[R] .jinit() : Cannot create Java virtual machine
Dear all, when using .jinit() I get the message .jinit() : Cannot create Java virtual machine (-1). The details: I am using the Dismo package.Dismo has a function 'maxent' that communi-cates with this program(MaxEnt).MaxEnt is available as a stand-alone Java program. It is normal when I execute the command :jar - paste(system.file(package=dismo), /java/maxent.jar, sep='') when I execute the function:xm - maxent(predictors, pres_train, factors='biome').The R show the error(Cannot create Java virtual machine) . Java is correct installed . My R version is 2.14.0. I don't know how to solve the problem. Will you help me out? Thank you,all. Yuwei Wang Cnic,CAS [[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 in fitted values in lm function
Hi, I have a data set of 1 rows and ran a linear regression by using the function lmres = lm(formula,data) then got the fitted value by using the value fit=fitted(lmres). but the number of rows in the fitted one is about 9548, What could be the reason for reduction in the number of rows in the fitted one -- View this message in context: http://r.789695.n4.nabble.com/help-in-fitted-values-in-lm-function-tp4038642p4038642.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] .jinit() : Cannot create Java virtual machine
Dear all, when using .jinit() I get the message .jinit() : Cannot create Java virtual machine (-1). sessionInfo() R version 2.14.0 (2011-10-31)Platform: i386-pc-mingw32/i386 (32-bit)locale:[1] LC_COLLATE=Chinese_People's Republic of China.936 [2] LC_CTYPE=Chinese_People's Republic of China.936 [3] LC_MONETARY=Chinese_People's Republic of China.936[4] LC_NUMERIC=C [5] LC_TIME=Chinese_People's Republic of China.936 attached base packages:[1] stats graphics grDevices utils datasets methods base other attached packages:[1] maptools_0.8-10 lattice_0.20-0 foreign_0.8-46 rJava_0.9-1[5] dismo_0.7-11raster_1.9-41 sp_0.9-91 loaded via a namespace (and not attached):[1] grid_2.14.0 The details: I am using the Dismo package.Dismo has a function 'maxent' that communi-cates with this program(MaxEnt).MaxEnt is available as a stand-alone Java program. It is normal when I execute the command :jar - paste(system.file(package=dismo), /java/maxent.jar, sep='') when I execute the function:xm - maxent(predictors, pres_train, factors='biome').The R show the error(Cannot create Java virtual machine) . Java is correct installed . My R version is 2.14.0. I don't know how to solve the problem. Will you help me out? Thank you,all. Yuwei Wang Cnic,CAS [[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] Error .jcall(mxe, S, fit, c(autorun, -e, afn, -o, dirout, : java.lang.NoSuchMethodError: density.Params.readFromArgs([Ljava/lang/String; )Ljava/lang/String;
Dear all, I get the error when I use maxent.jar: Error .jcall(mxe, S, fit, c(autorun, -e, afn, -o, dirout, : java.lang.NoSuchMethodError: density.Params.readFromArgs([Ljava/lang/String;)Ljava/lang/String; sessionInfo() result: R version 2.14.0 (2011-10-31)Platform: i386-pc-mingw32/i386 (32-bit)locale:[1] LC_COLLATE=Chinese_People's Republic of China.936 [2] LC_CTYPE=Chinese_People's Republic of China.936 [3] LC_MONETARY=Chinese_People's Republic of China.936[4] LC_NUMERIC=C [5] LC_TIME=Chinese_People's Republic of China.936attached base packages:[1] stats graphics grDevices utils datasets methods base other attached packages:[1] maptools_0.8-10 lattice_0.20-0 foreign_0.8-46 rJava_0.9-2[5] dismo_0.7-11raster_1.9-41 sp_0.9-91 loaded via a namespace (and not attached):[1] grid_2.14.0 The details: I am using the Dismo package.Dismo has a function 'maxent' that communi-cates with this program(MaxEnt).MaxEnt is available as a stand-alone Java program. It is normal when I execute the command :jar - paste(system.file(package=dismo), /java/maxent.jar, sep='') when I execute the function:xm - maxent(predictors, pres_train, factors='biome').The R show the error. Java is correct installed ,version is 1.60._18. My R version is 2.14.0. I don't know how to solve the problem. Will you help me out? Thank you,all. Yuwei Wang Cnic,CAS [[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] Confused with an error message related to plotrix library in the newer versions of R.
On 11/14/2011 05:59 PM, Prasanth V P wrote: require(plotrix) xy.pop- c(17,15,13,11,9,8,6,5,4,3,2,2,1,3) xx.pop- c(17,14,12,11,11,8,6,5,4,3,2,2,2,3) agelabels- c(0-4,5-9,10-14,15-19,20-24,25-29,30-34, 35-39,40-44,45-49,50-54,55-59,60-64,65+) xycol-color.gradient(c(0,0,0.5,0.15),c(0.25,0.5,0.5,1.75),c(0.5,1.5,1,0),18) xxcol-color.gradient(c(0,1,0.5,1),c(0.25,0.5,0.5,1.25),c(0.5,0.25,0.5,1.5),18) par(mar=pyramid.plot(xy.pop,xx.pop,labels=agelabels, labelcex=1.125, main=Population Pyramid -- Malawi, xycol=xycol, xxcol=xxcol)) Hi Prasanth V P, Just a typo. Try this: par(mar=pyramid.plot(xy.pop,xx.pop,labels=agelabels,labelcex=1.125, main=Population Pyramid -- Malawi, lxcol=xycol,rxcol=xxcol)) Nice plot. Jim __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] help in fitted values in lm function
Hi Hi, I have a data set of 1 rows and ran a linear regression by using the function lmres = lm(formula,data) then got the fitted value by using the value fit=fitted(lmres). but the number of rows in the fitted one is about 9548, What could be the reason for reduction in the number of rows in the fitted one Some NA values in your data? Petr -- View this message in context: http://r.789695.n4.nabble.com/help-in- fitted-values-in-lm-function-tp4038642p4038642.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] regular expression for selection
Dear all I am again (as usual) lost in regular expression use for selection. Here are my data: dput(mena) c(138516_10g_50ml_50c_250utes1_m53.00-_s1.imp, 138516_10g_50ml_50c_250utes1_m54.00_s1.imp, 138516_10g_50ml_50c_250utes1_m55.00_s1.imp, 138516_10g_50ml_50c_250utes1_m56.00_s1.imp, 138516_10g_50ml_50c_250utes1_m57.00_s1.imp, 138516_10g_50ml_50c_250utes1_m58.00_s1.imp, 138516_10g_50ml_50c_250utes1_m59.00_s1.imp) I want to select only values m foolowed by numbers from 53 to 59. I used sub(m5., , mena) which correctly selects those m53 - m59 values but, in contrary to my expectation, it replaced the selected values with specified replacement - in that case empty string. What I shall use if I want to get rid of all but m53-m59 from those strings? Regards Petr __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] regular expression for selection
Hi, Try grepl instead of sub, mena[grepl(m5., mena)] HTH, baptiste On 14 November 2011 21:45, Petr PIKAL petr.pi...@precheza.cz wrote: Dear all I am again (as usual) lost in regular expression use for selection. Here are my data: dput(mena) c(138516_10g_50ml_50c_250utes1_m53.00-_s1.imp, 138516_10g_50ml_50c_250utes1_m54.00_s1.imp, 138516_10g_50ml_50c_250utes1_m55.00_s1.imp, 138516_10g_50ml_50c_250utes1_m56.00_s1.imp, 138516_10g_50ml_50c_250utes1_m57.00_s1.imp, 138516_10g_50ml_50c_250utes1_m58.00_s1.imp, 138516_10g_50ml_50c_250utes1_m59.00_s1.imp) I want to select only values m foolowed by numbers from 53 to 59. I used sub(m5., , mena) which correctly selects those m53 - m59 values but, in contrary to my expectation, it replaced the selected values with specified replacement - in that case empty string. What I shall use if I want to get rid of all but m53-m59 from those strings? Regards Petr __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] regular expression for selection
On 11/14/2011 07:45 PM, Petr PIKAL wrote: Dear all I am again (as usual) lost in regular expression use for selection. Here are my data: dput(mena) c(138516_10g_50ml_50c_250utes1_m53.00-_s1.imp, 138516_10g_50ml_50c_250utes1_m54.00_s1.imp, 138516_10g_50ml_50c_250utes1_m55.00_s1.imp, 138516_10g_50ml_50c_250utes1_m56.00_s1.imp, 138516_10g_50ml_50c_250utes1_m57.00_s1.imp, 138516_10g_50ml_50c_250utes1_m58.00_s1.imp, 138516_10g_50ml_50c_250utes1_m59.00_s1.imp) I want to select only values m foolowed by numbers from 53 to 59. I used sub(m5., , mena) which correctly selects those m53 - m59 values but, in contrary to my expectation, it replaced the selected values with specified replacement - in that case empty string. What I shall use if I want to get rid of all but m53-m59 from those strings? Hi Petr, How about: grep(m5,mena) Jim __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] regular expression for selection
Hi Hi, Try grepl instead of sub, mena[grepl(m5., mena)] It does not select those m5? strings from those character vectors. I need as an output a vector m53, m54, m55, m56, m57, m58, m59 Regards Petr HTH, baptiste On 14 November 2011 21:45, Petr PIKAL petr.pi...@precheza.cz wrote: Dear all I am again (as usual) lost in regular expression use for selection. Here are my data: dput(mena) c(138516_10g_50ml_50c_250utes1_m53.00-_s1.imp, 138516_10g_50ml_50c_250utes1_m54.00_s1.imp, 138516_10g_50ml_50c_250utes1_m55.00_s1.imp, 138516_10g_50ml_50c_250utes1_m56.00_s1.imp, 138516_10g_50ml_50c_250utes1_m57.00_s1.imp, 138516_10g_50ml_50c_250utes1_m58.00_s1.imp, 138516_10g_50ml_50c_250utes1_m59.00_s1.imp) I want to select only values m foolowed by numbers from 53 to 59. I used sub(m5., , mena) which correctly selects those m53 - m59 values but, in contrary to my expectation, it replaced the selected values with specified replacement - in that case empty string. What I shall use if I want to get rid of all but m53-m59 from those strings? Regards Petr __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 with text separation
Good morning R list,
My apologies if this has *already* answered elsewhere, but I have not found
the answer that I am looking for.
I have a character string, i.e.
form-c('~ A + B + C + C / D + E + E / F + G + H + I + J + K + L * M')
Now, my aim is to find the position of all those instances of '*' and to
remove said '*'. However, I would also like to remove the preceding
variable name before the '*', the math operator preceding this, and also
the variable name after the '*'. So, here I would like to remove '+L*M'
So, far I have come up with the following code:
parts-strsplit(form,' ')
index-which(unlist(parts)==*)
for (i in 1:length(index)){
parts[[1]][index[i]]-list(NULL)
parts[[1]][index[i]+1]-list(NULL)
parts[[1]][index[i]-1]-list(NULL)
parts[[1]][index[i]-2]-list(NULL)
}
new.form-unlist(parts)
form-new.form[0]
for (i in 1: length(new.form)){
form-paste(form,new.form[i], sep=)
}
However, as you can see, I have had to use strsplit in, what I consider a
rather clumsy manner, as the character string (form) has to be in a certain
format. All variables and maths operators require a space between them in
order for strsplit to work in the manner I require.
I would very much like to accomplish what the above code already does, but
without the need for the initial character string having the need for the
aforementioned spaces.
If the list can offer help, I would be most appreciative.
Yours
Mike Griffiths
--
*Michael Griffiths, Ph.D
*Statistician
*Upstream Systems*
8th Floor
Portland House
Bressenden Place
SW1E 5BH
http://www.google.com/url?q=http%3A%2F%2Fwww.upstreamsystems.com%2Fsa=Dsntz=1usg=AFrqEzfKYfaAalqvahwrpywpJDL9DxUmWw
Tel +44 (0) 20 7869 5147
Fax +44 207 290 1321
Mob +44 789 4944 145
www.upstreamsystems.comhttp://www.google.com/url?q=http%3A%2F%2Fwww.upstreamsystems.com%2Fsa=Dsntz=1usg=AFrqEzfKYfaAalqvahwrpywpJDL9DxUmWw
*griffi...@upstreamsystems.com einst...@upstreamsystems.com*
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] regular expression for selection
Hi On 11/14/2011 07:45 PM, Petr PIKAL wrote: Dear all I am again (as usual) lost in regular expression use for selection. Here are my data: dput(mena) c(138516_10g_50ml_50c_250utes1_m53.00-_s1.imp, 138516_10g_50ml_50c_250utes1_m54.00_s1.imp, 138516_10g_50ml_50c_250utes1_m55.00_s1.imp, 138516_10g_50ml_50c_250utes1_m56.00_s1.imp, 138516_10g_50ml_50c_250utes1_m57.00_s1.imp, 138516_10g_50ml_50c_250utes1_m58.00_s1.imp, 138516_10g_50ml_50c_250utes1_m59.00_s1.imp) I want to select only values m foolowed by numbers from 53 to 59. I used sub(m5., , mena) which correctly selects those m53 - m59 values but, in contrary to my expectation, it replaced the selected values with specified replacement - in that case empty string. What I shall use if I want to get rid of all but m53-m59 from those strings? Hi Petr, How about: grep(m5,mena) It gives numeric values which tells me that there is a match in each string, but as a result I need only m53-m59 substrings. Regards Petr Jim __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Running totals
From: Joshua Wiley jwiley.ps...@gmail.com dat$RTotal - cumsum(dat$BAL) Wow, that's really great. I'm starting to really enjoy using R. My statistical needs are not that great, but I love the way that R handles tabular data. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] regular expression for selection
On 14.11.2011 10:22, Petr PIKAL wrote: Hi On 11/14/2011 07:45 PM, Petr PIKAL wrote: Dear all I am again (as usual) lost in regular expression use for selection. Here are my data: dput(mena) c(138516_10g_50ml_50c_250utes1_m53.00-_s1.imp, 138516_10g_50ml_50c_250utes1_m54.00_s1.imp, 138516_10g_50ml_50c_250utes1_m55.00_s1.imp, 138516_10g_50ml_50c_250utes1_m56.00_s1.imp, 138516_10g_50ml_50c_250utes1_m57.00_s1.imp, 138516_10g_50ml_50c_250utes1_m58.00_s1.imp, 138516_10g_50ml_50c_250utes1_m59.00_s1.imp) I want to select only values m foolowed by numbers from 53 to 59. I used sub(m5., , mena) which correctly selects those m53 - m59 values but, in contrary to my expectation, it replaced the selected values with specified replacement - in that case empty string. What I shall use if I want to get rid of all but m53-m59 from those strings? Hi Petr, How about: grep(m5,mena) It gives numeric values which tells me that there is a match in each string, but as a result I need only m53-m59 substrings. gsub(.*_(m5.).*, \\1, mena) Uwe Ligges Regards Petr 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-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Confused with an error message related to plotrix library in the newer versions of R.
Hi Jim, It's working perfectly fine with the rxcol parameter. I am just wondering how could I miss that..!!! By the way, many thanks for pointing it out... Otherwise, I would have been using the old version of R for just getting the required plot. Much Appreciated, Prasanth. -Original Message- From: Jim Lemon [mailto:j...@bitwrit.com.au] Sent: 14 November 2011 13:39 To: Prasanth V P Cc: r-help@r-project.org Subject: Re: [R] Confused with an error message related to plotrix library in the newer versions of R. On 11/14/2011 05:59 PM, Prasanth V P wrote: require(plotrix) xy.pop- c(17,15,13,11,9,8,6,5,4,3,2,2,1,3) xx.pop- c(17,14,12,11,11,8,6,5,4,3,2,2,2,3) agelabels- c(0-4,5-9,10-14,15-19,20-24,25-29,30-34, 35-39,40-44,45-49,50-54,55-59,60-64,65+) xycol-color.gradient(c(0,0,0.5,0.15),c(0.25,0.5,0.5,1.75),c(0.5,1.5,1,0), 18) xxcol-color.gradient(c(0,1,0.5,1),c(0.25,0.5,0.5,1.25),c(0.5,0.25,0.5,1.5 ),18) par(mar=pyramid.plot(xy.pop,xx.pop,labels=agelabels, labelcex=1.125, main=Population Pyramid -- Malawi, xycol=xycol, xxcol=xxcol)) Hi Prasanth V P, Just a typo. Try this: par(mar=pyramid.plot(xy.pop,xx.pop,labels=agelabels,labelcex=1.125, main=Population Pyramid -- Malawi, lxcol=xycol,rxcol=xxcol)) Nice plot. 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] Automatic Labeling of Document Clusters
I am performing document clustering on a set of documents using R. I performed hierarchical clustering using hclust and have identified the cluster corresponding to each data point. I would like to lablel each cluster automatically in order to identify the top keywords associated with each cluster. This would help me in validating the clusters. Are there any packages in R that helps us do automatic labelling of clusters??? A few clustering labeling methods are given here: http://en.wikipedia.org/wiki/Cluster_labeling http://erulemaking.ucsur.pitt.edu/doc/papers/dgo06-labeling.pdf Thanks you. Ravi -- View this message in context: http://r.789695.n4.nabble.com/Automatic-Labeling-of-Document-Clusters-tp4038849p4038849.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] regular expression for selection
Does library( stringr ) str_extract( mena, m5[0-9] ) achieve what you are looking for? Rgds, Rainer On Monday 14 November 2011 10:22:09 Petr PIKAL wrote: Hi On 11/14/2011 07:45 PM, Petr PIKAL wrote: Dear all I am again (as usual) lost in regular expression use for selection. Here are my data: dput(mena) c(138516_10g_50ml_50c_250utes1_m53.00-_s1.imp, 138516_10g_50ml_50c_250utes1_m54.00_s1.imp, 138516_10g_50ml_50c_250utes1_m55.00_s1.imp, 138516_10g_50ml_50c_250utes1_m56.00_s1.imp, 138516_10g_50ml_50c_250utes1_m57.00_s1.imp, 138516_10g_50ml_50c_250utes1_m58.00_s1.imp, 138516_10g_50ml_50c_250utes1_m59.00_s1.imp) I want to select only values m foolowed by numbers from 53 to 59. I used sub(m5., , mena) which correctly selects those m53 - m59 values but, in contrary to my expectation, it replaced the selected values with specified replacement - in that case empty string. What I shall use if I want to get rid of all but m53-m59 from those strings? Hi Petr, How about: grep(m5,mena) It gives numeric values which tells me that there is a match in each string, but as a result I need only m53-m59 substrings. Regards Petr 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-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] arrow egdes and lty
Dear R developers, I want to draw an arrow in a figure with lty=2. The lty argument also affects the edge of the arrow, which is unfortunate. Feature or bug? Is there some way to draw an arrow with intact edge, still with lty=2? Example code: plot(1:10) arrows(4, 5, 6, 7, lty=2) Best wishes, Matthias -- __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] What is the CADF test criterion=BIC report?
