up. When I use this, it opens a new
window, but the first device goes blank.
Hi Erin,
Maybe you want something like zoomInPlot (plotrix).
Jim
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Re: [R] a Chebyshev ....really important
On Thu, 29 Jul 2010 19:01:52 -0400 hussain abu-saaq hussain...@hotmail.com wrote: Hi. i have one question. is there any command to use a Chebyshev in R. i need them to fit the data and get a Chebyshev polynomial. thank you. Please try http://www.rseek.org/?cx=010923144343702598753%3Aboaz1reyxd4q=chebyshevsa=Search+functions%2C+lists%2C+and+morecof=FORID%3A11 or require(sos) findFn(chebyshev) or similar. Please check the posting guide. Regards Liviu __ 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] Flip axis on hist2d plot
I am plotting a heatmap using the hist2d function: require(gplots) x - rnorm(2000) y - rnorm(2000) hist2d(x, y, freq=TRUE, nbins=50, col = c(white,heat.colors(256))) However, I would like to flip the vertical y axis so that the upper left corner serves as the y-origin. How can I do that? Ralf __ 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] multiple graphics windows open with sessionInfo
On 29.07.2010 23:29, Erin Hodgess wrote:
Dear R People:
Hello again. I'm trying to have 3 graphics windows visible
simultaneously. I set up a zoo series.
Then I plot the original series. I use the locator function to select
2 values from the original series, which generates a subset of the
original series.
Next, I plot the subset.
The last step is to produce an EWMA chart from the subset series.
Fair enough. I've tried all sort of things, but can only have 2
graphics windows open with stuff in them. If I go into the blank
window and maximize it, then it appears. But other than that, it does
not.
xdate- seq(as.Date(1998-01-01),as.Date(2010-06-30),by=day)
length(xdate)
[1] 4564
xt- zoo(rnorm(4564),order=xdate)
#Here is the function itself:
eplot
function (x)
{
require(zoo)
require(qcc)
windows()
plot(x)
z- locator(2,type=l,col=red)
windows()
plot(window(x, start = min(z$x), end = max(z$x)))
windows()
ewma(window(x, start = min(z$x), end = max(z$x)))
dev.set(3)
plot(window(x, start = min(z$x), end = max(z$x)))
Erin,
actually, I do not udnerstand what you want to achieve with the last two
lines of the function.
Particularly note that dev.set(3) does only work if you have a certain
amount of open devices once you call the function.
Best,
Uwe
}
sessionInfo()
R version 2.11.1 (2010-05-31)
i386-pc-mingw32
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United
States.1252LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] qcc_2.0.1 zoo_1.6-3 proto_0.3-8
loaded via a namespace (and not attached):
[1] dynlm_0.2-3 grid_2.11.1 lattice_0.18-8
strucchange_1.4-0 tcltk_2.11.1 tools_2.11.1 traitr_0.7
Any help would be much appreciated.
Thanks,
Erin
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Re: [R] Need a help to plot bar for time series Rain data
On 07/30/2010 06:51 PM, Nyanzura wrote:
Hey Guys,
I am quite new to R, am trying to plot a bar plot for my monthly rainfall
data from 1920 to 1990. For every year I have the data from January to
December. I have created this code:
data-read.table(C://R//Data//Rain.txt, header=TRUE)
data-data[,2:13]
Rdata-data[1,]
for(i in 2:79){Rdata-c(Rdata,data[i,])}
times-ts(Rdata,start=1920,frequency=12)
pdf(plot_Rain,width=20,height=5)
barplot(times)
I am getting this error:
Error in barplot.default(times) : 'height' must be a vector or a matrix
Could anyone please tell me how should I specify/write the code to plot the
bars??
Hi Nyanzura,
I guess the first thing would be to see what:
class(times)
has to say. However, a plot with 852 bars might be a little hard to
interpret.
Jim
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Re: [R] Need a help to plot bar for time series Rain data
Hi Jim, Thank you very much, let me check as you suggested. But in addition what do you think could be easy to interpret? Could you advice me please. Nyanzura -- View this message in context: http://r.789695.n4.nabble.com/Need-a-help-to-plot-bar-for-time-series-Rain-data-tp2307739p2307858.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] 3d topographic map
sh...@ucar.edu wrote:
I would like to create a 3d topographic map using lat/lon and
z(height). I have been scouring the R help pages and have not located
the package I am looking for. Does anyone have a suggestion of package
that will work for this?
I have some code for generating some pretty cool 3D topographic maps,
even interactive ones. It's not very difficult to do, really, and much
of the code is actually just for generating nice colours for the map. :-)
I thought it was quite surprising and interesting to see how shallow
the ocean is many place, and how much the depth actually varies.
For instance, the North Sea (between the coast of Norway and the
coast of England) is only about 100 meters deep most places. But
in other places the ocean is several kilometers deep.
Anyway, here's the code:
# First download the SRTM30_Plus data file (about 55 MiB) from
# ftp://topex.ucsd.edu/pub/srtm30_plus/srtm30/data/w020n90.Bathymetry.srtm
# See also http://topex.ucsd.edu/WWW_html/srtm30_plus.html
# Bounding box
minlat=40
maxlat=90
minlong=-20
maxlong=20
# Range of bounding box
longrange=maxlong-minlong
latrange=maxlat-minlat
# Number of columns and rows of data in the bathymetry file
ncols=60 * 2 * longrange
nrows=60 * 2 * latrange
ntot=ncols*nrows # Total number of points -- probably too many to plot ...
steps=10 # ... so we use only every 'steps' point in each direction
ux=seq(1,ncols,by=steps) # X coordinates (longitude)
uy=seq(1,nrows,by=steps) # Y coordinates (latitude)
dat=expand.grid(x=ux,y=uy) # Create grid
dat=transform(dat,index=(y-1)*ncols+x) # Calculate byte index in file
# Transform indices to real coordinates
dat=transform(dat, long=ggplot2::rescale(x, from=c(1,ncols),
to=c(minlong+1/60/4, maxlong-1/60/4),
clip=FALSE),
lat=ggplot2::rescale(y, from=c(1,nrows),
to=c(maxlat-1/60/4, minlat+1/60/4), clip=FALSE))
# Name of file containing the bathymetry data
filename=w020n90.Bathymetry.srtm
# Read bathymetry data from the file
library(R.utils)
dat$z=readBinFragments(filename, what=integer, size=2, signed=TRUE,
idxs=dat$index,endian=big)
# Create matrix containing the data
dat.mat=matrix(dat$z,ncol=length(ux),byrow=TRUE)
dat.mat=t(dat.mat)[,nrow(dat.mat):1]
# Calculate topographic colours for elevation values
map.colours=function(z, water=c(-5000,0), land=c(0,1500), mountain,...)
{
z.min=min(z)
z.max=max(z)
# Divide the land gradient into two parts
land=c(land[1],mean(land),land[2])
# Number of unique water and land values
nw=length(unique(z[z0]))
nl=length(unique(z[z=0]))
# Create the output colour component vectors
h - s - v - rep(1, length(z))
# h-values for water
hvals=c(43/60,31/60)
# Create water colours
if(nw==1) h[z0]=hvals[2] else if(nw1)
h[z0]=approx(water,hvals,xout=z[z0],rule=2)$y
# h, s and v values for land
hvals=c(4/12,2/12,0/12)
svals=c(1,1,0)
vvals=c(.65,.9,.95)
# Create land colours
if(nl==1)
{ h[z=0] = hvals[1]; s[z=0] = svals[1]; v[z=0] = vvals[1]} else
if(nl1)
{
h[z=0]=approx(land,hvals,xout=z[z=0],rule=2)$y
s[z=0]=approx(land,svals,xout=z[z=0],rule=2)$y
v[z=0]=approx(land,vvals,xout=z[z=0],rule=2)$y
}
hsv(h,s,v)
}
# Basic contour plot -- not very pretty ...
with(dat, contour(unique(long),rev(unique(lat)),dat.mat))
# Colours make the whole thing look quite pretty ...
ncolours=100
image(unique(dat$long),rev(unique(dat$lat)),
matrix(1:length(dat.mat),nrow=nrow(dat.mat)),
col=map.colours(dat.mat),xlab=Longitude,ylab=Latitude)
# And it looks even prettier in 3D ...
zfacet - dat.mat[-nrow(dat.mat), -ncol(dat.mat)]
with(dat, persp(unique(long), rev(unique(lat)), dat.mat,
expand=.2, col=map.colours(zfacet), border=NA,
shade=.3, phi=60, theta=0, axes=FALSE))
# How about an *interactive* 3D map ...
# Try holding the left mouse button and dragging
# Now try the mouse wheel (or right button and dragging)
# Finally, try clicking the middle button (or wheel) and dragging
library(rgl)
with(dat, surface3d(unique(long), rev(unique(lat)), dat.mat/1000,
col=map.colours(dat.mat)))
# Note that the elevation values are of course very much exaggerated
# In 'real life', it would look something like this (i.e., completely flat)
with(dat, surface3d(unique(long), rev(unique(lat)), dat.mat/100,
col=map.colours(dat.mat)))
--
Karl Ove Hufthammer
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PLEASE
[R] Programming Statistical Functions
Hello, I'm new in R. I'm meteorological modeller and i will calculate some statistics for my model results. These statistis are the follow: ANB: Average Normalized Absolute BIAS MNB: Mean Normalized BIAS MNE: Mean Normalised Error STDE: Standard Deviation of Error FB: Fractional BIAS MG: Geometric Mean BIAS VG: Geometric Variance SKVAR: Skill Variance RMSE: Root Mean Square Error NMSE: Normalized Mean Square Error r: Correlation Coefficient CV: Coeficient of Variation FAC2: Fractional Predictions within a factor of two of observations Hc: Hit Rate IOA: Index of Agreement Au: Unpaired Peak Concentration Accuracy As: Spatially-paired Peak Concentration Accuracy And their expressions are in the upload file: http://r.789695.n4.nabble.com/file/n2307880/Statistics.doc Statistics.doc I think that someone was developed this statistical functions for use in R, but if don't exist, someone help me to programme it? Thank you! -- View this message in context: http://r.789695.n4.nabble.com/Programming-Statistical-Functions-tp2307880p2307880.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] super class
Is this what you wanted? setClass(class1, representation(xc1=numeric, xc2=character)) setClass(class2, representation(cx1=character, cx2=numeric)) setClassUnion(combinedClass, c(class1,class2)) getClass(combinedClass) -- View this message in context: http://r.789695.n4.nabble.com/super-class-tp831608p2307894.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] Programming Statistical Functions
Maybe and r site search would help? Try and figure out how to
calculate these yourself. If you need help send a minimal,
reproducible example to this list, and you will probably recieve help.
If you need a starting place for programming functions look at an
introduction to R.
#coefficient of variation
CV - function(x){mean(x)/sd(x)}
My $0.02.
Stephen
On Fri, Jul 30, 2010 at 7:53 AM, hector hec...@ceam.es wrote:
Hello,
I'm new in R. I'm meteorological modeller and i will calculate some
statistics for my model results.
These statistis are the follow:
ANB: Average Normalized Absolute BIAS
MNB: Mean Normalized BIAS
MNE: Mean Normalised Error
STDE: Standard Deviation of Error
FB: Fractional BIAS
MG: Geometric Mean BIAS
VG: Geometric Variance
SKVAR: Skill Variance
RMSE: Root Mean Square Error
NMSE: Normalized Mean Square Error
r: Correlation Coefficient
CV: Coeficient of Variation
FAC2: Fractional Predictions within a factor of two of observations
Hc: Hit Rate
IOA: Index of Agreement
Au: Unpaired Peak Concentration Accuracy
As: Spatially-paired Peak Concentration Accuracy
And their expressions are in the upload file:
http://r.789695.n4.nabble.com/file/n2307880/Statistics.doc Statistics.doc
I think that someone was developed this statistical functions for use in R,
but if don't exist, someone help me to programme it? Thank you!
--
View this message in context:
http://r.789695.n4.nabble.com/Programming-Statistical-Functions-tp2307880p2307880.html
Sent from the R help mailing list archive at Nabble.com.
__
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--
Stephen Sefick
| Auburn University |
| Department of Biological Sciences |
| 331 Funchess Hall |
| Auburn, Alabama |
| 36849 |
|___|
| sas0...@auburn.edu |
| http://www.auburn.edu/~sas0025 |
|___|
Let's not spend our time and resources thinking about things that are
so little or so large that all they really do for us is puff us up and
make us feel like gods. We are mammals, and have not exhausted the
annoying little problems of being mammals.
-K. Mullis
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Re: [R] (no subject)
Hi:
Avoiding loops in R by using vectorization is usually one of the best ways
to improve performance. Since we can't replicate your data (e.g., tslength
is not given), instead I'll generate a couple of functions to extract the
estimated beta from randomly generated data. The replicate() function comes
in handy for this type of simulation.
