Re: [R] Sweave encoding option
Hi Yihui, Thanks for your quick reply! Yes, it was a long vacation, but definitely not long enough :-). Seriously, I have not changed my R, my tex engine etc. Nothing. And I was running the command just a couple of weeks ago and everything was fine. But now I need to specify this encoding option Still puzzled. Tao From: Yihui Xie x...@yihui.name To: Shi, Tao shida...@yahoo.com Cc: r-help@r-project.org r-help@r-project.org Sent: Tuesday, September 4, 2012 7:40 PM Subject: Re: [R] Sweave encoding option What happened might be that your vacation took too long. The encoding argument was introduced in R 2.13.1 (July last year). Nothing has changed in your Rnw document, but things have always been changing in R, so the best thing to do is to check out help(Sweave). Regards, Yihui -- Yihui Xie xieyi...@gmail.com Phone: 515-294-2465 Web: http://yihui.name Department of Statistics, Iowa State University 2215 Snedecor Hall, Ames, IA On Tue, Sep 4, 2012 at 7:02 PM, Shi, Tao shida...@yahoo.com wrote: Hi list, I was running Sweave on one of my .rnw file. Everything was fine, until I came back from the vacation. Nothing changed (at least to my knowledge), but now I have this problem:   Sweave(myfile.rnw) Error: âCOLO001final.rnwâ is not ASCII and does not declare an encoding After snooping around on the web, I found this solution: Sweave(myfile.rnw, encoding=utf8) Now everything works fine. Could somebody explain to me what happened? Why I need to specify the encoding now for it to work? What has changed (beyond my knowledge) in my computer that is causing this error? I'm running R 2.15.1 on WinXP. Thanks! Tao __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Read data from .csv file as a matrix and compare the different between two matrix
On Sep 4, 2012, at 4:39 PM, s.s.m. fauzi wrote: Hi, I have two table matrix, and I would like to compare the different between two matrix. For example: Matrix 1: A B C A 0 1 0 B 0 0 1 C 0 0 0 Matrix 2: A B C A 0 1 0 B 0 0 0 C 0 0 0 Each column which have value 1, should also return value 1. As in this case/example, the result should appear like this (as below). The result of this differentiation should also be in matrix table and should be write in . csv file. Result of the differences: Differences? What differences? If you examined the matrix returned by: matrix1 == matrix2 it would look exactly like your desired result: A B C A 0 1 0 B 0 0 0 C 0 0 0 At the mean time, I'm able to load the .csv file and convert it to matrix matrix1 -read.table(matrix1.csv, header=T, sep=,) matrix1 - as.matrix(matrix1) matrix2 - read.table(matrix2.csv, header=T, sep=,) matrix2 - as.matrix(matrix2) But, I can't find a suitable script to compare the differences between the matrix and write it to file. Appreciate any help from the expert [[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 Alameda, CA, USA __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] run EGARCH package on REXCEl
Hi, I have limited experience on R and recently started using REXcel. Although I have been able to run both simple functions (like mean etc) and some complex ones (like Principal Component analysis, PCA) using RExcel, I am facing some problems while running EGARCH model. For this I have downloaded the 'betategarch' package for R to run EGARCH with student t dist. Although the package has been installed properly, whenever I run function, I get an error saying - could not find function tegarch.est. I'd appreciate any help on the above. Regards Ank [[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] POSIXlt and daylight savings time
I'll rephrase the question...
If you try...
as.POSIXlt('2004-10-31 02:00:00')
you get
[1] 2004-10-31
What do I need to do to make it return
[1] 2004-10-31 02:00:00
--
View this message in context:
http://r.789695.n4.nabble.com/POSIXlt-and-daylight-savings-time-tp4642253p4642272.html
Sent from the R help mailing list archive at Nabble.com.
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[R] How to effectively remove Outliers from a binary logistic regression in R
Hallo there, greetings from Germany. I have a simple question for you. I have run a binary logistic model, but there are lots of outliers distorting the real results. I have tried to get rid of the outliers using the following commands: remove = -c(56, 303, 365, 391, 512, 746, 859, 940, 1037, 1042, 1138, 1355) MIGRATION.rebuild - glm(MIGRATION, subset=remove) influence(MIGRATION.rebuild) influence.measures(MIGRATION.rebuild) BUT it did not work. My question is: *Do you know a simple R-command which erases outliers and rebuilds the model without them?* I am including my model below so that you may have an idea of how I am trying to do it. Thanks in advance for your help. Francisco M. da Rocha [[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] run EGARCH package on REXCEl
Ank, Welcome to R. I suspect that what you are missing is: require(betategarch) If you don't know it, you may be interested in the blog post: http://www.portfolioprobe.com/2012/07/06/a-practical-introduction-to-garch-modeling/ Also questions about garch are generally best sent to R-sig-finance (you have to subscribe before you can post). Though if I'm correct in my diagnosis, this was the right list for this question. Pat On 05/09/2012 07:34, Ankit Mital wrote: Hi, I have limited experience on R and recently started using REXcel. Although I have been able to run both simple functions (like mean etc) and some complex ones (like Principal Component analysis, PCA) using RExcel, I am facing some problems while running EGARCH model. For this I have downloaded the 'betategarch' package for R to run EGARCH with student t dist. Although the package has been installed properly, whenever I run function, I get an error saying - could not find function tegarch.est. I'd appreciate any help on the above. Regards Ank [[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. -- Patrick Burns pbu...@pburns.seanet.com twitter: @portfolioprobe http://www.portfolioprobe.com/blog http://www.burns-stat.com (home of 'Some hints for the R beginner' and 'The R Inferno') __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 effectively remove Outliers from a binary logistic regression in R
On 09/05/2012 05:40 PM, Marcus Tullius wrote: Hallo there, greetings from Germany. I have a simple question for you. I have run a binary logistic model, but there are lots of outliers distorting the real results. I have tried to get rid of the outliers using the following commands: remove = -c(56, 303, 365, 391, 512, 746, 859, 940, 1037, 1042, 1138, 1355) MIGRATION.rebuild- glm(MIGRATION, subset=remove) influence(MIGRATION.rebuild) influence.measures(MIGRATION.rebuild) BUT it did not work. My question is: *Do you know a simple R-command which erases outliers and rebuilds the model without them?* I am including my model below so that you may have an idea of how I am trying to do it. Hi Francisco, Your model didn't make it to the help list, but I think that the problem is in your attempt to use the subset argument in glm. The vector is supposed to include the indices of the values that you _want_ in the analysis, and it looks like you are trying to remove the values that you _don't_ want. Say you have 2000 rows in your data frame in the model. The subset argument should look something like this: glm(MIGRATION, subset=!(1:2000 %in% c(56,303,365,391,512,746,859,940,1037,1042,1138, 1355)) 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.
[R] Installing lumi and hdrcde
To whom it may concern. As I would like to analyse some array data I was keen on downloading the lumi package that depends obviously on hdrcde that is not available for r 2.12.1. I did not find instructions to solve or circumvent this problem. Installing hdrcde by hand did not work either. It was not detected by (.packages(all.available=TRUE)) if installed in the R library. Thanks Hermann Norpois This was my try to install the lumi package: source (http://bioconductur.org/biocLite.R;) Fehler in file(filenaReme, r, encoding = encoding) : kann Verbindung nicht öffnen Zusätzlich: Warnmeldung: In file(filename, r, encoding = encoding) : kann 'bioconductur.org' nicht auflösen source (http://bioconductor.org/biocLite.R;) BiocInstaller version 1.2.1, ?biocLite for help biocLite(lumi) BioC_mirror: 'http://www.bioconductor.org' Using R version 2.14, BiocInstaller version 1.2.1. Installing package(s) 'lumi' Installing package(s) into /home/hnorpois/R/i686-pc- linux-gnu-library/2.14 (as lib is unspecified) Warnung: dependency hdrcde is not available versuche URL ' http://www.bioconductor.org/packages/2.9/bioc/src/contrib/lumi_2.6.0.tar.gz' Content type 'application/x-gzip' length 11386679 bytes (10.9 Mb) URL geöffnet == downloaded 10.9 Mb ERROR: dependency hdrcde is not available for package lumi * removing /home/hnorpois/R/i686-pc-linux-gnu-library/2.14/lumi The downloaded packages are in /tmp/RtmpMNrvTz/downloaded_packages Warnmeldungen: 1: In install.packages(pkgs = pkgs, repos = repos, ...) : installation of package lumi had non-zero exit status 2: 'rgl' cannot be updated, installed directory '/usr/lib/R/site-library' not writeable [[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] linking HTML with R
hi, I am said to create a small form in html and after i click the submit button it should execute R function and move to next page of html can I know how can it be done??? can we link R and HTML??? which packages will help me in doing this??? are there any examples similar to this online??? Thanks in advance with regards, C. Punitha - Thank you, with regards, Punitha -- View this message in context: http://r.789695.n4.nabble.com/linking-HTML-with-R-tp4642276.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] Mailing List
Hello there, is there a way I can erase my name from the mailing list and still get mails concerning the topics I am interested in? I cannot handle all those emails coming in constantly. I do not have time for that. Greetings, Francisco [[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] POSIXlt and daylight savings time
Hello,
Jeff already answered to your question,
as.POSIXlt('2004-10-31 02:00:00', format = %Y-%m-%d %H:%M:%S)
And in my system and timezone (GMT) I get
as.POSIXlt('2004-10-31 02:00:00')
[1] 2004-10-31 02:00:00
So Jeff's point (b) should also be followed.
sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: i386-pc-mingw32/i386 (32-bit)
locale:
[1] LC_COLLATE=Portuguese_Portugal.1252 LC_CTYPE=Portuguese_Portugal.1252
[3] LC_MONETARY=Portuguese_Portugal.1252 LC_NUMERIC=C
[5] LC_TIME=Portuguese_Portugal.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] fortunes_1.4-2 tools_2.15.1
Hope this helps,
Rui Barradas
Em 05-09-2012 09:24, pdb escreveu:
I'll rephrase the question...
If you try...
as.POSIXlt('2004-10-31 02:00:00')
you get
[1] 2004-10-31
What do I need to do to make it return
[1] 2004-10-31 02:00:00
--
View this message in context:
http://r.789695.n4.nabble.com/POSIXlt-and-daylight-savings-time-tp4642253p4642272.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
and provide commented, minimal, self-contained, reproducible code.