Hello Paul,
just a guess: different sample sizes! In your first call, the sample is shorter
than in your second. Hence, you can test this, if you curtail your data set in
your second call and then you should obtain the same result, i.e.:
library(vars)
data(Canada)
test - summary(CADFtest(Canada[-c(1:13), 1], max.lag.y = 1))
test
Augmented DF test
ADF test
t-test statistic: -1.389086
p-value:0.855681
Max lag of the diff. dependent variable:1.00
Call:
dynlm(formula = formula(model), start = obs.1, end = obs.T)
Residuals:
Min 1Q Median 3Q Max
-0.79726 -0.20587 -0.03332 0.23840 0.70460
Coefficients:
Estimate Std. Error t value Pr(|t|)
(Intercept) 24.471789 17.521147 1.3970.167
trnd 0.009959 0.006941 1.4350.156
L(y, 1) -0.026068 0.018767 -1.3890.856
L(d(y), 1) 0.615983 0.092632 6.650 7.18e-09 ***
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
Residual standard error: 0.3533 on 65 degrees of freedom
Multiple R-squared: 0.413, Adjusted R-squared: 0.3859
F-statistic:NA on NA and NA DF, p-value: NA
Though, I am not the package maintainer who could provide you with more
insights, but the source code itself.
Best,
Bernhard
-Ursprüngliche Nachricht-
Von: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] Im
Auftrag von p99323...@ntu.edu.tw
Gesendet: Montag, 14. November 2011 04:35
An: r-help@r-project.org
Betreff: [R] What is the CADF test criterion=BIC report?
Hello:
I am a rookie in using R. When I used the unit root test in CADFtest, I
got the different t-test statistics between using criterion=BIC and no using
criterion. But when I checked the result with eviews, I find out that no using
criterion is correct. Why after using criterion=BIC, I got the different
result?
Paul
data(Canada)
ADFt - CADFtest(Canada[,1], max.lag.y = 14, criterion=BIC)
summary(ADFt)
Augmented DF test
ADF test
t-test statistic: -1.389086
p-value:0.855681
Max lag of the diff. dependent variable:1.00
Call:
dynlm(formula = formula(model), start = obs.1, end = obs.T)
Residuals:
Min 1Q Median 3Q Max
-0.79726 -0.20587 -0.03332 0.23840 0.70460
Coefficients:
Estimate Std. Error t value Pr(|t|)
(Intercept) 24.342321 17.435476 1.3960.167
trnd 0.009959 0.006941 1.4350.156
L(y, 1) -0.026068 0.018767 -1.3890.856
L(d(y), 1) 0.615983 0.092632 6.650 7.18e-09 ***
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
Residual standard error: 0.3533 on 65 degrees of freedom
Multiple R-squared: 0.413, Adjusted R-squared: 0.3859
F-statistic:NA on NA and NA DF, p-value: NA
ADFt1 - CADFtest(Canada[,1], max.lag.y =1)
summary(ADFt1)
Augmented DF test
ADF test
t-test statistic: -2.7285715
p-value:0.2282588
Max lag of the diff. dependent variable:1.000
Call:
dynlm(formula = formula(model), start = obs.1, end = obs.T)
Residuals:
Min 1Q Median 3Q Max
-0.84769 -0.24745 -0.02081 0.24187 0.82344
Coefficients:
Estimate Std. Error t value Pr(|t|)
(Intercept) 47.661910 17.439021 2.733 0.00776 **
trnd 0.019217 0.007005 2.743 0.00754 **
L(y, 1) -0.051256 0.018785 -2.729 0.22826
L(d(y), 1) 0.753011 0.075724 9.944 1.61e-15 ***
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
Residual standard error: 0.3937 on 78 degrees of freedom
Multiple R-squared: 0.5674, Adjusted R-squared: 0.5508
F-statistic:NA on NA and NA DF, p-value: NA
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Re: [R] Odp: Problem using read.xls - Everything converted to factors
Hi, I have this same problem using read.xls in a table that I have NA values. Look: Using the importing from a csv file using read.table summary(dados) TratV1V2 A:5 Min. :1.0 Min. :1.000 B:5 1st Qu.:1.0 1st Qu.:1.000 Median :1.5 Median :2.000 Mean :1.5 Mean :1.556 3rd Qu.:2.0 3rd Qu.:2.000 Max. :2.0 Max. :2.000 NA's :1.000 Now using read.xls summary(dados.xls) TratV1V2 A:5 Min. :1.0 1 :4 B:5 1st Qu.:1.0 2 :5 Median :1.5 NA :1 Mean :1.5 3rd Qu.:2.0 Max. :2.0 Look that the V2 variable in read.xls is wrong convert to factors. Anybody know how to fix it in read.xls? Thanks Ronaldo Em 03-06-2011 12:34, Petr PIKAL escreveu: Hi [R] Problem using read.xls - Everything converted to factors Hallo, I would like to use to read.xls function from the gdata package to read data from Microsoft Excel files but I experienced a problem: For example I used the following code: testfile-read.xls(/home/.../wsjecon0603.xls, #file path header=F, dec=,, na.strings=n.a., skip=5, sheet=2, col.names=c(Name, Firm,GDP1,GDP2,GDP3,GDP4,CPI5, CPI11,UNEMP5,UNEMP11,PROF03,PROF04,STARTS03,STARTS04), nrows=54, #colClasses=c (character,character,numeric,numeric,numeric,numeric,numeric,numeric,numeric,numeric,numeric,numeric,numeric,numeric) ) print(testfile) Although the xls file contains numeric values in all the columns except the ones which I named Name and Firm, everything in the data frame has factor as class. I tried to use the colClasses option as above and as well with 's around each word, but this does not work and I will Hm. That shall work. You have got some advice from Gabor but in case numeric columns come as non numeric I often find a problem with some kind of formating the original values. Numbers like 10 253,52 are treated as nonnumeric as there is extra space character between thousands and hundereds. Maybe also na.strings are not always marked as n.a. but sometimes the value is missing and I suppose this can lead to conversion of all column to character vector. always receive the following error: Fehler in is(object, Class) : versuche einen Slot className von einem Objekt der einfachen Klasse (list) ohne Slots anzufordern Calls: read.xls - read.csv - read.table - Anonymous - is After some hours of reasearch I figured out how I can manually change the classes of the columns: testfile$GDP2-as.numeric(levels(testfile$GDP2))[testfile$GDP2] testfile$Name-as.character(levels(testfile$Name))[testfile$Name] #and so on you can spare some time to use sapply testfile[,character columns]- sapply(testfile[,character columns], as.numeric) shall convert all character columns to numeric at once but you will get NAs to all values which could not be converted for any reason. Regards Petr This works, but is a lot of work since I have to import many different data sets. So I was wondering if there is another way to let the classes be recognized correctly. Additionally I would like to know if there is any way to import data from different sheets with the same layout at once into one data frame. I use Ubuntu 11.04 with Rkward if this is of any importance. Thanks in advance for your answers, Sebastian __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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. -- 4ª lei - Aja como se seu orientador estivesse sempre certo, na maior parte do tempo. --Herman, I. P. 2007. Following the law. NATURE, Vol 445, p. 228. Prof. Ronaldo Reis Júnior | .''`. UNIMONTES/DBG/Lab. Ecologia Comportamental e Computacional | : :' : Campus Universitário Prof. Darcy Ribeiro, Vila Mauricéia | `. `'` CP: 126, CEP: 39401-089, Montes Claros - MG - Brasil | `- Fone: (38) 3229-8192 | ronaldo.r...@unimontes.br | http://www.ppgcb.unimontes.br/lecc | LinuxUser#: 205366 [[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] regular expression for selection
Hi Thank you. It is a pure magic, something taught in Unseen University. this is what I got as a help for selecting only letters from set of character vector. vzor [1] 61A 62C/27 65A/27 66C/29 69A/29 70C/31 73A/31 [8] 74C/33 77A/33 81A/35 82C/37 85A/37 86C/39 89A/39 [15] 90C/41 93A/41 94C/43 97A/43 98C/45 101A/45 102C/47 [22] 105A/47 106C/49 109A/49 110C/51 113A/51 gsub([^A-z], , vzor) [1] A C A C A C A C A A C A C A C A C [18] A C A C A C A C A Therefore I expected that sub(m5., \\1, mena) or sub(m5., , mena) selects what I wanted. But it was not the case. Please can you correct me when I try to evaluate your solution? gsub(.*_(m5.).*, \\1, mena) or gsub(.*(m5.).*, \\1, mena) .* matches any characters () negation? or matching selection for back reference? Finally the expressin matches whole string and evaluates what is matched by parenthesised value. This evaluation is returned by backreference. Is it correct evaluation? Regards Petr On 14.11.2011 10:22, Petr PIKAL wrote: Hi On 11/14/2011 07:45 PM, Petr PIKAL wrote: Dear all I am again (as usual) lost in regular expression use for selection. Here are my data: dput(mena) c(138516_10g_50ml_50c_250utes1_m53.00-_s1.imp, 138516_10g_50ml_50c_250utes1_m54.00_s1.imp, 138516_10g_50ml_50c_250utes1_m55.00_s1.imp, 138516_10g_50ml_50c_250utes1_m56.00_s1.imp, 138516_10g_50ml_50c_250utes1_m57.00_s1.imp, 138516_10g_50ml_50c_250utes1_m58.00_s1.imp, 138516_10g_50ml_50c_250utes1_m59.00_s1.imp) I want to select only values m foolowed by numbers from 53 to 59. I used sub(m5., , mena) which correctly selects those m53 - m59 values but, in contrary to my expectation, it replaced the selected values with specified replacement - in that case empty string. What I shall use if I want to get rid of all but m53-m59 from those strings? Hi Petr, How about: grep(m5,mena) It gives numeric values which tells me that there is a match in each string, but as a result I need only m53-m59 substrings. gsub(.*_(m5.).*, \\1, mena) Uwe Ligges Regards Petr 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-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] regular expression for selection
On 14.11.2011 11:27, Petr PIKAL wrote: Hi Thank you. It is a pure magic, something taught in Unseen University. this is what I got as a help for selecting only letters from set of character vector. vzor [1] 61A 62C/27 65A/27 66C/29 69A/29 70C/31 73A/31 [8] 74C/33 77A/33 81A/35 82C/37 85A/37 86C/39 89A/39 [15] 90C/41 93A/41 94C/43 97A/43 98C/45 101A/45 102C/47 [22] 105A/47 106C/49 109A/49 110C/51 113A/51 gsub([^A-z], , vzor) [1] A C A C A C A C A A C A C A C A C [18] A C A C A C A C A Therefore I expected that sub(m5., \\1, mena) or sub(m5., , mena) selects what I wanted. But it was not the case. Please can you correct me when I try to evaluate your solution? gsub(.*_(m5.).*, \\1, mena) or gsub(.*(m5.).*, \\1, mena) .* matches any characters Yes. () negation? or matching selection for back reference? The latter. See books about ergular expressions. I think it is also mentioned in ?regexp and with an example in ?gsub Finally the expressin matches whole string and evaluates what is matched by parenthesised value. This evaluation is returned by backreference. Is it correct evaluation? Indeed, where \\1 is the first backreference. Best, Uwe Regards Petr On 14.11.2011 10:22, Petr PIKAL wrote: Hi On 11/14/2011 07:45 PM, Petr PIKAL wrote: Dear all I am again (as usual) lost in regular expression use for selection. Here are my data: dput(mena) c(138516_10g_50ml_50c_250utes1_m53.00-_s1.imp, 138516_10g_50ml_50c_250utes1_m54.00_s1.imp, 138516_10g_50ml_50c_250utes1_m55.00_s1.imp, 138516_10g_50ml_50c_250utes1_m56.00_s1.imp, 138516_10g_50ml_50c_250utes1_m57.00_s1.imp, 138516_10g_50ml_50c_250utes1_m58.00_s1.imp, 138516_10g_50ml_50c_250utes1_m59.00_s1.imp) I want to select only values m foolowed by numbers from 53 to 59. I used sub(m5., , mena) which correctly selects those m53 - m59 values but, in contrary to my expectation, it replaced the selected values with specified replacement - in that case empty string. What I shall use if I want to get rid of all but m53-m59 from those strings? Hi Petr, How about: grep(m5,mena) It gives numeric values which tells me that there is a match in each string, but as a result I need only m53-m59 substrings. gsub(.*_(m5.).*, \\1, mena) Uwe Ligges Regards Petr 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-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 include integrate in a function that can be solved with uniroot?
Hallo,
I am trying to define expectation as an integral
and use uniroot to find the distribution parameter
for a given expectation.
However I fail to understand how to define properly
the functions involved and pass the parameters correctly.
Can anyone help me out?
Thanks,
Gerrit Draisma.
This what I tried:
===
# exponential density
g - function(x,lambda){ lambda *exp(-lambda*x) }
# expectation with lambda=1/10
integrate(f = function(x,lambda=1/10) {x*g(x,lambda)}, 0,Inf)
10 with absolute error 6.7e-05
# *how to write this as a function?*
E - function(lambda) {
+ integrate( f = function(x,th){x*g(x,lambda)},
+ 0,Inf)$Value}
E(1/10)
NULL
# *how to include this function in uniroot to find lambda*
# *for a given expectation?*
mu - 10
uniroot(f-function(th){E(th)-mu},lower=1,upper=100)
Error in if (is.na(f.lower)) stop(f.lower = f(lower) is NA) :
argument is of length zero
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Re: [R] arrow egdes and lty
On 14-Nov-11 09:57:52, Matthias Gondan wrote: Dear R developers, I want to draw an arrow in a figure with lty=2. The lty argument also affects the edge of the arrow, which is unfortunate. Feature or bug? Is there some way to draw an arrow with intact edge, still with lty=2? Example code: plot(1:10) arrows(4, 5, 6, 7, lty=2) Best wishes, Matthias According to ?arrows, it would seem that there is no provision to draw the arrow shaft and the arrow head using different line types with a single call to arrows(). To the extent that this represents the absence of a desirable feature (since you desire it), I would designate it as a bug. It can be done with two calls to arrows(), as follows: plot(1:10) arrows(4, 5, 6, 7, lty=2, length=0) arrows(5.99, 6.99, 6, 7, lty=1) Of course, the first could also be done using lines(). Ted. E-Mail: (Ted Harding) ted.hard...@wlandres.net Fax-to-email: +44 (0)870 094 0861 Date: 14-Nov-11 Time: 10:39:32 -- XFMail -- __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] arrow egdes and lty
Hi, Dear R developers, I want to draw an arrow in a figure with lty=2. The lty argument also affects the edge of the arrow, which is unfortunate. Feature or bug? Is there some way to draw an arrow with intact edge, still with lty=2? AFAIK there is no such option in the arrow function, but you might try to play around with the shape package and its various arrowhead options. Example code: plot(1:10) arrows(4, 5, 6, 7, lty=2) library(shape) plot(1:10) Arrows(4, 5, 6, 7, lty=2) HTH, Denes Best wishes, Matthias -- __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 compute eigenvectors and eigenvalues?