(1) Create a function to construct the sample and run the model:
wf - function() {
x - sample(1:20, 10)
y - 2 + 1.5 * x + rnorm(20)
summary(lm(y ~ x))$coef[2]
}
system.time(replicate(1000, wf()))
user system elapsed
3.170.003.17
(2) Use a loop instead of replicate():
b - numeric(1000)
system.time(for(i in seq_along(b)) b[i] - wf())
user system elapsed
3.170.003.18
(3) Use lsfit() instead (only works for simple linear regression):
wf2 - function() {
x - sample(1:20, 10)
y - 2 + 1.5 * x + rnorm(10)
lsfit(x, y)$coef[2]
}
system.time(replicate(1000, wf2()))
user system elapsed
0.450.000.46
Hopefully you can adapt one or more of these functions to your needs.
Dennis
On Fri, Jul 30, 2010 at 1:18 AM, Natasa Tzortzaki tz_nat...@hotmail.comwrote:
hello,
i am new to R and trying to calculate the beta coefficient for standard
linear regression for a series of randomly generated numbers. I have created
this loop, but it runs really slow, is there a way to improve it?
#number of simulations
n.k-999
#create the matrix for regression coefficients generated from #random data
beta-matrix(0,1,n.k+1)
e-matrix(0,tslength,n.k+1)
for(k in 1:n.k+1)
{
for(i in 1:tslength)
{
beta[1,1]-beta1
e[i,k]-c(rnorm(1,0,var.all))
beta[1,k]-summary(lm(e[1:tslength,k]~t))$coefficient[2]
}
}
thanks
Anastasia Tzortzaki
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Re: [R] Need a help to plot bar for time series Rain data
On 07/30/2010 09:24 PM, Nyanzura wrote: Hi Jim, Thank you very much, let me check as you suggested. But in addition what do you think could be easy to interpret? Could you advice me please. I would probably start with: plot(times,type=l,...) if you can makes 'times' into a vector. Jim __ 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] Sweave line breaks
On Jul 30, 2010, at 4:13 AM, soeren.vo...@eawag.ch wrote: Hello, when I print x in Sweave, the lines do not wrap. However, I want them to wrap (perhaps at a specified width). How? Thanks, *S* keep.source=TRUE= x - Lorem ipsum dolor sit amet, consectetur adipisicing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum. print(x) @ See ?strwrap and ?paste. Also use cat() instead of print(). The double \\ at the end of each line tells LaTeX to force a line break. Since R will detect the \ as an escape character, you need to double them when cat()ing. I also add a newline (\n) so that the output after the \\ goes to the next line. cat(paste(strwrap(x, width = 70), collapse = \n), \n) Lorem ipsum dolor sit amet, consectetur adipisicing elit, sed do\\ eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim\\ ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut\\ aliquip ex ea commodo consequat. Duis aute irure dolor in\\ reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla\\ pariatur. Excepteur sint occaecat cupidatat non proident, sunt in\\ culpa qui officia deserunt mollit anim id est laborum. 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] Data Handling
Hi, I am trying to convert my dataset into xts. I have tried the following : data1-read.table(data1.txt,header=F) data2-read.table(data2.txt,header=F) data1.xtsas.xts(data1,descr=my new xts object) However, I get an error : Error in as.POSIXlt.character(x, tz, ...) : character string is not in a standard unambiguous format I understand that my date and time format might not be accepted and have tried to convert this but failed. Could you suggest something ? My date is in the format : dd/mm/ My time is in the format : hh:00 Thank you in advance -- View this message in context: http://r.789695.n4.nabble.com/Data-Handling-tp2307770p2307936.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] Ouput several lines of cat
Hi, set sep=\n x - c(X XXX,X XX.XX,- ( XX.XX XXX ) ) cat(x,file=x.txt,sep=\n) - A R learner. -- View this message in context: http://r.789695.n4.nabble.com/Ouput-several-lines-of-cat-tp2307900p2307945.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] Data Handling
On Fri, Jul 30, 2010 at 9:02 AM, Lily_stats sund...@gmail.com wrote: Hi, I am trying to convert my dataset into xts. I have tried the following : data1-read.table(data1.txt,header=F) data2-read.table(data2.txt,header=F) data1.xtsas.xts(data1,descr=my new xts object) However, I get an error : Error in as.POSIXlt.character(x, tz, ...) : character string is not in a standard unambiguous format I understand that my date and time format might not be accepted and have tried to convert this but failed. Could you suggest something ? My date is in the format : dd/mm/ My time is in the format : hh:00 Thank you in advance -- View this message in context: http://r.789695.n4.nabble.com/Data-Handling-tp2307770p2307936.html Sent from the R help mailing list archive at Nabble.com. Can't say too much since there is no detail in your post but you can do something like this: library(xts) # this also loads zoo library(chron) # if you wish to use chron z - read.zoo(...) x - as.xts(z) where you may need to use FUN= and possibly the index.column= and other arguments to read.zoo. See ?read.zoo and the R News 4/1 article on dates. __ 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] simple table/matrix problem
Hi
Given three vectors
x - c(fish=3, dogs=5, bats=2)
y - c(dogs=1, hogs=3)
z - c(bats=3, dogs=5)
How do I create a multi-way table like the following?
out
x y z
bats 2 0 3
dogs 5 1 5
fish 3 0 0
hogs 0 3 0
('out' is a matrix).
See how the first line shows 'x' has 2 bats, 'y' has zero bats, and 'z'
has 3 bats
and so on for each line.
The real application would have a matrix of size ~10 by ~1.
--
Robin K. S. Hankin
Uncertainty Analyst
University of Cambridge
19 Silver Street
Cambridge CB3 9EP
01223-764877
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] simple table/matrix problem
Try this:
Reduce(function(...)merge(..., by = 'ind', all = TRUE), lapply(list(x, y,
z), stack))
On Fri, Jul 30, 2010 at 10:39 AM, Robin Hankin rk...@cam.ac.uk wrote:
Hi
Given three vectors
x - c(fish=3, dogs=5, bats=2)
y - c(dogs=1, hogs=3)
z - c(bats=3, dogs=5)
How do I create a multi-way table like the following?
out
x y z
bats 2 0 3
dogs 5 1 5
fish 3 0 0
hogs 0 3 0
('out' is a matrix).
See how the first line shows 'x' has 2 bats, 'y' has zero bats, and 'z' has
3 bats
and so on for each line.
The real application would have a matrix of size ~10 by ~1.
--
Robin K. S. Hankin
Uncertainty Analyst
University of Cambridge
19 Silver Street
Cambridge CB3 9EP
01223-764877
__
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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.
--
Henrique Dallazuanna
Curitiba-Paraná-Brasil
25° 25' 40 S 49° 16' 22 O
[[alternative HTML version deleted]]
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] how to get higher derivatives with deriv
On Jul 29, 2010, at 11:27 PM, Wu Gong wrote:
## specify the function string
f.str - x^alpha
## higher derivatives
DD - function(f.str, x = 2, alpha=3,order = 1){
expr.s - parse(text=f.str)
while(order=1) {
expr.s - D(expr.s,x)
order - order-1}
eval(expr.s)
}
compute
DD(f.str,x=1,alpha=0.5,order=1)
Somewhat more elegant things can be done, consider for instance
f
function (x,alpha) x^alpha
ddf - f
body(ddf) - D(D(body(f),x),x)
ddf
function (x, alpha)
x^((alpha - 1) - 1) * (alpha - 1) * alpha
ddf(1,.5)
[1] -0.25
(wrapping this as a function which accepts an order argument is left as an
exercise, because I'm too lazy)
--
Peter Dalgaard
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Email: pd@cbs.dk Priv: pda...@gmail.com
__
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and provide commented, minimal, self-contained, reproducible code.
[R] bonjour
Bonjour, je suis une étudiante en épidémiologie. j'utilise R pour mes analyses, et un souci dans le calcul de l'AIC,BIC, et je pense calcul la déviance puis à partir de là calculer ces informations manuellement mais j'ai trouvé quelque chose et je ne suis pas très si c'est la déviance que j'ai trouvé. si quelqu'un peut m'aider? je vous remercie beaucoup. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] how to get higher derivatives with deriv
I am not as lazy as Peter (but neither am I as good as him)! So, please
allow me to take a stab at completing his exercise:
Deriv - function(fn, order=1) {
ddf - fn
body(ddf) - D(body(f),x)
if (order 1) {
for (i in 2:order) {
body(ddf) - D(body(ddf),x)
}
}
ddf
}
f - function (x,alpha) x^alpha
x - seq(0, 3, length=100)
plot(x, f(x, alpha=1.5), type=l, ylab=)
lines(x, Deriv(f, 1)(x, alpha=1.5), col=2)
lines(x, Deriv(f, 2)(x, alpha=1.5), col=3)
Thanks for the elegant solution, Peter.
Best,
Ravi.
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of peter dalgaard
Sent: Friday, July 30, 2010 9:52 AM
To: Wu Gong
Cc: r-help@r-project.org
Subject: Re: [R] how to get higher derivatives with deriv
On Jul 29, 2010, at 11:27 PM, Wu Gong wrote:
## specify the function string
f.str - x^alpha
## higher derivatives
DD - function(f.str, x = 2, alpha=3,order = 1){
expr.s - parse(text=f.str)
while(order=1) {
expr.s - D(expr.s,x)
order - order-1}
eval(expr.s)
}
compute
DD(f.str,x=1,alpha=0.5,order=1)
Somewhat more elegant things can be done, consider for instance
f
function (x,alpha) x^alpha
ddf - f
body(ddf) - D(D(body(f),x),x)
ddf
function (x, alpha)
x^((alpha - 1) - 1) * (alpha - 1) * alpha
ddf(1,.5)
[1] -0.25
(wrapping this as a function which accepts an order argument is left as an
exercise, because I'm too lazy)
--
Peter Dalgaard
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Email: pd@cbs.dk Priv: pda...@gmail.com
__
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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.
__
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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] help for creating arff file..i have the codes??
I need to create an arff file.i have the necesaary codes as two parts and i need to combine them..if there is anyone who can help i'll send the codes..thank you. -- View this message in context: http://r.789695.n4.nabble.com/help-for-creating-arff-file-i-have-the-codes-tp2308039p2308039.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] bonjour
Thanx Ivan, first of all, my english is power but i will try . my question is about the calculation of AIC, BIC by using svyglm in order to choose the best model in multiple regression. thanx Le 30 juillet 2010 16:17, Ivan Calandra ivan.calan...@uni-hamburg.de a écrit : Salut, Commence par écrire en anglais. Il y a peut-être une liste spécifique en français, mais je ne la connais pas. Ensuite, lis le posting guide (lien disponible à la fin de chaque email posté sur la liste R). Si ces 2 étapes sont bien respectées, tu devrais obtenir des réponses. HTH, Ivan Le 7/30/2010 16:08, aline uwimana a écrit : Bonjour, je suis une étudiante en épidémiologie. j'utilise R pour mes analyses, et un souci dans le calcul de l'AIC,BIC, et je pense calcul la déviance puis à partir de là calculer ces informations manuellement mais j'ai trouvé quelque chose et je ne suis pas très si c'est la déviance que j'ai trouvé. si quelqu'un peut m'aider? je vous remercie beaucoup. [[alternative HTML version deleted]] __r-h...@r-project.org mailing listhttps://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] how to get higher derivatives with deriv
On Jul 30, 2010, at 4:28 PM, Ravi Varadhan wrote:
I am not as lazy as Peter (but neither am I as good as him)! So, please
allow me to take a stab at completing his exercise:
Deriv - function(fn, order=1) {
ddf - fn
body(ddf) - D(body(f),x)
### Typo: body(ddf) or body(fn)
if (order 1) {
for (i in 2:order) {
body(ddf) - D(body(ddf),x)
}
}
ddf
}
Yes.
One thing: body() and body-() are relatively expensive operations, and only
really needed on the way in and the way out, so you might want to use a
temporary variable.
--
Peter Dalgaard
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Email: pd@cbs.dk Priv: pda...@gmail.com
__
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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] COXPH: how to get the score test and likelihood ratio test for a specific variable in a multivariate Coxph ?
Hello, I would like to get the likelihood ratio and score tests for specific variables in a multivariate coxph model. The default is Wald, so the tests for each separate variable is based on Wald's test. I have the other tests for the full model but I don't know how to get them for each variable. Any idea? David Biau. [[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] hi! l have a question please help me
Is this a question from your homework?
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 Fri, Jul 30, 2010 at 8:14 AM, leepama butch...@hanmail.net wrote:
1)
dmatrix1-function(n,p,rho,sigma,k){
muvec1=zeros(1,p)
truep-as.matrix(c(3,1.5,0,0,2,0,0,0))
A=eye(p)
for(i in 1:p){
for(j in 1:p){
A[i,j]=rho^(abs(i-j))
X=mvrnorm(n,muvec1,A)
y=X%*%truep+as.matrix(rnorm(n,0,sigma))
Y=X[1:k,]
w=y[1:k]
Z=X[(k+1):n,]
z=y[(k+1):n]}}
return(list(X,Y,w,Z,z))
}
I made this code which performs design matrix..