__
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] predict rpart newdata - introduce only values variables used in the tree
agent dunham crosspide at hotmail.com writes: I've a tree which included at first 23 variables. Then I've pruned this tree, and there are only 8 variables involved. Are you sure the others are not being considered as surrogate variables? Is there a way to introduce only this 8 values? No. Why? See my previous answer. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Read data from .csv file as a matrix and compare the different between two matrix
Hello, Em 05-09-2012 07:26, David Winsemius escreveu: On Sep 4, 2012, at 4:39 PM, s.s.m. fauzi wrote: Hi, I have two table matrix, and I would like to compare the different between two matrix. For example: Matrix 1: A B C A 0 1 0 B 0 0 1 C 0 0 0 Matrix 2: A B C A 0 1 0 B 0 0 0 C 0 0 0 Each column which have value 1, should also return value 1. As in this case/example, the result should appear like this (as below). The result of this differentiation should also be in matrix table and should be write in . csv file. Result of the differences: Differences? What differences? In fact, this doesn't seem to be a differences problem, but a logical one: - result is 1 iff both operands are 1. So the solution could be # multiply to return an integer, not T/F 1*(matrix1 matrix2) Rui Barradas If you examined the matrix returned by: matrix1 == matrix2 it would look exactly like your desired result: A B C A 0 1 0 B 0 0 0 C 0 0 0 At the mean time, I'm able to load the .csv file and convert it to matrix matrix1 -read.table(matrix1.csv, header=T, sep=,) matrix1 - as.matrix(matrix1) matrix2 - read.table(matrix2.csv, header=T, sep=,) matrix2 - as.matrix(matrix2) But, I can't find a suitable script to compare the differences between the matrix and write it to file. Appreciate any help from the expert [[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 Alameda, CA, USA __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Mailing List
Since noone but you knows what you are interested in - unlikely. You could try to set up your mailclient with rules, deleting mails coming from the list that do not contain certain keywords. On 05.09.2012, at 12:00, Marcus Tullius wrote: Hello there, is there a way I can erase my name from the mailing list and still get mails concerning the topics I am interested in? I cannot handle all those emails coming in constantly. I do not have time for that. Greetings, Francisco [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] repace values in raster based on values in another raster
Hi The key information is how landuse.raster and fire.did.not.occurr objects looks like. e.g. for matrix you can do set.seed(333) mat-matrix(rnorm(20),5,4) mat[mat0]-NA fat-matrix(sample(1:5, 20, replace=T),5,4) lat-100 mat[fat==1]-lat mat [,1][,2] [,3][,4] [1,] -0.08281164 100.000 -1.1249003 100.000 [2,] NA NA -0.8743036 NA [3,] -2.05128979 NA NA NA [4,] NA NA -0.5839751 100.000 [5,] -1.52596060 -0.5604825 -0.8232986 -0.3804572 if lat is one value. If it is matrix with the same dimensions as mat you need to do it differently. lat-matrix(runif(20)*100, 5,4) mat[fat==1]-lat Warning message: In mat[fat == 1] - lat : number of items to replace is not a multiple of replacement length mat [,1] [,2] [,3] [,4] [1,] -0.08281164 24.1093483 -1.1249003 38.9556712 [2,] NA NA -0.8743036 NA [3,] -2.05128979 NA NA NA [4,] NA NA -0.5839751 61.7859617 [5,] -1.52596060 -0.5604825 -0.8232986 -0.3804572 mat[which(fat==1)]-lat[which(fat==1)] mat [,1] [,2] [,3] [,4] [1,] -0.08281164 41.0170721 -1.1249003 15.3955547 [2,] NA NA -0.8743036 NA [3,] -2.05128979 NA NA NA [4,] NA NA -0.5839751 3.0707204 [5,] -1.52596060 -0.5604825 -0.8232986 -0.3804572 Regards Petr -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-bounces@r- project.org] On Behalf Of sean_parks Sent: Wednesday, September 05, 2012 12:58 AM To: r-help@r-project.org Subject: [R] repace values in raster based on values in another raster Hi, I am attempting to create a new raster based on values of another raster. In the Arc world, this is called a conditional statement or con statement. I am having quite a bit of difficulty figuring this out in R. Here is some pseudo-code: if (fire.did.not.occurr == 1) then (new. raster = landuse.raster) Here is some real code and the associated error: landuse.raster - raster(C:/temp/landuse.raster.tif) new.raster - landuse.raster new.raster[new.raster 0] - NA new.raster[fire.did.not.occurr == 1] - landuse.raster Error in x@data@values[i] - value : incompatible types (from S4 to integer) in subassignment type fix If I replace the landuse.raster with a specific number in the final command, then the operation works, but I would like to replace with the values in the landuse.raster. Please help. FYI: Please know that I have searched the forums and have not found anything helpful. Perhaps I am using incorrect search criteria. Thanks, Sean -- View this message in context: http://r.789695.n4.nabble.com/repace- values-in-raster-based-on-values-in-another-raster-tp4642245.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting- guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Mailing List
On Sep 5, 2012, at 3:00 AM, Marcus Tullius wrote: Hello there, is there a way I can erase my name from the mailing list and still get mails concerning the topics If you change your subscription options to daily digest ( at the page where you signed up), you can just read the top of the digest. I am interested in? I cannot handle all those emails coming in constantly. I do not have time for that. Greetings, Francisco David Winsemius, MD Alameda, CA, USA __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] cenboxplot(): Reporting Limit Twice Correct Concentration [RESOLVED]
On Wed, 5 Sep 2012, Nordlund, Dan (DSHS/RDA) wrote: The line is drawn at 0.01 because there is a censored record where quant=0.01, i.e. sb.t[which(sb.t$quant==0.01 sb.t$ceneq1==TRUE),] site sampdateera param quant ceneq1 floor ceiling 34169 MW-5 1995-01-10 Pre-mining SbTot 0.01 TRUE 00.01 Dan, Thanks for seeing what I missed evary time I went though the data. I knew it had to be some mis-classified observation but after three times through I thought that I had corrected all the misfits and didn't see that one. New eyeballs are invaluable after one's looked at data or code a long time. Very much appreciated, Rich __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Histogram to KDE
On Fri, Aug 31, 2012 at 12:15 PM, David L Carlson dcarl...@tamu.edu wrote:
Using a data.frame x with columns bins and counts:
x - structure(list(bins = c(3.5, 4.5, 5.5, 6.5, 7.5, 8.5, 9.5, 10.5,
11.5, 12.5, 13.5, 14.5, 15.5), counts = c(1, 1, 2, 3, 6, 18,
19, 23, 8, 10, 6, 2, 1)), .Names = c(bins, counts), row.names =
4:16,
class = data.frame)
This will give you a plot of the kde estimate:
Thanks.
xkde - density(rep(bins, counts), bw=SJ)
plot(xkde)
As for the standard error or the confidence interval, you would probably
need to use bootstrapping.
On a similar note - is there a way in R to directly resample /
cross-validate from a histogram of a data-set without recreating the
original data-set ?
-Original Message-
Hello,
I wanted to know if there was way to convert a histogram of a data-set
to a
kernel density estimate directly in R ?
Specifically, I have a histogram [bins, counts] of samples {X1 ...
XN} of a quantized variable X where there is one bin for each level of
X,
and I'ld like to directly get a kde estimate of the pdf of X from the
histogram. Therefore, there is no additional quantization of X in the
histogram. Most KDE methods in R seem to require the original sample
set - and I would like to avoid re-creating the samples from the
histogram. Is there some quick way of doing this using one of the
standard
kde methods in R ?
Also, a general statistical question - is there some measure of the
standard error or confidence interval or similar of a KDE of a data-set
?
Thanks,
-fj
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] Installing lumi and hdrcde
On 05.09.2012 11:41, Hermann Norpois wrote: To whom it may concern. As I would like to analyse some array data I was keen on downloading the lumi package that depends obviously on hdrcde that is not available for r 2.12.1. I did not find instructions to solve or circumvent this problem. Installing hdrcde by hand did not work either. It was not detected by (.packages(all.available=TRUE)) if installed in the R library. Thanks Hermann Norpois This was my try to install the lumi package: source (http://bioconductur.org/biocLite.R;) This can easily be solved by using the correct spelling for bioconductor. Uwe Ligges Fehler in file(filenaReme, r, encoding = encoding) : kann Verbindung nicht öffnen Zusätzlich: Warnmeldung: In file(filename, r, encoding = encoding) : kann 'bioconductur.org' nicht auflösen source (http://bioconductor.org/biocLite.R;) BiocInstaller version 1.2.1, ?biocLite for help biocLite(lumi) BioC_mirror: 'http://www.bioconductor.org' Using R version 2.14, BiocInstaller version 1.2.1. Installing package(s) 'lumi' Installing package(s) into ‘/home/hnorpois/R/i686-pc- linux-gnu-library/2.14’ (as ‘lib’ is unspecified) Warnung: dependency ‘hdrcde’ is not available versuche URL ' http://www.bioconductor.org/packages/2.9/bioc/src/contrib/lumi_2.6.0.tar.gz' Content type 'application/x-gzip' length 11386679 bytes (10.9 Mb) URL geöffnet == downloaded 10.9 Mb ERROR: dependency ‘hdrcde’ is not available for package ‘lumi’ * removing ‘/home/hnorpois/R/i686-pc-linux-gnu-library/2.14/lumi’ The downloaded packages are in ‘/tmp/RtmpMNrvTz/downloaded_packages’ Warnmeldungen: 1: In install.packages(pkgs = pkgs, repos = repos, ...) : installation of package ‘lumi’ had non-zero exit status 2: 'rgl' cannot be updated, installed directory '/usr/lib/R/site-library' not writeable [[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] Smooth contour of a matrix
Hi R users I'm looking for a way to do a contour plot of the attached 2D matrix. Using contour() gives me some ugly contour lines that I would like to smooth. Any ideas? oliverjack38 http://r.789695.n4.nabble.com/file/n4642291/param1-4.txt param1-4.txt -- View this message in context: http://r.789695.n4.nabble.com/Smooth-contour-of-a-matrix-tp4642291.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] Mailing List
You might prefer to read list via the web or a news reader or an RSS feed, in which case http://dir.gmane.org/gmane.comp.lang.r.general might be helpful. Keith J On 05/09/2012 13:47, David Winsemius wrote: On Sep 5, 2012, at 3:00 AM, Marcus Tullius wrote: Hello there, is there a way I can erase my name from the mailing list and still get mails concerning the topics If you change your subscription options to daily digest ( at the page where you signed up), you can just read the top of the digest. I am interested in? I cannot handle all those emails coming in constantly. I do not have time for that. Greetings, Francisco David Winsemius, MD Alameda, CA, USA __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] cex.lab ignored in plot.zoo for multiple plots
Hello everyone, a problem with the plot.zoo function. In the parameters of the function, cex.lab is ignored. I tried to reduce the size of the yaxis labels by at least 50%. -- Example: sample - as.zoo(EuStockMarkets) par(las=1) plot.zoo(sample, plot.type=multiple, main=Time Series, xlab=Date, yaxt=n, cex.lab=0.5, xaxs=i) # Try playing with different values for cex.lab par(las=0) --- Any hints or suggestions? THX Nico [[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] linking HTML with R
Hi, I think the simplest way to do this is using a small piece of php code. See http://stats.stackexchange.com/questions/4279/how-can-i-integrate-r-with-php There are several webpages about this topic, but all of them are very ancient. I have the plan to write a text about this Greetz Frans www.digipsy.nl -Oorspronkelijk bericht- Van: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] Namens punitha Verzonden: woensdag 5 september 2012 11:49 Aan: r-help@r-project.org Onderwerp: [R] linking HTML with R hi, I am said to create a small form in html and after i click the submit button it should execute R function and move to next page of html can I know how can it be done??? can we link R and HTML??? which packages will help me in doing this??? are there any examples similar to this online??? Thanks in advance with regards, C. Punitha - Thank you, with regards, Punitha -- View this message in context: http://r.789695.n4.nabble.com/linking-HTML-with-R-tp4642276.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Improvement of Regression Model
Hello folks, I am on learning phase of R. I have developed Regression Model over six predictor variables. while development, i found my all data are not very linear. So, may because of this the prediction of my model is not exact. Here is the summary of model : Call: lm(formula = y ~ x_1 + x_2 + x_3 + x_4 + x_5 + x_6) Residuals: Min 1Q Median 3Q Max -125.302 -26.2100.702 26.261 111.511 Coefficients: Estimate Std. Error t value Pr(|t|) (Intercept) 48.629440.27999 173.684 2e-16 *** x_1 -0.678310.08053 -8.423 2e-16 *** x_2 0.074760.49578 0.151 0.880143 x_3 -0.229810.06489 -3.541 0.000399 *** x_4 0.018450.09070 0.203 0.838814 x_5 3.769520.67006 5.626 1.87e-08 *** x_6 0.076980.01565 4.919 8.75e-07 *** --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 Residual standard error: 33.76 on 19710 degrees of freedom Multiple R-squared: 0.006298, Adjusted R-squared: 0.005995 F-statistic: 20.82 on 6 and 19710 DF, p-value: 2.2e-16 I have certain questions with this model 1. Any way to improve the accuracy of this model? 2.Which of the value is most useful among Residual standard error,degrees of freedom, Multiple R-squared, Adjusted R-squared, F-statisti, p-value for choosing best model from numbers of model ? 3.Is it appropriate to use polynomial model with these data? 4.In case when i am using polynomial model for regression, which degree is most appropriate for it? Thanks Vignesh attachment: Rplot.pngattachment: Rplot01.pngattachment: Rplot02.pngattachment: Rplot03.pngattachment: Rplot04.pngattachment: Rplot05.png__ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Installing lumi and hdrcde
On 09/05/2012 02:41 AM, Hermann Norpois wrote: To whom it may concern. As I would like to analyse some array data I was keen on downloading the lumi package that depends obviously on hdrcde that is not available for r 2.12.1. I did not find instructions to solve or circumvent this problem. Installing hdrcde by hand did not work either. It was not detected by (.packages(all.available=TRUE)) if installed in the R library. Thanks Hermann Norpois This was my try to install the lumi package: source (http://bioconductur.org/biocLite.R;) Fehler in file(filenaReme, r, encoding = encoding) : kann Verbindung nicht öffnen Zusätzlich: Warnmeldung: In file(filename, r, encoding = encoding) : kann 'bioconductur.org' nicht auflösen source (http://bioconductor.org/biocLite.R;) BiocInstaller version 1.2.1, ?biocLite for help biocLite(lumi) BioC_mirror: 'http://www.bioconductor.org' Using R version 2.14, BiocInstaller version 1.2.1. Installing package(s) 'lumi' Installing package(s) into ‘/home/hnorpois/R/i686-pc- linux-gnu-library/2.14’ (as ‘lib’ is unspecified) Warnung: dependency ‘hdrcde’ is not available versuche URL ' http://www.bioconductor.org/packages/2.9/bioc/src/contrib/lumi_2.6.0.tar.gz' Content type 'application/x-gzip' length 11386679 bytes (10.9 Mb) URL geöffnet == downloaded 10.9 Mb ERROR: dependency ‘hdrcde’ is not available for package ‘lumi’ * removing ‘/home/hnorpois/R/i686-pc-linux-gnu-library/2.14/lumi’ If I use R-2.14 and install.packages(hdrcde, repos=http://cran.fhcrc.org;) I get In getDependencies(pkgs, dependencies, available, lib) : package 'hdrcde' is not available (for R version 2.14.0 alpha) but if I use R-2.15 the package installs correctly. Likewise with biocLite(lumi). So I think the easiest solution is to use a current version of R. Please ask questions about Bioconductor packages on the Bioconductor mailing list http://bioconductor.org/help/mailing-list/ Martin The downloaded packages are in ‘/tmp/RtmpMNrvTz/downloaded_packages’ Warnmeldungen: 1: In install.packages(pkgs = pkgs, repos = repos, ...) : installation of package ‘lumi’ had non-zero exit status 2: 'rgl' cannot be updated, installed directory '/usr/lib/R/site-library' not writeable [[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. -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Horizontal grid in background of barplot
A horribly pedestrian alternative to plotrix:
barplot(x,beside=TRUE, ylim=c(0,90), etc.)