Hello. Consider the following matrix: mp - matrix(c(0,1/4,1/4,3/4,0,1/4,1/4,3/4,1/2),3,3,byrow=T) mp [,1] [,2] [,3] [1,] 0.00 0.25 0.25 [2,] 0.75 0.00 0.25 [3,] 0.25 0.75 0.50 The eigenvectors of the previous matrix are 1, 0.25 and 0.25 and it is not a diagonalizable matrix. When you try to find the eigenvalues and eigenvectors with R, R responses: eigen(mp) $values [1] 1.00 -0.25 -0.25 $vectors [,1] [,2] [,3] [1,] 0.3207501 1.068531e-08 -1.068531e-08 [2,] 0.4490502 -7.071068e-01 -7.071068e-01 [3,] 0.8339504 7.071068e-01 7.071068e-01 The eigenvalues are correct but the eigenvectors aren't. Moreover, if you try to compute the inverse of the matrix of eigenvectors, R is not aware that this matrix is singular: solve(eigen(mp)$vectors) [,1] [,2] [,3] [1,] 6.235383e-01 6.235383e-01 6.235383e-01 [2,] 3.743456e+07 -9.358641e+06 -9.358640e+06 [3,] -3.743456e+07 9.358640e+06 9.358641e+06 My question is: how can I fix it? Arnau. Arnau Mir Torres Edifici A. Turmeda Campus UIB Ctra. Valldemossa, km. 7,5 07122 Palma de Mca. tel: (+34) 971172987 fax: (+34) 971173003 email: arnau@uib.es URL: http://dmi.uib.es/~arnau [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] [R-pkgs] LaF 0.3: fast access to large ASCII files
The LaF package provides methods for fast access to large ASCII files. Currently the following file formats are supported: * comma separated format (csv) and other separated formats and * fixed width format. It is assumed that the files are too large to fit into memory, although the package can also be used to efficiently access files that do fit into memory. In order to process files that are too large to fit into memory, methods are provided to access and process file blockwise. Furthermore, an opened file can be indexed as one would a data.frame. In this way subsets. or specific columns can be read into memory. For example, assuming that an object laf has been created using one of the functions laf_open_csv or laf_open_fwf, the third column from the file can be read into memory using: col - laf[,3] The LaF-manual vignette contains a description of all functionality provided: http://laf-r.googlecode.com/files/LaF-manual_0.3.pdf The Laf-benchmark vignette compares the performance of LaF to the standard R-routines read.table and read.fwf: http://laf-r.googlecode.com/files/LaF-benchmark_0.3.pdf ___ R-packages mailing list r-packa...@r-project.org https://stat.ethz.ch/mailman/listinfo/r-packages __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] arrow egdes and lty
Ted Harding ted.hard...@wlandres.net on Mon, 14 Nov 2011 10:39:35 + writes: On 14-Nov-11 09:57:52, Matthias Gondan wrote: Dear R developers, I want to draw an arrow in a figure with lty=2. The lty argument also affects the edge of the arrow, which is unfortunate. Feature or bug? Is there some way to draw an arrow with intact edge, still with lty=2? Example code: plot(1:10) arrows(4, 5, 6, 7, lty=2) Best wishes, Matthias According to ?arrows, it would seem that there is no provision to draw the arrow shaft and the arrow head using different line types with a single call to arrows(). To the extent that this represents the absence of a desirable feature (since you desire it), I would designate it as a bug. It can be done with two calls to arrows(), as follows: plot(1:10) arrows(4, 5, 6, 7, lty=2, length=0) arrows(5.99, 6.99, 6, 7, lty=1) Another possibility is to use p.arrows() from package 'sfsmisc' which draws nice arrow heads; and if you like to keep them simple, do *not* fill them : install.packages(sfsmisc) require(sfsmisc) example(arrows) # - show R's standard arrows() ## The example from the p.arrows() help page: plot(x,y, main=p.arrows(.)) p.arrows(x[s], y[s], x[s+1], y[s+1], col= 1:3, fill = dark blue) ## not filling the arrow heads -- and using lty : plot(x,y, main=p.arrows(.)) p.arrows(x[s], y[s], x[s+1], y[s+1], col= 1:3, lty = 2, fill = NA) Of course, the first could also be done using lines(). Ted. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] [R-pkgs] amap new version (multidimensional analysis)
Dear R users, Thanks to a new contributor, Luigi Cerulo, amap provides 2 more metrics, and another agglomeration linkage for distance computation, and hierarchical clustering. The new centroid linkage method implemented in the cluster3 software tool (http://bonsai.hgc.jp/~mdehoon/software/cluster/software.htm). In this method the pseudoitem of a cluster is computed as the average of the items coordinates, and clusters are aggregated with the same distance metrics used between items. This approach reveals very effective in the context of gene functional expressions analysis. This update makes amap even more convenient for gene expression analysis, but not only; amap provides a lot of tools for robust statistics (rank based metrics, robust principal component analysis) with very fast implementations. Antoine Lucas. ___ R-packages mailing list r-packa...@r-project.org https://stat.ethz.ch/mailman/listinfo/r-packages __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] aov output question
Hello, I currently get anova results out of the aov function (see below) I use the model.tables and I believe it gives me back the model parameters of the fit (betas), however I don't see the intercept (beta_0) and don't understand what the rep output means and there is no description in the documentation. Another question: is there a function that outputs the results in a more meaningful way e.g. show the percentage of variation of each factor towards the response I believe the formula would be something like: for factor X: (Sum_Sq_X / Sum_Sq_Total)*100 Thanks in advance, Best regards, Giovanni #throughput.aov - aov(Throughput~No_databases*Partitioning*No_middlewares*Queue_size,data=throughput) throughput.aov Call: aov(formula = Throughput ~ No_databases + Partitioning + No_middlewares + Queue_size, data = throughput) Terms: No_databases Partitioning No_middlewares Queue_size Residuals Sum of Squares 43146975 73949061130 20710 195504055 Deg. of Freedom11 2 1 433 Residual standard error: 671.9453 Estimated effects may be unbalanced summary(throughput.aov) DfSum Sq Mean Sq F valuePr(F) No_databases 1 43146975 43146975 95.5614 2.2e-16 *** Partitioning 1 7394 7394 0.01640.8982 No_middlewares 2 9061130 4530565 10.0342 5.497e-05 *** Queue_size 1 2071020710 0.04590.8305 Residuals 433 195504055 451511 --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 model.tables(throughput.aov,type=effects,se=TRUE) Design is unbalanced - use se.contrast() for se's Tables of effects No_databases 1 4 -317.1 310 rep 217.0 222 Partitioning sharding replication 4.303 -3.91 rep 209.000 230.00 No_middlewares 1 2 4 -97.93 -108.2 199 rep 139.00 150.0 150 Queue_size 40 100 -6.852 6.883 rep 220.000 219.000 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Fit continuous distribution to truncated empirical values
Hello David, thanks for your answer. I have done as you told me, however the fit is very poor, much worse than that obtained from using the whole dataset (without upper bound). Any idea? Thanks, Michele On Nov 4, 2011, at 8:56 PM, David Winsemius wrote: On Nov 3, 2011, at 7:54 AM, Michele Mazzucco wrote: Hi all, I am trying to fit a distribution to some data about survival times. I am interested only in a specific interval, e.g., while the data lies in the interval (0,, 600), I want the best for the interval (0,..., 24). I have tried both fitdistr (MASS package) and fitdist (from the fitdistrplus package), but I could not get them working, e.g. fitdistr(left, weibull, upper=24) Error in optim(x = c(529L, 528L, 527L, 526L, 525L, 524L, 523L, 522L, 521L, : L-BFGS-B needs finite values of 'fn' In addition: Warning message: In dweibull(x, shape, scale, log) : NaNs produced Am I doing something wrong? You didn't supply data to test, but shouldn't you supply a lower bound if you want to fit weibull? It is, after all, bounded at 0. left - c(529L, 528L, 527L, 526L, 525L, 524L, 523L, 522L, 521L, 50*runif(100)) fitdistr(left, weibull, upper=24) Error in optim(x = c(529, 528, 527, 526, 525, 524, 523, 522, 521, 18.3964251773432, : L-BFGS-B needs finite values of 'fn' In addition: Warning message: In dweibull(x, shape, scale, log) : NaNs produced fitdistr(left, weibull, upper=24, lower=0.5) shape scale 0.58195013 24. ( 0.04046087) ( 3.38621367) Thanks, Michele p.s. I have seen similar posts, e.g., http://tolstoy.newcastle.edu.au/R/help/05/02/11558.html, but I am not sure whether I can apply the same approach here. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. David Winsemius, MD Heritage Laboratories West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] correlations between columns for each row
Hello fellow R-users, Iâve been mulling this problem over for some time now and have decided it is something I have to deal with but canât, so here goes: I have a dataset (called maindata, it is 271 columns *13890 rows so I wont post the entire thing here, Iâll just explain the situation!) I am trying to calculate inter-environment correlation (rF = cov A,B / sq.root(varA * varB ) for each row of the dataset. the values needed are (in 80 of the columns 2*40) in columns 174-213, and 214-253 respectively which represent two environments (A or B). Each of those columns is labelled with Xnumber.A/B e.g. X208.A is column 174 (which also relates to the first column in the B environment groups, col.214, X208.B) effectively the equation is: rF=cov (columns[174:213] , [214:253]) / sqrt( (var[174:213]) * (var[214:253]) ) I want each of the 13890 rows to then have the rF value at the end of it (which will then be used later against other variables) Can anyone help me with this problem? Iâve tried allsorts and I have run out of ideas. Thanks in advance, Rob [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to compute eigenvectors and eigenvalues?
Consider the following matrix:
mp - matrix(c(0,1/4,1/4,3/4,0,1/4,1/4,3/4,1/2),3,3,byrow=T)
mp
[,1] [,2] [,3]
[1,] 0.00 0.25 0.25
[2,] 0.75 0.00 0.25
[3,] 0.25 0.75 0.50
The eigenvectors of the previous matrix are 1, 0.25 and 0.25 and it is not a
diagonalizable matrix.
When you try to find the eigenvalues and eigenvectors with R, R responses:
eigen(mp)
$values
[1] 1.00 -0.25 -0.25
$vectors
[,1] [,2] [,3]
[1,] 0.3207501 1.068531e-08 -1.068531e-08
[2,] 0.4490502 -7.071068e-01 -7.071068e-01
[3,] 0.8339504 7.071068e-01 7.071068e-01
The eigenvalues are correct but the eigenvectors aren't.
Well, let's look at 4*mp which is an integer matrix:
(M - matrix(c(rep(c(0, 3, 1, 1), 2),2), 3,3)); em - eigen(M); V -
em$vectors; lam - em$values
[,1] [,2] [,3]
[1,]011
[2,]301
[3,]132
all.equal(M, V %*% diag(lam) %*% solve(V))
[1] TRUE
zapsmall(V %*% diag(lam) %*% solve(V))
[,1] [,2] [,3]
[1,]011
[2,]301
[3,]132
So, as you see V is not singular,
and the basic property of the eigenvalue decomposition is
fulfilled:
M = V Lambda V^{-1}
or
M V = V Lambda
i.e. each column of V *is* eigenvector to the corresponding
eigenvalue.
Moreover, if you try to compute the inverse of the matrix of eigenvectors,
R is not aware that this matrix is singular:
solve(eigen(mp)$vectors)
[,1] [,2] [,3]
[1,] 6.235383e-01 6.235383e-01 6.235383e-01
[2,] 3.743456e+07 -9.358641e+06 -9.358640e+06
[3,] -3.743456e+07 9.358640e+06 9.358641e+06
it isn't...
My question is: how can I fix it?
No need to fix anything, as nothing is broken ;-)
Martin Maechler, ETH Zurich
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Re: [R] State space model
I found an old thread on R-Sig-Finance with the same problem and a possible
solution https://stat.ethz.ch/pipermail/r-sig-finance/2007q2/001362.html
I've used with success a few times but it seems a bit slow.
If anyone has a better way of modelling state-dependent volatility using
one of the available packages please let me know.
Kristian
2011/11/12 Kristian Lind kristian.langgaard.l...@gmail.com
Hi,
I'm trying to estimate the parameters of a state space model of the
following form
measurement eq:
z_t = a + b*y_t + eps_t
transition eq
y_t+h = (I -exp(-hL))theta + exp(-hL)y_t+ eta_{t+h}.
The problem is that the distribution of the innovations of the transition
equation depend on the previous value of the state variable.
To be exact: y_t|y_{t-1} ~N(mu, Q_t) where Q is a diagonal matrix with
elements equal to
Q_{i,t} =
sigma_i*(1-exp(-kappa_i*h)/kappa_i*(theta_i/2*(1-exp(kappa_i*h)+exp(-kappa_i*h)y_{t-1,i}
The fkf returns the filtered states variables so y_{t-1,i} is available. I
just can't figure out how to write my program in such a way that this
information is included and updated in the state space model for each
iteration in optim. Any suggestions on how to solve this are much
appreciated.
Thank you,
Kristian.
Below my program where the variance matrices are just identity matrices
and the data is just random numbers. I used the example from the FKF
package as framework.
library(FKF) #loading Fast Kalman Filter package
library(Matrix) # matrix exponential package
library(BB)
library(alabama)
x - matrix(abs(rnorm(400)), nrow=10, ncol=40)
m - 2 # m is the number of state variables
n - ncol(x) # is the length of the observed sample
d - nrow(x) # is the number of observed variables.
h - 1/52
## creating state space representation of 2-factor CIR model
CIR2ss - function(K_1, K_2, sigma_1, sigma_2, lambda_1, lambda_2,
theta_1, theta_2, delta_0, delta_1, delta_2) {
## defining auxilary parameters,
phi_11 - sqrt((K_1+lambda_1)^2+2*sigma_1^2*delta_1)
phi_21 - sqrt((K_2+lambda_2)^2+2*sigma_2^2*delta_2)
phi_12 - K_1+lambda_1+phi_11
phi_22 - K_2+lambda_2+phi_21
phi_13 - 2*K_1*theta_1/sigma_1^2
phi_23 - 2*K_2*theta_2/sigma_2^2
a - array(1, c(d,n))
phi_14 - numeric(d)
phi_24 - numeric(d)
b1 - numeric(d)
b2 - numeric(d)
for(t in 1:d){
phi_14[t] - 2*phi_11+phi_12*(exp(phi_11*t)-1)
phi_24[t] - 2*phi_21+phi_22*(exp(phi_21*t)-1)
a[t] - delta_0 -
phi_13/(t)*log(2*phi_11*exp(phi_12*(t)/2)/phi_14[t])-
phi_23/(t)*log(2*phi_21*exp(phi_22*(t)/2)/phi_24[t])
b1[t] - (delta_1/(t))*2*(exp(phi_11*(t))-1)/phi_14[t]
b2[t] - (delta_2/(t))*2*(exp(phi_21*(t))-1)/phi_24[t]
}
b - array(c(b1,b2), c(d,m,n))
j - -matrix(c(K_1, 0, 0, K_2), c(2,2))*h
explh - as.matrix(expm(j))
Tt - array(explh, c(m,m,n)) #array giving the factor of the
transition equation
Zt - b #array giving the factor of the measurement equation
ct - a #matrix giving the intercept of the measurement equation
dt - as.matrix((diag(m)-explh)%*%c(theta_1, theta_2)) #matrix giving
the intercept of the transition equation
GGt - array(diag(d), c(d,d,1)) #array giving the variance of the
disturbances of the measurement equation
HHt - diag(m) #array giving the variance of the innovations of the
transition equation
a0 - c(0.5, 0.5) #vector giving the initial value/estimation of the
state variable
P0 - matrix(1e6, nrow = 2, ncol = 2) # matrix giving the variance of
a0
return(list(a0 = a0, P0 = P0, ct = ct, dt = dt, Zt = Zt, Tt = Tt, GGt
= GGt,
HHt = HHt))
}
## Objective function passed to optim
objective - function(parm, yt) {
sp - CIR2ss(parm[K_1], parm[K_2], parm[sigma_1], parm[sigma_2],
parm[lambda_1], parm[lambda_2],
parm[theta_1], parm[theta_2], parm[delta_0],
parm[delta_1], parm[delta_2])
ans - fkf(a0 = sp$a0, P0 = sp$P0, dt = sp$dt, ct = sp$ct, Tt = sp$Tt,
Zt = sp$Zt, HHt = sp$HHt, GGt = sp$GGt, yt = yt)
return(-ans$logLik)
}
parm - c(K_1 = 0.6048, K_2 = 0.656, sigma_1 =0.1855, sigma_2 =0.5524,
lambda_1 =0.55, lambda_2 =0.009, theta_1 = 0.173, theta_2 =
0.12,
delta_0 =0.686, delta_1 =-0.003, delta_2=0.0025)
hin - function(parm, yt){
h- numeric(2)
h[1] - 2*parm[1]*parm[7]-parm[3]^2
h[2] - 2*parm[2]*parm[8]-parm[4]^2
h
}
##optimizing objective function
fit - auglag(par = parm, fn = objective, yt = x, control.outer =
list(method = CG), hin = hin)
print(fit)
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Re: [R] Help with text separation
Hi,
On Mon, Nov 14, 2011 at 4:20 AM, Michael Griffiths
griffi...@upstreamsystems.com wrote:
Good morning R list,
My apologies if this has *already* answered elsewhere, but I have not found
the answer that I am looking for.
I have a character string, i.e.
form-c('~ A + B + C + C / D + E + E / F + G + H + I + J + K + L * M')
Now, my aim is to find the position of all those instances of '*' and to
remove said '*'. However, I would also like to remove the preceding
variable name before the '*', the math operator preceding this, and also
the variable name after the '*'. So, here I would like to remove '+L*M'
You just want to get rid of them? gsub() it is.
I've changed your formula a little bit to better demonstrate what's going on:
form-c('~ A + B * C + C / D + E + E / F * G + H + I + J + K + L * M')
gsub( \\+ [A-Z] \\* [A-Z], , form)
[1] ~ A + C / D + E + E / F * G + H + I + J + K
That regular expression will take out a
space
+
any capital letter
space
*
space
any capital letter.
It will take out all occurrences of that sequence, but won't take out
occurrences of * not in that sequence.
If you don't want the spaces, you don't need them. Just take them out
of the regular expression as well.
Not that strsplit() was remotely the right tool here, but you can
split into characters without a separator:
form - 'abcd'
strsplit(form, '')
[[1]]
[1] a b c d
Sarah
So, far I have come up with the following code:
parts-strsplit(form,' ')
index-which(unlist(parts)==*)
for (i in 1:length(index)){
parts[[1]][index[i]]-list(NULL)
parts[[1]][index[i]+1]-list(NULL)
parts[[1]][index[i]-1]-list(NULL)
parts[[1]][index[i]-2]-list(NULL)
}
new.form-unlist(parts)
form-new.form[0]
for (i in 1: length(new.form)){
form-paste(form,new.form[i], sep=)
}
However, as you can see, I have had to use strsplit in, what I consider a
rather clumsy manner, as the character string (form) has to be in a certain
format. All variables and maths operators require a space between them in
order for strsplit to work in the manner I require.
I would very much like to accomplish what the above code already does, but
without the need for the initial character string having the need for the
aforementioned spaces.
If the list can offer help, I would be most appreciative.
Yours
Mike Griffiths
--
Sarah Goslee
http://www.functionaldiversity.org
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[R] Fwd: How to compute eigenvectors and eigenvalues?
Inicio del mensaje reenviado:
De: Arnau Mir arnau@uib.es
Fecha: 14 de noviembre de 2011 13:24:31 GMT+01:00
Para: Martin Maechler maech...@stat.math.ethz.ch
Asunto: Re: [R] How to compute eigenvectors and eigenvalues?
Sorry, but I can't explain very well.
The matrix 4*mp is:
4*mp
[,1] [,2] [,3]
[1,]011
[2,]301
[3,]132
The eigenvalues are:
lam
[1] 4 -1 -1
There is only one eigenvector linearly independent with eigenvalue -1. This
eigenvector is c(0,1,-1) but R computes two eigenvectors:
V
[,1] [,2] [,3]
[1,] 0.3207501 1.068531e-08 -1.068531e-08
[2,] 0.4490502 -7.071068e-01 -7.071068e-01
[3,] 0.8339504 7.071068e-01 7.071068e-01
One is
V[,2]
[1] 1.068531e-08 -7.071068e-01 7.071068e-01
and the other one:
V[,3]
[1] -1.068531e-08 -7.071068e-01 7.071068e-01
The first component of these two vectors must be zero but due to numerical
errors, R computes 1.068531e-08 and -1.068531e-08 respectively.
So, the matrix V is singular but R isn't aware of.
You are right when you say:
V %*% diag(lam) %*% solve(V)
[,1] [,2] [,3]
[1,] 8.788496e-09 1.00e+001
[2,] 3.00e+00 -9.313226e-101
[3,] 1.00e+00 3.00e+002
but this expression doesn't make any sense because solve(V) doesn't exist.
What I want is that R responses that mp or 4*mp is not diagonalizable and
solve(V) doesn't exist.
Arnau.
El 14/11/2011, a las 13:06, Martin Maechler escribió:
Consider the following matrix:
mp - matrix(c(0,1/4,1/4,3/4,0,1/4,1/4,3/4,1/2),3,3,byrow=T)
mp
[,1] [,2] [,3]
[1,] 0.00 0.25 0.25
[2,] 0.75 0.00 0.25
[3,] 0.25 0.75 0.50
The eigenvectors of the previous matrix are 1, 0.25 and 0.25 and it is not
a diagonalizable matrix.
When you try to find the eigenvalues and eigenvectors with R, R responses:
eigen(mp)
$values
[1] 1.00 -0.25 -0.25
$vectors
[,1] [,2] [,3]
[1,] 0.3207501 1.068531e-08 -1.068531e-08
[2,] 0.4490502 -7.071068e-01 -7.071068e-01
[3,] 0.8339504 7.071068e-01 7.071068e-01
The eigenvalues are correct but the eigenvectors aren't.
Well, let's look at 4*mp which is an integer matrix:
(M - matrix(c(rep(c(0, 3, 1, 1), 2),2), 3,3)); em - eigen(M); V -
em$vectors; lam - em$values
[,1] [,2] [,3]
[1,]011
[2,]301
[3,]132
all.equal(M, V %*% diag(lam) %*% solve(V))
[1] TRUE
zapsmall(V %*% diag(lam) %*% solve(V))
[,1] [,2] [,3]
[1,]011
[2,]301
[3,]132
So, as you see V is not singular,
and the basic property of the eigenvalue decomposition is
fulfilled:
M = V Lambda V^{-1}
or
M V = V Lambda
i.e. each column of V *is* eigenvector to the corresponding
eigenvalue.