Can you help me how to make several data set??
the code i made compute only one data set...
2) we generate 50 data with 30 variables. The true regression
vector is such that
bj = 3 â 0.1j j = 1, . . . , 10,
bj = â5 + 0.3j j = 20, . . . , 25,
bj = 0 for the others j.
The noise is such that sigma = 9 and the correlations are such that (j, k)
=
exp (â|jâk|/2 for (j, k) â {11, . . . , 25}2 and the others variables
are
i.i.d. N(0, 1),
also independent from x11, . . . , x25
how to simulate this data set
3)we simulated 50 data sets and 40 predictors.
β=(3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0)
and Ï=15. The predictors X were generated as follows:
xi=Z1+xi
, Z1â¼N.(0,1), i=1, . . . ,5,
xi=Z2+xi
, Z2â¼N.(0,1), i=6, . . . ,10,
xi=Z3+xi
, Z3â¼N.(0,1), i=11, . . . ,15,
xiâ¼N.(0,1), xi independent identically distributed, i=16, : : : , 40
how to simulate this data set
--
View this message in context:
http://r.789695.n4.nabble.com/hi-l-have-a-question-please-help-me-tp2307569p2307569.html
Sent from the R help mailing list archive at Nabble.com.
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Re: [R] Out-of-sample predictions with boosting model
Thanks, Ben. Specifying the data in this way should give me what I need - I can do this in a loop fairly easily and wind up with what I want in the end. And I should've been more specific, I think that mboost can handle time-series data, it's the fact that the data is a panel bit that was giving me issues--I'd like to think about using base learners that can handle panel data in the future so if you have any suggestions there I'd be happy to hear them. Also, don't worry, the models I specify are tuned and I have thought about what base learners are appropriate; I left it as a blackbox for the exposition of my post. :) Anyway, many thanks, Travis -- View this message in context: http://r.789695.n4.nabble.com/Out-of-sample-predictions-with-boosting-model-tp2305458p2308082.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] logos and goodies
Interesting topic and question. I hope someone who knows will answer this. 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 Fri, Jul 30, 2010 at 5:06 AM, c...@witthoft.com wrote: I've got a couple questions related to my search (in vain) for an R tshirt or coffee mug. The first question is simply: is there a higher-resolution R logo available than the one at r-developer.org? (or the modified one provided by useR conference pages) Next: what are the chances of someone in the R management setting up a cafepress.com R store for shirts, coffee mugs, etc? I just sort of figured what with Firefox, Ubuntu, etc. selling product, R could do so as well. (I have all the gear I need to make myself a tshirt w/ the logo, but not as high quality as cafepress does) The other thing I noticed is that the link to the R logos' directory, http://developer.r-project.org/Logo, is blocked to the general public. Luckily, if you know the name of the image files is Rlogo-[1-6].png, you can still download the images. Any reason the /Logo directory itself couldn't be made read-accessible? Carl __ 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.
[R] Next release of R planned to be 2.12.0
This mainly as a thumbs-up to sysadmins planning installation for the Fall semester: Only a small number of low-impact bugs have been found since the 2.11.1 release so we have decided NOT to do a 2.11.2, but head straight for 2.12.0 some time in October. For the R Core Team Peter Dalgaard -- Peter Dalgaard Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd@cbs.dk Priv: pda...@gmail.com ___ r-annou...@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-announce __ 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] COXPH: how to get the score test and likelihood ratio test for a specific variable in a multivariate Coxph ?
On Jul 30, 2010, at 11:08 AM, Biau David wrote: Hello, I would like to get the likelihood ratio and score tests for specific variables in a multivariate coxph model. The default is Wald, so the tests for each separate variable is based on Wald's test. I have the other tests for the full model but I don't know how to get them for each variable. Any idea? The first idea would be to specify which function in which package you are asking questions about. In the case of coxph in the survival package, for instance, you do get a likelihood ratio test (== differences in log-likelihoods) by default. A score test is, at least as as I understand it for individual variables, equivalent to a Wald test, so I don't really understand your question, since youa re already getting all of that in the survival package. (You can extract a score value and loglik values from a coxph object by: (with the first example in the coxph help page) coxph(Surv(time, status) ~ x + strata(sex), test1)$score xoxph(Surv(time, status) ~ x + strata(sex), test1)$loglik But anova(coxph-object) would give you these values in a neater bundle. #Analysis of Deviance Table # Cox model: response is Surv(time, status) #Terms added sequentially (first to last) # loglik Chisq Df Pr(|Chi|) # NULL -3.8712 # x-3.3277 1.0871 1 0.2971 The question about getting them for each variable does not make a lot of sense to me, since likelihood tests are model comparisons. You can only make such statements about the consequences of adding or deleting a variable to/from an existing model. -- David Winsemius, MD 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] logos and goodies
On Jul 30, 2010, at 4:06 AM, c...@witthoft.com wrote: I've got a couple questions related to my search (in vain) for an R tshirt or coffee mug. The first question is simply: is there a higher-resolution R logo available than the one at r-developer.org? (or the modified one provided by useR conference pages) I think that's a setup error, it is not even accessible to the Core Team... (Ideally, there should be a usage policy statement in the directory, but you know what paves the road to Hell.) If you had been able to see the directory, you might have seen one attempt of a vector graphics version in Rlogo-1.svg. There was a thread on the issue on R-devel at the end of February, outlining the procedure for creating it. I am sure that it could be improved substantially with some additional fiddling (the present one was intended for highly compressed icons; it looks rather irregular at large magnifications). Next: what are the chances of someone in the R management setting up a cafepress.com R store for shirts, coffee mugs, etc? I just sort of figured what with Firefox, Ubuntu, etc. selling product, R could do so as well. (I have all the gear I need to make myself a tshirt w/ the logo, but not as high quality as cafepress does) The other thing I noticed is that the link to the R logos' directory, http://developer.r-project.org/Logo, is blocked to the general public. Luckily, if you know the name of the image files is Rlogo-[1-6].png, you can still download the images. Any reason the /Logo directory itself couldn't be made read-accessible? Carl __ 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 Dalgaard Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd@cbs.dk Priv: pda...@gmail.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] Re : COXPH: how to get the score test and likelihood ratio test for a specific variable in a multivariate Coxph ?
Thx for the answer. I am using survival. I didn't know that the Wald and score tests were the same for individual variables in a coxph; I Thought the score test was the multivariate version of the Log-rank. However, say I have only one variable in the model, I should expect the test for the full model and the one for a single variable to be the same? Then it seems to me that the default test is the Wald and that the Wald and the Score are different. cox_lr_age - coxph(Surv(tilr, ev_lr==1)~age, data=tam) summary(cox_lr_age) Call: coxph(formula = Surv(tilr, ev_lr == 1) ~ age, data = tam) n=2156 (76 observations deleted due to missingness) coef exp(coef) se(coef) z Pr(|z|) age 0.019504 1.019696 0.004651 4.193 2.75e-05 *** --- Signif. codes: 0 â***â 0.001 â**â 0.01 â*â 0.05 â.â 0.1 â â 1 exp(coef) exp(-coef) lower .95 upper .95 age 1.020 0.9807 1.010 1.029 Rsquare= 0.008 (max possible= 0.669 ) Likelihood ratio test= 18.4 on 1 df, p=1.787e-05 Wald test= 17.58 on 1 df, p=2.751e-05 Score (logrank) test = 17.86 on 1 df, p=2.375e-05 David Biau. De : David Winsemius dwinsem...@comcast.net Cc : r help list r-help@r-project.org Envoyé le : Ven 30 juillet 2010, 17h 34min 28s Objet : Re: [R] COXPH: how to get the score test and likelihood ratio test for a specific variable in a multivariate Coxph ? On Jul 30, 2010, at 11:08 AM, Biau David wrote: Hello, I would like to get the likelihood ratio and score tests for specific variables in a multivariate coxph model. The default is Wald, so the tests for each separate variable is based on Wald's test. I have the other tests for the full model but I don't know how to get them for each variable. Any idea? The first idea would be to specify which function in which package you are asking questions about. In the case of coxph in the survival package, for instance, you do get a likelihood ratio test (== differences in log-likelihoods) by default. A score test is, at least as as I understand it for individual variables, equivalent to a Wald test, so I don't really understand your question, since youa re already getting all of that in the survival package. (You can extract a score value and loglik values from a coxph object by: (with the first example in the coxph help page) coxph(Surv(time, status) ~ x + strata(sex), test1)$score xoxph(Surv(time, status) ~ x + strata(sex), test1)$loglik But anova(coxph-object) would give you these values in a neater bundle. #Analysis of Deviance Table # Cox model: response is Surv(time, status) #Terms added sequentially (first to last) # loglik Chisq Df Pr(|Chi|) # NULL -3.8712 # x-3.3277 1.0871 1 0.2971 The question about getting them for each variable does not make a lot of sense to me, since likelihood tests are model comparisons. You can only make such statements about the consequences of adding or deleting a variable to/from an existing model. --David Winsemius, MD 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.
Re: [R] how to get higher derivatives with deriv
Hi Peter,
Here is my homework :)
DD - function(f,order=1){
f.str - body(f)
while(order=1) {
f.str - paste('D(',f.str,',x)',sep=)
order - order-1}
ddf - f
body(ddf) - eval(parse(text=f.str))
ddf}
f - function(x,alpha) x^alpha
DD(f)(2,3)
g - function(x,alpha) x^alpha+2*x^(alpha-1)
DD(g,2)(2,3)
It would be better to handle expressions directly, but I can only paste
strings. The reason why I didn't prefer using body() is that the derivative
only works on a mathematical function not a R function. The body(f) would
cause error when function is constructed by {}.
-
A R learner.
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[R] Need to read an Excel File
I am trying to read an Excel file using the following: a-read.xls(mydata.xls, sheet=1) The file mydata.xls is stored in the working directory. However I am getting the following error. Can anyone help. Error in findPerl(verbose = verbose) : perl executable not found. Use perl= argument to specify the correct path. Error in file.exists(tfn) : invalid 'file' argument -- View this message in context: http://r.789695.n4.nabble.com/Need-to-read-an-Excel-File-tp2307915p2307915.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] Ouput several lines of cat
Hello, I am brand new to R. I need to know how to output the contents of cat function into a text file. The cat is used to output several lines of string in the following format: X XXX X XX.XX - ( XX.XX XXX ) I need to get the output of all these lines into a text file. I tried to put a file name in the cat function. However the output file only displays single line output. Thanks -- View this message in context: http://r.789695.n4.nabble.com/Ouput-several-lines-of-cat-tp2307900p2307900.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] (no subject)
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org]
On Behalf Of Natasa Tzortzaki
Sent: Friday, July 30, 2010 1:19 AM
To: r-help@r-project.org
Subject: [R] (no subject)
hello,
i am new to R and trying to calculate the beta coefficient for standard
linear regression for a series of randomly generated numbers. I have
created this loop, but it runs really slow, is there a way to improve it?
#number of simulations
n.k-999
#create the matrix for regression coefficients generated from #random data
beta-matrix(0,1,n.k+1)
e-matrix(0,tslength,n.k+1)
for(k in 1:n.k+1)
{
for(i in 1:tslength)
{
beta[1,1]-beta1
e[i,k]-c(rnorm(1,0,var.all))
beta[1,k]-summary(lm(e[1:tslength,k]~t))$coefficient[2]
}
}
thanks
Anastasia Tzortzaki
Anastasia,
You haven't provided a reproducible example, so I am going to guess at some of
what you are doing. You also have used some function names for your variable
names which I like to avoid, so I have used 'b' as the name of the vector for
collecting beta coefficients and 'ts' for the predictor variable. I have set
var.all equal to 1.
To speed up your process, you want to eliminate looping as much as possible.
In addition, you should pre-allocate space for vectors that you are going to
fill up in a loop. Your e values can all be generated at once outside of your
loop. I also used the coef() extractor function directly on the lm() object.