par('usr')# just getting plot limits
[1] 0.44 15.56 0.00 90.00
par(new=T)
lines(c(0.44,15.56),c(20,20))
lines(c(0.44,15.56),c(40,40))
etc.
[[alternative HTML version deleted]]
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] Improvement of Regression Model
These questions are off topic for this list. Try a statistical list like stats.stackexchange.com. Probably better yet, as your statistical skills sound like they are somewhat limited, consult a local statistician for help. -- Bert On Wed, Sep 5, 2012 at 7:54 AM, Vignesh Prajapati vign...@tatvic.com wrote: Hello folks, I am on learning phase of R. I have developed Regression Model over six predictor variables. while development, i found my all data are not very linear. So, may because of this the prediction of my model is not exact. Here is the summary of model : Call: lm(formula = y ~ x_1 + x_2 + x_3 + x_4 + x_5 + x_6) Residuals: Min 1Q Median 3Q Max -125.302 -26.2100.702 26.261 111.511 Coefficients: Estimate Std. Error t value Pr(|t|) (Intercept) 48.629440.27999 173.684 2e-16 *** x_1 -0.678310.08053 -8.423 2e-16 *** x_2 0.074760.49578 0.151 0.880143 x_3 -0.229810.06489 -3.541 0.000399 *** x_4 0.018450.09070 0.203 0.838814 x_5 3.769520.67006 5.626 1.87e-08 *** x_6 0.076980.01565 4.919 8.75e-07 *** --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 Residual standard error: 33.76 on 19710 degrees of freedom Multiple R-squared: 0.006298, Adjusted R-squared: 0.005995 F-statistic: 20.82 on 6 and 19710 DF, p-value: 2.2e-16 I have certain questions with this model 1. Any way to improve the accuracy of this model? 2.Which of the value is most useful among Residual standard error,degrees of freedom, Multiple R-squared, Adjusted R-squared, F-statisti, p-value for choosing best model from numbers of model ? 3.Is it appropriate to use polynomial model with these data? 4.In case when i am using polynomial model for regression, which degree is most appropriate for it? Thanks Vignesh __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Bert Gunter Genentech Nonclinical Biostatistics Internal Contact Info: Phone: 467-7374 Website: http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Improvement of Regression Model
a) This sounds like homework. This is not a homework support forum. b) If it is not homework, you should take one or more classes on statistics. Your questions are more about theory than R and this is not a statistics theory mailing list. c) You ask questions about the use of your data, but you provide no data or reproducible, self-contained R code, so even if it is not homework you are not providing us with a sporting chance at understanding your questions. Read the Posting Guide. --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/BatteriesO.O#. #.O#. with /Software/Embedded Controllers) .OO#. .OO#. rocks...1k --- Sent from my phone. Please excuse my brevity. Vignesh Prajapati vign...@tatvic.com wrote: Hello folks, I am on learning phase of R. I have developed Regression Model over six predictor variables. while development, i found my all data are not very linear. So, may because of this the prediction of my model is not exact. Here is the summary of model : Call: lm(formula = y ~ x_1 + x_2 + x_3 + x_4 + x_5 + x_6) Residuals: Min 1Q Median 3Q Max -125.302 -26.2100.702 26.261 111.511 Coefficients: Estimate Std. Error t value Pr(|t|) (Intercept) 48.629440.27999 173.684 2e-16 *** x_1 -0.678310.08053 -8.423 2e-16 *** x_2 0.074760.49578 0.151 0.880143 x_3 -0.229810.06489 -3.541 0.000399 *** x_4 0.018450.09070 0.203 0.838814 x_5 3.769520.67006 5.626 1.87e-08 *** x_6 0.076980.01565 4.919 8.75e-07 *** --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 Residual standard error: 33.76 on 19710 degrees of freedom Multiple R-squared: 0.006298, Adjusted R-squared: 0.005995 F-statistic: 20.82 on 6 and 19710 DF, p-value: 2.2e-16 I have certain questions with this model 1. Any way to improve the accuracy of this model? 2.Which of the value is most useful among Residual standard error,degrees of freedom, Multiple R-squared, Adjusted R-squared, F-statisti, p-value for choosing best model from numbers of model ? 3.Is it appropriate to use polynomial model with these data? 4.In case when i am using polynomial model for regression, which degree is most appropriate for it? Thanks Vignesh __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] how to visualise the smoothers of a model averaged GAM ?
Hi, It is not clear to me what a model-averaged (sensu MuMIn package) GAM is... How is the smoother averaged and how can I see it ? My model is: M.gam.auto - gam (Leksite ~ s(Altmean,k=4) + s(Class_unfav_prop, k=4) + + s(Visib2000, k=4) + s(Ddisturbance, k=4) + s(Steppe_prop, k=4) + s(autocov2, k=4), family=binomial, data= leks) When i extract the confidence intervals for the average models (all models with delta AIC 2), I get: confint (avgmod) 2.5 % 97.5 % (Intercept) -0.705495919 0.090974395 s(Altmean).1 -1.032000478 0.846255206 s(Altmean).2 -0.131526964 3.181165030 s(Altmean).3 -0.479038766 1.511470593 s(autocov2).1 -0.594732400 5.030680753 s(autocov2).2 -3.932830030 18.377288299 s(autocov2).3 -5.859925892 3.269061133 s(Ddisturbance).1 -0.324700903 0.609412974 s(Ddisturbance).2 -0.016172651 5.880936668 s(Ddisturbance).3 -0.881357264 0.862160976 s(Steppe_prop).1 -0.002864215 0.002861629 s(Steppe_prop).2 -0.022374707 0.022389396 s(Steppe_prop).3 0.191842041 1.242861265 s(Class_unfav_prop).1 -0.119628517 0.109562147 s(Class_unfav_prop).2 -0.246237564 0.274136388 s(Class_unfav_prop).3 -0.588583036 0.189353845 s(Visib2000).1-0.003592773 0.003593891 s(Visib2000).2-0.012680896 0.012686619 s(Visib2000).3-0.489773942 0.206553913 Not sure of this means nor how to visualize the smoothers... Help would be appreciated. Francisco Moreira Institute of Agronomy Technical University of Lisbon -- View this message in context: http://r.789695.n4.nabble.com/how-to-visualise-the-smoothers-of-a-model-averaged-GAM-tp4642302.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] how to visualise the smoothers of a model averaged GAM ?
Hi, If i understand what you mean, you can do Plot(M.gam.auto) You Will get the centered predictions for smooths, you can also extract predictions for each term using (predict(M.gam.auto, type=terms)). The results you got are thé coefficients for each of you smooths pieces (as k=4, you get 3), but they re not interpretable as they are. Hope this could help Youssef Le 2012-09-05 à 11:50, fmoreira fmore...@isa.utl.pt a écrit : Hi, It is not clear to me what a model-averaged (sensu MuMIn package) GAM is... How is the smoother averaged and how can I see it ? My model is: M.gam.auto - gam (Leksite ~ s(Altmean,k=4) + s(Class_unfav_prop, k=4) + + s(Visib2000, k=4) + s(Ddisturbance, k=4) + s(Steppe_prop, k=4) + s(autocov2, k=4), family=binomial, data= leks) When i extract the confidence intervals for the average models (all models with delta AIC 2), I get: confint (avgmod) 2.5 % 97.5 % (Intercept) -0.705495919 0.090974395 s(Altmean).1 -1.032000478 0.846255206 s(Altmean).2 -0.131526964 3.181165030 s(Altmean).3 -0.479038766 1.511470593 s(autocov2).1 -0.594732400 5.030680753 s(autocov2).2 -3.932830030 18.377288299 s(autocov2).3 -5.859925892 3.269061133 s(Ddisturbance).1 -0.324700903 0.609412974 s(Ddisturbance).2 -0.016172651 5.880936668 s(Ddisturbance).3 -0.881357264 0.862160976 s(Steppe_prop).1 -0.002864215 0.002861629 s(Steppe_prop).2 -0.022374707 0.022389396 s(Steppe_prop).3 0.191842041 1.242861265 s(Class_unfav_prop).1 -0.119628517 0.109562147 s(Class_unfav_prop).2 -0.246237564 0.274136388 s(Class_unfav_prop).3 -0.588583036 0.189353845 s(Visib2000).1-0.003592773 0.003593891 s(Visib2000).2-0.012680896 0.012686619 s(Visib2000).3-0.489773942 0.206553913 Not sure of this means nor how to visualize the smoothers... Help would be appreciated. Francisco Moreira Institute of Agronomy Technical University of Lisbon -- View this message in context: http://r.789695.n4.nabble.com/how-to-visualise-the-smoothers-of-a-model-averaged-GAM-tp4642302.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] cex.lab ignored in plot.zoo for multiple plots
On Sep 5, 2012, at 8:06 AM, Nicolai Schneider wrote: Hello everyone, a problem with the plot.zoo function. In the parameters of the function, cex.lab is ignored. I tried to reduce the size of the yaxis labels by at least 50%. -- Example: sample - as.zoo(EuStockMarkets) par(las=1) plot.zoo(sample, plot.type=multiple, main=Time Series, xlab=Date, yaxt=n, cex.lab=0.5, xaxs=i) # Try playing with different values for cex.lab I would have thought that the parameter to use would be 'cex.axis'. Testing seems to confirm theory in this case. par(las=0) --- -- David Winsemius, MD Alameda, CA, USA __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] how to visualise the smoothers of a model averaged GAM ?