Moreover, if you try to compute the inverse of the matrix of eigenvectors,
R is not aware that this matrix is singular:
solve(eigen(mp)$vectors)
[,1] [,2] [,3]
[1,] 6.235383e-01 6.235383e-01 6.235383e-01
[2,] 3.743456e+07 -9.358641e+06 -9.358640e+06
[3,] -3.743456e+07 9.358640e+06 9.358641e+06
it isn't...
My question is: how can I fix it?
No need to fix anything, as nothing is broken ;-)
Martin Maechler, ETH Zurich
Arnau Mir Torres
Edifici A. Turmeda
Campus UIB
Ctra. Valldemossa, km. 7,5
07122 Palma de Mca.
tel: (+34) 971172987
fax: (+34) 971173003
email: arnau@uib.es
URL: http://dmi.uib.es/~arnau
Arnau Mir Torres
Edifici A. Turmeda
Campus UIB
Ctra. Valldemossa, km. 7,5
07122 Palma de Mca.
tel: (+34) 971172987
fax: (+34) 971173003
email: arnau@uib.es
URL: http://dmi.uib.es/~arnau
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Re: [R] How to compute eigenvectors and eigenvalues?
Dear Arnau, In this and a subsequent message, you seem to incorrectly infer that the two equal eigenvalues of the matrix imply that it's singular. The rank of the matrix is equal to the number of *nonzero* eigenvalues, here 3, and so the matrix is nonsingular. That two eigenvalues are equal simply implies that the corresponding eigenvectors span a subspace of dimension 2; the 2 corresponding eigenvectors reported by R are (within rounding error) a basis for this subspace. I hope this helps, John John Fox Senator William McMaster Professor of Social Statistics Department of Sociology McMaster University Hamilton, Ontario, Canada http://socserv.mcmaster.ca/jfox -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-bounces@r- project.org] On Behalf Of Arnau Mir Sent: November-14-11 5:53 AM To: r-help@r-project.org Subject: [R] How to compute eigenvectors and eigenvalues? Hello. Consider the following matrix: mp - matrix(c(0,1/4,1/4,3/4,0,1/4,1/4,3/4,1/2),3,3,byrow=T) mp [,1] [,2] [,3] [1,] 0.00 0.25 0.25 [2,] 0.75 0.00 0.25 [3,] 0.25 0.75 0.50 The eigenvectors of the previous matrix are 1, 0.25 and 0.25 and it is not a diagonalizable matrix. When you try to find the eigenvalues and eigenvectors with R, R responses: eigen(mp) $values [1] 1.00 -0.25 -0.25 $vectors [,1] [,2] [,3] [1,] 0.3207501 1.068531e-08 -1.068531e-08 [2,] 0.4490502 -7.071068e-01 -7.071068e-01 [3,] 0.8339504 7.071068e-01 7.071068e-01 The eigenvalues are correct but the eigenvectors aren't. Moreover, if you try to compute the inverse of the matrix of eigenvectors, R is not aware that this matrix is singular: solve(eigen(mp)$vectors) [,1] [,2] [,3] [1,] 6.235383e-01 6.235383e-01 6.235383e-01 [2,] 3.743456e+07 - 9.358641e+06 -9.358640e+06 [3,] -3.743456e+07 9.358640e+06 9.358641e+06 My question is: how can I fix it? Arnau. Arnau Mir Torres Edifici A. Turmeda Campus UIB Ctra. Valldemossa, km. 7,5 07122 Palma de Mca. tel: (+34) 971172987 fax: (+34) 971173003 email: arnau@uib.es URL: http://dmi.uib.es/~arnau [[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] help in fitted values in lm function
Yes there are few NA in the Data -- View this message in context: http://r.789695.n4.nabble.com/help-in-fitted-values-in-lm-function-tp4038642p4039207.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] What is the CADF test criterion=BIC report?
In order for the information criteria to be able to select the model, all the models have to be estimated on the same sample. Therefore, all the models are estimated and compared using the same sample used for the model containing the largest number of lags. You can find this and other details in Lupi, C. (2009). Unit Root CADF Testing with R, Journal of Statistical Software, 2009, 32(2), 1-19 -- View this message in context: http://r.789695.n4.nabble.com/What-is-the-CADF-test-criterion-BIC-report-tp4038700p4039259.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] parralellization without clustering (snow)
Hi, I'm running R in supercomputer where clusters already are configurered, i.e. number of procesors are predefined and I cannot change it. Can I still use package like snow? I'm worrying that command like makeCluster won't be very 'healthy'. Or its ok to use it? Thanks in advance, Tomas -- View this message in context: http://r.789695.n4.nabble.com/parralellization-without-clustering-snow-tp4039275p4039275.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] Enquiry about 2nd-order interactions survival analysis
David's answers were correct. You are looking deep into the code when there is no reason to to so. 1. h(t|(X=x,Z=z)) = exp(Beta0 + XZBeta1) Most statisticians will tell you that this is an unwise model. The reason is that if you replace X with X+1 the fit changes, which is almost never desirable. What if someone coded your dummy variable as 1/0 instead of 0/1 -- wouldn't you want to get the same fit Therefore the default in R for the model lm(y ~ x*z) is to fit y = b0 + b1 x + b2 z + b3 xz You can get exactly the model you specify as lm(y ~ x:z), or as temp - x*z; lm(y ~ temp) Statistically, this is almost surely a mistake. 2. The model formulas work across packages. I used lm() above, but survreg is no different. Formula processing is done by the model.matrix() function, which survreg, lm, glm, all call. My C code is all downstream of this, and irrelevant to your question. Terry T On Sun, 2011-11-13 at 14:39 +0800, Kenji Ryusuke wrote: Dr Terry Therneau, Firstly I do apologize upon unsolicited email. I know about Dr Terry through R package survival and alot of your papers. As we know Equation(1) is a normal parametric survival analysis, I'ld like to modify it to be a 2nd-order interactions as in Equation(2) :- h(t|X=x) = exp(Beta0 + XBeta1) --- (1) h(t|(X=x,Z=z)) = exp(Beta0 + XZBeta1) -- (2) Where x and z are two covariates: x = dummy variable (1 or 0) z = factors (people name) I would like to modify survreg() to be a second-order interactions regression while there is no 2nd-order interactions survival regression as I searched over www.rseek.org. I tried to read through the codes of survreg(), but I am stuck (cannot understand) at survreg6.c survreg6.c apply C Language which involves Cholesky decomposition multi-matrix (first-order interactions) calculation. 1) chinv2.c 2) cholesky3.c 3) chsolve2.c (only solve the equations of first-order interactions) I do appreciate if Dr Terry willing to enlighten me. Thank you. Best, Ryusuke __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 include integrate in a function that can be solved with uniroot?
Try this:
EV - function(lamb){
fnc - function(x) x * dexp(x, lamb)
integrate(fnc, 0, Inf)$value
}
Your problem is that there's nothing to translate th to lambda in your
code for E.
Michael
On Mon, Nov 14, 2011 at 5:32 AM, Gerrit Draisma gdrai...@xs4all.nl wrote:
Hallo,
I am trying to define expectation as an integral
and use uniroot to find the distribution parameter
for a given expectation.
However I fail to understand how to define properly
the functions involved and pass the parameters correctly.
Can anyone help me out?
Thanks,
Gerrit Draisma.
This what I tried:
===
# exponential density
g - function(x,lambda){ lambda *exp(-lambda*x) }
# expectation with lambda=1/10
integrate(f = function(x,lambda=1/10) {x*g(x,lambda)}, 0,Inf)
10 with absolute error 6.7e-05
# *how to write this as a function?*
E - function(lambda) {
+ integrate( f = function(x,th){x*g(x,lambda)},
+ 0,Inf)$Value}
E(1/10)
NULL
# *how to include this function in uniroot to find lambda*
# *for a given expectation?*
mu - 10
uniroot(f-function(th){E(th)-mu},lower=1,upper=100)
Error in if (is.na(f.lower)) stop(f.lower = f(lower) is NA) :
argument is of length zero
__
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and provide commented, minimal, self-contained, reproducible code.
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Help with text separation
Thank you Sarah,
Your reply was very helpful. I have the added difficulty that I am not only
dealing with single A-Z characters, but quite often have the following
situation:
form-c('~Sentence+LEGAL+Intro+Intro/Intro1+Intro*LEGAL+benefit+benefit/benefit1+product+action+mean+CTA*help')
and again, I need to remove the +'CTA*help' part of the character string.
However, in another instance I may have
form-c('~Sentence*LEGAL+Intro+Intro/Intro1+Intro*LEGAL+benefit+benefit/benefit1+product+action+mean+CTA*help')
In this case I would need to remove 'Sentence*LEGAL+' from form.
Can this be accomplished in the same manner?
Many thanks, once again, for your help
Mike Griffiths
On Mon, Nov 14, 2011 at 12:09 PM, Sarah Goslee sarah.gos...@gmail.comwrote:
Hi,
On Mon, Nov 14, 2011 at 4:20 AM, Michael Griffiths
griffi...@upstreamsystems.com wrote:
Good morning R list,
My apologies if this has *already* answered elsewhere, but I have not
found
the answer that I am looking for.
I have a character string, i.e.
form-c('~ A + B + C + C / D + E + E / F + G + H + I + J + K + L * M')
Now, my aim is to find the position of all those instances of '*' and to
remove said '*'. However, I would also like to remove the preceding
variable name before the '*', the math operator preceding this, and also
the variable name after the '*'. So, here I would like to remove '+L*M'
You just want to get rid of them? gsub() it is.
I've changed your formula a little bit to better demonstrate what's going
on:
form-c('~ A + B * C + C / D + E + E / F * G + H + I + J + K + L * M')
gsub( \\+ [A-Z] \\* [A-Z], , form)
[1] ~ A + C / D + E + E / F * G + H + I + J + K
That regular expression will take out a
space
+
any capital letter
space
*
space
any capital letter.
It will take out all occurrences of that sequence, but won't take out
occurrences of * not in that sequence.
If you don't want the spaces, you don't need them. Just take them out
of the regular expression as well.
Not that strsplit() was remotely the right tool here, but you can
split into characters without a separator:
form - 'abcd'
strsplit(form, '')
[[1]]
[1] a b c d
Sarah
So, far I have come up with the following code:
parts-strsplit(form,' ')
index-which(unlist(parts)==*)
for (i in 1:length(index)){
parts[[1]][index[i]]-list(NULL)
parts[[1]][index[i]+1]-list(NULL)
parts[[1]][index[i]-1]-list(NULL)
parts[[1]][index[i]-2]-list(NULL)
}
new.form-unlist(parts)
form-new.form[0]
for (i in 1: length(new.form)){
form-paste(form,new.form[i], sep=)
}
However, as you can see, I have had to use strsplit in, what I consider a
rather clumsy manner, as the character string (form) has to be in a
certain
format. All variables and maths operators require a space between them in
order for strsplit to work in the manner I require.
I would very much like to accomplish what the above code already does,
but
without the need for the initial character string having the need for the
aforementioned spaces.
If the list can offer help, I would be most appreciative.
Yours
Mike Griffiths
--
Sarah Goslee
http://www.functionaldiversity.org
--
*Michael Griffiths, Ph.D
*Statistician
*Upstream Systems*
8th Floor
Portland House
Bressenden Place
SW1E 5BH
http://www.google.com/url?q=http%3A%2F%2Fwww.upstreamsystems.com%2Fsa=Dsntz=1usg=AFrqEzfKYfaAalqvahwrpywpJDL9DxUmWw
Tel +44 (0) 20 7869 5147
Fax +44 207 290 1321
Mob +44 789 4944 145
www.upstreamsystems.comhttp://www.google.com/url?q=http%3A%2F%2Fwww.upstreamsystems.com%2Fsa=Dsntz=1usg=AFrqEzfKYfaAalqvahwrpywpJDL9DxUmWw
*griffi...@upstreamsystems.com einst...@upstreamsystems.com*
http://www.upstreamsystems.com/
[[alternative HTML version deleted]]
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] Installing binaries from R-Forge
Hello.
I just installed R 2.14.0 and then did
install.packages(splm, repos=http://R-Forge.R-project.org;)
in order to replicate your problem.
It worked almost fine. The only problem I had was with some missing
packages: being a fresh install, all suggested and required packages had
to be installed before 'splm', which is automatically done by
install.packages using the 'repos' specified: but some ('spam',
'ibdreg', 'lmtest', 'deldir', 'coda', 'sandwich') aren't available on
R-forge, so I had to install them separately beforehand.
The error you get is typical of moments when the required binary isn't
available yet, because the version is very recent and the automated
compiling process hasn't completed its runs. This isn't a problem with
'splm' because the current version is some months old. In turn, R 2.14.0
was 9 days old at the time of your message, so maybe recompiling wasn't
done yet.
An alternative install, also not requiring the very last R version, is
to download splm_0.9-05.zip to a local folder and install from there. If
you are on Windows, you can always do this through the graphical menu
(Packages install from local .zip file). If on Linux, same but through
command line.
It would be useful to know
- whether the problem persists now
- which system are you using etc.
This last piece of information is **required posting info**, and cited
in the posting guide (which in turn is required reading for
non-programmers alike). You can do
sessionInfo()
Let me know how you get along with this.
Giovanni
Giovanni Millo, PhD
Research Dept.,
Assicurazioni Generali SpA
Via Machiavelli 4,
34132 Trieste (Italy)
tel. +39 040 671184
fax +39 040 671160
--- Original message ---
Message: 3
Date: Wed, 9 Nov 2011 07:39:09 -0500
From: Downey, Patrick pdow...@urban.org
To: r-help@r-project.org
Subject: [R] Installing binaries from R-Forge
Message-ID:
0f96478603980b46aaafba77069582ed131c7...@uiexch.urban.org
Content-Type: text/plain; charset=us-ascii
Hello,
I'm attempting to install the splm package from R-Forge.
https://r-forge.r-project.org/R/?group_id=352
The page says, In order to successfully install the packages provided
on
R-Forge, you have to switch to the most recent version of R... It later
says To install this package directly within R type:
install.packages(splm, repos=http://R-Forge.R-project.org;).
I just installed R-2.14 and I still get the following error message.
Warning message:
In getDependencies(pkgs, dependencies, available, lib) :
package 'splm' is not available (for R version 2.14.0)
Can someone please help? I understand that there is relevant information
in
the posting guide, but I'm not a programmer and it's difficult for me to
understand. I thought I've followed the advice from previous posts
(notably, upgrade).
Thank you,
Mitch
--- end original message ---
Ai sensi del D.Lgs. 196/2003 si precisa che le informazi...{{dropped:12}}
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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] how to include integrate in a function that can be solved with uniroot?
You need to explicitly pass th to your function with the ... argument
of integrate.
E - function(th){
integrate(function(x,th) x*g(x, th), 0, Inf, th)$value
}
Also, it's value, not Value, which might be producing errors of another sort.
Michael
On Mon, Nov 14, 2011 at 9:16 AM, Gerrit Draisma gdrai...@xs4all.nl wrote:
Thanks Michael,
I see now how to include integrate function in the EV function.
And apologies:
I now realize that my code was sloppy.
I intended to write
E- function(th) {
+ integrate( f = function(x,th){x*g(x,th)},
+ 0,Inf)$Value}
E(1/10)
But that does not work either,
Gerrit.
Op 11/14/2011 2:50 PM, R. Michael Weylandt schreef:
Try this:
EV- function(lamb){
fnc- function(x) x * dexp(x, lamb)
integrate(fnc, 0, Inf)$value
}
Your problem is that there's nothing to translate th to lambda in your
code for E.
Michael
On Mon, Nov 14, 2011 at 5:32 AM, Gerrit Draismagdrai...@xs4all.nl
wrote:
Hallo,
I am trying to define expectation as an integral
and use uniroot to find the distribution parameter
for a given expectation.
However I fail to understand how to define properly
the functions involved and pass the parameters correctly.
Can anyone help me out?
Thanks,
Gerrit Draisma.
This what I tried:
===
# exponential density
g- function(x,lambda){ lambda *exp(-lambda*x) }
# expectation with lambda=1/10
integrate(f = function(x,lambda=1/10) {x*g(x,lambda)}, 0,Inf)
10 with absolute error 6.7e-05
# *how to write this as a function?*
E- function(lambda) {
+ integrate( f = function(x,th){x*g(x,lambda)},
+ 0,Inf)$Value}
E(1/10)
NULL
# *how to include this function in uniroot to find lambda*
# *for a given expectation?*
mu- 10
uniroot(f-function(th){E(th)-mu},lower=1,upper=100)
Error in if (is.na(f.lower)) stop(f.lower = f(lower) is NA) :
argument is of length zero
__
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PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/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] Running totals
Glad it worked! The one gotcha is that it does not handle missing values, so for example: cumsum(c(1, 2, 3, NA, 4)) [1] 1 3 6 NA NA both the NA, and everything after it become NA (missing). If you find yourself working with tables and frequencies and the like, you may also like (if you have not already seen): ?table # tabulate data ?function pulls up documentation ## example table(c(john, jane, jane, jane)) jane john 31 ?xtabs # cross tabulation ## examples using the built in mtcars dataset ## (vs and am are 0/1 data) xtabs( ~ vs + am, data = mtcars) am vs 0 1 0 12 6 1 7 7 You may also like the vcd (visualizing categorical data) package by Michael Friendly: Keeping with the mtcars data, we might want to visualize that little cross tab: require(vcd) pairs(xtabs(~ vs + am, data = mtcars)) Cheers, Josh On Mon, Nov 14, 2011 at 1:30 AM, Mark Carter mcturra2...@yahoo.co.uk wrote: From: Joshua Wiley jwiley.ps...@gmail.com dat$RTotal - cumsum(dat$BAL) Wow, that's really great. I'm starting to really enjoy using R. My statistical needs are not that great, but I love the way that R handles tabular data. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Joshua Wiley Ph.D. Student, Health Psychology Programmer Analyst II, ATS Statistical Consulting Group University of California, Los Angeles https://joshuawiley.com/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Help with text separation
Hi
r-help-boun...@r-project.org napsal dne 14.11.2011 14:54:05:
Thank you Sarah,
Your reply was very helpful. I have the added difficulty that I am not
only
dealing with single A-Z characters, but quite often have the following
situation:
form-c('~Sentence+LEGAL+Intro+Intro/Intro1+Intro*LEGAL+benefit+benefit/
benefit1+product+action+mean+CTA*help')
and again, I need to remove the +'CTA*help' part of the character
string.
However, in another instance I may have
form-c('~Sentence*LEGAL+Intro+Intro/Intro1+Intro*LEGAL+benefit+benefit/
benefit1+product+action+mean+CTA*help')
In this case I would need to remove 'Sentence*LEGAL+' from form.
Can this be accomplished in the same manner?