So, you could do something like the following:
# number of simulations
n.k - 999
# predictor variable
ts - 1:100
tslength - length(ts)
var.all - 1
# pre-allocate vector to collect beta coefficients
b - numeric(n.k)
# generate your e values all at once
# columns contain values for each simuation trial
e - matrix(rnorm(n.k*tslength,0,var.all), ncol = n.k)
# run your analyses
for(k in 1:n.k)
{
b[k] - coef(lm(e[,k] ~ ts))[2]
}
Hope this is helpful,
Dan
Daniel Nordlund
Bothell, WA USA
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[R] Data Handling
Hi, I am very new to R so these questions may seem simple! I have a huge 2 sets of data(matrix 5x2++) in the following formats , for example data.txt and data2.txt: Date Time X Y 03/03/1983 20:00 0.1 990 I would like to recreate a new matrix which filters through data.txt and data2.txt to get something as below : Date Time X_data1 X_data2 Y_data1 Y_data2 31/12/2000 12:00 2.25 0 990 So I basically need : 1) When Date AND Time from data1.txt and data2.txt match, list the corresponding X and Y values (X_data1,X_data2,Y_data1,Y_data2) Thank you in advance, and I hope I have been clear enough in my message -- View this message in context: http://r.789695.n4.nabble.com/Data-Handling-tp2307770p2307770.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] Reading .eps file created in Illustrator
Hello, I am trying to import an .eps file created with Adobe Illustrator and plot it in a Quartz window (I am using R 2.11.1 GUI 1.34 Leopard build 32-bit (5589) on MacOSx.5.8). I thought of using the PostScriptTrace() to convert my .eps file to RGML, and then use readPicture to plot the file, but the first step already fails (cf below). I also had a look at the add.image( ) example, which does work on my screen. Ultimately, I would like to plot my picture and let the user click on different parts to run different actions. Thanks for any help or alternative ways to do this, Patrick PostScriptTrace(test.eps) /bin/sh: gs: command not found Erreur dans PostScriptTrace(test.eps) : status 32512 in running command 'gs -q -dBATCH -dNOPAUSE - sDEVICE=pswrite -sOutputFile=/dev/null -sstdout=test.eps.xml capturetest.eps' [[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] Having problem to define a subclass, please help me
Here I am having problem to define a subclass, specially if I define that
subclass after defining initialize() method for its superclass. Here is my code:
setClass(a, representation=list(x=numeric, y=numeric),
prototype=list(x=rnorm(10), y=rnorm(10)))
[1] a
setMethod(initialize, a, function(.Object, x, y, ...) {
+ if (length(x) != length(y)) x = y = rep(5, 4)
+ .obj...@x = x
+ .obj...@y = y
+ .Object })
[1] initialize
setClass(b, representation=list(x1=character), contains=a)
Error in .local(.Object, ...) : element 1 is empty;
the part of the args list of 'length' being evaluated was:
(x)
Can anyone please point me where I am doing wrong?
Thanks,
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[R] finding a function or a line while debugging?
guRus Is there a way by which I can search for a particular function or a particular line of code within the maze of all the R codes that are interlinked? Say for instance I am running a code using quantstrat package and on a particular line I get the error saying x is missing in is.array(x). I want to figure out where is.array is in all the codes that my code refers to? How do I do this? Is there like a grep or search function that can say tell me that 'here is the function inside which is.array(X) is being called' etc? out-try(applyStrategy(strategy=stratSMA5D , portfolios=portfolio.st)) Error in is.array(x) : 'x' is missing Thx -- 'Raghu' [[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] Data Handling
Convert your datasets into xts objects and then do a cbind ordering by the column you want. Do a ?cbind. HTH Raghu On Fri, Jul 30, 2010 at 10:33 AM, Lily_stats [via R] ml-node+2307770-1033893256-309...@n4.nabble.comml-node%2b2307770-1033893256-309...@n4.nabble.com wrote: Hi, I am very new to R so these questions may seem simple! I have a huge 2 sets of data(matrix 5x2++) in the following formats , for example data.txt and data2.txt: Date Time X Y 03/03/1983 20:00 0.1 990 I would like to recreate a new matrix which filters through data.txt and data2.txt to get something as below : Date Time X_data1 X_data2 Y_data1 Y_data2 31/12/2000 12:00 2.25 0990 So I basically need : 1) When Date AND Time from data1.txt and data2.txt match, list the corresponding X and Y values (X_data1,X_data2,Y_data1,Y_data2) Thank you in advance, and I hope I have been clear enough in my message -- View message @ http://r.789695.n4.nabble.com/Data-Handling-tp2307770p2307770.html To start a new topic under R help, email ml-node+789696-608741344-309...@n4.nabble.comml-node%2b789696-608741344-309...@n4.nabble.com To unsubscribe from R help, click here (link removed) . -- 'Raghu' -- View this message in context: http://r.789695.n4.nabble.com/Data-Handling-tp2307770p2307836.html Sent from the R help mailing list archive at Nabble.com. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Data Handling
Please try: data - xts(data[,2:n], order.by=as.POSIXct(strptime(data[,1], %d/%m/%Y))) Use similar strptime for hours also.n=number of columns. Good Luck Raghu On Fri, Jul 30, 2010 at 2:02 PM, Lily_stats [via R] ml-node+2307936-1777222343-309...@n4.nabble.comml-node%2b2307936-1777222343-309...@n4.nabble.com wrote: Hi, I am trying to convert my dataset into xts. I have tried the following : data1-read.table(data1.txt,header=F) data2-read.table(data2.txt,header=F) data1.xtsas.xts(data1,descr=my new xts object) However, I get an error : Error in as.POSIXlt.character(x, tz, ...) : character string is not in a standard unambiguous format I understand that my date and time format might not be accepted and have tried to convert this but failed. Could you suggest something ? My date is in the format : dd/mm/ My time is in the format : hh:00 Thank you in advance -- View message @ http://r.789695.n4.nabble.com/Data-Handling-tp2307770p2307936.html To start a new topic under R help, email ml-node+789696-608741344-309...@n4.nabble.comml-node%2b789696-608741344-309...@n4.nabble.com To unsubscribe from R help, click here (link removed) . -- 'Raghu' -- View this message in context: http://r.789695.n4.nabble.com/Data-Handling-tp2307770p2307959.html Sent from the R help mailing list archive at Nabble.com. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Computation of largest eigenvalue
Hello, I am looking for an R function to compute only the largest eigenvalue (Perron-Frobenius eigenvalue) and its corresponding eigenvector of a square matrix (in fact, even only of a non-negative matrix). The function should also be able to deal with very large but sparse matrices. Any idea? Best regards, Christian Weiß -- Dr. Christian H. Weiß Fachbereich Mathematik Technische Universität Darmstadt Schlossgartenstraße 7 64289 Darmstadt -Deutschland- Tel.: +6151/16-3787 Email: we...@mathematik.tu-darmstadt.de Homepage: http://www3.mathematik.tu-darmstadt.de/fileadmin/home/users/157/person/Person.html -- Dein Leben wird auch dadurch nicht flach und dumm, wenn du weißt, daß dein Kampf erfolglos sein wird. Es ist viel flacher, wenn du für etwas Gutes und Ideales kämpfst und nun meinst, du müsstest es auch erreichen. Sind denn Ideale zum Erreichen da? Leben wir denn, um den Tod abzuschaffen? - HERMANN HESSE __ 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] creation package
Dear r-help, I create a package. When I installed this package (I use this command : R CMD check namepackage),I find an error: * checking whether package 'namepackage' can be installed ... ERROR Installation failed. Could you help me to find solution for this error. Best Regards [[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] ColSideColor width in heatmap.2
Dear R users, I am trying to add a ColSideColor- bar to a heatmap created with heatmap.2. I had to adjust the width of the heatmap, for which I used asp = 0.8. Now the ColSideColor- Bar does not fit to the width of the heatmap anymore. Does anyone have an idea, how I can adjust the width of the bar? Here is a simplified example: library(gplots) m - matrix(1:300,30,10) heatmap.2 ( m, asp =0.8, dendrogram = none, key = FALSE, density.info = none, trace = none, ColSideColors = c(yellow,orange,red,pink,purple,blue,lightblue,lightgreen,green,black)) Thanks, Anna [[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] R Equivalent of SAS Datastep Line-Hold (@@) Specifier?
Hello Dr. Venables and Joshua, Thank you for your replies to my post. Dr. Venables's solution is particularly elegant. I looked at the the help file for scan() and it seems pretty clear how this works. Two arguments (file= and what=) are submitted to the function. These are specified in order and so do not specifically need to be named. The what= argument can take the form of a list as it does here. Naming 6 variables in the list and initializing them to either 0 or tells R how many variables it's going to read, their names, and their type. So presumably when R encounters the first of 12 additional values in each row, it assumes that it should continually recycle the same six variables that were specified until it reaches the end of the row. And so it keeps on reading. Is this correct? Thanks, Paul --- On Fri, 7/30/10, bill.venab...@csiro.au bill.venab...@csiro.au wrote: From: bill.venab...@csiro.au bill.venab...@csiro.au Subject: RE: [R] R Equivalent of SAS Datastep Line-Hold (@@) Specifier? To: jwiley.ps...@gmail.com, pjmiller...@yahoo.com Cc: r-help@r-project.org Received: Friday, July 30, 2010, 2:44 AM There is a much simpler way. con - textConnection( A 1 101 M 55 5 A 1 104 F 27 0 A 1 106 M 31 35 A 1 107 F 44 21 A 1 109 M 47 15 A 1 111 F 69 70 A 1 112 F 31 10 A 1 114 F 50 0 A 1 116 M 32 20 A 1 118 F 39 25 A 1 119 F 54 0 A 1 121 M 70 38 A 1 123 F 57 55 A 1 124 M 37 18 A 1 126 F 41 0 A 1 128 F 48 8 A 1 131 F 35 0 A 1 134 F 28 0 A 1 135 M 27 40 A 1 138 F 42 12 A 2 202 M 58 68 A 2 203 M 42 22 A 2 206 M 26 30 A 2 207 F 36 0 A 2 210 F 35 25 A 2 211 M 51 0 A 2 214 M 51 60 A 2 216 F 42 15 A 2 217 F 50 50 A 2 219 F 41 35 A 2 222 F 59 0 A 2 223 F 38 10 A 2 225 F 32 0 A 2 226 F 28 16 A 2 229 M 42 48 A 2 231 F 51 45 A 2 234 F 26 90 A 2 235 M 42 0 A 3 301 M 38 28 A 3 302 M 41 20 A 3 304 M 65 75 A 3 306 F 64 0 A 3 307 F 30 30 A 3 309 F 64 5 A 3 311 M 39 80 A 3 314 F 57 85 A 3 315 M 61 12 A 3 318 F 45 95 A 3 319 F 34 26 A 3 321 M 39 10 A 3 324 M 27 0 A 3 325 F 56 35 B 1 102 M 19 68 B 1 103 F 51 10 B 1 105 M 45 20 B 1 108 F 44 65 B 1 110 M 32 25 B 1 113 M 61 75 B 1 115 M 45 83 B 1 117 F 21 0 B 1 120 F 19 55 B 1 122 F 38 0 B 1 125 M 37 72 B 1 127 F 53 40 B 1 129 M 48 0 B 1 130 F 36 80 B 1 132 M 49 20 B 1 133 F 28 0 B 1 136 F 34 45 B 1 137 F 57 95 B 1 139 F 47 40 B 1 140 M 29 0 B 2 201 F 63 10 B 2 204 M 36 49 B 2 205 M 36 16 B 2 208 F 48 12 B 2 209 F 42 40 B 2 212 F 32 0 B 2 213 M 24 88 B 2 215 M 40 59 B 2 218 M 31 24 B 2 220 F 45 72 B 2 221 F 27 55 B 2 224 M 56 70 B 2 227 F 41 0 B 2 228 F 24 65 B 2 230 M 44 30 B 2 232 M 37 32 B 2 233 F 33 0 B 3 303 M 40 26 B 3 305 M 46 15 B 3 308 M 59 82 B 3 310 F 62 38 B 3 312 M 52 40 B 3 313 F 33 40 B 3 316 M 62 87 B 3 317 M 52 60 B 3 320 F 32 2 B 3 322 F 43 0 B 3 323 F 51 35 ) Example_Trial - data.frame(scan(con, list(Trt = , Centre = 0, Patient = 0, Sex = , Age = 0, Score = 0))) ## head(Example_Trial) Trt Centre Patient Sex Age Score 1 A 1 101 M 55 5 2 A 1 104 F 27 0 3 A 1 106 M 31 35 4 A 1 107 F 44 21 5 A 1 109 M 47 15 6 A 1 111 F 69 70 Rather than use a textConnection, you would probably just use a file. -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Joshua Wiley Sent: Friday, 30 July 2010 4:59 PM To: Paul Miller Cc: r-help@r-project.org Subject: Re: [R] R Equivalent of SAS Datastep Line-Hold (@@) Specifier? This gets you to a matrix, though it is messy and you would still have to convert some of the columns from character to numeric, but maybe it will give you an idea. matrix(data = unlist(strsplit(x = readLines(textConnection( A 1 101 M 55 5 A 1 104 F 27 0 A 1 106 M 31 35 A 1 107 F 44 21 A 1 109 M 47 15 A 1 111 F 69 70 A 1 112 F 31 10 A 1 114 F 50 0 A 1 116 M 32 20 A 1 118 F 39 25 A 1 119 F 54 0 A 1 121 M 70 38 A 1 123 F 57 55 A 1 124 M 37 18 A 1 126 F 41 0 A 1 128 F 48 8 A 1 131 F 35 0 A 1 134 F 28 0 A 1 135 M 27 40 A 1 138 F 42 12 A 2 202 M 58 68 A 2 203 M 42 22 A 2 206 M 26 30 A 2 207 F 36 0 A 2 210 F 35 25 A 2 211 M 51 0 A 2 214 M 51 60 A 2 216 F 42 15 A 2 217 F 50 50 A 2 219 F 41 35 A 2 222 F 59 0 A 2 223 F 38 10 A 2 225 F 32 0 A 2 226 F 28 16 A 2 229 M 42 48 A 2 231 F 51 45 A 2 234 F 26 90 A 2 235 M 42 0 A 3 301 M 38 28 A 3 302 M 41 20 A 3 304 M 65 75 A 3 306 F 64 0 A 3 307 F 30 30 A 3 309 F 64 5 A 3 311 M 39 80 A 3 314 F 57 85 A 3 315 M 61 12 A 3 318 F 45 95 A 3 319 F 34 26 A 3 321 M 39 10 A 3 324 M 27 0 A 3 325 F 56 35 B 1 102 M 19 68 B 1 103 F 51 10 B 1 105 M 45 20 B 1 108 F 44 65 B 1 110 M 32 25 B 1 113 M 61 75 B 1 115 M 45 83 B 1 117 F 21 0 B 1 120 F 19 55 B 1 122 F 38 0 B 1 125 M 37 72 B
Re: [R] simple table/matrix problem
Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com
-Original Message-
From: r-help-boun...@r-project.org
[mailto:r-help-boun...@r-project.org] On Behalf Of Robin Hankin
Sent: Friday, July 30, 2010 6:40 AM
To: r-help@r-project.org
Subject: [R] simple table/matrix problem
Hi
Given three vectors
x - c(fish=3, dogs=5, bats=2)
y - c(dogs=1, hogs=3)
z - c(bats=3, dogs=5)
How do I create a multi-way table like the following?