Maybe I should have added further details to my previous message. So, after running dd - dredge (M.gam.auto) avgmod - model.avg(dd, subset = delta 2) I ask for the confidence intervals using confint (avgmod) What you are suggesting would result in the visualization of the initial model, not of this averaged one...right? -- View this message in context: http://r.789695.n4.nabble.com/how-to-visualise-the-smoothers-of-a-model-averaged-GAM-tp4642302p4642307.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] model.table (anova)
Hello everybody, I have a problem with the model.table of anova. I have data (datos2) with 4 cluster (V7), calculated with daisy and hclust. str(datos2) 'data.frame': 56 obs. of 7 variables: $ Estacion: Factor w/ 56 levels Abradelo,AltoDoRodicio,..: 1 2 3 4 5 6 7 8 9 10 ... $ Invierno: num 36 53.9 37.1 63.6 12.5 ... $ X : int 643449 616292 562796 669916 625025 631194 511201 524431 641809 590324 ... $ X.1 : int 4734442 4684126 4696309 4743224 4723028 4833932 4649389 4701030 4706108 4765782 ... $ X.2 : int 826 981 553 1364 432 421 473 424 697 731 ... $ X.3 : num 87961 82902 30608 84260 94169 ... $ V7 : int 1 1 2 1 3 4 2 2 1 4 ... I made the anova test: sig.test - aov(V7~Invierno+X+X.1+X.2+X.3,data=datos2) summary(sig.test) Df Sum Sq Mean Sq F value Pr(F) Invierno 1 0.010.01 0.014 0.9064 X1 0.810.81 1.784 0.1877 X.1 1 32.61 32.61 72.026 2.97e-11 *** X.2 1 1.401.40 3.098 0.0845 . X.3 1 0.740.74 1.639 0.2063 Residuals 50 22.640.45 --- Signif. codes: 0 *** 0.001 ** 0.01 * 0.05 . 0.1 1 Now i would like to now the differences between each cluster, for this model.tables: mod - model.tables(sig.test,mean) Tables of means Grand mean 2.178571 Invierno Invierno 3.642384106 5.849889625 7.726269316 8.830022075 10.04415011 10.15452539 2.1615 2.1628 2.1639 2.1646 2.1653 2.1653 11.9205298 12.25165563 12.47240618 13.35540839 13.90728477 14.34878587 2.1664 2.1666 2.1667 2.1672 2.1676 2.1678 14.6799117 15.56291391 16.11479029 18.98454746 19.09492274 20.52980132 2.1680 2.1686 2.1689 2.1706 2.1707 2.1715 23.73068433 24.28256071 24.39293598 25.05518764 25.71743929 26.1589404 2.1734 2.1737 2.1738 2.1742 2.1746 2.1749 26.26931567 29.13907285 29.69094923 29.8013245 31.01545254 33.99558499 2.1749 2.1766 2.1770 2.1770 2.1777 2.1795 35.7615894 35.98233996 36.42384106 37.08609272 38.0794702 39.18322296 2.1806 2.1807 2.1810 2.1814 2.1819 2.1826 44.81236203 45.36423841 49.88962472 51.87637969 53.09050773 53.42163355 2.1859 2.1863 2.1890 2.1901 2.1909 2.1911 53.75275938 53.86313466 54.52538631 54.74613687 57.61589404 58.60927152 2.1913 2.1913 2.1917 2.1919 2.1936 2.1942 60.26490066 63.35540839 63.57615894 64.56953642 2.1951 2.1970 2.1971 2.1977 X X 497771 505372 508273 510859 511201 513379 516145 518427 524431 525267 526634 2.3693 2.3603 2.3464 2.3529 2.3850 2.3565 2.3218 2.3784 2.3245 2.3400 2.3120 531549 536101 540986 544158 547280 549546 555930 558736 560019 560578 562796 2.3085 2.2778 2.2838 2.2569 2.2480 2.2909 2.2708 2.2397 2.2067 2.2101 2.2390 570876 574209 576464 583167 585343 585393 589733 590324 594370 597892 598421 2.1876 2.2207 2.2228 2.1681 2.1689 2.2040 2.1982 2.1907 2.1252 2.1852 2.1306 598945 612930 613230 615988 616292 618769 623277 625025 625827 631194 632785 2.1654 2.0910 2.1139 2.1112 2.1276 2.0689 2.0768 2.0578 2.1086 2.0921 2.0430 636959 639190 639736 640275 641809 643449 648423 654995 657933 664123 669916 2.0585 2.0225 2.0379 2.0679 2.0327 2.0401 2.0285 1.9861 1.9910 2.0179 2.0076 670351 1.9719 X.1 X.1 4639803 4644255 4648384 4649389 4658771 4664595 4669787 4669863 4674072 4675170 0.871 0.969 0.964 1.144 1.293 1.143 1.334 1.199 1.554 1.500 4676811 4684126 4685177 4688943 4691376 4692421 4695132 4696309 4698702 4701030 1.360 1.425 1.565 1.612 1.425 1.802 1.533 1.721 1.822 1.870 4702027 4703493 4703623 4706108 4711638 4714422 4717609 4718574 4720490 4723028 1.853 1.623 1.728 1.726 2.095 2.102 1.855 2.057 2.046 2.013 4732806 4734442 4741204 4741500 4743224 4747354 4751251 4757557 4761493 4765782 2.264 2.097 2.281 2.418 2.123 2.512 2.469 2.681 2.561 2.600 4771652 4775147 4777923 4780523 4786917 4788103 4798361 4799728 4812691 4815885 2.817 2.828 2.809 2.755 2.881 3.046 3.225 3.060 3.173 3.421 4822868 4824470 4827467 4833932 4835419 4839683 3.330 3.385 3.417 3.460 3.535 3.647 . . . str(mod) List of 2 $ tables:List of 6 ..$ Grand mean: num 2.18 ..$ Invierno : mtable [1:52(1d)] 2.16 2.16 2.16 2.16 2.17 ... .. ..- attr(*, dimnames)=List of 1 .. .. ..$ Invierno: chr [1:52] 3.642384106 5.849889625 7.726269316 8.830022075 ... ..$ X : mtable [1:56(1d)] 2.37 2.36 2.35 2.35 2.39 ... .. ..- attr(*, dimnames)=List of 1 .. .. ..$ X: chr [1:56] 497771 505372 508273 510859 ... ..$ X.1 : mtable [1:56(1d)] 0.871 0.969 0.964 1.144 1.293 ... .. ..- attr(*, dimnames)=List of 1 .. .. ..$ X.1: chr [1:56] 4639803 4644255 4648384 4649389 ... ..$ X.2 : mtable [1:55(1d)] 2.29 2.41 2.23 2.13 2.51 ... .. ..- attr(*, dimnames)=List of 1 .. .. ..$ X.2: chr
[R] Simulating key-press or keyword events on a Mac
Hello all, Can someone please tell me how I can simulate a key press (particularly arrow keys and space bar) on a Mac? Any help is much appreciated. Cheers [[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] Comparing Von Bertalanffy Growth Curves
April Lindeman aprillinde...@yahoo.com wrote on 09/04/2012 01:43:06 PM: I am trying to compare Vbert growth curves from several years of fish data. I am following the code provided by: http:// www.ncfaculty.net/dogle/fishR/gnrlex/VonBertalanffy/VonBertalanffy.pdf . Specifically the section on VBGM Comparisons between groups. This code is pretty cut and dry. I am able to run it perfectly with the fake data that is provided. But when I run it with my own data I get stuck with this line: fitGen - nls(vbGen,data=LMB,start=svGen) I get this error code: Error in numericDeriv(form[[3L]], names(ind), env) : Missing value or an infinity produced when evaluating the model. Does anyone know how to fix it? I have no missing values and do not know how to fix the infinity produced. Here is my data set: structure(list(Age = c(1L, 2L, 3L, 5L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 5L, 1L, 2L, 3L, 4L, 5L, 1L, 2L, 3L, 4L, 5L, 1L, 2L, 3L, 4L, 5L, 1L, 2L, 3L, 4L, 5L), MM = c(155. 79, 296.37, 325.77, 374.65, 181.46, 258.31, 321.88, 355.6, 139.75, 230.72, 319.61, 344.84, 130.92, 236.34, 290.53, 360.33, 400.61, 155. 33, 240.87, 315.46, 345.05, 378.2, 134.71, 256.66, 333.71, 362.99, 381.46, 153.91, 217.21, 287.8, 357.28, 385.62, 222.25, 288.93, 294. 05, 332.79, 367.39), Year = c(2005L, 2005L, 2005L, 2005L, 2006L, 2006L, 2006L, 2006L, 2007L, 2007L, 2007L, 2007L, 2008L, 2008L, 2008L, 2008L, 2008L, 2009L, 2009L, 2009L, 2009L, 2009L, 2010L, 2010L, 2010L, 2010L, 2010L, 2011L, 2011L, 2011L, 2011L, 2011L, 2012L, 2012L, 2012L, 2012L, 2012L)), .Names = c(Age, MM, Year), class = data.frame, row.names = c(NA, -37L)) As another person commented, you skipped the step where you attached the data attach(LMB) In case it's helpful here is all my code before this point: str(LMB) Why are you carrying out these as.integer() conversions? It's not clear to me that they are necessary. MMi=as.integer(MM) Yearf=as.factor(Year) Agei=as.integer(Age) As another person commented, you skipped the step where you attached the needed packages. I found I had to install and attach 7 packages to get your code to run! But this could have been avoided by simply supplying us with the starting values: svCom - list(Linf=430, K=0.5, t0=0) ( svCom - vbStarts(MMi~Agei,data=LMB)) You copied this code from the example in the pdf, but in that example they had only 2 groups. You have 8 years. So, this should be: svGen - lapply(svCom, rep, length(unique(Year))) ( svGen - lapply(svCom,rep,2) ) Wow. I didn't know you use the extraction function, [], in a formula. This is very good to know! Thanks for educating me!! vbGen - MMi~Linf[Yearf]*(1-exp(-K[Yearf]*(Age-t0[Yearf]))+error) fitGen - nls(vbGen,data=LMB,start=svGen) Thank you, April Here's the whole reproducible snippet of code ... # the data LMB - structure(list(Age = c(1L, 2L, 3L, 5L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 5L, 1L, 2L, 3L, 4L, 5L, 1L, 2L, 3L, 4L, 5L, 1L, 2L, 3L, 4L, 5L, 1L, 2L, 3L, 4L, 5L), MM = c(155.79, 296.37, 325.77, 374.65, 181.46, 258.31, 321.88, 355.6, 139.75, 230.72, 319.61, 344.84, 130.92, 236.34, 290.53, 360.33, 400.61, 155.33, 240.87, 315.46, 345.05, 378.2, 134.71, 256.66, 333.71, 362.99, 381.46, 153.91, 217.21, 287.8, 357.28, 385.62, 222.25, 288.93, 294.05, 332.79, 367.39), Year = c(2005L, 2005L, 2005L, 2005L, 2006L, 2006L, 2006L, 2006L, 2007L, 2007L, 2007L, 2007L, 2008L, 2008L, 2008L, 2008L, 2008L, 2009L, 2009L, 2009L, 2009L, 2009L, 2010L, 2010L, 2010L, 2010L, 2010L, 2011L, 2011L, 2011L, 2011L, 2011L, 2012L, 2012L, 2012L, 2012L, 2012L)), .Names = c(Age, MM, Year), class = data.frame, row.names = c(NA, -37L)) # attach the data attach(LMB) # provide starting values svCom - list(Linf=430, K=0.5, t0=0) # repeat the starting values for each year svGen - lapply(svCom, rep, length(unique(Year))) # define a new variable, uniquely numbered for each year Yearf - as.factor(Year) # fit a single model with different parameter estimates for each year fitGen - nls(MM ~ Linf[Yearf]*(1-exp(-K[Yearf]*(Age-t0[Yearf]))), data=LMB, start=svGen) fitGen Jean [[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] Recoding categorical gender variable into numeric factors
I currently have a data set in which gender is inputed as Male and Female , and I'm trying to convert this into 1 and 0. I found a website which reccomended using two commands: data$scode[data$sex==M] - 1 data$scode[data$sex==F] - 2 to convert to numbers, and: data$scode - factor(data$scode) to convert this variable to a factor. My issue is that, after I use the first command, *only* the female values get converted to a number. I am left with a column filled with 2's and blank spaces. Instead of typing both lines of the first command, I copy and pasted the first line and changed the letter representing gender. I also made sure that both letters were exactly as they appear in the dataset. My questions are: is there any visible issue with my syntax, and are there any other methods to accomplish this? I'm also very new to R, so complex syntax is beyond me. Conrad Baldner -- View this message in context: http://r.789695.n4.nabble.com/Recoding-categorical-gender-variable-into-numeric-factors-tp4642316.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] POSIXlt and daylight savings time
pdb wrote:
as.POSIXlt('2004-10-31 02:00:00')
[1] 2004-10-31
as.POSIXlt('2004-10-31 03:00:00')
[1] 2004-10-31 03:00:00
How do I tell as.POSIXlt() to ignore daylight savings and just convert to
a time as is? I've read about the 'isdst' but it is still unclear what to
do.