Hm. I am not at all an expert in regular expressions but recently I
learned some ways (thanks Uwe)
sub(^(~)\\+(.+)\\+$, \\1\\2, gsub([[:alnum:]]+\\*[[:alnum:]]+, ,
form))
[1] ~Intro+Intro/Intro1++benefit+benefit/benefit1+product+action+mean
this will remove all values xx*y from your form together with
leading and trailing +
I wonder if any automatic process can remove only one from several
xx*y substrings.
Regards
Petr
PS and still it is not perfect as there is one middle + more.
Many thanks, once again, for your help
Mike Griffiths
On Mon, Nov 14, 2011 at 12:09 PM, Sarah Goslee
sarah.gos...@gmail.comwrote:
Hi,
On Mon, Nov 14, 2011 at 4:20 AM, Michael Griffiths
griffi...@upstreamsystems.com wrote:
Good morning R list,
My apologies if this has *already* answered elsewhere, but I have
not
found
the answer that I am looking for.
I have a character string, i.e.
form-c('~ A + B + C + C / D + E + E / F + G + H + I + J + K + L *
M')
Now, my aim is to find the position of all those instances of '*'
and to
remove said '*'. However, I would also like to remove the preceding
variable name before the '*', the math operator preceding this, and
also
the variable name after the '*'. So, here I would like to remove
'+L*M'
You just want to get rid of them? gsub() it is.
I've changed your formula a little bit to better demonstrate what's
going
on:
form-c('~ A + B * C + C / D + E + E / F * G + H + I + J + K + L *
M')
gsub( \\+ [A-Z] \\* [A-Z], , form)
[1] ~ A + C / D + E + E / F * G + H + I + J + K
That regular expression will take out a
space
+
any capital letter
space
*
space
any capital letter.
It will take out all occurrences of that sequence, but won't take out
occurrences of * not in that sequence.
If you don't want the spaces, you don't need them. Just take them out
of the regular expression as well.
Not that strsplit() was remotely the right tool here, but you can
split into characters without a separator:
form - 'abcd'
strsplit(form, '')
[[1]]
[1] a b c d
Sarah
So, far I have come up with the following code:
parts-strsplit(form,' ')
index-which(unlist(parts)==*)
for (i in 1:length(index)){
parts[[1]][index[i]]-list(NULL)
parts[[1]][index[i]+1]-list(NULL)
parts[[1]][index[i]-1]-list(NULL)
parts[[1]][index[i]-2]-list(NULL)
}
new.form-unlist(parts)
form-new.form[0]
for (i in 1: length(new.form)){
form-paste(form,new.form[i], sep=)
}
However, as you can see, I have had to use strsplit in, what I
consider a
rather clumsy manner, as the character string (form) has to be in a
certain
format. All variables and maths operators require a space between
them in
order for strsplit to work in the manner I require.
I would very much like to accomplish what the above code already
does,
but
without the need for the initial character string having the need
for the
aforementioned spaces.
If the list can offer help, I would be most appreciative.
Yours
Mike Griffiths
--
Sarah Goslee
http://www.functionaldiversity.org
--
*Michael Griffiths, Ph.D
*Statistician
*Upstream Systems*
8th Floor
Portland House
Bressenden Place
SW1E 5BH
http://www.google.com/url?q=http%3A%2F%2Fwww.upstreamsystems.com%
2Fsa=Dsntz=1usg=AFrqEzfKYfaAalqvahwrpywpJDL9DxUmWw
Tel +44 (0) 20 7869 5147
Fax +44 207 290 1321
Mob +44 789 4944 145
www.upstreamsystems.comhttp://www.google.com/url?q=http%3A%2F%
2Fwww.upstreamsystems.com%2Fsa=Dsntz=1usg=AFrqEzfKYfaAalqvahwrpywpJDL9DxUmWw
*griffi...@upstreamsystems.com einst...@upstreamsystems.com*
http://www.upstreamsystems.com/
[[alternative HTML version deleted]]
__
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PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
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PLEASE do
Re: [R] Upgrade R?
Hello Kevin, Thank you. I will delete the folder and run an application called CCleaner (free). That will remove all the broken registry entries. There should be a problem free update path for R installation. As you rightfully mentioned the R- manual is not clear about package update issues. I received many helpful suggestions on the update path but some of the them were contradictory in the order of steps to be taken. I am also using statConn (DCOM) interface for programming. So my problems are multifold. I will compile the answers I received on the R version update issue and publish them so that that the experts could put them into more effective use. Sincerely, Cem -Original Message- From: Kevin Burton [mailto:rkevinbur...@charter.net] Sent: Sunday, November 13, 2011 4:11 PM To: 'Cem Girit' Subject: RE: [R] Upgrade R? I don't know if it was correct but I just removed the directory and then searched and removed all instances in the registry that referred to 2.13.1 (in my case searching for this seemed to only return references to 'R'). I have since been given some links that address specific registry entries but I haven't had any problem yet with my 'slash and burn' approach. It removed it from the 'Install/Uninstall' list with windows so it seems to have be removed and the disk space that 2.13.2 took up has been reclaimed. Hope this helps. Let me know if you find any more definitive answers. Thanks. Kevin -Original Message- From: Cem Girit [mailto:gi...@comcast.net] Sent: Saturday, November 12, 2011 6:33 PM To: 'Kevin Burton' Subject: RE: [R] Upgrade R? Hello Kevin, I am getting the same error utCompiledCode... since I installed R2.14 while R2.13 existed. How did you get rid of R2.13 eventually? Did you just delete it? If so, how did you clean the registry? Thank you, Cem -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Kevin Burton Sent: Thursday, November 10, 2011 11:54 AM To: 'jose Bartolomei'; 'R Help' Subject: Re: [R] Upgrade R? The problem with this documentation is two-fold. One it seems to concentrate on building from source which I don't need. Two it doesn't address the upgade. I have a number of packages and so I need to do what has been suggested and install the latest version *first*. Then copy the libraries (packages). Then uninstall the previous version. It is on this last step that I am stuck on right now. The last link on uninstalling R manually was what I needed. Thank you. Kevin From: jose Bartolomei [mailto:surfpr...@hotmail.com] Sent: Thursday, November 10, 2011 10:19 AM To: rkevinbur...@charter.net; R Help Subject: RE: [R] Upgrade R? Hi, Don't know if this will help you but... In my short experience and following the guidelines you should first uninstall R. http://cran.r-project.org/doc/manuals/R-admin.html#Installing-R-under-Window s Unistall it from the Windows control panel. The old R version libraries file will be kept on machine. For example : C:\Program Files\R\R-2.13.0\library Then install the new version via: http://cran.r-project.org/doc/manuals/R-admin.html#Installing-R-under-Window s You can copy/paste libraries from the old version R library file to the new one. C:\Program Files\R\R-2.14.0\library There is too an function named: ?update.packagee If above was what you did, then there is a post on Uninstalling R manually: http://learnserver.csd.univie.ac.at/rcomwiki/doku.php?id=wiki:uninstalling_r _manually Regards, Jose From: rkevinbur...@charter.net To: r-help@r-project.org Date: Thu, 10 Nov 2011 09:07:20 -0600 Subject: Re: [R] Upgrade R? Since apparently there is no one familiar with this error message let me rephrase the question. Is there a 'manual' process to fully remove a version of 'R' from my machine? This is a Window PC running Windows 7. Thank you. Kevin From: Kevin Burton [mailto:rkevinbur...@charter.net] Sent: Monday, November 07, 2011 2:23 PM To: 'r-help@r-project.org' Subject: Upgrade R? I am trying to upgrade to R 2.14 from R 2.13.1 I have compied all the libraries from the 'library' directory in my existing installation (2.13.1) to the installed R 2.14. Now I want to uninstall the old installation (R 2.13.1) and I get the error: Internal Error: Cannot find utCompiledCode record for this version of the uninstaller. Any ideas? Kevin [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list
[R] lme4:glmer with nested data
Dear all, I have the following dataset with results from an experiment with individual bats that performed two tasks related to prey capture under different conditions: X variables: indiv - 5 individual bats used in the experiment; all of which performed both tasks task - 2 tasks that each individual bat had to perform dist - 5 repeated measures of individual bats at 5 different distances from the object all x variables I treat as categorical factors with levels Y - I have 8 dependent variables related to the structure of ultrasound calls emitted by bats when performing each task. I know I can use them together in the same model with the function “cbind()” but each variable behaves a bit differently. Thus, I guess it would be better to build 8 separate models. I believe indiv should be a random effect in the model; dist and task should be fixed effects. I´d like to use the “glmer” (lme4) function to test two hypotheses: Main hypothesis: There are differences in Y measurements between tasks, which are related also to distance from the object. Secondary hypothesis: Differences in Y measurements between tasks do not depend on the individual. I guess the simplest model for an AIC model selection would be: print(Model.01-glmer(y~task*dist+(1|indiv)) - so any model that provides more details should have a lower (better) AIC score. I’m not sure if I’m coding the model correctly, so my hypothesis would be properly tested. 1- Literature suggests to get rid of the pseudo-replication: my repeated measures (“dist”) seem to behave like longitudinal data (as it is basically a time series). This way, indiv would be nested in dist. Furthermore, dist levels have different variance, so it would be good to group the data and somehow tell the model, that it should ignore differences in variance. (1|dist:indiv) or (dist|indiv)? I am still wondering if the “weights=” argument would apply here? 2- “dist” is nested in “task”, as for both tasks I have the same distances measured. According to the description of the package “lme4”, I should write: print(Model.02-glmer(y~task*dist+(1|indiv)+(1|task:dist)) 3- according to the text -book “The R book” I understand that I should do the following (as mentioned for the ratliver treatment-dataset): rename factor levels to unique labels: taskdist-task:dist taskdistindiv-task:dist:indiv print(Model.03-glmer(y~task+(1|taskdist)+(1|taskdistindiv))) Or, pooling 1 and 3 together myself I would end up with: print(Model.04-glmer(y~dist*task+(1|indiv)+(1|task:dist)+(1|dist:indiv)) I doubt that all of them actually describe correctly what I want the model to answer... I did not find any directly related comment in the R help. Thank you for your attention and for any help you may provide. -- __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Understand Ncells and Vcells, from gc()
Dear all, I am working on a 64 bits Linux system. I issue the following R commands: rm(list=ls()) # To remove all objects in the workspace. gc() # To free memory. used (Mb) gc trigger (Mb) max used (Mb) Ncells 124250 6.7 35 18.7 35 18.7 Vcells 124547 1.0 786432 6.0 476934 3.7 gc() # I had to do it again, don't know why! used (Mb) gc trigger (Mb) max used (Mb) Ncells 124257 6.7 35 18.7 35 18.7 Vcells 124574 1.0 786432 6.0 476934 3.7 gc() # Just to be sure things have stabilized. used (Mb) gc trigger (Mb) max used (Mb) Ncells 124257 6.7 35 18.7 35 18.7 Vcells 124574 1.0 786432 6.0 476934 3.7 x - as.integer(3) object.size(x) 48 bytes gc() # To free memory. used (Mb) gc trigger (Mb) max used (Mb) Ncells 124255 6.7 35 18.7 35 18.7 Vcells 124550 1.0 786432 6.0 476934 3.7 gc() # I had to do it again, don't know why! used (Mb) gc trigger (Mb) max used (Mb) Ncells 124259 6.7 35 18.7 35 18.7 Vcells 124575 1.0 786432 6.0 476934 3.7 gc() # Just to be sure things have stabilized. used (Mb) gc trigger (Mb) max used (Mb) Ncells 124259 6.7 35 18.7 35 18.7 Vcells 124575 1.0 786432 6.0 476934 3.7 My questions are: 1) Why should I use the command gc() two times before the values displayed do not change anymore? 2) object.size(x) is 48 bytes on my system. As I understand it, this is 8 bytes for storing the value 3L and 40 bytes (on my 64 bits OS) to store the header of x. Am-I right? (Note that I understand it would be the same for x - c(3L,4L)) 3) If 2) is OK, then you can see that Ncells increased by 2 units and Vcells by 1 unit. I think that 1 unit of Vcells = 8 bytes. Is it TRUE? (This is written in help(gc)) And in my mind, 1 unit of Ncells should be 20 bytes, so that: 1 unit of Vcells + 2 units of Ncells = 8 + 2*20 = 48, the size of x as returned by the command object.size(x). BUT, when you look at help(gc), one can read: 'gc' returns a matrix with rows 'Ncells' (_cons cells_), usually 28 bytes each on 32-bit systems and 56 bytes on 64-bit systems, So, can you please help me to undertsand all of this? Thanks in advance. Best regards, Pierre -- Pierre Lafaye de Micheaux Adresse courrier: Département de Mathématiques et Statistique Université de Montréal CP 6128, succ. Centre-ville Montréal, Québec H3C 3J7 CANADA Adresse physique: Département de Mathématiques et Statistique Bureau 4249, Pavillon André-Aisenstadt 2920, chemin de la Tour Montréal, Québec H3T 1J4 CANADA Tél.: (00-1) 514-343-6607 / Fax: (00-1) 514-343-5700 laf...@dms.umontreal.ca http://www.biostatisticien.eu -- Pierre Lafaye de Micheaux Adresse courrier: Département de Mathématiques et Statistique Université de Montréal CP 6128, succ. Centre-ville Montréal, Québec H3C 3J7 CANADA Adresse physique: Département de Mathématiques et Statistique Bureau 4249, Pavillon André-Aisenstadt 2920, chemin de la Tour Montréal, Québec H3T 1J4 CANADA Tél.: (00-1) 514-343-6607 / Fax: (00-1) 514-343-5700 laf...@dms.umontreal.ca http://www.biostatisticien.eu [[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] Help with text separation
Hi,
On Mon, Nov 14, 2011 at 8:54 AM, Michael Griffiths
griffi...@upstreamsystems.com wrote:
Thank you Sarah,
Your reply was very helpful. I have the added difficulty that I am not only
dealing with single A-Z characters, but quite often have the following
situation:
form-c('~Sentence+LEGAL+Intro+Intro/Intro1+Intro*LEGAL+benefit+benefit/benefit1+product+action+mean+CTA*help')
and again, I need to remove the +'CTA*help' part of the character string.
However, in another instance I may have
form-c('~Sentence*LEGAL+Intro+Intro/Intro1+Intro*LEGAL+benefit+benefit/benefit1+product+action+mean+CTA*help')
In this case I would need to remove 'Sentence*LEGAL+' from form.
Can this be accomplished in the same manner?
Regular expressions are *very* powerful, so yes. You should read a good
intro to regular expressions, and pay careful attention to the word markers,
then take a look at the specifics of R's implementation.
Why do I send you to the help? Because the possible answers all look a
lot like this:
form-c('~Sentence*LEGAL+Intro+Intro/Intro1+Intro*LEGAL+benefit+benefit/benefit1+product+action+mean+CTA*help')
gsub(\\+w**w*\\, , form)
[1]
~Sentence*LEGAL+Intro+Intro/Intro1+benefit+benefit/benefit1+product+action+mean
Sarah
Many thanks, once again, for your help
Mike Griffiths
On Mon, Nov 14, 2011 at 12:09 PM, Sarah Goslee sarah.gos...@gmail.com
wrote:
Hi,
On Mon, Nov 14, 2011 at 4:20 AM, Michael Griffiths
griffi...@upstreamsystems.com wrote:
Good morning R list,
My apologies if this has *already* answered elsewhere, but I have not
found
the answer that I am looking for.
I have a character string, i.e.
form-c('~ A + B + C + C / D + E + E / F + G + H + I + J + K + L * M')
Now, my aim is to find the position of all those instances of '*' and to
remove said '*'. However, I would also like to remove the preceding
variable name before the '*', the math operator preceding this, and also
the variable name after the '*'. So, here I would like to remove '+L*M'
You just want to get rid of them? gsub() it is.
I've changed your formula a little bit to better demonstrate what's going
on:
form-c('~ A + B * C + C / D + E + E / F * G + H + I + J + K + L * M')
gsub( \\+ [A-Z] \\* [A-Z], , form)
[1] ~ A + C / D + E + E / F * G + H + I + J + K
That regular expression will take out a
space
+
any capital letter
space
*
space
any capital letter.
It will take out all occurrences of that sequence, but won't take out
occurrences of * not in that sequence.
If you don't want the spaces, you don't need them. Just take them out
of the regular expression as well.
Not that strsplit() was remotely the right tool here, but you can
split into characters without a separator:
form - 'abcd'
strsplit(form, '')
[[1]]
[1] a b c d
Sarah
So, far I have come up with the following code:
parts-strsplit(form,' ')
index-which(unlist(parts)==*)
for (i in 1:length(index)){
parts[[1]][index[i]]-list(NULL)
parts[[1]][index[i]+1]-list(NULL)
parts[[1]][index[i]-1]-list(NULL)
parts[[1]][index[i]-2]-list(NULL)
}
new.form-unlist(parts)
form-new.form[0]
for (i in 1: length(new.form)){
form-paste(form,new.form[i], sep=)
}
However, as you can see, I have had to use strsplit in, what I consider
a
rather clumsy manner, as the character string (form) has to be in a
certain
format. All variables and maths operators require a space between them
in
order for strsplit to work in the manner I require.
I would very much like to accomplish what the above code already does,
but
without the need for the initial character string having the need for
the
aforementioned spaces.
If the list can offer help, I would be most appreciative.