out
x y z
bats 2 0 3
dogs 5 1 5
fish 3 0 0
hogs 0 3 0
You could try using a matrix subscript to a matrix
to insert the values, as in:
f - function (dataList)
{
animals - sort(unique(a - unlist(lapply(dataList, names),
use.names = FALSE)))
variables - names(dataList)
retval - array(0, dim = c(length(animals), length(variables)),
dimnames = list(animals, variables))
retval[cbind(match(a, animals), rep(seq_along(dataList),
vapply(dataList, length, integer(1] -
unlist(dataList, use.names = FALSE)
retval
}
f(list(x=x,y=y,z=z))
x y z
bats 2 0 3
dogs 5 1 5
fish 3 0 0
hogs 0 3 0
Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com
('out' is a matrix).
See how the first line shows 'x' has 2 bats, 'y' has zero
bats, and 'z'
has 3 bats
and so on for each line.
The real application would have a matrix of size ~10 by ~1.
--
Robin K. S. Hankin
Uncertainty Analyst
University of Cambridge
19 Silver Street
Cambridge CB3 9EP
01223-764877
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[R] Using R for Multiple Regression
Hi, Subject: Using R for Multiple Regression I am new to statistic but am interested in applying mathematical models to solve biological problems. I have used a linear model to generate the test data. When using this data I expect R to correctly identify the model but that does not seem to be the case. I am certain that I am doing something wrong but not able to figure it out. Model: Y = m1x1 + m2x2+ m3X3 + c m1=5 m2=6 m3=0 c=2 Model Identified by R using lm(formula = y ~ x1 + x2 + x3) (Intercept) 8.000e+01 x1 1.100e+01 x2 NA x3 NA The data I am using is as follows: y x1 x2 x3 91 1 14 2 102 2 15 5 113 3 16 8 124 4 17 11 135 5 18 14 146 6 19 17 157 7 20 20 168 8 21 23 179 9 22 26 190 10 23 29 Kind regards Dr. Ambikesh Jayal, Department of Information Systems, Computing and Mathematics Room 134 St John's Building Brunel University Uxbridge, Middlesex UB8 3PH, UK Website: http://sites.google.com/site/ambi1999/ [[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] multiple graphics windows open
Hi Erin,
Could you please add a simple self contained code for us to try and help you
with?
(giving us code with doesn't help)
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 Thu, Jul 29, 2010 at 10:21 PM, Erin Hodgess erinm.hodg...@gmail.comwrote:
Dear R People:
Now I have a function with 3 graphics windows. I'd like for them all
to be visible. However, the first window goes blank. Here is the
basic setup. The first plot is the entire series. The user selects
two points, which in turns generates a subset plot and an EWMA subset
plot. Finally, if things worked right, the user should be able to
click on Tile Vertically and see all 3 windows. Also, there should
be a line segment on the original plot connecting the two selected
points.
library(zoo)
xdate - seq(as.Date(1998-01-01),as.Date(2010-06-30),by=day)
length(xdate)
[1] 4564
xt - zoo(rnorm(4564),order=xdate)
eplot
function (x)
{
x11()
plot(x)
z - locator(2)
x11()
plot(window(x, start = min(z$x), end = max(z$x)))
dev.set(dev.prev())
segments(z$x[1],z$y[1],z$x[2],z$y[2],col=red)
dev.set(dev.next())
x11()
ewma(window(x, start = min(z$x), end = max(z$x)))
dev.set(dev.prev())
return(z)
}
eplot(xt)
$x
[1] 9400.369 11592.073
$y
[1] 3.641633 3.353061
How do I get that original plot to appear without losing any of the
other plots, please?
Thanks,
Erin
--
Erin Hodgess
Associate Professor
Department of Computer and Mathematical Sciences
University of Houston - Downtown
mailto: erinm.hodg...@gmail.com
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[[alternative HTML version deleted]]
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] hi! l have a question please help me
yes!! I join group study that study R-programming... so I really tried..only to fail and made many erros.. I really don't know how to perform this... -- View this message in context: http://r.789695.n4.nabble.com/hi-l-have-a-question-please-help-me-tp2307569p2308091.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] finding a function or a line while debugging?
On 30/07/2010 8:04 AM, Raghu wrote: guRus Is there a way by which I can search for a particular function or a particular line of code within the maze of all the R codes that are interlinked? Say for instance I am running a code using quantstrat package and on a particular line I get the error saying x is missing in is.array(x). I want to figure out where is.array is in all the codes that my code refers to? How do I do this? Is there like a grep or search function that can say tell me that 'here is the function inside which is.array(X) is being called' etc? out-try(applyStrategy(strategy=stratSMA5D , portfolios=portfolio.st)) Error in is.array(x) : 'x' is missing ?traceback 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] Need to read an Excel File
On Fri, Jul 30, 2010 at 8:39 AM, rajibshibly rajibshi...@yahoo.com wrote: I am trying to read an Excel file using the following: a-read.xls(mydata.xls, sheet=1) The file mydata.xls is stored in the working directory. However I am getting the following error. Can anyone help. Error in findPerl(verbose = verbose) : perl executable not found. Use perl= argument to specify the correct path. Error in file.exists(tfn) : invalid 'file' argument The error message seems self explanatory. It says it could not find perl and it is advising you to use the perl= argument of read.xls to specify where perl is. Alternately add perl to your path so it can find it. The ?read.xls help page includes examples of using the perl argument. Please ensure you communicate which package you are using next time (I gather from the context its gdata but it might not be obvious). __ 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] standard error for predicted mean count from ZIP
Does anyone have code for computing the standard error of the predicted mean count from a zero-inflated Poisson regression model estimated by the zeroinfl() function from the pscl package (and yes, we've checked with A. Z. already)? Thank you Brian Brian S. Cade, PhD U. S. Geological Survey Fort Collins Science Center 2150 Centre Ave., Bldg. C Fort Collins, CO 80526-8818 email: brian_c...@usgs.gov tel: 970 226-9326 [[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] finding a function or a line while debugging?
On 30/07/2010 8:04 AM, Raghu wrote: guRus Is there a way by which I can search for a particular function or a particular line of code within the maze of all the R codes that are interlinked? Say for instance I am running a code using quantstrat package and on a particular line I get the error saying x is missing in is.array(x). I want to figure out where is.array is in all the codes that my code refers to? How do I do this? Is there like a grep or search function that can say tell me that 'here is the function inside which is.array(X) is being called' etc? out-try(applyStrategy(strategy=stratSMA5D , portfolios=portfolio.st)) Error in is.array(x) : 'x' is missing ?traceback For more info, see the somewhat outdated http://www.stats.uwo.ca/faculty/murdoch/software/debuggingR pages. 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] Ouput several lines of cat
On 30-Jul-10 12:20:35, rajibshibly wrote: Hello, I am brand new to R. I need to know how to output the contents of cat function into a text file. The cat is used to output several lines of string in the following format: X XXX X XX.XX - ( XX.XX XXX ) I need to get the output of all these lines into a text file. I tried to put a file name in the cat function. However the output file only displays single line output. Thanks cat() is somewhat special in that, by default, it does not output a new line after each element in the list being output: cat(A B C,D E F,G H I) # A B C D E F G H I However, you can get it to inset one by using the sep argument (default sep = as in the above output): cat(A B C,D E F,G H I,sep=\n) # A B C # D E F # G H I See the description in '?cat'. The name cat, as in UNIX 'cat', is an abbreviation for catenate, which means to string things together in a chain. Hence the default behaviour above (but with spaces inserted to separate the original elements). For a true catenation, with nothing separating the chained elements, see: cat(A B C,D E F,G H I,sep=) # A B CD E FG H I Hoping this helps. Ted. E-Mail: (Ted Harding) ted.hard...@manchester.ac.uk Fax-to-email: +44 (0)870 094 0861 Date: 30-Jul-10 Time: 17:44:26 -- XFMail -- __ 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] problems about dynamic GMM
Dear all, I am a new user of R, and I would like to use R to estimate dynamaic GMM of Arellano and Bond (1991). The package I used is plm and its code pgmm. However, the regression cannot run and it showed an error message: Error in solve.default(Reduce(+, A2)) : system is computationally singular: reciprocal condition number = 2.27327e-27. Could I please ask, how could I deal with this problems, or are there any other package which can help me estimate dynamic GMM? Many thanks for help. -- Hao-pang __ 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] Re : COXPH: how to get the score test and likelihood ratio test for a specific variable in a multivariate Coxph ?
On Jul 30, 2010, at 11:53 AM, Biau David wrote: Thx for the answer. I am using survival. I didn't know that the Wald and score tests were the same for individual variables in a coxph; I Thought the score test was the multivariate version of the Log-rank. However, say I have only one variable in the model, I should expect the test for the full model and the one for a single variable to be the same? I don't understand what you are saying. What full model? Then it seems to me that the default test is the Wald and that the Wald and the Score are different. Numerically it would appear. cox_lr_age - coxph(Surv(tilr, ev_lr==1)~age, data=tam) summary(cox_lr_age) Call: coxph(formula = Surv(tilr, ev_lr == 1) ~ age, data = tam) n=2156 (76 observations deleted due to missingness) coef exp(coef) se(coef) z Pr(|z|) age 0.019504 1.019696 0.004651 4.193 2.75e-05 *** --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 exp(coef) exp(-coef) lower .95 upper .95 age 1.020 0.9807 1.010 1.029 Rsquare= 0.008 (max possible= 0.669 ) Likelihood ratio test= 18.4 on 1 df, p=1.787e-05 Wald test= 17.58 on 1 df, p=2.751e-05 Score (logrank) test = 17.86 on 1 df, p=2.375e-05 You can find the methods used by executing: #require(survival) getAnywhere(summary.coxph) You had not earlier indicated what functions and output you had questions about. The Score test to which you refer above has the additional parenthetical indication that it is a logrank statistic. Looking in Therneau and Gramsch's, Modeling Survival Data in the index, we find that an approximate intersection of cited pages for score test and log rank-test includes page 53-54 where we see the explanation that a) Wald test is deprecated as the least reliable and b) that a Wald test based on one-iteration is closely related to the efficient score test (but it is not clear that this is the test referred to in this output. Reading between the lines it appears that the score test above might not actually be from a Cox model but is rather from a log-rank procedure. I hope Therneau can clarify. -- David. David Biau. De : David Winsemius dwinsem...@comcast.net À : Biau David djmb...@yahoo.fr Cc : r help list r-help@r-project.org Envoyé le : Ven 30 juillet 2010, 17h 34min 28s Objet : Re: [R] COXPH: how to get the score test and likelihood ratio test for a specific variable in a multivariate Coxph ? On Jul 30, 2010, at 11:08 AM, Biau David wrote: Hello, I would like to get the likelihood ratio and score tests for specific variables in a multivariate coxph model. The default is Wald, so the tests for each separate variable is based on Wald's test. I have the other tests for the full model but I don't know how to get them for each variable. Any idea? The first idea would be to specify which function in which package you are asking questions about. In the case of coxph in the survival package, for instance, you do get a likelihood ratio test (== differences in log-likelihoods) by default. A score test is, at least as as I understand it for individual variables, equivalent to a Wald test, so I don't really understand your question, since youa re already getting all of that in the survival package. (You can extract a score value and loglik values from a coxph object by: (with the first example in the coxph help page) coxph(Surv(time, status) ~ x + strata(sex), test1)$score xoxph(Surv(time, status) ~ x + strata(sex), test1)$loglik But anova(coxph-object) would give you these values in a neater bundle. #Analysis of Deviance Table # Cox model: response is Surv(time, status) #Terms added sequentially (first to last) # loglik Chisq Df Pr(|Chi|) # NULL -3.8712 # x-3.3277 1.0871 10.2971 The question about getting them for each variable does not make a lot of sense to me, since likelihood tests are model comparisons. You can only make such statements about the consequences of adding or deleting a variable to/from an existing model. --David Winsemius, MD West Hartford, CT David Winsemius, MD 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] hi! l have a question please help me
Then please read this: http://www.r-project.org/posting-guide.html *Basic statistics and classroom homework:* R-help is not intended for these. If you want learning materials for R you can check out: http://stats.stackexchange.com/questions/138/resources-for-learning-r And: http://www.r-statistics.com/2009/10/free-statistics-e-books-for-download/ Good luck. 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 Fri, Jul 30, 2010 at 6:19 PM, leepama butch...@hanmail.net wrote: yes!! I join group study that study R-programming... so I really tried..only to fail and made many erros.. I really don't know how to perform this... -- View this message in context: http://r.789695.n4.nabble.com/hi-l-have-a-question-please-help-me-tp2307569p2308091.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] newton.method
Sometimes it is easier to just write it. See below.