There *was* no 02:00:00 in your local timezone, so you’re trying to specifiy
a point in time that just didn’t exist. If you really want to do this, use
the UTC timezone, by setting the ‘tz’ argument in as.POSIXct/as.POSIXlt to
UTC (or GMT).
--
Karl Ove Hufthammer
E-mail: k...@huftis.org
Jabber: huf...@jabber.no
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Simulating key-press or keyword events on a Mac
This is very off-topic here. --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/BatteriesO.O#. #.O#. with /Software/Embedded Controllers) .OO#. .OO#. rocks...1k --- Sent from my phone. Please excuse my brevity. Reza Salimi-Khorshidi worx.of.m...@gmail.com wrote: Hello all, Can someone please tell me how I can simulate a key press (particularly arrow keys and space bar) on a Mac? Any help is much appreciated. Cheers [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Recoding categorical gender variable into numeric factors
Hi Conrad, On Wed, Sep 5, 2012 at 3:14 PM, Conradsb csbal...@vt.edu wrote: I currently have a data set in which gender is inputed as Male and Female , and I'm trying to convert this into 1 and 0. This is usually not necessary, and makes things more confusing. Male and Female is clear and self-explanatory: 0 and 1 are not. I found a website which reccomended using two commands: data$scode[data$sex==M] - 1 data$scode[data$sex==F] - 2 Nope, 1 is the character 1, not the number 1 in R. Also, you said the values were Male and Female, not F and M. To convert Male to 1 and Female to 2 you can use data$scode[data$sex==Male] - 1 data$scode[data$sex==Female] - 2 Notice Male and Female, instead of M and F, and 1 and 2 instead of 1 and 2 to convert to numbers, and: data$scode - factor(data$scode) to convert this variable to a factor. No need to convert it to a factor first. Just use data$sex - factor(data$sex) My issue is that, after I use the first command, *only* the female values get converted to a number. I am left with a column filled with 2's and blank spaces. Strange, especially if sex is actually Male and Female, in which case scode should be all NA. If you want to follow up on this, please post the result of dput(dat[sex]) Instead of typing both lines of the first command, I copy and pasted the first line and changed the letter representing gender. I also made sure that both letters were exactly as they appear in the dataset. My questions are: is there any visible issue with my syntax, and are there any other methods to accomplish this? In this case you don't actually need to convert to numeric. Just use data$scode - factor(scode) If you really need to convert characters to numbers, it is often convenient to use factors as intermediate steps, like this: dat - data.frame(sex=sample(c(Male, Female), 10, replace=TRUE)) dat$sex.n - as.numeric( as.character( factor( dat$sex, levels = c(Female, Male), labels = c(0, 1 Best, Ista I'm also very new to R, so complex syntax is beyond me. Conrad Baldner -- View this message in context: http://r.789695.n4.nabble.com/Recoding-categorical-gender-variable-into-numeric-factors-tp4642316.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Recoding categorical gender variable into numeric factors
I can't replicate your problem. I created a data set with Male and Female since that is what you indicate, but your commands use M and F which is different. When I use Male and Female the recoding is just as expected, but you don't even need to do this. You probably already have a factor since R routinely turns character fields into factors: data - data.frame(sex=c(rep(Male, 5), rep(Female, 5))) data sex 1Male 2Male 3Male 4Male 5Male 6 Female 7 Female 8 Female 9 Female 10 Female str(data) 'data.frame': 10 obs. of 1 variable: $ sex: Factor w/ 2 levels Female,Male: 2 2 2 2 2 1 1 1 1 1 So data$sex is a Factor with two levels Female=1 and Male=2. If the result of str(data) looks like this, you have a character array (chr): str(data) 'data.frame': 10 obs. of 1 variable: $ sex: chr Male Male Male Male ... If you want to convert a character array to a factor just use the command: data$sex - factor(data$sex) By default, R orders the character strings alphabetically before converting to factors so Female becomes 1 and Male becomes 2. -- David L Carlson Associate Professor of Anthropology Texas AM University College Station, TX 77843-4352 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-bounces@r- project.org] On Behalf Of Conradsb Sent: Wednesday, September 05, 2012 2:14 PM To: r-help@r-project.org Subject: [R] Recoding categorical gender variable into numeric factors I currently have a data set in which gender is inputed as Male and Female , and I'm trying to convert this into 1 and 0. I found a website which reccomended using two commands: data$scode[data$sex==M] - 1 data$scode[data$sex==F] - 2 to convert to numbers, and: data$scode - factor(data$scode) to convert this variable to a factor. My issue is that, after I use the first command, *only* the female values get converted to a number. I am left with a column filled with 2's and blank spaces. Instead of typing both lines of the first command, I copy and pasted the first line and changed the letter representing gender. I also made sure that both letters were exactly as they appear in the dataset. My questions are: is there any visible issue with my syntax, and are there any other methods to accomplish this? I'm also very new to R, so complex syntax is beyond me. Conrad Baldner -- View this message in context: http://r.789695.n4.nabble.com/Recoding- categorical-gender-variable-into-numeric-factors-tp4642316.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting- guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] help w/ uploading table frm R to green plump
Hi, Does anyone know how to upload a table to green plumb have it be distributed? I know how to upload using sqlSave(chann, d, tablename=castaneg.wh_d, rownames=F, colnames=T) but how can I make my table be distributed randomly on the server. In SAS you can use the option distribute_on=random Thanks in advance for your help -- View this message in context: http://r.789695.n4.nabble.com/help-w-uploading-table-frm-R-to-green-plump-tp4642319.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] Outliers in Binary Logistic Regressions
Hallo folks, I know I should not ask the same question again. But I have a problem I cannot solve and without the solution I am stuck and lost, unable to get along with my work! Someone suggested I should try the code below in order to eliminate the outliers from my data. I did as I was told, but I got a negative reply. The code did not function. I am including it here so that, if possible, someone may correct it for me. That would really be very much appreciated! My data has 1439 rows. *RR.rebuild - glm(RR, subset=remove) glm(RR, subset=!(1:1439 %in% c(56,303,365,391,512,746,859,940,1037,1042,1138,1355)) influence(RR.rebuild) influence.measures(RR.rebuild)* Many thanks in advance for any help and sorry for being annoyingly persistent! Francisco [[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] showing ticks for censored data in survfit() in the rms package
The answer to this may be obvious, but I was wondering in the rms package and the survfit(), how you can plot the censored time points as ticks. Take for example, library(survival) library(rms) foo - data.frame(Time=c(1,2,3,4,5,6,10), Status=c(1,1,0,0,1,1,1)) answer - survfit(Surv(foo$Time, foo$Status==1) ~1) # this shows the censored time points as ticks at Time = 3 and 4 plot(answer) # how do you achieve something similar with survplot() survplot(answer) Thanks, Andrew __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] using sqldf's read.csv.sql to read a file with NA for missing
I'm trying to use sqdf's function read.csv.sql to read CSV files in which the missing values are represented by NA's. Plain old read.csv works fine on these files, but they are rather large and I'd like to filter using sql-like statements. However, even if I specify field.types correctly and nrows=-1, it still turns the columns with NA's into chars or 0. I'm trying to make this OS independent, so I don't think I can use a filter to convert the NA's to NULL's or whatever SQLite would understand. I can accept it everything has to be read in as char and then convert to doubles with as.numeric, but I'm looking for speed. Here is code I thought would read the file (I've attached a small sample.) It almost works if there are no NA's in the initial rows, but it still turns NA's into 0's instead of NA or something I can change into NA; and it returns characters if there are NA's in the initial rows. (0 is a possible value so I can't filter out the 0's.) field.types - list(V1='char', V2='char', V3='real', V4='int', V5='real', V6='int', V7='real') dtst - read.csv.sql(./tmp.csv, header=FALSE, field.types=field.types, nrows=-1) str(dtst) 'data.frame': 32 obs. of 7 variables: $ V1: chr 2012-07-01 2012-07-01 2012-07-01 2012-07-01 ... $ V2: chr 15:50:00 15:51:00 15:52:00 15:53:00 ... $ V3: chr NA NA NA NA ... $ V4: int 0 0 0 0 0 0 0 0 0 0 ... $ V5: chr NA NA NA NA ... $ V6: int 0 0 0 0 0 0 0 0 0 0 ... $ V7: chr NA NA NA NA ... Any suggestions? Thanks, -- David L. Reiner This e-mail and any materials attached hereto, including, without limitation, all content hereof and thereof (collectively, XR Content) are confidential and proprietary to XR Trading, LLC (XR) and/or its affiliates, and are protected by intellectual property laws. Without the prior written consent of XR, the XR Content may not (i) be disclosed to any third party or (ii) be reproduced or otherwise used by anyone other than current employees of XR or its affiliates, on behalf of XR or its affiliates. THE XR CONTENT IS PROVIDED AS IS, WITHOUT REPRESENTATIONS OR WARRANTIES OF ANY KIND. TO THE MAXIMUM EXTENT PERMISSIBLE UNDER APPLICABLE LAW, XR HEREBY DISCLAIMS ANY AND ALL WARRANTIES, EXPRESS AND IMPLIED, RELATING TO THE XR CONTENT, AND NEITHER XR NOR ANY OF ITS AFFILIATES SHALL IN ANY EVENT BE LIABLE FOR ANY DAMAGES OF ANY NATURE WHATSOEVER, INCLUDING, BUT NOT LIMITED TO, DIRECT, INDIRECT, CONSEQUENTIAL, SPECIAL AND PUNITIVE DAMAGES, LOSS OF PROFITS AND TRADING LOSSES, RESULTING FROM ANY PERSON'S USE OR RELIANCE UPON, OR INABILITY TO USE, ANY XR CONTENT, EVEN IF XR IS ADVISED OF THE POSSIBILITY OF SUCH DAMAGES OR IF SUCH DAMAGES WERE FORESEEABLE. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 sqldf's read.csv.sql to read a file with NA for missing