Yours
Mike Griffiths
--
Sarah Goslee
http://www.functionaldiversity.org
__
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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] help in fitted values in lm function
If you want fitted() to return NAs in the positions where there were NA's in data, use na.action=na.exclude in your call to lm(). E.g., z - data.frame(y=1:5, x=c(1,NA,3,3,5)) fitted(lm(y~x, data=z)) 1345 1.25 3.25 3.25 5.25 fitted(lm(y~x, data=z, na.action=na.exclude)) 12345 1.25 NA 3.25 3.25 5.25 I think the help file for model.matrix has more detail, including how to use options() to set the na.action for your R session. Bill Dunlap Spotfire, TIBCO Software wdunlap tibco.com -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of arunkumar Sent: Monday, November 14, 2011 3:36 AM To: r-help@r-project.org Subject: Re: [R] help in fitted values in lm function Yes there are few NA in the Data -- View this message in context: http://r.789695.n4.nabble.com/help-in-fitted-values-in-lm-function- tp4038642p4039207.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] lme4:glmer with nested data
1. Post this on the R-sig-mixed-models list, not here. 2. (The following advice should be treated cautiously): Forget it! With only 5 bats, you have too little information to estimate variance components. Treat the bats as fixed effects and fit via lm (or glm if some of your responses are not gaussian). As your statistical skills seem a mite weak, I would also suggest that you collaborate with your local statistician. As I would not submit my brain (diminished as it may be) to someone whose training comes largely from reading Brain surgery for Dummies, neither would I trust the data analysis of someone whose statistical background is analogously informed. Apologies if I have misjudged. Cheers, Bert On Mon, Nov 14, 2011 at 5:44 AM, hij...@gmx.net wrote: Dear all, I have the following dataset with results from an experiment with individual bats that performed two tasks related to prey capture under different conditions: X variables: indiv - 5 individual bats used in the experiment; all of which performed both tasks task - 2 tasks that each individual bat had to perform dist - 5 repeated measures of individual bats at 5 different distances from the object all x variables I treat as categorical factors with levels Y - I have 8 dependent variables related to the structure of ultrasound calls emitted by bats when performing each task. I know I can use them together in the same model with the function cbind() but each variable behaves a bit differently. Thus, I guess it would be better to build 8 separate models. I believe indiv should be a random effect in the model; dist and task should be fixed effects. I´d like to use the glmer (lme4) function to test two hypotheses: Main hypothesis: There are differences in Y measurements between tasks, which are related also to distance from the object. Secondary hypothesis: Differences in Y measurements between tasks do not depend on the individual. I guess the simplest model for an AIC model selection would be: print(Model.01-glmer(y~task*dist+(1|indiv)) - so any model that provides more details should have a lower (better) AIC score. Im not sure if Im coding the model correctly, so my hypothesis would be properly tested. 1- Literature suggests to get rid of the pseudo-replication: my repeated measures (dist) seem to behave like longitudinal data (as it is basically a time series). This way, indiv would be nested in dist. Furthermore, dist levels have different variance, so it would be good to group the data and somehow tell the model, that it should ignore differences in variance. (1|dist:indiv) or (dist|indiv)? I am still wondering if the weights= argument would apply here? 2- dist is nested in task, as for both tasks I have the same distances measured. According to the description of the package lme4, I should write: print(Model.02-glmer(y~task*dist+(1|indiv)+(1|task:dist)) 3- according to the text -book The R book I understand that I should do the following (as mentioned for the ratliver treatment-dataset): rename factor levels to unique labels: taskdist-task:dist taskdistindiv-task:dist:indiv print(Model.03-glmer(y~task+(1|taskdist)+(1|taskdistindiv))) Or, pooling 1 and 3 together myself I would end up with: print(Model.04-glmer(y~dist*task+(1|indiv)+(1|task:dist)+(1|dist:indiv)) I doubt that all of them actually describe correctly what I want the model to answer... I did not find any directly related comment in the R help. Thank you for your attention and for any help you may provide. -- __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 [[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] help in fitted values in lm function
This caught me learning R, and no doubt thousands of others. When would one ever want the results of fitted() or residuals() to NOT match the data frame rows which went into the model? Certainly making shrinking the results the default is not what 99% of user will want if they need to access residuals: They will want a list of residuals padded with NAs to plot or use in further analyses in the originating data frame. IMHO, the default na.action for lm() should be “na.exclude (which, believe it or not, INcludes NAs in the results…) Best, tim On 14 Nov 2011, at 3:49 PM, William Dunlap wrote: If you want fitted() to return NAs in the positions where there were NA's in data, use na.action=na.exclude in your call to lm(). E.g., z - data.frame(y=1:5, x=c(1,NA,3,3,5)) fitted(lm(y~x, data=z)) 1345 1.25 3.25 3.25 5.25 fitted(lm(y~x, data=z, na.action=na.exclude)) 12345 1.25 NA 3.25 3.25 5.25 I think the help file for model.matrix has more detail, including how to use options() to set the na.action for your R session. Bill Dunlap Spotfire, TIBCO Software wdunlap tibco.com -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of arunkumar Sent: Monday, November 14, 2011 3:36 AM To: r-help@r-project.org Subject: Re: [R] help in fitted values in lm function Yes there are few NA in the Data -- View this message in context: http://r.789695.n4.nabble.com/help-in-fitted-values-in-lm-function- tp4038642p4039207.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@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Fit continuous distribution to truncated empirical values
On Nov 14, 2011, at 6:11 AM, Michele Mazzucco wrote: Hello David, thanks for your answer. I have done as you told me, however the fit is very poor, much worse than that obtained from using the whole dataset (without upper bound). Any idea? Counter questions in the absence of data: ??? Is there a reason from domain specific knowledge and theory to expect that the procedure you are attempting should be correct? ??? Why would you want to exclude data? ??? Why are you not looking for more general tutorials (such as the one by Ricci) rather than asking what is as yet an open-ended question on fitting methods that surely does not admit an answer easily provided on a mailing list? -- David. Thanks, Michele On Nov 4, 2011, at 8:56 PM, David Winsemius wrote: On Nov 3, 2011, at 7:54 AM, Michele Mazzucco wrote: Hi all, I am trying to fit a distribution to some data about survival times. I am interested only in a specific interval, e.g., while the data lies in the interval (0,, 600), I want the best for the interval (0,..., 24). I have tried both fitdistr (MASS package) and fitdist (from the fitdistrplus package), but I could not get them working, e.g. fitdistr(left, weibull, upper=24) Error in optim(x = c(529L, 528L, 527L, 526L, 525L, 524L, 523L, 522L, 521L, : L-BFGS-B needs finite values of 'fn' In addition: Warning message: In dweibull(x, shape, scale, log) : NaNs produced Am I doing something wrong? You didn't supply data to test, but shouldn't you supply a lower bound if you want to fit weibull? It is, after all, bounded at 0. left - c(529L, 528L, 527L, 526L, 525L, 524L, 523L, 522L, 521L, 50*runif(100)) fitdistr(left, weibull, upper=24) Error in optim(x = c(529, 528, 527, 526, 525, 524, 523, 522, 521, 18.3964251773432, : L-BFGS-B needs finite values of 'fn' In addition: Warning message: In dweibull(x, shape, scale, log) : NaNs produced fitdistr(left, weibull, upper=24, lower=0.5) shape scale 0.58195013 24. ( 0.04046087) ( 3.38621367) Thanks, Michele p.s. I have seen similar posts, e.g., http://tolstoy.newcastle.edu.au/R/help/05/02/11558.html , but I am not sure whether I can apply the same approach here. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. David Winsemius, MD Heritage Laboratories West Hartford, CT David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] max min values within dataframe
dear R-team I need to find the min, max values for each patient from dataset and keep the output of it as a dataframe with the following columns - Patient nr - Region (remains same per patient) - Min score - Max score Patient Region Score Time 11 X19 28 21 X20 126 31 X22 100 41 X25 191 52 Y121 62 Y122 72 Y254 82 Y267 93 X 61 10 3 X 64 11 3 X21 31 12 3 X22 68 13 3 X23 31 14 3 X24 38 15 3 X21 15 16 3 X22 24 17 3 X23 15 18 3 X24 243 19 3 X25 77 20 4 Y 65 21 4 Y22 28 22 4 Y23 75 23 4 Y24 19 24 5 Y233 25 5 Y241 26 5 Y23 33 27 5 Y24 13 28 5 Y25 42 29 5 Y26 21 30 5 Y274 31 6 Y244 32 6 Y328 So far I could find the min and max values for each patient, but the output of it is not (yet) what I need. Patient.nr = unique(Patient) aggregate(Score, list(Patient), max) Group.1 x 1 1 25 2 2 26 3 3 25 4 4 24 5 5 27 6 6 32 aggregate(Score, list(Patient), min) Group.1 x 1 1 19 2 2 12 3 3 6 4 4 6 5 5 23 6 6 24 I would like to do same but writing this new information (min, max values) in a dataframe with following columns - Patient nr - Region (remains same per patient) - Min score - Max score Can anybody help me with this? Thanks Laura [[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] Upgrade R?
I am also using statConn so I will let you know if I hear anything new. -Original Message- From: Cem Girit [mailto:gi...@comcast.net] Sent: Monday, November 14, 2011 8:52 AM To: 'Kevin Burton' Cc: r-help@r-project.org Subject: RE: [R] Upgrade R? Hello Kevin, Thank you. I will delete the folder and run an application called CCleaner (free). That will remove all the broken registry entries. There should be a problem free update path for R installation. As you rightfully mentioned the R- manual is not clear about package update issues. I received many helpful suggestions on the update path but some of the them were contradictory in the order of steps to be taken. I am also using statConn (DCOM) interface for programming. So my problems are multifold. I will compile the answers I received on the R version update issue and publish them so that that the experts could put them into more effective use. Sincerely, Cem -Original Message- From: Kevin Burton [mailto:rkevinbur...@charter.net] Sent: Sunday, November 13, 2011 4:11 PM To: 'Cem Girit' Subject: RE: [R] Upgrade R? I don't know if it was correct but I just removed the directory and then searched and removed all instances in the registry that referred to 2.13.1 (in my case searching for this seemed to only return references to 'R'). I have since been given some links that address specific registry entries but I haven't had any problem yet with my 'slash and burn' approach. It removed it from the 'Install/Uninstall' list with windows so it seems to have be removed and the disk space that 2.13.2 took up has been reclaimed. Hope this helps. Let me know if you find any more definitive answers. Thanks. Kevin -Original Message- From: Cem Girit [mailto:gi...@comcast.net] Sent: Saturday, November 12, 2011 6:33 PM To: 'Kevin Burton' Subject: RE: [R] Upgrade R? Hello Kevin, I am getting the same error utCompiledCode... since I installed R2.14 while R2.13 existed. How did you get rid of R2.13 eventually? Did you just delete it? If so, how did you clean the registry? Thank you, Cem -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Kevin Burton Sent: Thursday, November 10, 2011 11:54 AM To: 'jose Bartolomei'; 'R Help' Subject: Re: [R] Upgrade R? The problem with this documentation is two-fold. One it seems to concentrate on building from source which I don't need. Two it doesn't address the upgade. I have a number of packages and so I need to do what has been suggested and install the latest version *first*. Then copy the libraries (packages). Then uninstall the previous version. It is on this last step that I am stuck on right now. The last link on uninstalling R manually was what I needed. Thank you. Kevin From: jose Bartolomei [mailto:surfpr...@hotmail.com] Sent: Thursday, November 10, 2011 10:19 AM To: rkevinbur...@charter.net; R Help Subject: RE: [R] Upgrade R? Hi, Don't know if this will help you but... In my short experience and following the guidelines you should first uninstall R. http://cran.r-project.org/doc/manuals/R-admin.html#Installing-R-under-Window s Unistall it from the Windows control panel. The old R version libraries file will be kept on machine. For example : C:\Program Files\R\R-2.13.0\library Then install the new version via: http://cran.r-project.org/doc/manuals/R-admin.html#Installing-R-under-Window s You can copy/paste libraries from the old version R library file to the new one. C:\Program Files\R\R-2.14.0\library There is too an function named: ?update.packagee If above was what you did, then there is a post on Uninstalling R manually: http://learnserver.csd.univie.ac.at/rcomwiki/doku.php?id=wiki:uninstalling_r _manually Regards, Jose From: rkevinbur...@charter.net To: r-help@r-project.org Date: Thu, 10 Nov 2011 09:07:20 -0600 Subject: Re: [R] Upgrade R? Since apparently there is no one familiar with this error message let me rephrase the question. Is there a 'manual' process to fully remove a version of 'R' from my machine? This is a Window PC running Windows 7. Thank you. Kevin From: Kevin Burton [mailto:rkevinbur...@charter.net] Sent: Monday, November 07, 2011 2:23 PM To: 'r-help@r-project.org' Subject: Upgrade R? I am trying to upgrade to R 2.14 from R 2.13.1 I have compied all the libraries from the 'library' directory in my existing installation (2.13.1) to the installed R 2.14. Now I want to uninstall the old installation (R 2.13.1) and I get the error: Internal Error: Cannot find utCompiledCode record for this version of the uninstaller. Any ideas? Kevin [[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
Re: [R] max min values within dataframe
Hi Laura, This looks suspiciously like homework. Nonetheless, you may wish to check out ?cbind. Sarah On Mon, Nov 14, 2011 at 11:10 AM, B Laura gm.spam2...@gmail.com wrote: dear R-team I need to find the min, max values for each patient from dataset and keep the output of it as a dataframe with the following columns - Patient nr - Region (remains same per patient) - Min score - Max score Patient Region Score Time 1 1 X 19 28 2 1 X 20 126 3 1 X 22 100 4 1 X 25 191 5 2 Y 12 1 6 2 Y 12 2 7 2 Y 25 4 8 2 Y 26 7 9 3 X 6 1 10 3 X 6 4 11 3 X 21 31 12 3 X 22 68 13 3 X 23 31 14 3 X 24 38 15 3 X 21 15 16 3 X 22 24 17 3 X 23 15 18 3 X 24 243 19 3 X 25 77 20 4 Y 6 5 21 4 Y 22 28 22 4 Y 23 75 23 4 Y 24 19 24 5 Y 23 3 25 5 Y 24 1 26 5 Y 23 33 27 5 Y 24 13 28 5 Y 25 42 29 5 Y 26 21 30 5 Y 27 4 31 6 Y 24 4 32 6 Y 32 8 So far I could find the min and max values for each patient, but the output of it is not (yet) what I need. Patient.nr = unique(Patient) aggregate(Score, list(Patient), max) Group.1 x 1 1 25 2 2 26 3 3 25 4 4 24 5 5 27 6 6 32 aggregate(Score, list(Patient), min) Group.1 x 1 1 19 2 2 12 3 3 6 4 4 6 5 5 23 6 6 24 I would like to do same but writing this new information (min, max values) in a dataframe with following columns - Patient nr - Region (remains same per patient) - Min score - Max score Can anybody help me with this? Thanks Laura -- Sarah Goslee http://www.functionaldiversity.org __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] rugarch data format?