On 10-07-30 06:00 AM, r-help-requ...@r-project.org wrote:
Date: Thu, 29 Jul 2010 11:15:05 -0700 (PDT)
From: sammynysj...@caa.columbia.edu
To:r-help@r-project.org
Subject: Re: [R] newton.method
Message-ID:1280427305687-2306895.p...@n4.nabble.com
Content-Type: text/plain; charset=us-ascii
newton.method is in package 'animation'.
Thanks Ravi.
BBSolve/BBOptim seems to work very well although I am not familiar with the
optimization methods being used there. Is there a way to specify a tolerance
in the function to get the required precision.
I did something like this to use newton method.
require(animation)
newton.method(f, init=2, tol=10*exp(-8))
But it gives bogus results.
If someone could point me a correct working version of newton method for
finding roots and its usage, that would be helpful.
cheers,
Sam
tfn-function(x) {
f = 2.5*exp(-0.5*(2*0.045 - x)) + 2.5*exp(-0.045) + 2.5*exp(-1.5*x) - 100
return(f)
}
tgr-function(x) {
g = 0.5*2.5*exp(-0.5*(2*0.045 - x)) -1.5*2.5*exp(-1.5*x)
return(g)
}
newt-function(start, fun, grad) {
x-start
newx-x+100 # to avoid stopping
while( 1 != 0) {
f-fun(x)
g-grad(x)
newx-x-f/g
cat(x, newx, f, g:,x,' ',newx,' ',f,' ',g,\n)
if ((100+x) == (100+newx)) return(newx)
tmp-readline(continue?)
x-newx
}
}
You can try
newt(7,tfn, tgr)
newt(-7,tfn,tgr)
and get both roots quite quickly.
However, I'd probably used uniroot by preference as a general tool. The scripts above are
meant for learning purposes.
Best,
John Nash
PS. I did check tgr with numDeriv -- always worth doing.
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Re: [R] Computation of largest eigenvalue
There is the arpack() function in igraph package for computing leading eigenvalues, but I am not sure how well it can handle very large matrices. I have coded up an accelerated power method and have used it on dense matrices of order 5000. It takes around 9-10 secs for the dominant eigenvalue and corresponding eigenvector. How very large is your matrix? Ravi. -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Christian Weiß Sent: Friday, July 30, 2010 9:32 AM To: r-help@r-project.org Subject: [R] Computation of largest eigenvalue Hello, I am looking for an R function to compute only the largest eigenvalue (Perron-Frobenius eigenvalue) and its corresponding eigenvector of a square matrix (in fact, even only of a non-negative matrix). The function should also be able to deal with very large but sparse matrices. Any idea? Best regards, Christian Weiß -- Dr. Christian H. Weiß Fachbereich Mathematik Technische Universität Darmstadt Schlossgartenstraße 7 64289 Darmstadt -Deutschland- Tel.: +6151/16-3787 Email: we...@mathematik.tu-darmstadt.de Homepage: http://www3.mathematik.tu-darmstadt.de/fileadmin/home/users/157/person/Perso n.html -- Dein Leben wird auch dadurch nicht flach und dumm, wenn du weißt, daß dein Kampf erfolglos sein wird. Es ist viel flacher, wenn du für etwas Gutes und Ideales kämpfst und nun meinst, du müsstest es auch erreichen. Sind denn Ideale zum Erreichen da? Leben wir denn, um den Tod abzuschaffen? - HERMANN HESSE __ 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] Re : COXPH: how to get the score test and likelihood ratio test for a specific variable in a multivariate Coxph ?
The Wald, score, and LR tests are discussed in full in my book. They are not the same. The LR test is the difference between LR(beta=0) and LR(beta=final). The score test is a Taylor series approximation to this using an expansion around beta=0. The Wald test is a similar Taylor series approximation, but around beta=final. If there are no tied times the score test = Log-rank test. If there are ties, then they are just a tiny bit different: the paper using the log-rank has an n-1 in his variance term and the Cox model has an n. Neither is right or wrong, just a different choice. Terry Therneau __ 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] Formatting datetime data for gantt.chart.
Overall goal: I'd like to have a visual representation of when certain computer applications are running over the course of a day (data will come from a SQL query later, but I'm using a csv for now). My idea is to use a gantt chart, but I'm running into issues with the start and end time. I'm wondering if it's because I need to use hours instead of days as my unit of time. Problem #1 I'm trying to use strptime to convert a datetime string (7/12/2010 5:30:05 PM) to POSIX so I can use it as a start/end time in a gantt chart. ( I need to measure hours instead of days, so as.POSIXct/lt won't work for me. I'd also like to retain date info so I can create weekly/monthly averages)) When tested, I get this: strptime(7/12/2010 5:30:05 PM, %X) [1] NA When I delete the date, I get: strptime(5:30:05 PM, %X) [1] 2010-07-30 05:30:05 The full date string in the first example seems pretty unambiguous, so I'm not sure why it is not being recognized and %X should show the full datetime string - any suggestions? #2 I will read the data from a csv file (and eventually, a database). A secondary problem I've run into is converting the entire list of times - will I need to create a loop to handle them all or is there a function similar to tapply() that I can use? Thanks in advance for your time, akn [[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] reading dates in Excel into R
I just do not want the dates format change randomly (seems to me) each time I read it from excel2007 file into R. When I export the excel2007 fiel into csv file and use read.csv function then the dates all come out good (as mm/dd/ in csv file). I guess I have to first import into csv file before reading into R. Just avoid reading from Excel2007 files directly. Thanks, Hongying Date: Fri, 30 Jul 2010 10:24:50 +0100 Subject: Re: [R] reading dates in Excel into R From: fra...@gmail.com To: peter.alsp...@plantandfood.co.nz CC: colorl...@hotmail.com; r-help@r-project.org To read the data into R 1) I format my dates as -MM-DD in Excel (or OpenOffice Calc), 2) (change =na() to NA) 3) Check that required number of significant decimal places are displayed, 4) export as csv and 5) Use readSeries() function from Rmetrics timeSeries package to read the data into R. For what it is worth I have found this approach flexible . Best Regards John On 29 July 2010 22:18, Peter Alspach peter.alsp...@plantandfood.co.nz wrote: Tena koe What do you want to control? You can govern the format used in R using the appropriate R functions. I doubt it would be useful to have dates read from Excel depend on the format set for displaying those dates in Excel. HTH ,,, Peter Alspach -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r- project.org] On Behalf Of Hongying Li Sent: Friday, 30 July 2010 5:33 a.m. To: r-help@r-project.org Subject: [R] reading dates in Excel into R I am reading dates in Excel2007 into R. Here are the functions I used: library(RODBC) channel-odbcConnectExcel2007(myfile.xlsx) tmp-sqlFetch(channel,1,as.is=T) The dates in myfile.xlsx are all in this format: mm/dd/. But when I read it to R, some columns look like -mm-dd 00:00:00, some columns look like -mm-dd, and some columns are numbers. I do not know how I can control this. Any help? Thanks! _ Hotmail is redefining busy with tools for the New Busy. Get more from your inbox. N:WL:en-US:WM_HMP:042010_2 [[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. -- John C Frain Economics Department Trinity College Dublin Dublin 2 Ireland www.tcd.ie/Economics/staff/frainj/home.html mailto:fra...@tcd.ie mailto:fra...@gmail.com [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] R on Mac OS X 10.6 freezing up
I am running R and R64 on a MacBook Pro (2.66GHz, 8GB, OS X 10.6) and it keeps freezing up on me (i.e. have to force quit or kill). Same problem with both R and R64. I am not doing heavy computation, mostly just editing some scripts in the GUI. Also the computer is plenty fast with sufficient memory. I looked around but haven't seen anything on this problem. Thanks! -- Jesse Poland Research Geneticist USDA-ARS Cornell University c: 607-339-7771 __ 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] (no subject)
On Fri, Jul 30, 2010 at 4:59 AM, Daniel Nordlund djnordl...@verizon.net wrote: You haven't provided a reproducible example, so I am going to guess at some of what you are doing. You also have used some function names for your variable names which I like to avoid, so I have used 'b' as the name of the vector for collecting beta coefficients and 'ts' for the predictor variable. I have set var.all equal to 1. A minor point: one should probably avoid using 'ts' as a variable name too, since it's a function in the stats package. -- Gray Calhoun Assistant Professor of Economics, Iowa State University http://www.econ.iastate.edu/~gcalhoun/ __ 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] Re : Re : COXPH: how to get the score test and likelihood ratio test for a specific variable in a multivariate Coxph ?