I see the attachment didn't go through. here is the text: 2012-07-01,15:50:00,NA,0,NA,0,NA 2012-07-01,15:51:00,NA,0,NA,0,NA 2012-07-01,15:52:00,NA,0,NA,0,NA 2012-07-01,15:53:00,NA,0,NA,0,NA 2012-07-01,15:54:00,NA,0,NA,0,NA 2012-07-01,15:55:00,NA,0,NA,0,NA 2012-07-01,15:56:00,NA,0,NA,0,NA 2012-07-01,15:57:00,NA,0,NA,0,NA 2012-07-01,15:58:00,NA,0,NA,0,NA 2012-07-01,15:59:00,NA,0,NA,0,NA 2012-07-01,16:00:00,1358.5,1,1358.5,4,NA 2012-07-01,16:01:00,NA,0,1358.25,2,NA 2012-07-01,16:02:00,NA,0,1358.25,2,NA 2012-07-01,16:03:00,NA,0,1358.25,2,NA 2012-07-01,16:04:00,NA,0,1358.25,2,NA 2012-07-01,16:05:00,NA,0,1358.25,2,NA 2012-07-01,16:06:00,1358.25,2,1358.25,2,NA 2012-07-01,16:07:00,1358.25,2,1358.25,2,NA 2012-07-01,16:08:00,1358,3,1358,2,NA 2012-07-01,16:09:00,1358.25,2,1358.25,2,NA 2012-07-01,16:10:00,1358.25,2,1358.25,2,NA 2012-07-01,16:11:00,1358.25,2,1358.25,2,NA 2012-07-01,16:12:00,1357.5,3,1357.5,3,NA 2012-07-01,16:13:00,1357.25,10,1357.25,3,1357.25 2012-07-01,16:14:00,NA,0,1357.25,10,1357.125 2012-07-01,16:15:00,1357,20,1357,18,1357 2012-07-01,16:16:00,1357,20,1357,18,1357 2012-07-01,16:17:00,1357,20,1357,18,1357 2012-07-01,16:18:00,1357,20,1357,18,1357 2012-07-01,16:19:00,1357,20,1357,18,1357 2012-07-01,16:20:00,1357,20,1357,18,1357 2012-07-01,16:21:00,1357,20,1357,18,1357 -- David -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of David Reiner Sent: Wednesday, September 05, 2012 4:32 PM To: r-help@r-project.org Subject: [R] using sqldf's read.csv.sql to read a file with NA for missing I'm trying to use sqdf's function read.csv.sql to read CSV files in which the missing values are represented by NA's. Plain old read.csv works fine on these files, but they are rather large and I'd like to filter using sql-like statements. However, even if I specify field.types correctly and nrows=-1, it still turns the columns with NA's into chars or 0. I'm trying to make this OS independent, so I don't think I can use a filter to convert the NA's to NULL's or whatever SQLite would understand. I can accept it everything has to be read in as char and then convert to doubles with as.numeric, but I'm looking for speed. Here is code I thought would read the file (I've attached a small sample.) It almost works if there are no NA's in the initial rows, but it still turns NA's into 0's instead of NA or something I can change into NA; and it returns characters if there are NA's in the initial rows. (0 is a possible value so I can't filter out the 0's.) field.types - list(V1='char', V2='char', V3='real', V4='int', V5='real', V6='int', V7='real') dtst - read.csv.sql(./tmp.csv, header=FALSE, field.types=field.types, nrows=-1) str(dtst) 'data.frame': 32 obs. of 7 variables: $ V1: chr 2012-07-01 2012-07-01 2012-07-01 2012-07-01 ... $ V2: chr 15:50:00 15:51:00 15:52:00 15:53:00 ... $ V3: chr NA NA NA NA ... $ V4: int 0 0 0 0 0 0 0 0 0 0 ... $ V5: chr NA NA NA NA ... $ V6: int 0 0 0 0 0 0 0 0 0 0 ... $ V7: chr NA NA NA NA ... Any suggestions? Thanks, -- David L. Reiner This e-mail and any materials attached hereto, including, without limitation, all content hereof and thereof (collectively, XR Content) are confidential and proprietary to XR Trading, LLC (XR) and/or its affiliates, and are protected by intellectual property laws. Without the prior written consent of XR, the XR Content may not (i) be disclosed to any third party or (ii) be reproduced or otherwise used by anyone other than current employees of XR or its affiliates, on behalf of XR or its affiliates. THE XR CONTENT IS PROVIDED AS IS, WITHOUT REPRESENTATIONS OR WARRANTIES OF ANY KIND. TO THE MAXIMUM EXTENT PERMISSIBLE UNDER APPLICABLE LAW, XR HEREBY DISCLAIMS ANY AND ALL WARRANTIES, EXPRESS AND IMPLIED, RELATING TO THE XR CONTENT, AND NEITHER XR NOR ANY OF ITS AFFILIATES SHALL IN ANY EVENT BE LIABLE FOR ANY DAMAGES OF ANY NATURE WHATSOEVER, INCLUDING, BUT NOT LIMITED TO, DIRECT, INDIRECT, CONSEQUENTIAL, SPECIAL AND PUNITIVE DAMAGES, LOSS OF PROFITS AND TRADING LOSSES, RESULTING FROM ANY PERSON'S USE OR RELIANCE UPON, OR INABILITY TO USE, ANY XR CONTENT, EVEN IF XR IS ADVISED OF THE POSSIBILITY OF SUCH DAMAGES OR IF SUCH DAMAGES WERE FORESEEABLE. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 sqldf's read.csv.sql to read a file with NA for missing
On Wed, Sep 5, 2012 at 5:31 PM, David Reiner david.rei...@xrtrading.com wrote: I'm trying to use sqdf's function read.csv.sql to read CSV files in which the missing values are represented by NA's. Plain old read.csv works fine on these files, but they are rather large and I'd like to filter using sql-like statements. However, even if I specify field.types correctly and nrows=-1, it still turns the columns with NA's into chars or 0. I'm trying to make this OS independent, so I don't think I can use a filter to convert the NA's to NULL's or whatever SQLite would understand. I can accept it everything has to be read in as char and then convert to doubles with as.numeric, but I'm looking for speed. Here is code I thought would read the file (I've attached a small sample.) It almost works if there are no NA's in the initial rows, but it still turns NA's into 0's instead of NA or something I can change into NA; and it returns characters if there are NA's in the initial rows. (0 is a possible value so I can't filter out the 0's.) field.types - list(V1='char', V2='char', V3='real', V4='int', V5='real', V6='int', V7='real') dtst - read.csv.sql(./tmp.csv, header=FALSE, field.types=field.types, nrows=-1) str(dtst) 'data.frame': 32 obs. of 7 variables: $ V1: chr 2012-07-01 2012-07-01 2012-07-01 2012-07-01 ... $ V2: chr 15:50:00 15:51:00 15:52:00 15:53:00 ... $ V3: chr NA NA NA NA ... $ V4: int 0 0 0 0 0 0 0 0 0 0 ... $ V5: chr NA NA NA NA ... $ V6: int 0 0 0 0 0 0 0 0 0 0 ... $ V7: chr NA NA NA NA ... See FAQ#14 on the sqldf home page noting the part at the end of the answer about csvfix. -- Statistics Software Consulting GKX Group, GKX Associates Inc. tel: 1-877-GKX-GROUP email: ggrothendieck at 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] using sqldf's read.csv.sql to read a file with NA for missing
You will probably have to contact the maintainer of package sqldf (G. Grothendieck ggrothendi...@gmail.com) as it appears that the package does not support missing values. I tried stripping out the NAs so that the fields were empty, but the results are the same. Fields specified as numeric are converted to character. Inserting a complete record at the top of the data prevents the conversion to text, but NA's are still converted to zeros. As a workaround, you could replace NA's with before reading the file and then convert this value to NA within R. -- David L Carlson Associate Professor of Anthropology Texas AM University College Station, TX 77843-4352 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-bounces@r- project.org] On Behalf Of David Reiner Sent: Wednesday, September 05, 2012 4:40 PM To: r-help@r-project.org Subject: Re: [R] using sqldf's read.csv.sql to read a file with NA for missing I see the attachment didn't go through. here is the text: 2012-07-01,15:50:00,NA,0,NA,0,NA 2012-07-01,15:51:00,NA,0,NA,0,NA 2012-07-01,15:52:00,NA,0,NA,0,NA 2012-07-01,15:53:00,NA,0,NA,0,NA 2012-07-01,15:54:00,NA,0,NA,0,NA 2012-07-01,15:55:00,NA,0,NA,0,NA 2012-07-01,15:56:00,NA,0,NA,0,NA 2012-07-01,15:57:00,NA,0,NA,0,NA 2012-07-01,15:58:00,NA,0,NA,0,NA 2012-07-01,15:59:00,NA,0,NA,0,NA 2012-07-01,16:00:00,1358.5,1,1358.5,4,NA 2012-07-01,16:01:00,NA,0,1358.25,2,NA 2012-07-01,16:02:00,NA,0,1358.25,2,NA 2012-07-01,16:03:00,NA,0,1358.25,2,NA 2012-07-01,16:04:00,NA,0,1358.25,2,NA 2012-07-01,16:05:00,NA,0,1358.25,2,NA 2012-07-01,16:06:00,1358.25,2,1358.25,2,NA 2012-07-01,16:07:00,1358.25,2,1358.25,2,NA 2012-07-01,16:08:00,1358,3,1358,2,NA 2012-07-01,16:09:00,1358.25,2,1358.25,2,NA 2012-07-01,16:10:00,1358.25,2,1358.25,2,NA 2012-07-01,16:11:00,1358.25,2,1358.25,2,NA 2012-07-01,16:12:00,1357.5,3,1357.5,3,NA 2012-07-01,16:13:00,1357.25,10,1357.25,3,1357.25 2012-07-01,16:14:00,NA,0,1357.25,10,1357.125 2012-07-01,16:15:00,1357,20,1357,18,1357 2012-07-01,16:16:00,1357,20,1357,18,1357 2012-07-01,16:17:00,1357,20,1357,18,1357 2012-07-01,16:18:00,1357,20,1357,18,1357 2012-07-01,16:19:00,1357,20,1357,18,1357 2012-07-01,16:20:00,1357,20,1357,18,1357 2012-07-01,16:21:00,1357,20,1357,18,1357 -- David -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-bounces@r- project.org] On Behalf Of David Reiner Sent: Wednesday, September 05, 2012 4:32 PM To: r-help@r-project.org Subject: [R] using sqldf's read.csv.sql to read a file with NA for missing I'm trying to use sqdf's function read.csv.sql to read CSV files in which the missing values are represented by NA's. Plain old read.csv works fine on these files, but they are rather large and I'd like to filter using sql-like statements. However, even if I specify field.types correctly and nrows=-1, it still turns the columns with NA's into chars or 0. I'm trying to make this OS independent, so I don't think I can use a filter to convert the NA's to NULL's or whatever SQLite would understand. I can accept it everything has to be read in as char and then convert to doubles with as.numeric, but I'm looking for speed. Here is code I thought would read the file (I've attached a small sample.) It almost works if there are no NA's in the initial rows, but it still turns NA's into 0's instead of NA or something I can change into NA; and it returns characters if there are NA's in the initial rows. (0 is a possible value so I can't filter out the 0's.) field.types - list(V1='char', V2='char', V3='real', V4='int', V5='real', V6='int', V7='real') dtst - read.csv.sql(./tmp.csv, header=FALSE, field.types=field.types, nrows=-1) str(dtst) 'data.frame': 32 obs. of 7 variables: $ V1: chr 2012-07-01 2012-07-01 2012-07-01 2012-07-01 ... $ V2: chr 15:50:00 15:51:00 15:52:00 15:53:00 ... $ V3: chr NA NA NA NA ... $ V4: int 0 0 0 0 0 0 0 0 0 0 ... $ V5: chr NA NA NA NA ... $ V6: int 0 0 0 0 0 0 0 0 0 0 ... $ V7: chr NA NA NA NA ... Any suggestions? Thanks, -- David L. Reiner This e-mail and any materials attached hereto, including, without limitation, all content hereof and thereof (collectively, XR Content) are confidential and proprietary to XR Trading, LLC (XR) and/or its affiliates, and are protected by intellectual property laws. Without the prior written consent of XR, the XR Content may not (i) be disclosed to any third party or (ii) be reproduced or otherwise used by anyone other than current employees of XR or its affiliates, on behalf of XR or its affiliates. THE XR CONTENT IS PROVIDED AS IS, WITHOUT REPRESENTATIONS OR WARRANTIES OF ANY KIND. TO THE MAXIMUM EXTENT PERMISSIBLE UNDER APPLICABLE LAW, XR HEREBY DISCLAIMS ANY AND ALL WARRANTIES, EXPRESS AND IMPLIED, RELATING TO THE XR CONTENT, AND NEITHER XR NOR ANY OF ITS AFFILIATES SHALL IN ANY EVENT BE LIABLE FOR
Re: [R] showing ticks for censored data in survfit() in the rms package
On Sep 5, 2012, at 2:05 PM, Andrew Yee wrote: The answer to this may be obvious, but I was wondering in the rms package and the survfit(), how you can plot the censored time points as ticks. survfit() is not in rms. Take for example, library(survival) library(rms) foo - data.frame(Time=c(1,2,3,4,5,6,10), Status=c(1,1,0,0,1,1,1)) answer - survfit(Surv(foo$Time, foo$Status==1) ~1) # this shows the censored time points as ticks at Time = 3 and 4 plot(answer) # how do you achieve something similar with survplot() survplot(answer) You should read more widely in the survival help pages. Since rms is in many cases built on top of the survival package. That 'answer'-object is of class survfit and there is a lines() method for survfit-objects. help(survfit) # follow links to lines lines(answer) # ticks appear. -- David Winsemius, MD Alameda, CA, USA __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] analysis of bitmaps
I'm interested in using R to perform some statistical analysis of bitmaps. When I search, I see a lot of information about outputting bitmaps, but I'm not finding much about loading a bitmap into a data frame so that it can be analyzed. Would someone have a quick pointer to help me out? [[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] Model Description