I am sorry to ask this group but the maintainer of this package did not leave an email address. Has anyone used or is using the 'rugarch' package with time-series data (ts)? I try to fit a GARCH model to my data using the following: gf - ugarchfit(data=l[[MEN]]$series, spec=spec) and I get: Error in .extractdata(data) : rgarch--error: class of data object not recognized class(l[[MEN]]$series) [1] ts The documentation states that : data A univariate data object. Can be a numeric vector, matrix, data.frame, zoo, xts, timeSeries, ts or irts object. I am not sure what I am doing wrong. Thank you. Kevin [[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] Fit continuous distribution to truncated empirical values
David, here is the smallest dataset # Bid Price SurvivalCensored 0.030.029 1 1 0.030.029 11 1 0.030.029 10 1 0.030.029 9 1 0.030.029 8 1 0.030.029 7 1 0.030.029 6 1 0.030.029 5 1 0.030.029 4 1 0.030.029 3 1 0.030.029 2 1 0.030.029 1 1 0.030.029 1 1 0.030.029 1 1 0.030.029 9 1 0.030.029 8 1 0.030.029 7 1 0.030.029 6 1 0.030.029 5 1 0.030.029 4 1 0.030.029 3 1 0.030.029 2 1 0.030.029 1 1 0.030.029 16 1 0.030.029 15 1 0.030.029 14 1 0.030.029 13 1 0.030.029 12 1 0.030.029 11 1 0.030.029 10 1 0.030.029 9 1 0.030.029 8 1 0.030.029 7 1 0.030.029 6 1 0.030.029 5 1 0.030.029 4 1 0.030.029 3 1 0.030.029 2 1 0.030.029 1 1 0.030.029 6 1 0.030.029 5 1 0.030.029 4 1 0.030.029 3 1 0.030.029 2 1 0.030.029 1 1 0.030.029 7 1 0.030.029 6 1 0.030.029 5 1 0.030.029 4 1 0.030.029 3 1 0.030.029 2 1 0.030.029 1 1 0.030.029 5 1 0.030.029 4 1 0.030.029 3 1 0.030.029 2 1 0.030.029 1 1 0.030.029 4 1 0.030.029 3 1 0.030.029 2 1 0.030.029 1 1 0.030.029 6 1 0.030.029 5 1 0.030.029 4 1 0.030.029 3 1 0.030.029 2 1 0.030.029 1 1 0.030.029 30 1 0.030.029 29 1 0.030.029 28 1 0.030.029 27 1 0.030.029 26 1 0.030.029 25 1 0.030.029 24 1 0.030.029 23 1 0.030.029 22 1 0.030.029 21 1 0.030.029 20 1 0.030.029 19 1 0.030.029 18 1 0.030.029 17 1 0.030.029 16 1 0.030.029 15 1 0.030.029 14 1 0.030.029 13 1 0.030.029 12 1 0.030.029 11 1 0.030.029 10 1 0.030.029 9 1 0.030.029 8 1 0.030.029 7 1 0.030.029 6 1 0.030.029 5 1 0.030.029 4 1 0.030.029 3 1 0.030.029 2 1 0.030.029 1 1 0.030.029 8 1 0.030.029 7 1 0.030.029 6 1 0.030.029 5 1 0.030.029 4 1 0.030.029 3 1 0.030.029 2 1 0.030.029 1 1 0.030.029 4 1 0.030.029 3 1 0.030.029 2 1 0.030.029 1 1 0.030.027 71 0 0.030.027 70 0 0.030.027 69 0 0.030.027 68 0 0.030.027 67 0 0.030.027 66 0 0.030.027 65 0 0.030.027 64 0 0.030.027 63 0 0.030.027 62 0 0.030.027 61 0 0.030.027 60 0 0.030.027 59 0 0.030.027 58 0 0.030.027 57 0 0.030.027 56 0 0.030.027 55 0 0.030.027 54 0 0.030.027 53 0 0.030.027 52 0 0.030.027 51 0 0.030.027 50 0 0.030.027 49 0 0.030.027 48 0 0.030.027 47 0 0.030.027 46 0 0.030.027 45 0 0.030.027 44 0 0.030.027 43 0 0.030.027 42 0 0.030.027 41 0 0.030.027 40 0 0.030.027 39 0 0.030.027 38 0 0.030.027 37 0 0.030.027 36 0 0.030.027 35 0 0.030.027 34 0 0.030.027 33 0 0.030.027 32 0 0.030.027 31 0 0.030.027 30 0 0.030.027 29 0 0.030.027 28 0 0.030.027 27 0 0.030.027 26 0 0.030.027 25 0 0.030.027 24 0 0.030.027 23 0 0.030.027 22 0 0.030.027 21 0 0.030.027 20 0 0.030.027 19 0 0.030.027 18 0 0.030.027 17 0 0.030.027 16 0 0.030.027 15 0 0.030.027 14 0 0.030.027 13 0 0.030.027 12 0 0.030.027 11 0 0.030.027 10 0 0.030.027 9 0 0.030.027 8 0 0.030.027 7 0 0.030.027 6 0 0.030.027 5 0 0.030.027 4 0 0.030.027 3 0 0.030.027 2 0 0.030.027 1 0 This is column # 3 1 11 10 9 8 7 6 5 4 3 2 1 1 1 9 8 7 6 5 4 3 2 1 16 15 14 13 12 11 10 9 8 7 6 5 4 3 2 1 6 5 4 3 2 1 7 6 5 4 3 2 1 5 4 3 2 1 4 3 2 1 6 5 4 3 2 1 30 29 28 27 26 25
Re: [R] Fit continuous distribution to truncated empirical values
A non-helpful reply on a language issue. Truncated data are quite different than censored data and require different methodologies to analyze. You -- and many others in their postings -- have appeared to confuse the two here. -- Bert On Mon, Nov 14, 2011 at 8:20 AM, Michele Mazzucco michelemazzu...@gmail.com wrote: David, here is the smallest dataset # Bid Price SurvivalCensored 0.030.029 1 1 0.030.029 11 1 0.030.029 10 1 0.030.029 9 1 0.030.029 8 1 0.030.029 7 1 0.030.029 6 1 0.030.029 5 1 0.030.029 4 1 0.030.029 3 1 0.030.029 2 1 0.030.029 1 1 0.030.029 1 1 0.030.029 1 1 0.030.029 9 1 0.030.029 8 1 0.030.029 7 1 0.030.029 6 1 0.030.029 5 1 0.030.029 4 1 0.030.029 3 1 0.030.029 2 1 0.030.029 1 1 0.030.029 16 1 0.030.029 15 1 0.030.029 14 1 0.030.029 13 1 0.030.029 12 1 0.030.029 11 1 0.030.029 10 1 0.030.029 9 1 0.030.029 8 1 0.030.029 7 1 0.030.029 6 1 0.030.029 5 1 0.030.029 4 1 0.030.029 3 1 0.030.029 2 1 0.030.029 1 1 0.030.029 6 1 0.030.029 5 1 0.030.029 4 1 0.030.029 3 1 0.030.029 2 1 0.030.029 1 1 0.030.029 7 1 0.030.029 6 1 0.030.029 5 1 0.030.029 4 1 0.030.029 3 1 0.030.029 2 1 0.030.029 1 1 0.030.029 5 1 0.030.029 4 1 0.030.029 3 1 0.030.029 2 1 0.030.029 1 1 0.030.029 4 1 0.030.029 3 1 0.030.029 2 1 0.030.029 1 1 0.030.029 6 1 0.030.029 5 1 0.030.029 4 1 0.030.029 3 1 0.030.029 2 1 0.030.029 1 1 0.030.029 30 1 0.030.029 29 1 0.030.029 28 1 0.030.029 27 1 0.030.029 26 1 0.030.029 25 1 0.030.029 24 1 0.030.029 23 1 0.030.029 22 1 0.030.029 21 1 0.030.029 20 1 0.030.029 19 1 0.030.029 18 1 0.030.029 17 1 0.030.029 16 1 0.030.029 15 1 0.030.029 14 1 0.030.029 13 1 0.030.029 12 1 0.030.029 11 1 0.030.029 10 1 0.030.029 9 1 0.030.029 8 1 0.030.029 7 1 0.030.029 6 1 0.030.029 5 1 0.030.029 4 1 0.030.029 3 1 0.030.029 2 1 0.030.029 1 1 0.030.029 8 1 0.030.029 7 1 0.030.029 6 1 0.030.029 5 1 0.030.029 4 1 0.030.029 3 1 0.030.029 2 1 0.030.029 1 1 0.030.029 4 1 0.030.029 3 1 0.030.029 2 1 0.030.029 1 1 0.030.027 71 0 0.030.027 70 0 0.030.027 69 0 0.030.027 68 0 0.030.027 67 0 0.030.027 66 0 0.030.027 65 0 0.030.027 64 0 0.030.027 63 0 0.030.027 62 0 0.030.027 61 0 0.030.027 60 0 0.030.027 59 0 0.030.027 58 0 0.030.027 57 0 0.030.027 56 0 0.030.027 55 0 0.030.027 54 0 0.030.027 53 0 0.030.027 52 0 0.030.027 51 0 0.030.027 50 0 0.030.027 49 0 0.030.027 48 0 0.030.027 47 0 0.030.027 46 0 0.030.027 45 0 0.030.027 44 0 0.030.027 43 0 0.030.027 42 0 0.030.027 41 0 0.030.027 40 0 0.030.027 39 0 0.030.027 38 0 0.030.027 37 0 0.030.027 36 0 0.030.027 35 0 0.030.027 34 0 0.030.027 33 0 0.030.027 32 0 0.030.027 31 0 0.030.027 30 0 0.030.027 29 0 0.030.027 28 0 0.030.027 27 0 0.030.027 26 0 0.030.027 25 0 0.030.027 24 0 0.030.027 23 0 0.030.027 22 0 0.030.027 21 0 0.030.027 20 0 0.030.027 19 0 0.030.027 18 0 0.030.027 17 0 0.030.027 16 0 0.030.027 15 0 0.030.027 14 0 0.030.027 13 0 0.030.027 12 0 0.030.027 11 0
Re: [R] max min values within dataframe
Hi Laura, You were close. Just use range() instead of min/max: ## your data (read in and then pasted the output of dput() to make it easy) dat - structure(list(Patient = c(1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 6L, 6L), Region = structure(c(1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L), .Label = c(X, Y), class = factor), Score = c(19L, 20L, 22L, 25L, 12L, 12L, 25L, 26L, 6L, 6L, 21L, 22L, 23L, 24L, 21L, 22L, 23L, 24L, 25L, 6L, 22L, 23L, 24L, 23L, 24L, 23L, 24L, 25L, 26L, 27L, 24L, 32L ), Time = c(28L, 126L, 100L, 191L, 1L, 2L, 4L, 7L, 1L, 4L, 31L, 68L, 31L, 38L, 15L, 24L, 15L, 243L, 77L, 5L, 28L, 75L, 19L, 3L, 1L, 33L, 13L, 42L, 21L, 4L, 4L, 8L)), .Names = c(Patient, Region, Score, Time), class = data.frame, row.names = c(1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32)) tmp - with(dat, aggregate(Score, list(Patient), range)) tmpreg - with(dat, Region[!duplicated(Patient)]) results - data.frame(tmp$Group.1, tmpreg, tmp$x) colnames(results) - c(Patient, Region, Min, Max) Note it is a little tricky to get the results in a data frame, because tmp is a bit of an odd data frame---due to the way aggregate works, the the first column of the data frame is a regular vector, but the second column actually contains a two column matrix. To get it into regular form, I extracted them separately when creating 'results'. Cheers, Josh On Mon, Nov 14, 2011 at 8:10 AM, B Laura gm.spam2...@gmail.com wrote: dear R-team I need to find the min, max values for each patient from dataset and keep the output of it as a dataframe with the following columns - Patient nr - Region (remains same per patient) - Min score - Max score Patient Region Score Time 1 1 X 19 28 2 1 X 20 126 3 1 X 22 100 4 1 X 25 191 5 2 Y 12 1 6 2 Y 12 2 7 2 Y 25 4 8 2 Y 26 7 9 3 X 6 1 10 3 X 6 4 11 3 X 21 31 12 3 X 22 68 13 3 X 23 31 14 3 X 24 38 15 3 X 21 15 16 3 X 22 24 17 3 X 23 15 18 3 X 24 243 19 3 X 25 77 20 4 Y 6 5 21 4 Y 22 28 22 4 Y 23 75 23 4 Y 24 19 24 5 Y 23 3 25 5 Y 24 1 26 5 Y 23 33 27 5 Y 24 13 28 5 Y 25 42 29 5 Y 26 21 30 5 Y 27 4 31 6 Y 24 4 32 6 Y 32 8 So far I could find the min and max values for each patient, but the output of it is not (yet) what I need. Patient.nr = unique(Patient) aggregate(Score, list(Patient), max) Group.1 x 1 1 25 2 2 26 3 3 25 4 4 24 5 5 27 6 6 32 aggregate(Score, list(Patient), min) Group.1 x 1 1 19 2 2 12 3 3 6 4 4 6 5 5 23 6 6 24 I would like to do same but writing this new information (min, max values) in a dataframe with following columns - Patient nr - Region (remains same per patient) - Min score - Max score Can anybody help me with this? Thanks Laura [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Joshua Wiley Ph.D. Student, Health Psychology Programmer Analyst II, ATS Statistical Consulting Group University of California, Los Angeles https://joshuawiley.com/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Very simple loop
I'm very new to R and am trying to create my first loop. I have: x -c(0:200) A - dpois(x,exp(4.5355343)) B - dpois(x,exp(4.5355343 + 0.0118638)) C - dpois(x,exp(4.5355343 -0.0234615)) D - dpois(x,exp(4.5355343 + 0.0316557)) E - dpois(x,exp(4.5355343 + 0.0004716)) F - dpois(x,exp(4.5355343 + 0.056437)) G - dpois(x,exp(4.5355343 + 0.1225822)) and would like to to get A[K] + B[K] + C[K] + D[K] + E[K] + F[K] G[K] for K(0:200) And then plot these cumulative values. Many thanks. -- View this message in context: http://r.789695.n4.nabble.com/Very-simple-loop-tp4039895p4039895.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] size of pdf/eps output
Hello, I am using a grid.layout for combining multiple ggplot-plots. So far I am doing it this way to get a pdf/eps: pdf(/path/to/my/file.pdf) #or postscript(/path/to/my/file.eps) grid.newpage() pushViewport(viewport(layout = grid.layout(nrow=2, ncol=2, widths = unit(c(7.5,7), cm), heights = unit(rep(5, 2), cm print(plot1, vp = viewport(layout.pos.row = 1, layout.pos.col = 1)) print(plot2, vp = viewport(layout.pos.row = 1, layout.pos.col = 2)) print(plot3, vp = viewport(layout.pos.row = 2, layout.pos.col = 1)) dev.off() With that method I get really nice plots but there is much white space around them. I'd like to crop the pdf/eps automatically to the maximum extend of the plot. How can that be done? Is that a setting with viewport? Thank you very much for your help /Johannes -- __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Very simple loop
Hi, On Mon, Nov 14, 2011 at 10:59 AM, Davg davidgrim...@hotmail.com wrote: I'm very new to R and am trying to create my first loop. I have: x -c(0:200) A - dpois(x,exp(4.5355343)) B - dpois(x,exp(4.5355343 + 0.0118638)) C - dpois(x,exp(4.5355343 -0.0234615)) D - dpois(x,exp(4.5355343 + 0.0316557)) E - dpois(x,exp(4.5355343 + 0.0004716)) F - dpois(x,exp(4.5355343 + 0.056437)) G - dpois(x,exp(4.5355343 + 0.1225822)) and would like to to get A[K] + B[K] + C[K] + D[K] + E[K] + F[K] G[K] for K(0:200) R indexing starts with 1, so even though x starts with 0, the corresponding index is 1:201 You don't need a loop at all: R can easily handle this with: all.sum - A + B + C + D + E + F + G And then plot these cumulative values. What kind of plot? You might check out ?hist and ?plot for ideas. Sarah -- Sarah Goslee http://www.functionaldiversity.org __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Very simple loop
x -c(0:200) A - dpois(x,exp(4.5355343)) B - dpois(x,exp(4.5355343 + 0.0118638)) C - dpois(x,exp(4.5355343 -0.0234615)) D - dpois(x,exp(4.5355343 + 0.0316557)) E - dpois(x,exp(4.5355343 + 0.0004716)) F - dpois(x,exp(4.5355343 + 0.056437)) G - dpois(x,exp(4.5355343 + 0.1225822)) total - A + B + C + D + E + F + G matplot(cbind(A, B, C, D, E, F, G, total)) On Mon, Nov 14, 2011 at 10:59 AM, Davg davidgrim...@hotmail.com wrote: I'm very new to R and am trying to create my first loop. I have: x -c(0:200) A - dpois(x,exp(4.5355343)) B - dpois(x,exp(4.5355343 + 0.0118638)) C - dpois(x,exp(4.5355343 -0.0234615)) D - dpois(x,exp(4.5355343 + 0.0316557)) E - dpois(x,exp(4.5355343 + 0.0004716)) F - dpois(x,exp(4.5355343 + 0.056437)) G - dpois(x,exp(4.5355343 + 0.1225822)) and would like to to get A[K] + B[K] + C[K] + D[K] + E[K] + F[K] G[K] for K(0:200) And then plot these cumulative values. Many thanks. -- View this message in context: http://r.789695.n4.nabble.com/Very-simple-loop-tp4039895p4039895.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. -- Jim Holtman Data Munger Guru What is the problem that you are trying to solve? Tell me what you want to do, not how you want to do it. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Very simple loop
x -c(0:200)
dat - data.frame(
A = dpois(x,exp(4.5355343)),
B = dpois(x,exp(4.5355343 + 0.0118638)),
C = dpois(x,exp(4.5355343 -0.0234615)),
D = dpois(x,exp(4.5355343 + 0.0316557)),
E = dpois(x,exp(4.5355343 + 0.0004716)),
F = dpois(x,exp(4.5355343 + 0.056437)),
G = dpois(x,exp(4.5355343 + 0.1225822)))
## using a looping approach
## instantiate a vector to hold results
results - vector(numeric, length = length(x))
for(i in 1:201) {# R starts indexing at 1, not 0
results[i] - dat[i, A] + dat[i, B] + dat[i, C] +
dat[i, D] + dat[i, E] + dat[i, F] + dat[i, G]
}
## find and plot cumulatively values
plot(x, cumsum(results))
You may be wondering why I put all the variables in a data frame. It
is because it will be much easier in the long run. This accomplishes
the same thing as the loop, with a fraction of the effort and much
much faster (loops can be slow in R, and vectorizing is preferred).
plot(x, cumsum(rowSums(dat)))
rowSums() is a vectorized function that finds the (duh) sums of each
row, then I just find the cumulative sum, and plot.
Hope this helps,
Josh
On Mon, Nov 14, 2011 at 7:59 AM, Davg davidgrim...@hotmail.com wrote:
I'm very new to R and am trying to create my first loop.
I have:
x -c(0:200)
A - dpois(x,exp(4.5355343))
B - dpois(x,exp(4.5355343 + 0.0118638))
C - dpois(x,exp(4.5355343 -0.0234615))
D - dpois(x,exp(4.5355343 + 0.0316557))
E - dpois(x,exp(4.5355343 + 0.0004716))
F - dpois(x,exp(4.5355343 + 0.056437))
G - dpois(x,exp(4.5355343 + 0.1225822))
and would like to to get A[K] + B[K] + C[K] + D[K] + E[K] + F[K] G[K]
for K(0:200)
And then plot these cumulative values.
Many thanks.
--
View this message in context:
http://r.789695.n4.nabble.com/Very-simple-loop-tp4039895p4039895.html
Sent from the R help mailing list archive at Nabble.com.
__
R-help@r-project.org mailing list
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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.
--
Joshua Wiley
Ph.D. Student, Health Psychology
Programmer Analyst II, ATS Statistical Consulting Group
University of California, Los Angeles
https://joshuawiley.com/
__
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] Very simple loop
But the awesome thing is you don't need a for loop at all thanks to the magic of R's vectorization! This will do it (and much faster than an R level loop would): x = 0:200 # Note that you don't need a c() since you aren't concatenating 0:200 with anything A - dpois(x,exp(4.5355343)) B - dpois(x,exp(4.5355343 + 0.0118638)) C - dpois(x,exp(4.5355343 -0.0234615)) D - dpois(x,exp(4.5355343 + 0.0316557)) E - dpois(x,exp(4.5355343 + 0.0004716)) F - dpois(x,exp(4.5355343 + 0.056437)) G - dpois(x,exp(4.5355343 + 0.1225822)) Y = A + B + C + D+ E+ F + G plot(x, Y) I'd advise you to look around for a good R guide: (there are quite a few free online, many tailored to specific disciplines) vectorization is pretty sweet and if you don't get into it early, you'll find R to be much more cumbersome and slow than it truly is. Hope this helps, Michael On Mon, Nov 14, 2011 at 10:59 AM, Davg davidgrim...@hotmail.com wrote: I'm very new to R and am trying to create my first loop. I have: x -c(0:200) A - dpois(x,exp(4.5355343)) B - dpois(x,exp(4.5355343 + 0.0118638)) C - dpois(x,exp(4.5355343 -0.0234615)) D - dpois(x,exp(4.5355343 + 0.0316557)) E - dpois(x,exp(4.5355343 + 0.0004716)) F - dpois(x,exp(4.5355343 + 0.056437)) G - dpois(x,exp(4.5355343 + 0.1225822)) and would like to to get A[K] + B[K] + C[K] + D[K] + E[K] + F[K] G[K] for K(0:200) And then plot these cumulative values. Many thanks. -- View this message in context: http://r.789695.n4.nabble.com/Very-simple-loop-tp4039895p4039895.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] max min values within dataframe
I took a stab at this using ddply() from the plyr package. How's this
look to you?
x- textConnection(Col Patient Region Score Time
11 X19 28
21 X20 126
31 X22 100
41 X25 191
52 Y121
62 Y122
72 Y254
82 Y267
93 X 61
10 3 X 64
11 3 X21 31
12 3 X22 68
13 3 X23 31
14 3 X24 38
15 3 X21 15
16 3 X22 24
17 3 X23 15
18 3 X24 243
19 3 X25 77
20 4 Y 65
21 4 Y22 28
22 4 Y23 75
23 4 Y24 19
24 5 Y233
25 5 Y241
26 5 Y23 33
27 5 Y24 13
28 5 Y25 42
29 5 Y26 21
30 5 Y274
31 6 Y244
32 6 Y328)
V = read.table(x, header = T)[,-1]
closeAllConnections()
rm(x)
# Everything above is just stuff to get the data in.
R - ddply(V, c(Patient,Region), function(d) {c(max =
max(d$Score),min = min(d$Score))})
Patient Region max min
1 1 X 25 19
2 2 Y 26 12
3 3 X 25 6
4 4 Y 24 6
5 5 Y 27 23
6 6 Y 32 24
Michael
On Mon, Nov 14, 2011 at 11:32 AM, Joshua Wiley jwiley.ps...@gmail.com wrote:
Hi Laura,
You were close. Just use range() instead of min/max:
## your data (read in and then pasted the output of dput() to make it easy)
dat - structure(list(Patient = c(1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 3L,
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L, 5L, 5L,
5L, 5L, 5L, 5L, 5L, 6L, 6L), Region = structure(c(1L, 1L, 1L,
1L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L), .Label = c(X,
Y), class = factor), Score = c(19L, 20L, 22L, 25L, 12L, 12L,
25L, 26L, 6L, 6L, 21L, 22L, 23L, 24L, 21L, 22L, 23L, 24L, 25L,
6L, 22L, 23L, 24L, 23L, 24L, 23L, 24L, 25L, 26L, 27L, 24L, 32L
), Time = c(28L, 126L, 100L, 191L, 1L, 2L, 4L, 7L, 1L, 4L, 31L,
68L, 31L, 38L, 15L, 24L, 15L, 243L, 77L, 5L, 28L, 75L, 19L, 3L,
1L, 33L, 13L, 42L, 21L, 4L, 4L, 8L)), .Names = c(Patient, Region,
Score, Time), class = data.frame, row.names = c(1, 2,
3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14,
15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25,
26, 27, 28, 29, 30, 31, 32))
tmp - with(dat, aggregate(Score, list(Patient), range))
tmpreg - with(dat, Region[!duplicated(Patient)])
results - data.frame(tmp$Group.1, tmpreg, tmp$x)
colnames(results) - c(Patient, Region, Min, Max)
Note it is a little tricky to get the results in a data frame, because
tmp is a bit of an odd data frame---due to the way aggregate works,
the the first column of the data frame is a regular vector, but the
second column actually contains a two column matrix. To get it into
regular form, I extracted them separately when creating 'results'.