Well thank you very much for these explanations. Unfortunately, I must admit the book I have for survival analysis seems less precise as to which test to use and why. Still, in coxph (survival), if I have multiple variables in a model, say X_1, X_2, and X_3, how do I test their respective coefficients \beta_1, \beta_2, and \beta_3 with the LR, score and Wald? I guess i can do it by comparing the model with all three variables to those without each of the variables, but is there not a more straightforward manner? David Biau. De : Therneau, Terry M., Ph.D. thern...@mayo.edu À : David Winsemius dwinsem...@comcast.net; Biau David djmb...@yahoo.fr Cc : r help list r-help@r-project.org Envoyé le : Ven 30 juillet 2010, 19h 07min 15s Objet : RE: Re : [R] COXPH: how to get the score test and likelihood ratio test for a specific variable in a multivariate Coxph ? The Wald, score, and LR tests are discussed in full in my book. They are not the same. The LR test is the difference between LR(beta=0) and LR(beta=final). The score test is a Taylor series approximation to this using an expansion around beta=0. The Wald test is a similar Taylor series approximation, but around beta=final. If there are no tied times the score test = Log-rank test. If there are ties, then they are just a tiny bit different: the paper using the log-rank has an n-1 in his variance term and the Cox model has an n. Neither is right or wrong, just a different choice. Terry Therneau [[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] R on Mac OS X 10.6 freezing up
Jesse Poland wrote: I am running R and R64 on a MacBook Pro (2.66GHz, 8GB, OS X 10.6) and it keeps freezing up on me (i.e. have to force quit or kill). Same problem with both R and R64. I am not doing heavy computation, mostly just editing some scripts in the GUI. Also the computer is plenty fast with sufficient memory. I looked around but haven't seen anything on this problem. Thanks! There's an R-sig-mac mailing list, which may be a better place to seek help. If you can replicate the problem easily, I would expect that you could help the developers considerably if you could (say) connect to the R process and do a traceback showing where things get stuck. -- Peter Dalgaard Center for Statistics, Copenhagen Business School Phone: (+45)38153501 Email: pd@cbs.dk Priv: pda...@gmail.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] Summing by index
# build a sample data frame illustrating the problem ids-c(rep(1234,5),rep(5436,3),rep(7864,4)) years-c(seq(1990,1994,by=1),seq(1991,1993,by=1),seq(1990,1993,by=1)) data-seq(14,25,by=1) data[6]-NA DF-data.frame(Id=ids,Year=years,Data=data) DF Id Year Data 1 1234 1990 14 2 1234 1991 15 3 1234 1992 16 4 1234 1993 17 5 1234 1994 18 6 5436 1991 NA 7 5436 1992 20 8 5436 1993 21 9 7864 1990 22 10 7864 1991 23 11 7864 1992 24 12 7864 1993 25 # The result wanted is a sum of DF$Data, by DF$Id. collect the sum of $Data for each $Id # the result would take the form # Id, sum for each Id # Try using BY result-by(DF$Data,INDICES=Data$Id,FUN=sum,na.rm=T) Error in names(IND) - deparse(substitute(INDICES))[1L] : 'names' attribute [1] must be the same length as the vector [0] idx-as.list(Data$Id) idx2-list(1234,1234,1234,1234,1234,5436,5436,5436,7864,7864,7864,7864) result-by(DF$Data,INDICES=idx,FUN=sum,na.rm=T) result [1] 215 result-by(DF$Data,INDICES=idx2,FUN=sum,na.rm=T) Error in tapply(1L:12L, list(1234, 1234, 1234, 1234, 1234, 5436, 5436, : arguments must have same length idx list() idx[1] [[1]] NULL idx2 [[1]] [1] 1234 [[2]] [1] 1234 [[3]] [1] 1234 [[4]] [1] 1234 [[5]] [1] 1234 [[6]] [1] 5436 [[7]] [1] 5436 [[8]] [1] 5436 [[9]] [1] 7864 [[10]] [1] 7864 [[11]] [1] 7864 [[12]] [1] 7864 aggregate(DF$Data, by=idx2,sum,na.rm=T) Error in aggregate.data.frame(as.data.frame(x), ...) : arguments must have same length The instruction that the INDICES must have the same length is confusing me. the number of indices will always be less than the number of rows because the indices are repeated, we want to sum over multiple instances of the indices to collect the Sum by index. I'm confused. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Summing by index
On Jul 30, 2010, at 2:41 PM, steven mosher wrote: # build a sample data frame illustrating the problem ids-c(rep(1234,5),rep(5436,3),rep(7864,4)) years-c(seq(1990,1994,by=1),seq(1991,1993,by=1),seq(1990,1993,by=1)) data-seq(14,25,by=1) data[6]-NA DF-data.frame(Id=ids,Year=years,Data=data) DF Id Year Data 1 1234 1990 14 2 1234 1991 15 3 1234 1992 16 4 1234 1993 17 5 1234 1994 18 6 5436 1991 NA 7 5436 1992 20 8 5436 1993 21 9 7864 1990 22 10 7864 1991 23 11 7864 1992 24 12 7864 1993 25 # The result wanted is a sum of DF$Data, by DF$Id. collect the sum of $Data for each $Id # the result would take the form # Id, sum for each Id # Try using BY result-by(DF$Data,INDICES=Data$Id,FUN=sum,na.rm=T) Try instead: result-by(DF$Data,INDICES=DF$Id,FUN=sum,na.rm=T) -- David. Error in names(IND) - deparse(substitute(INDICES))[1L] : 'names' attribute [1] must be the same length as the vector [0] idx-as.list(Data$Id) idx2- list(1234,1234,1234,1234,1234,5436,5436,5436,7864,7864,7864,7864) result-by(DF$Data,INDICES=idx,FUN=sum,na.rm=T) result [1] 215 result-by(DF$Data,INDICES=idx2,FUN=sum,na.rm=T) Error in tapply(1L:12L, list(1234, 1234, 1234, 1234, 1234, 5436, 5436, : arguments must have same length idx list() idx[1] [[1]] NULL idx2 [[1]] [1] 1234 [[2]] [1] 1234 [[3]] [1] 1234 [[4]] [1] 1234 [[5]] [1] 1234 [[6]] [1] 5436 [[7]] [1] 5436 [[8]] [1] 5436 [[9]] [1] 7864 [[10]] [1] 7864 [[11]] [1] 7864 [[12]] [1] 7864 aggregate(DF$Data, by=idx2,sum,na.rm=T) Error in aggregate.data.frame(as.data.frame(x), ...) : arguments must have same length The instruction that the INDICES must have the same length is confusing me. the number of indices will always be less than the number of rows because the indices are repeated, we want to sum over multiple instances of the indices to collect the Sum by index. I'm confused. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Summing by index
ha. that was a stupid mistake. Thanks. On Fri, Jul 30, 2010 at 11:46 AM, David Winsemius dwinsem...@comcast.netwrote: On Jul 30, 2010, at 2:41 PM, steven mosher wrote: # build a sample data frame illustrating the problem ids-c(rep(1234,5),rep(5436,3),rep(7864,4)) years-c(seq(1990,1994,by=1),seq(1991,1993,by=1),seq(1990,1993,by=1)) data-seq(14,25,by=1) data[6]-NA DF-data.frame(Id=ids,Year=years,Data=data) DF Id Year Data 1 1234 1990 14 2 1234 1991 15 3 1234 1992 16 4 1234 1993 17 5 1234 1994 18 6 5436 1991 NA 7 5436 1992 20 8 5436 1993 21 9 7864 1990 22 10 7864 1991 23 11 7864 1992 24 12 7864 1993 25 # The result wanted is a sum of DF$Data, by DF$Id. collect the sum of $Data for each $Id # the result would take the form # Id, sum for each Id # Try using BY result-by(DF$Data,INDICES=Data$Id,FUN=sum,na.rm=T) Try instead: result-by(DF$Data,INDICES=DF$Id,FUN=sum,na.rm=T) -- David. Error in names(IND) - deparse(substitute(INDICES))[1L] : 'names' attribute [1] must be the same length as the vector [0] idx-as.list(Data$Id) idx2-list(1234,1234,1234,1234,1234,5436,5436,5436,7864,7864,7864,7864) result-by(DF$Data,INDICES=idx,FUN=sum,na.rm=T) result [1] 215 result-by(DF$Data,INDICES=idx2,FUN=sum,na.rm=T) Error in tapply(1L:12L, list(1234, 1234, 1234, 1234, 1234, 5436, 5436, : arguments must have same length idx list() idx[1] [[1]] NULL idx2 [[1]] [1] 1234 [[2]] [1] 1234 [[3]] [1] 1234 [[4]] [1] 1234 [[5]] [1] 1234 [[6]] [1] 5436 [[7]] [1] 5436 [[8]] [1] 5436 [[9]] [1] 7864 [[10]] [1] 7864 [[11]] [1] 7864 [[12]] [1] 7864 aggregate(DF$Data, by=idx2,sum,na.rm=T) Error in aggregate.data.frame(as.data.frame(x), ...) : arguments must have same length The instruction that the INDICES must have the same length is confusing me. the number of indices will always be less than the number of rows because the indices are repeated, we want to sum over multiple instances of the indices to collect the Sum by index. I'm confused. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. David Winsemius, MD West Hartford, CT [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Layering multiple persp plots
Hi all, I've got two persp plots with Identical X and Y's, and I'd like to plot them on the same graph, so that it is obvious where one plot is above the other. I can't find any mention of this anywhere. Do I need to use wireframe? Any help is appreciated. Thanks, -- Ian Bentley M.Sc. Candidate Queen's University Kingston, Ontario [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Summing by index
Thanks again david. To finish out the example. DF Id Year Data 1 1234 1990 14 2 1234 1991 15 3 1234 1992 16 4 1234 1993 17 5 1234 1994 18 6 5436 1991 NA 7 5436 1992 20 8 5436 1993 21 9 7864 1990 22 10 7864 1991 23 11 7864 1992 24 12 7864 1993 25 result-by(DF$Data,INDICES=DF$Id,FUN=sum,na.rm=T) id-as.numeric(unlist(names(result))) sums-unlist(result[]) DF2-data.frame(Id=id,Sums=sums) DF2 Id Sums 1 1234 80 2 5436 41 3 7864 94 Thanks again. On Fri, Jul 30, 2010 at 11:46 AM, David Winsemius dwinsem...@comcast.netwrote: On Jul 30, 2010, at 2:41 PM, steven mosher wrote: # build a sample data frame illustrating the problem ids-c(rep(1234,5),rep(5436,3),rep(7864,4)) years-c(seq(1990,1994,by=1),seq(1991,1993,by=1),seq(1990,1993,by=1)) data-seq(14,25,by=1) data[6]-NA DF-data.frame(Id=ids,Year=years,Data=data) DF Id Year Data 1 1234 1990 14 2 1234 1991 15 3 1234 1992 16 4 1234 1993 17 5 1234 1994 18 6 5436 1991 NA 7 5436 1992 20 8 5436 1993 21 9 7864 1990 22 10 7864 1991 23 11 7864 1992 24 12 7864 1993 25 # The result wanted is a sum of DF$Data, by DF$Id. collect the sum of $Data for each $Id # the result would take the form # Id, sum for each Id # Try using BY result-by(DF$Data,INDICES=Data$Id,FUN=sum,na.rm=T) Try instead: result-by(DF$Data,INDICES=DF$Id,FUN=sum,na.rm=T) -- David. Error in names(IND) - deparse(substitute(INDICES))[1L] : 'names' attribute [1] must be the same length as the vector [0] idx-as.list(Data$Id) idx2-list(1234,1234,1234,1234,1234,5436,5436,5436,7864,7864,7864,7864) result-by(DF$Data,INDICES=idx,FUN=sum,na.rm=T) result [1] 215 result-by(DF$Data,INDICES=idx2,FUN=sum,na.rm=T) Error in tapply(1L:12L, list(1234, 1234, 1234, 1234, 1234, 5436, 5436, : arguments must have same length idx list() idx[1] [[1]] NULL idx2 [[1]] [1] 1234 [[2]] [1] 1234 [[3]] [1] 1234 [[4]] [1] 1234 [[5]] [1] 1234 [[6]] [1] 5436 [[7]] [1] 5436 [[8]] [1] 5436 [[9]] [1] 7864 [[10]] [1] 7864 [[11]] [1] 7864 [[12]] [1] 7864 aggregate(DF$Data, by=idx2,sum,na.rm=T) Error in aggregate.data.frame(as.data.frame(x), ...) : arguments must have same length The instruction that the INDICES must have the same length is confusing me. the number of indices will always be less than the number of rows because the indices are repeated, we want to sum over multiple instances of the indices to collect the Sum by index. I'm confused. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. David Winsemius, MD West Hartford, CT [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] hi! l have a question please help me
hey!!! this is not classroom homework!! To do main programming, I find some good training problems in paper... I tried to do that...but failed so please help me Nobody help me...I relly don't know how to perform this... If you solve this probelm,I will study your work to solve main problem... so please help me -- View this message in context: http://r.789695.n4.nabble.com/hi-l-have-a-question-please-help-me-tp2307569p2308257.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Summing by index
Hi, R has a buildin function ?rowsum rowsum(DF$Data,DF$Id,na.rm=T) - A R learner. -- View this message in context: http://r.789695.n4.nabble.com/Summing-by-index-tp2308332p2308411.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] Layering multiple persp plots
On 30/07/2010 1:22 PM, Ian Bentley wrote: Hi all, I've got two persp plots with Identical X and Y's, and I'd like to plot them on the same graph, so that it is obvious where one plot is above the other. I can't find any mention of this anywhere. Do I need to use wireframe? persp() can't do that. persp3d() in the rgl package can. I'm not sure about wireframe(). (If you use persp3d, take note of the fact that the colours are specified slightly differently. See ?persp3d). 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] reading dates in Excel into R
On Fri, Jul 30, 2010 at 1:17 PM, Hongying Li colorl...@hotmail.com wrote: I just do not want the dates format change randomly (seems to me) each time I read it from excel2007 file into R. When I export the excel2007 fiel into csv file and use read.csv function then the dates all come out good (as mm/dd/ in csv file). I guess I have to first import into csv file before reading into R. Just avoid reading from Excel2007 files directly. Thanks, Hongying You could try the various alternatives in the list on this page: http://rwiki.sciviews.org/doku.php?id=tips:data-io:ms_windowss=excel and see if any of them work in the way you wish. __ 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] newton.method
I have written versions of these in C++ but my point is to learn R and
discover all these methods in it.
thanks
On Fri, Jul 30, 2010 at 12:55 PM, Prof. John C Nash [via R]
ml-node+2308224-1876059272-368...@n4.nabble.comml-node%2b2308224-1876059272-368...@n4.nabble.com
wrote:
Sometimes it is easier to just write it. See below.
On 10-07-30 06:00 AM, [hidden
email]http://user/SendEmail.jtp?type=nodenode=2308224i=0wrote:
Date: Thu, 29 Jul 2010 11:15:05 -0700 (PDT)
From: sammyny[hidden
email]http://user/SendEmail.jtp?type=nodenode=2308224i=1
To:[hidden email] http://user/SendEmail.jtp?type=nodenode=2308224i=2
Subject: Re: [R] newton.method
Message-ID:[hidden
email]http://user/SendEmail.jtp?type=nodenode=2308224i=3
Content-Type: text/plain; charset=us-ascii
newton.method is in package 'animation'.
Thanks Ravi.
BBSolve/BBOptim seems to work very well although I am not familiar with
the
optimization methods being used there. Is there a way to specify a
tolerance
in the function to get the required precision.
I did something like this to use newton method.
require(animation)
newton.method(f, init=2, tol=10*exp(-8))
But it gives bogus results.