Hello dear, I am new to R, Have developed the model for prediction. I dont know exactly about the followed terms residual standard error degrees of freedom, multiple R-squared, adjusted R-squared F-statistics p-values Thanks in advance. [[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] Outliers in Binary Logistic Regressions
Hi, Not sure how your data looks like. With the sample data below, the code works. Try this: set.seed(1) dat1-data.frame(MIGRATION=sample(c(0,1),100,replace=TRUE),distance=sample(40:80,100,replace=TRUE)) RR.rebuild-glm(MIGRATION~distance,data=dat1,subset=!(1:100 %in% c(56,23,20,9,19)),family=binomial(link=logit)) RR.rebuild #Call: glm(formula = MIGRATION ~ distance, family = binomial(link = logit), # data = dat1, subset = !(1:100 %in% c(56, 23, 20, 9, 19))) #Coefficients: #(Intercept) distance #-0.0781611 -0.0004483 #Degrees of Freedom: 94 Total (i.e. Null); 93 Residual #Null Deviance: 131.4 #Residual Deviance: 131.4 AIC: 135.4 A.K. - Original Message - From: Marcus Tullius tull...@europe.com To: r-help@r-project.org Cc: Sent: Wednesday, September 5, 2012 3:42 PM Subject: [R] Outliers in Binary Logistic Regressions Hallo folks, I know I should not ask the same question again. But I have a problem I cannot solve and without the solution I am stuck and lost, unable to get along with my work! Someone suggested I should try the code below in order to eliminate the outliers from my data. I did as I was told, but I got a negative reply. The code did not function. I am including it here so that, if possible, someone may correct it for me. That would really be very much appreciated! My data has 1439 rows. *RR.rebuild - glm(RR, subset=remove) glm(RR, subset=!(1:1439 %in% c(56,303,365,391,512,746,859,940,1037,1042,1138,1355)) influence(RR.rebuild) influence.measures(RR.rebuild)* Many thanks in advance for any help and sorry for being annoyingly persistent! Francisco [[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] Maximum-likelihood fitting of a functional relationship(Ripley Thompson) type analysis
Hello all, Based on Ripley Thompson, Analyst, 1987 , I am trying to do a regression of my data which assumes a linear relationship between measurements by two modalities of the same physiological parameter. The complication is that my errors are heterogeneous, i.e. not only both X Y variables have significant variances, their ratio and individual values differ greatly between subjects. I believe a simple linear regression (which ignores the variances) is underestimating the slope of the relationship while a method like deming regression is overestimating (or underestimating depending on what I give as the ratio) since it assumes a constant ratio of the variable. Therefore, I have concluded that I need to do the full MLFR type of analysis suggested in that paper. Looking through archives and such, I could not find a direct implementation for R. I think a related method is that implemeted in leiv package which implements errors-in-variables methods. Admittedly, I am bit lazy and I did not dig into leiv implementation to figure out the differences and whether giving the ratio of the standard errors of Y to those of X for each point actually is correct. I am wondering if anyone has implemented this method in R and has an example that I can look that. While at it, I am wondering what is the way to estimate the 95% confidence interval in the results both for leiv and MLFR. Thanks, Turgut __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Summarizing data containing data/time information (as factor)
Dear R user I want to create a table (as below) to summarize the attached data (Test.csv, which can be read into R by using 'read.csv(Test.csv, header=F)' ), to indicate the day that there are any data available, e.g.value=1 if there are any data available for that day, otherwise value=0. 28/04 29/0430/0401/05 02/05 532703 0 1 1 10 532704 1 1 1 11 532705 0 0 1 10 Only Column A (Names: automatically stored as integer if being read into R) and Column B (date/time: automatically stored as factor if being read into R) are useful for this task. Could anyone kindly provide me some hints/ideas about how to write some code to to this job please? Many thanks in advance! Best wishes HJ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Model Description
On Sep 5, 2012, at 1:58 PM, mahout user wrote: Hello dear, I am new to R, Have developed the model for prediction. I dont know exactly about the followed terms residual standard error degrees of freedom, multiple R-squared, adjusted R-squared F-statistics p-values Thanks in advance. The r-help mailing list is not the place to go to correct your lack of knowledge about basic statistics. It is for questions about difficulties you have in constructing correct R code that persist after good faith efforts at self-education using the many contributed efforts at documentation. You may want to try instead: http://stats.stackexchange.com/ -- David Winsemius, MD Alameda, CA, USA __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] analysis of bitmaps
There are several packages to do this, with probably rgdal as the most general for reading - it will read many image formats as a SpatialGridDataFrame (class from package sp). This class behaves like a data.frame in many ways and can be coerced to one with as.data.frame. Non-spatial image formats will be provided with a default set of coordinates. You might also be interested in packages pixmap, raster, jpeg, png, tiff and several others that can be found on CRAN to do with bitmap, image or raster. It really depends on your needs and the form that your data are in. Cheers, Mike. On Thu, Sep 6, 2012 at 7:09 AM, Scott Swigart sc...@cascadeinsights.com wrote: I'm interested in using R to perform some statistical analysis of bitmaps. When I search, I see a lot of information about outputting bitmaps, but I'm not finding much about loading a bitmap into a data frame so that it can be analyzed. Would someone have a quick pointer to help me out? [[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. -- Michael Sumner Hobart, Australia e-mail: mdsum...@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] Summarizing data containing data/time information (as factor)
On Sep 5, 2012, at 4:57 PM, HJ YAN wrote: Dear R user I want to create a table (as below) to summarize the attached data (Test.csv, which can be read into R by using 'read.csv(Test.csv, header=F)' ), Unfortunately you did not read theinformation about posting attachments carefully enough and you csv filewas scrubbed by the mailserver.. I will attempt to recreate it: dat - read.table(text= 28/04 29/0430/0401/05 02/05 + 532703 0 1 1 10 + 532704 1 1 1 11 + 532705 0 0 1 10, header=TRUE) sdat - stack(dat) sdat$id - rownames(dat) sdat2 - sdat[sdat$values0, c(3,2,1)] sdat2$ind - factor( sub(\\., /, sdat2$ind)) sdat2$ind - factor( sub(X, , sdat2$ind)) At this point I think I have something similar to your original and will show how xtabs() can be used: xtabs(values ~id+ind, data=sdat2) ind id 01/05 02/05 28/04 29/04 30/04 532703 1 0 0 1 1 532704 1 1 1 1 1 532705 1 0 0 0 1 The dates are not sorted the same but if you used Date formatted values, they might. sdat2$dt - as.Date( sdat2$ind, format=%d/%m) xtabs(values ~id+dt, data=sdat2) dt id 2012-04-28 2012-04-29 2012-04-30 2012-05-01 2012-05-02 532703 0 1 1 1 0 532704 1 1 1 1 1 532705 0 0 1 1 0 to indicate the day that there are any data available, e.g.value=1 if there are any data available for that day, otherwise value=0. 28/04 29/0430/0401/05 02/05 532703 0 1 1 10 532704 1 1 1 11 532705 0 0 1 10 Only Column A (Names: automatically stored as integer if being read into R) and Column B (date/time: automatically stored as factor if being read into R) are useful for this task. Could anyone kindly provide me some hints/ideas about how to write some code to to this job please? Many thanks in advance! Best wishes HJ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 Alameda, CA, USA __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] merge a list of data frames
I have a list of data frames:
str(data)
List of 4
$ :'data.frame': 700773 obs. of 3 variables:
..$ V1: chr [1:700773] 200130446465779 200070050127778 200030633708779
200010587002779 ...
..$ V2: int [1:700773] 0 0 0 0 0 0 0 0 0 0 ...
..$ V3: num [1:700773] 1 1 1 1 1 ...
$ :'data.frame': 700773 obs. of 3 variables:
..$ V1: chr [1:700773] 200130446465779 200070050127778 200030633708779
200010587002779 ...
..$ V2: int [1:700773] 0 0 0 0 0 0 0 0 0 0 ...
..$ V3: num [1:700773] 1 1 1 1 1 ...
$ :'data.frame': 700773 obs. of 3 variables:
..$ V1: chr [1:700773] 200130446465779 200070050127778 200030633708779
200010587002779 ...
..$ V2: int [1:700773] 0 0 0 0 0 0 0 0 0 0 ...
..$ V3: num [1:700773] 1 1 1 1 1 ...
$ :'data.frame': 700773 obs. of 3 variables:
..$ V1: chr [1:700773] 200160325893778 200130647544079 200130446465779
200120186959078 ...
..$ V2: int [1:700773] 0 0 0 0 0 0 0 0 0 0 ...
..$ V3: num [1:700773] 1 1 1 1 1 1 1 1 1 1 ...
I want to merge them.
I tried to follow
http://rwiki.sciviews.org/doku.php?id=tips%3adata-frames%3amerge
and did:
data.1 - Reduce(function(f1,f2) merge(f1,f2,by=c(V1),all=TRUE), data)
Warning message:
In merge.data.frame(f1, f2, by = c(V1), all = TRUE) :
column names 'V2.x', 'V3.x', 'V2.y', 'V3.y' are duplicated in the result
str(data.1)
'data.frame': 700773 obs. of 9 variables:
$ V1 : chr 10001099079 10001254078 10001499078
10001541779 ...
$ V2.x: int 0 0 0 0 0 0 0 0 0 0 ...
$ V3.x: num 0.476 0.748 0.442 0.483 0.577 ...
$ V2.y: int 0 0 0 0 0 0 0 0 0 0 ...
$ V3.y: num 0.476 0.748 0.442 0.483 0.577 ...
$ V2.x: int 0 0 0 0 0 0 0 0 0 0 ...
$ V3.x: num 0.476 0.752 0.443 0.485 0.578 ...
$ V2.y: int 0 0 0 0 0 0 0 0 0 0 ...
$ V3.y: num 0.47 0.733 0.57 0.416 0.616 ...
I don't like the warning and I don't like that I now have to use [n] to
access identically named columns, but, I guess, this is better than
this:
library('reshape')
data.1 - merge_all(data,by=V1,all=TRUE)
Error in merge.data.frame(dfs[[1]], Recall(dfs[-1]), all = TRUE, sort = FALSE,
:
formal argument all matched by multiple actual arguments
data.1 - merge_all(data,by=V1,sort=TRUE,all=TRUE)
Error in merge.data.frame(dfs[[1]], Recall(dfs[-1]), all = TRUE, sort = FALSE,
:
formal argument all matched by multiple actual arguments
data.1 - merge_all(data,by=V1,sort=TRUE)
Error in merge.data.frame(dfs[[1]], Recall(dfs[-1]), all = TRUE, sort = FALSE,
:
formal argument sort matched by multiple actual arguments
data.1 - merge_all(data,by=V1)
Error in `[.data.frame`(df, , match(names(dfs[[1]]), names(df))) :
undefined columns selected
data.1 - merge_all(data,by=c(V1))
Error in `[.data.frame`(df, , match(names(dfs[[1]]), names(df))) :
undefined columns selected
what does 'formal argument sort matched by multiple actual arguments' mean?
thanks.
--
Sam Steingold (http://sds.podval.org/) on Ubuntu 12.04 (precise) X 11.0.11103000
http://www.childpsy.net/ http://ffii.org http://pmw.org.il
http://dhimmi.com http://palestinefacts.org http://iris.org.il
I just forgot my whole philosophy of life!!!
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/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] merge a list of data frames
On Sep 5, 2012, at 8:51 PM, Sam Steingold wrote:
I have a list of data frames:
str(data)
List of 4
$ :'data.frame': 700773 obs. of 3 variables:
..$ V1: chr [1:700773] 200130446465779 200070050127778 200030633708779
200010587002779 ...