If someone could point me a correct working version of newton method for
finding roots and its usage, that would be helpful.
cheers,
Sam
tfn-function(x) {
f = 2.5*exp(-0.5*(2*0.045 - x)) + 2.5*exp(-0.045) + 2.5*exp(-1.5*x) - 100
return(f)
}
tgr-function(x) {
g = 0.5*2.5*exp(-0.5*(2*0.045 - x)) -1.5*2.5*exp(-1.5*x)
return(g)
}
newt-function(start, fun, grad) {
x-start
newx-x+100 # to avoid stopping
while( 1 != 0) {
f-fun(x)
g-grad(x)
newx-x-f/g
cat(x, newx, f, g:,x,' ',newx,' ',f,' ',g,\n)
if ((100+x) == (100+newx)) return(newx)
tmp-readline(continue?)
x-newx
}
}
You can try
newt(7,tfn, tgr)
newt(-7,tfn,tgr)
and get both roots quite quickly.
However, I'd probably used uniroot by preference as a general tool. The
scripts above are
meant for learning purposes.
Best,
John Nash
PS. I did check tgr with numDeriv -- always worth doing.
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[R] Using data frame col names and variables
Hi to you all! I'm new to R and to this mailing list, so do please excuse me if my question sounds stupid. Currently I'm working with a data frame called results. In each column of results I have a set of results for different experiments (all results are numerical) realized in different dates, so that each row corresponds to a day. To make it clear when displaying the results, I gave names to the columns with the names of the experiments realized. I also gave names to the rows based on the day the experiments where realized. My problem now is that I'm trying to separate this experiments based on a criteria that is not important for the moment. What I want to be able to do is, given an experiment name, obtain the time series of the results of that experiment. I know I can do this by typing results$nameoftheexperiment But what if I have a variable name which contains the experiment's name? Doing the following results$name doesn't work, as expected, since there is no column with name name. Any help would be appreciated. Thank you very much! [[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] Fw: Having problem to define a subclass, please help me
Dear all, apart from my previous question, I would also like to ask one more
question here, which is as follows:
#let me 1st define a class and a subclass
setClass(a, representation=list(x=numeric, y=numeric),
prototype=list(x=rep(1,3),y=rep(2,3)))
setClass(b, representation=list(x1=character, y1=character),
prototype=list(x1=rep(A,3),y1=rep(B,3)), contains=a)
#Now I define the method for initialize() for class a
setMethod(initialize, a, function(.Object, x, y, ...) {
if (length(x) != length(y)) x=y=rep(10,4)
.obj...@x = x
.obj...@y = y
.Object })
new(a, x=rnorm(4), y=rnorm(4))
new(a, x=rnorm(4), y=rnorm(3))
#Next I define method for initialize() for subclass b
setMethod(initialize, b, function(.Object, x1, y1, ...) {
if (length(x1) == length(y1)) x1=y1=rep(bbb,4)
.obj...@x1 = x1
.obj...@y1 = y1
.Object })
new(b, x1=letters[1:3], x2=letters[2:4], x=rnorm(4), y=rnorm(3))
An object of class b
Slot x1:
[1] bbb bbb bbb bbb
Slot y1:
[1] bbb bbb bbb bbb
Slot x:
[1] 1 1 1
Slot y:
[1] 2 2 2
new(b, x1=letters[1:3], x2=letters[2:4], x=rnorm(4), y=rnorm(4))
Error in checkSlotAssignment(object, name, value) :
assignment of an object of class numeric is not valid for slot y1 in an
object of class b; is(value, character) is not TRUE
Here my questions are:
1. Why I am getting the prototype object in next to previous example for slots
x y?
2. Why just previous example generates some error?
3. The method initialize() function for a subclass requires explicit
description of all slots of it's superclass? If yes why? In my understanding,
all defined law for super-class should be inherited by it's sub-class,
therefore no need to define again.
I would be really grateful if someone clarify those.
Thanks
--- On Fri, 7/30/10, Megh Dal megh700...@yahoo.com wrote:
From: Megh Dal megh700...@yahoo.com
Subject: Having problem to define a subclass, please help me
To: r-h...@stat.math.ethz.ch
Date: Friday, July 30, 2010, 4:46 PM
Here I am having problem to define a
subclass, specially if I define that subclass after defining
initialize() method for its superclass. Here is my code:
setClass(a, representation=list(x=numeric,
y=numeric), prototype=list(x=rnorm(10), y=rnorm(10)))
[1] a
setMethod(initialize, a, function(.Object, x, y,
...) {
+
if (length(x) != length(y)) x = y = rep(5,
4)
+
.obj...@x = x
+
.obj...@y = y
+
.Object })
[1] initialize
setClass(b, representation=list(x1=character),
contains=a)
Error in .local(.Object, ...) : element 1 is empty;
the part of the args list of 'length'
being evaluated was:
(x)
Can anyone please point me where I am doing wrong?
Thanks,
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[R] Problem with par and bubble plot
Hi all. I have been trying to plot 9 bubble plots on each page of a PDF file. For this, I'm using : par(mfcol = c(3,3), mar = c(3,3,3,3), oma = c(0,0,0,0)); However, when plotting the bubble plot (gstats package), it plots the graph on a full page. I tried to plot something else with plot(x,y) and it works as intended. So I'm guessing the problem comes from the bubble plot itself. Anyone suggestion? Best regards, Phil -- View this message in context: http://r.789695.n4.nabble.com/Problem-with-par-and-bubble-plot-tp2308452p2308452.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] Using data frame col names and variables
On Jul 30, 2010, at 2:12 PM, Cadmium 2 wrote: Hi to you all! I'm new to R and to this mailing list, so do please excuse me if my question sounds stupid. Currently I'm working with a data frame called results. In each column of results I have a set of results for different experiments (all results are numerical) realized in different dates, so that each row corresponds to a day. To make it clear when displaying the results, I gave names to the columns with the names of the experiments realized. I also gave names to the rows based on the day the experiments where realized. My problem now is that I'm trying to separate this experiments based on a criteria that is not important for the moment. What I want to be able to do is, given an experiment name, obtain the time series of the results of that experiment. I know I can do this by typing results$nameoftheexperiment But what if I have a variable name which contains the experiment's name? Doing the following results$name doesn't work, as expected, since there is no column with name name. Try: results[ , name] And read the the help page for ?Extract. The $ formalism does not evaluate its argument whereas the [ function does. -- David. Any help would be appreciated. Thank you very much! [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. David Winsemius, MD 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] svydesign syntax
On Thu, 22 Jul 2010, R user wrote: This message is for those familiar with the survey package. I need to fit a weighted Cox model to accommodate the sampling weights as I have a case-control study with controls sampled at random from a database in a ratio 2:1 to cases (whom were all sampled). I want to make sure I am using the right svydesign syntax to specify this sampling design. Can anyone please check if the statement below is appropriate for my design? #group represents the case (total of 132) vs control (253 out of the total of 853 controls) groups; prob is 1 for cases and 253/853 for controls and ssize=132 for cases and 853 otherwise; dstr=svydesign(id=~1, strata=~group, prob=~prob, fpc=~ssize, data=noNA) This is technically correct but probably not for what you want. You probably want dstr=svydesign(id=~1, strata=~group, prob=~prob, data=noNA) or dstr = twophase(id=list(~1,~1), strata=list(NULL, ~group), data=noNA) Your svydesign() call treats the database as the full population. This could be correct, but usually people want estimates for the 'superpopulation' from which the population was sampled. The first option above is very slightly conservative, the second describes the two phases of sampling that give first the whole database and then your subsample. -thomas Thomas Lumley Professor of Biostatistics University of Washington, Seattle __ 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 dates in Excel into R
I've wasted a lot of time trying to read in dates from Excel. Even importing .csv files has not guarantees and often produces garbage instead of dates. What I found works best is saving the Excel data base as a tab-delimited file .txt (after having formatted the dates in the format you need, e.g., mm/dd/). And then you can read it (including dates) into R no problems. Dimitri On Fri, Jul 30, 2010 at 1:31 PM, Gabor Grothendieck ggrothendi...@gmail.com wrote: On Fri, Jul 30, 2010 at 1:17 PM, Hongying Li colorl...@hotmail.com wrote: I just do not want the dates format change randomly (seems to me) each time I read it from excel2007 file into R. When I export the excel2007 fiel into csv file and use read.csv function then the dates all come out good (as mm/dd/ in csv file). I guess I have to first import into csv file before reading into R. Just avoid reading from Excel2007 files directly. Thanks, Hongying You could try the various alternatives in the list on this page: http://rwiki.sciviews.org/doku.php?id=tips:data-io:ms_windowss=excel and see if any of them work in the way you wish. __ 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. -- Dimitri Liakhovitski Ninah Consulting www.ninah.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] reading dates in Excel into R
Hi Hongying, There is a manual on the R website about data import and export that explains different options. --Gray On 7/30/10, Hongying Li colorl...@hotmail.com wrote: I just do not want the dates format change randomly (seems to me) each time I read it from excel2007 file into R. When I export the excel2007 fiel into csv file and use read.csv function then the dates all come out good (as mm/dd/ in csv file). I guess I have to first import into csv file before reading into R. Just avoid reading from Excel2007 files directly. Thanks, Hongying Date: Fri, 30 Jul 2010 10:24:50 +0100 Subject: Re: [R] reading dates in Excel into R From: fra...@gmail.com To: peter.alsp...@plantandfood.co.nz CC: colorl...@hotmail.com; r-help@r-project.org To read the data into R 1) I format my dates as -MM-DD in Excel (or OpenOffice Calc), 2) (change =na() to NA) 3) Check that required number of significant decimal places are displayed, 4) export as csv and 5) Use readSeries() function from Rmetrics timeSeries package to read the data into R. For what it is worth I have found this approach flexible . Best Regards John On 29 July 2010 22:18, Peter Alspach peter.alsp...@plantandfood.co.nz wrote: Tena koe What do you want to control? You can govern the format used in R using the appropriate R functions. I doubt it would be useful to have dates read from Excel depend on the format set for displaying those dates in Excel. HTH ,,, Peter Alspach -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r- project.org] On Behalf Of Hongying Li Sent: Friday, 30 July 2010 5:33 a.m. To: r-help@r-project.org Subject: [R] reading dates in Excel into R I am reading dates in Excel2007 into R. Here are the functions I used: library(RODBC) channel-odbcConnectExcel2007(myfile.xlsx) tmp-sqlFetch(channel,1,as.is=T) The dates in myfile.xlsx are all in this format: mm/dd/. But when I read it to R, some columns look like -mm-dd 00:00:00, some columns look like -mm-dd, and some columns are numbers. I do not know how I can control this. Any help? Thanks! _ Hotmail is redefining busy with tools for the New Busy. Get more from your inbox. N:WL:en-US:WM_HMP:042010_2 [[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. -- John C Frain Economics Department Trinity College Dublin Dublin 2 Ireland www.tcd.ie/Economics/staff/frainj/home.html mailto:fra...@tcd.ie mailto:fra...@gmail.com [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Gray Calhoun Assistant Professor of Economics, Iowa State University http://www.econ.iastate.edu/~gcalhoun/ __ 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] Fw: Re: R statical-script for analysis (India)
Nilesh M. Vaghela Research Scholar c/o Prof. N. V. Sastry, Department of Chemistry, Sardar Patel University Vallabhvidyanagar-388 120 Gujarat, India --- On Thu, 29/7/10, Kurt Hornik kurt.hor...@wu.ac.at wrote: From: Kurt Hornik kurt.hor...@wu.ac.at Subject: Re: R statical-script for analysis (India) To: Nilesh Vaghela nilesh_sp...@yahoo.in Cc: c...@r-project.org Date: Thursday, 29 July, 2010, 8:17 AM Nilesh Vaghela writes: Dear Sir, I am doing research work on solution behavior of the ionic liquids by surface tension and conductivity measurements. We get some references (see attachment) in which the data analysis of the were done by R statical programme. We want to do same. But we do not know how to write script for analysis of the data.Basically it is Philips equation for cmc determination. Please explain me and be needful in my research work. Kind regards [[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] conditonal if
Hi,
I have problem with my R program. Actually, it just a simple program, but I do
not know the error is. Here is part of my program:
if (tau2ca==0) {MVvc - 0.01} else {MVvc - tau2ca}
ri_vc - si2/MVvc
vi_vc - ri_vc + 1
Y_bar_vc - sum(y/vi_vc)/sum((1/vi_vc))
tau2MVvc - sum((1/vi_vc)*(y - Y_bar_vc)^2)/(k-1)
But then, there is an error displayed in workspace
Error in if (tau2ca == 0) { : missing value where TRUE/FALSE needed
I do not know why there is an error like that. I think I type the program
correctly. Also, I just want to make sure whether my program below is right or
not.
for (l in 1:k)
{if (a[l]==0 | b[l]==0 | c[l]==0 | d[l]==0)
{ a[l] - a[l]+0.5
b[l] - b[l]+0.5
c[1] - c[1]+0.5
d[1] - d[1]+0.5
}
}
Looking forward to hearing from you.
Many thanks,
-pwikie-
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