..$ V2: int [1:700773] 0 0 0 0 0 0 0 0 0 0 ...
..$ V3: num [1:700773] 1 1 1 1 1 ...
$ :'data.frame': 700773 obs. of 3 variables:
..$ V1: chr [1:700773] 200130446465779 200070050127778 200030633708779
200010587002779 ...
..$ V2: int [1:700773] 0 0 0 0 0 0 0 0 0 0 ...
..$ V3: num [1:700773] 1 1 1 1 1 ...
$ :'data.frame': 700773 obs. of 3 variables:
..$ V1: chr [1:700773] 200130446465779 200070050127778 200030633708779
200010587002779 ...
..$ V2: int [1:700773] 0 0 0 0 0 0 0 0 0 0 ...
..$ V3: num [1:700773] 1 1 1 1 1 ...
$ :'data.frame': 700773 obs. of 3 variables:
..$ V1: chr [1:700773] 200160325893778 200130647544079 200130446465779
200120186959078 ...
..$ V2: int [1:700773] 0 0 0 0 0 0 0 0 0 0 ...
..$ V3: num [1:700773] 1 1 1 1 1 1 1 1 1 1 ...
I want to merge them.
Why? What are you expecting?
I tried to follow
http://rwiki.sciviews.org/doku.php?id=tips%3adata-frames%3amerge
and did:
data.1 - Reduce(function(f1,f2) merge(f1,f2,by=c(V1),all=TRUE), data)
Warning message:
In merge.data.frame(f1, f2, by = c(V1), all = TRUE) :
column names 'V2.x', 'V3.x', 'V2.y', 'V3.y' are duplicated in the result
str(data.1)
'data.frame': 700773 obs. of 9 variables:
$ V1 : chr 10001099079 10001254078 10001499078
10001541779 ...
$ V2.x: int 0 0 0 0 0 0 0 0 0 0 ...
$ V3.x: num 0.476 0.748 0.442 0.483 0.577 ...
$ V2.y: int 0 0 0 0 0 0 0 0 0 0 ...
$ V3.y: num 0.476 0.748 0.442 0.483 0.577 ...
$ V2.x: int 0 0 0 0 0 0 0 0 0 0 ...
$ V3.x: num 0.476 0.752 0.443 0.485 0.578 ...
$ V2.y: int 0 0 0 0 0 0 0 0 0 0 ...
$ V3.y: num 0.47 0.733 0.57 0.416 0.616 ...
I don't like the warning and I don't like that I now have to use [n] to
access identically named columns,
Perhaps it would make more sense to explain what your goal was, rather than
showing us two divergent efforts, neither of which is satisfactory? Perhaps?
--
David.
but, I guess, this is better than
this:
library('reshape')
data.1 - merge_all(data,by=V1,all=TRUE)
Error in merge.data.frame(dfs[[1]], Recall(dfs[-1]), all = TRUE, sort =
FALSE, :
formal argument all matched by multiple actual arguments
data.1 - merge_all(data,by=V1,sort=TRUE,all=TRUE)
Error in merge.data.frame(dfs[[1]], Recall(dfs[-1]), all = TRUE, sort =
FALSE, :
formal argument all matched by multiple actual arguments
data.1 - merge_all(data,by=V1,sort=TRUE)
Error in merge.data.frame(dfs[[1]], Recall(dfs[-1]), all = TRUE, sort =
FALSE, :
formal argument sort matched by multiple actual arguments
data.1 - merge_all(data,by=V1)
Error in `[.data.frame`(df, , match(names(dfs[[1]]), names(df))) :
undefined columns selected
data.1 - merge_all(data,by=c(V1))
Error in `[.data.frame`(df, , match(names(dfs[[1]]), names(df))) :
undefined columns selected
what does 'formal argument sort matched by multiple actual arguments' mean?
thanks.
--
Sam Steingold (http://sds.podval.org/) on Ubuntu 12.04 (precise) X
11.0.11103000
http://www.childpsy.net/ http://ffii.org http://pmw.org.il
http://dhimmi.com http://palestinefacts.org http://iris.org.il
I just forgot my whole philosophy of life!!!
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/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
Alameda, CA, USA
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Summarizing data containing data/time information (as factor)
Hi, I couldn't find any attached data. Could you dput() the data? A.K. - Original Message - From: HJ YAN yhj...@googlemail.com To: r-help@r-project.org Cc: Sent: Wednesday, September 5, 2012 7:57 PM Subject: [R] Summarizing data containing data/time information (as factor) Dear R user I want to create a table (as below) to summarize the attached data (Test.csv, which can be read into R by using 'read.csv(Test.csv, header=F)' ), to indicate the day that there are any data available, e.g.value=1 if there are any data available for that day, otherwise value=0. 28/04 29/04 30/04 01/05 02/05 532703 0 1 1 1 0 532704 1 1 1 1 1 532705 0 0 1 1 0 Only Column A (Names: automatically stored as integer if being read into R) and Column B (date/time: automatically stored as factor if being read into R) are useful for this task. Could anyone kindly provide me some hints/ideas about how to write some code to to this job please? Many thanks in advance! Best wishes HJ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Maximum likelihood fitting of a functional relationship (MLFR)
Hello all, Evidently my previous message met some filter due to subject line. I am re-sending my message. I apologize if this was sent out twice. Based on Ripley Thompson, Analyst, 1987 , I am trying to do a regression of my data which assumes a linear relationship between measurements by two modalities of the same physiological parameter. The complication is that my errors are heterogeneous, i.e. not only both X Y variables have significant variances, their ratio and individual values differ greatly between subjects. I believe a simple linear regression (which ignores the variances) is underestimating the slope of the relationship while a method like deming regression is overestimating (or underestimating depending on what I give as the ratio) since it assumes a constant ratio of the variable. Therefore, I have concluded that I need to do the full MLFR type of analysis suggested in that paper. Looking through archives and such, I could not find a direct implementation for R. I think a related method is that implemeted in leiv package which implements errors-in-variables methods. Admittedly, I am bit lazy and I did not dig into leiv implementation to figure out the differences and whether giving the ratio of the standard errors of Y to those of X for each point actually is correct. I am wondering if anyone has implemented this method in R and has an example that I can look that. While at it, I am wondering what is the way to estimate the 95% confidence interval in the results both for leiv and MLFR. Thanks, Turgut __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] How to extract p value from the lmekin object obtained by fitting mixed model with function lmekin() in package coxme?
Hi, R experts I am currently using lmekin() function in coxme package to fit a mixed effect model for family based genetic data. How can I extract the p value from a lmekin object? When I print the object in R console, I can see the p value and Z value are just over there. But I can not extract them by the coef() function. kinfit$coefficient$fixed (kinfit is the name of the lmekin object) just include the intercept and the value of fixed effects. Where are p and Z values? Thank you! -- Tianxiao Joshua Zhang, Ph.D. student Human and Statistical Genetics Program Division of Biology and Biomedical Sciences Washington University in St. Louis [[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] merge a list of data frames
I don't really know what you want, but if you have many columns with the same
names I am wondering why this is so. Do you really want to merge, which puts
all of the non-key columns side-by-side in one data frame? If so, why don't you
start by renaming the columns so they will make sense in the combined data
frame?
If you really want the column names to stay the same, perhaps you want to stack
the data frames vertically with rbind?
---
Jeff NewmillerThe . . Go Live...
DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go...
Live: OO#.. Dead: OO#.. Playing
Research Engineer (Solar/BatteriesO.O#. #.O#. with
/Software/Embedded Controllers) .OO#. .OO#. rocks...1k
---
Sent from my phone. Please excuse my brevity.
Sam Steingold s...@gnu.org wrote:
I have a list of data frames:
str(data)
List of 4
$ :'data.frame': 700773 obs. of 3 variables:
..$ V1: chr [1:700773] 200130446465779 200070050127778
200030633708779 200010587002779 ...
..$ V2: int [1:700773] 0 0 0 0 0 0 0 0 0 0 ...
..$ V3: num [1:700773] 1 1 1 1 1 ...
$ :'data.frame': 700773 obs. of 3 variables:
..$ V1: chr [1:700773] 200130446465779 200070050127778
200030633708779 200010587002779 ...
..$ V2: int [1:700773] 0 0 0 0 0 0 0 0 0 0 ...
..$ V3: num [1:700773] 1 1 1 1 1 ...
$ :'data.frame': 700773 obs. of 3 variables:
..$ V1: chr [1:700773] 200130446465779 200070050127778
200030633708779 200010587002779 ...
..$ V2: int [1:700773] 0 0 0 0 0 0 0 0 0 0 ...
..$ V3: num [1:700773] 1 1 1 1 1 ...
$ :'data.frame': 700773 obs. of 3 variables:
..$ V1: chr [1:700773] 200160325893778 200130647544079
200130446465779 200120186959078 ...
..$ V2: int [1:700773] 0 0 0 0 0 0 0 0 0 0 ...
..$ V3: num [1:700773] 1 1 1 1 1 1 1 1 1 1 ...
I want to merge them.
I tried to follow
http://rwiki.sciviews.org/doku.php?id=tips%3adata-frames%3amerge
and did:
data.1 - Reduce(function(f1,f2) merge(f1,f2,by=c(V1),all=TRUE),
data)
Warning message:
In merge.data.frame(f1, f2, by = c(V1), all = TRUE) :
column names 'V2.x', 'V3.x', 'V2.y', 'V3.y' are duplicated in the
result
str(data.1)
'data.frame': 700773 obs. of 9 variables:
$ V1 : chr 10001099079 10001254078 10001499078
10001541779 ...
$ V2.x: int 0 0 0 0 0 0 0 0 0 0 ...
$ V3.x: num 0.476 0.748 0.442 0.483 0.577 ...
$ V2.y: int 0 0 0 0 0 0 0 0 0 0 ...
$ V3.y: num 0.476 0.748 0.442 0.483 0.577 ...
$ V2.x: int 0 0 0 0 0 0 0 0 0 0 ...
$ V3.x: num 0.476 0.752 0.443 0.485 0.578 ...
$ V2.y: int 0 0 0 0 0 0 0 0 0 0 ...
$ V3.y: num 0.47 0.733 0.57 0.416 0.616 ...
I don't like the warning and I don't like that I now have to use [n] to
access identically named columns, but, I guess, this is better than
this:
library('reshape')
data.1 - merge_all(data,by=V1,all=TRUE)
Error in merge.data.frame(dfs[[1]], Recall(dfs[-1]), all = TRUE, sort =
FALSE, :
formal argument all matched by multiple actual arguments
data.1 - merge_all(data,by=V1,sort=TRUE,all=TRUE)
Error in merge.data.frame(dfs[[1]], Recall(dfs[-1]), all = TRUE, sort =
FALSE, :
formal argument all matched by multiple actual arguments
data.1 - merge_all(data,by=V1,sort=TRUE)
Error in merge.data.frame(dfs[[1]], Recall(dfs[-1]), all = TRUE, sort =
FALSE, :
formal argument sort matched by multiple actual arguments
data.1 - merge_all(data,by=V1)
Error in `[.data.frame`(df, , match(names(dfs[[1]]), names(df))) :
undefined columns selected
data.1 - merge_all(data,by=c(V1))
Error in `[.data.frame`(df, , match(names(dfs[[1]]), names(df))) :
undefined columns selected
what does 'formal argument sort matched by multiple actual arguments'
mean?
thanks.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to extract p value from the lmekin object obtained by fitting mixed model with function lmekin() in package coxme?
Perhaps what you want to explore is the object returned from the summary method rather than the fit object? coef(summary(kinfit)) --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/BatteriesO.O#. #.O#. with /Software/Embedded Controllers) .OO#. .OO#. rocks...1k --- Sent from my phone. Please excuse my brevity. Tian-Xiao Zhang ztx...@gmail.com wrote: Hi, R experts I am currently using lmekin() function in coxme package to fit a mixed effect model for family based genetic data. How can I extract the p value from a lmekin object? When I print the object in R console, I can see the p value and Z value are just over there. But I can not extract them by the coef() function. kinfit$coefficient$fixed (kinfit is the name of the lmekin object) just include the intercept and the value of fixed effects. Where are p and Z values? Thank you! __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