Cheers,
Josh
On Mon, Nov 14, 2011 at 8:10 AM, B Laura gm.spam2...@gmail.com wrote:
dear R-team
I need to find the min, max values for each patient from dataset and keep
the output of it as a dataframe with the following columns
- Patient nr
- Region (remains same per patient)
- Min score
- Max score
Patient Region Score Time
1 1 X 19 28
2 1 X 20 126
3 1 X 22 100
4 1 X 25 191
5 2 Y 12 1
6 2 Y 12 2
7 2 Y 25 4
8 2 Y 26 7
9 3 X 6 1
10 3 X 6 4
11 3 X 21 31
12 3 X 22 68
13 3 X 23 31
14 3 X 24 38
15 3 X 21 15
16 3 X 22 24
17 3 X 23 15
18 3 X 24 243
19 3 X 25 77
20 4 Y 6 5
21 4 Y 22 28
22 4 Y 23 75
23 4 Y 24 19
24 5 Y 23 3
25 5 Y 24 1
26 5 Y 23 33
27 5 Y 24 13
28 5 Y 25 42
29 5 Y 26 21
30 5 Y 27 4
31 6 Y 24 4
32 6 Y 32 8
So far I could find the min and max values for each patient, but the output
of it is not (yet) what I need.
Patient.nr = unique(Patient)
aggregate(Score, list(Patient), max)
Group.1 x
1 1 25
2 2 26
3 3 25
4 4 24
5 5 27
6 6 32
aggregate(Score, list(Patient), min)
Group.1 x
1 1 19
2 2 12
3 3 6
4 4 6
5 5 23
6 6 24
I would like to do same but writing this new information (min, max values)
in a dataframe with following columns
- Patient nr
- Region (remains
[R] unable to get R CMD to work as expected on a 64 bit windows machine
Hi,
I've just downloaded and installed R 2.14.0 using the windows binary on
a 64bit windows machine running windows 7.
Rterm / RGui work as expected, as does
R CMD --help
and
R CMD BATCH --help
however
R CMD check --help
returns no information and I seem to be unable to check a package.
Various other options also seem to not be working as expected, i.e.
R CMD REMOVE aa
(where aa is just a garbage name) appears to do nothing (whereas the
same command on a 32bit windows machine returns with a message that
package aa does not exist.)
Just invoking R on the command line appears to do nothing on 64 bit
windows as opposed to starting a command line version of R (ala Rterm)
on 32 bit windows.
Any pointers as to what I've done wrong during the installation would be
appreciated.
Cheers
Martyn
sessionInfo()
R version 2.14.0 (2011-10-31)
Platform: x86_64-pc-mingw32/x64 (64-bit)
locale:
[1] LC_COLLATE=English_United Kingdom.1252
[2] LC_CTYPE=English_United Kingdom.1252
[3] LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United Kingdom.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
The Numerical Algorithms Group Ltd is a company registered in England
and Wales with company number 1249803. The registered office is:
Wilkinson House, Jordan Hill Road, Oxford OX2 8DR, United Kingdom.
This e-mail has been scanned for all viruses by Star. Th...{{dropped:4}}
__
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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] unable to get R CMD to work as expected on a 64 bit windows machine
Hi Martyn,
My guess is that you need to add the directory where R is located to
your Windows PATH variable. It sounds like Windows just doesn't know
where to find R.
HTH,
Josh
On Mon, Nov 14, 2011 at 8:48 AM, Martyn Byng martyn.b...@nag.co.uk wrote:
Hi,
I've just downloaded and installed R 2.14.0 using the windows binary on
a 64bit windows machine running windows 7.
Rterm / RGui work as expected, as does
R CMD --help
and
R CMD BATCH --help
however
R CMD check --help
returns no information and I seem to be unable to check a package.
Various other options also seem to not be working as expected, i.e.
R CMD REMOVE aa
(where aa is just a garbage name) appears to do nothing (whereas the
same command on a 32bit windows machine returns with a message that
package aa does not exist.)
Just invoking R on the command line appears to do nothing on 64 bit
windows as opposed to starting a command line version of R (ala Rterm)
on 32 bit windows.
Any pointers as to what I've done wrong during the installation would be
appreciated.
Cheers
Martyn
sessionInfo()
R version 2.14.0 (2011-10-31)
Platform: x86_64-pc-mingw32/x64 (64-bit)
locale:
[1] LC_COLLATE=English_United Kingdom.1252
[2] LC_CTYPE=English_United Kingdom.1252
[3] LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United Kingdom.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
The Numerical Algorithms Group Ltd is a company registered in England
and Wales with company number 1249803. The registered office is:
Wilkinson House, Jordan Hill Road, Oxford OX2 8DR, United Kingdom.
This e-mail has been scanned for all viruses by Star. Th...{{dropped:4}}
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Joshua Wiley
Ph.D. Student, Health Psychology
Programmer Analyst II, ATS Statistical Consulting Group
University of California, Los Angeles
https://joshuawiley.com/
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Help with text separation
On Nov 14, 2011, at 4:20 AM, Michael Griffiths wrote:
Good morning R list,
My apologies if this has *already* answered elsewhere, but I have
not found
the answer that I am looking for.
I have a character string, i.e.
form-c('~ A + B + C + C / D + E + E / F + G + H + I + J + K + L * M')
Now, my aim is to find the position of all those instances of '*'
and to
remove said '*'. However, I would also like to remove the preceding
variable name before the '*', the math operator preceding this, and
also
the variable name after the '*'. So, here I would like to remove
'+L*M'
This would be a very narrow implementation that requires the +/spc/
alnum/spc/*/alnum sequence exactly;
sub(\\+*\\s*[[:alnum:]]*\\s*\\*.[[:alnum:]]*, , form)
[1] ~ A + B + C + C / D + E + E / F + G + H + I + J + K
This is a more general implementation using the * operator that
matches each of the preceding item 0 or more times.
form-c('~ A + B + C + C / D + E + E / F + G + H + I + J + K + L * M',
'~ A + B + C + C / D + E + E / F + G + H + I + J + K + L*M',
'~ A + B + C + C / D + E + E / F + G + H + I + J + K +Llll*M'
)
sub(\\+*\\s*[[:alnum:]]*\\s*\\*.[[:alnum:]]*, , form)
[1] ~ A + B + C + C / D + E + E / F + G + H + I + J + K
[2] ~ A + B + C + C / D + E + E / F + G + H + I + J + K
[3] ~ A + B + C + C / D + E + E / F + G + H + I + J + K
---stripped out code---
--
David Winsemius, MD
West Hartford, CT
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] unable to get R CMD to work as expected on a 64 bit windows machine
Hi Josh,
Thanks for that, which directory needs to be in the path?
There is a file called R.exe in
C:\Program Files\R\R-2.14.0\bin
C:\Program Files\R\R-2.14.0\bin\x64
and
C:\Program Files\R\R-2.14.0\bin\i386
I currently have
C:\Program Files\R\R-2.14.0\bin\x64
in the path (which is, I'm guessing why R CMD --help works), do I need the
others in the path as well, and if so, in what order?
Cheers
Martyn
-Original Message-
From: Joshua Wiley [mailto:jwiley.ps...@gmail.com]
Sent: 14 November 2011 16:57
To: Martyn Byng
Cc: r-help@r-project.org
Subject: Re: [R] unable to get R CMD to work as expected on a 64 bit windows
machine
Hi Martyn,
My guess is that you need to add the directory where R is located to
your Windows PATH variable. It sounds like Windows just doesn't know
where to find R.
HTH,
Josh
On Mon, Nov 14, 2011 at 8:48 AM, Martyn Byng martyn.b...@nag.co.uk wrote:
Hi,
I've just downloaded and installed R 2.14.0 using the windows binary on
a 64bit windows machine running windows 7.
Rterm / RGui work as expected, as does
R CMD --help
and
R CMD BATCH --help
however
R CMD check --help
returns no information and I seem to be unable to check a package.
Various other options also seem to not be working as expected, i.e.
R CMD REMOVE aa
(where aa is just a garbage name) appears to do nothing (whereas the
same command on a 32bit windows machine returns with a message that
package aa does not exist.)
Just invoking R on the command line appears to do nothing on 64 bit
windows as opposed to starting a command line version of R (ala Rterm)
on 32 bit windows.
Any pointers as to what I've done wrong during the installation would be
appreciated.
Cheers
Martyn
sessionInfo()
R version 2.14.0 (2011-10-31)
Platform: x86_64-pc-mingw32/x64 (64-bit)
locale:
[1] LC_COLLATE=English_United Kingdom.1252
[2] LC_CTYPE=English_United Kingdom.1252
[3] LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United Kingdom.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
The Numerical Algorithms Group Ltd is a company registered in England
and Wales with company number 1249803. The registered office is:
Wilkinson House, Jordan Hill Road, Oxford OX2 8DR, United Kingdom.
This e-mail has been scanned for all viruses by Star. Th...{{dropped:4}}
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Joshua Wiley
Ph.D. Student, Health Psychology
Programmer Analyst II, ATS Statistical Consulting Group
University of California, Los Angeles
https://joshuawiley.com/
This e-mail has been scanned for all viruses by Star.
The Numerical Algorithms Group Ltd is a company registered in England
and Wales with company number 1249803. The registered office is:
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] Fit continuous distribution to truncated empirical values
Bert, I think there is a misunderstanding here. Some data is censored, but I want to fit the data with a distribution in the interval [0,24] only. Also, please note that I have other datasets having values larger than 1000. Cheers, Michele On 14 Nov 2011, at 18:28, Bert Gunter wrote: A non-helpful reply on a language issue. Truncated data are quite different than censored data and require different methodologies to analyze. You -- and many others in their postings -- have appeared to confuse the two here. -- Bert On Mon, Nov 14, 2011 at 8:20 AM, Michele Mazzucco michelemazzu...@gmail.com wrote: David, here is the smallest dataset # Bid Price SurvivalCensored 0.030.029 1 1 0.030.029 11 1 0.030.029 10 1 0.030.029 9 1 0.030.029 8 1 0.030.029 7 1 0.030.029 6 1 0.030.029 5 1 0.030.029 4 1 0.030.029 3 1 0.030.029 2 1 0.030.029 1 1 0.030.029 1 1 0.030.029 1 1 0.030.029 9 1 0.030.029 8 1 0.030.029 7 1 0.030.029 6 1 0.030.029 5 1 0.030.029 4 1 0.030.029 3 1 0.030.029 2 1 0.030.029 1 1 0.030.029 16 1 0.030.029 15 1 0.030.029 14 1 0.030.029 13 1 0.030.029 12 1 0.030.029 11 1 0.030.029 10 1 0.030.029 9 1 0.030.029 8 1 0.030.029 7 1 0.030.029 6 1 0.030.029 5 1 0.030.029 4 1 0.030.029 3 1 0.030.029 2 1 0.030.029 1 1 0.030.029 6 1 0.030.029 5 1 0.030.029 4 1 0.030.029 3 1 0.030.029 2 1 0.030.029 1 1 0.030.029 7 1 0.030.029 6 1 0.030.029 5 1 0.030.029 4 1 0.030.029 3 1 0.030.029 2 1 0.030.029 1 1 0.030.029 5 1 0.030.029 4 1 0.030.029 3 1 0.030.029 2 1 0.030.029 1 1 0.030.029 4 1 0.030.029 3 1 0.030.029 2 1 0.030.029 1 1 0.030.029 6 1 0.030.029 5 1 0.030.029 4 1 0.030.029 3 1 0.030.029 2 1 0.030.029 1 1 0.030.029 30 1 0.030.029 29 1 0.030.029 28 1 0.030.029 27 1 0.030.029 26 1 0.030.029 25 1 0.030.029 24 1 0.030.029 23 1 0.030.029 22 1 0.030.029 21 1 0.030.029 20 1 0.030.029 19 1 0.030.029 18 1 0.030.029 17 1 0.030.029 16 1 0.030.029 15 1 0.030.029 14 1 0.030.029 13 1 0.030.029 12 1 0.030.029 11 1 0.030.029 10 1 0.030.029 9 1 0.030.029 8 1 0.030.029 7 1 0.030.029 6 1 0.030.029 5 1 0.030.029 4 1 0.030.029 3 1 0.030.029 2 1 0.030.029 1 1 0.030.029 8 1 0.030.029 7 1 0.030.029 6 1 0.030.029 5 1 0.030.029 4 1 0.030.029 3 1 0.030.029 2 1 0.030.029 1 1 0.030.029 4 1 0.030.029 3 1 0.030.029 2 1 0.030.029 1 1 0.030.027 71 0 0.030.027 70 0 0.030.027 69 0 0.030.027 68 0 0.030.027 67 0 0.030.027 66 0 0.030.027 65 0 0.030.027 64 0 0.030.027 63 0 0.030.027 62 0 0.030.027 61 0 0.030.027 60 0 0.030.027 59 0 0.030.027 58 0 0.030.027 57 0 0.030.027 56 0 0.030.027 55 0 0.030.027 54 0 0.030.027 53 0 0.030.027 52 0 0.030.027 51 0 0.030.027 50 0 0.030.027 49 0 0.030.027 48 0 0.030.027 47 0 0.030.027 46 0 0.030.027 45 0 0.030.027 44 0 0.030.027 43 0 0.030.027 42 0 0.030.027 41 0 0.030.027 40 0 0.030.027 39 0 0.030.027 38 0 0.030.027 37 0 0.030.027 36 0 0.030.027 35 0 0.030.027 34 0 0.030.027 33 0 0.030.027 32 0 0.030.027 31 0 0.030.027 30 0 0.030.027 29 0 0.030.027 28 0 0.030.027 27 0 0.030.027 26 0 0.030.027 25 0 0.030.027 24 0 0.030.027 23 0 0.030.027 22 0 0.030.027 21 0 0.030.027 20 0 0.030.027 19 0 0.030.027 18 0 0.030.027 17 0 0.030.027 16 0
Re: [R] Very simple loop
Dear David, You do not need a loop. The vectors are equaly sized, so sum them and then plot the vector with the sums: total - A+B+C+D+E+F+G plot (total, type=l) Regards, Emilio 2011/11/14 Davg davidgrim...@hotmail.com I'm very new to R and am trying to create my first loop. I have: x -c(0:200) A - dpois(x,exp(4.5355343)) B - dpois(x,exp(4.5355343 + 0.0118638)) C - dpois(x,exp(4.5355343 -0.0234615)) D - dpois(x,exp(4.5355343 + 0.0316557)) E - dpois(x,exp(4.5355343 + 0.0004716)) F - dpois(x,exp(4.5355343 + 0.056437)) G - dpois(x,exp(4.5355343 + 0.1225822)) and would like to to get A[K] + B[K] + C[K] + D[K] + E[K] + F[K] G[K] for K(0:200) And then plot these cumulative values. Many thanks. -- View this message in context: http://r.789695.n4.nabble.com/Very-simple-loop-tp4039895p4039895.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. -- _ *Emilio López Cano* +34 665 676 225 Department of Statistics ans Operations Research Universidad Rey Juan Carlos http://www.urjc.es http://www.urjc.es http://www.urjc.es [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R v2.13.2 - Cannot find Rcmd on path?
FYI, you can use tools such as Path Manager 1.1.1 (GPL) on Windows: http://www.softpedia.com/get/System/System-Miscellaneous/Path-Manager.shtml to list, modify (add, remove, reorder, remove duplicates, normalize) your PATH environment variable. For each directory it identifies in PATH it will also let you know whether it is valid or not and list files that exist in that directory, iff valid. So, if you don't see Rcmd.exe where you expect it to be, you know you did something wrong when setting PATH. My $.02 /Henrik On Sun, Nov 13, 2011 at 9:50 PM, Yihui Xie x...@yihui.name wrote: Well, I just mean to give the user an option during installation -- like you did in Rtools. I have decided not to argue on this issue any more. Thanks a lot anyway! 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 Sun, Nov 13, 2011 at 4:20 PM, Duncan Murdoch murdoch.dun...@gmail.com wrote: On 11-11-13 1:15 PM, Yihui Xie wrote: I remember I was torn into pieces a few months back when I made a wishlist here that R adds its bin path to PATH on Windows during installation. People had tons of reasons of objection. Although I do not use these batchfiles (usually I do not actually use Windows), I see there is a motivation behind them: there needs to be an easy way for Windows users to use R in command line (e.g. R CMD build...). You may argue that it is easy to understand PATH and modify it manually, and I will say nothing but thank Windows again. Sorry this seems to be off-topic. I don't remember any rending and tearing, but I do remember objections to modifying the path during installation. I wouldn't want to write code to do that, because it's hard: - Most people don't want to put R first, because it may hide something important. - Putting it last won't work if an earlier version is already there. So you need to examine the path and correct it, an automatic change is unlikely to be successful. But if you want to write code to do that, just go ahead and do it. Put it in a package, even. Duncan Murdoch Regards, Yihui -- Yihui Xiexieyi...@gmail.com Phone: 515-294-2465 Web: http://yihui.name Department of Statistics, Iowa State University 2215 Snedecor Hall, Ames, IA __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] unable to get R CMD to work as expected on a 64 bit windows machine
See if
Rcmd check --help
works.
I've always been use that form (I'm on Win7 64-bit).
/Henrik
On Mon, Nov 14, 2011 at 9:06 AM, Martyn Byng martyn.b...@nag.co.uk wrote:
Hi Josh,
Thanks for that, which directory needs to be in the path?
There is a file called R.exe in
C:\Program Files\R\R-2.14.0\bin
C:\Program Files\R\R-2.14.0\bin\x64
and
C:\Program Files\R\R-2.14.0\bin\i386
I currently have
C:\Program Files\R\R-2.14.0\bin\x64
in the path (which is, I'm guessing why R CMD --help works), do I need the
others in the path as well, and if so, in what order?
Cheers
Martyn
-Original Message-
From: Joshua Wiley [mailto:jwiley.ps...@gmail.com]
Sent: 14 November 2011 16:57
To: Martyn Byng
Cc: r-help@r-project.org
Subject: Re: [R] unable to get R CMD to work as expected on a 64 bit
windows machine
Hi Martyn,
My guess is that you need to add the directory where R is located to
your Windows PATH variable. It sounds like Windows just doesn't know
where to find R.
HTH,
Josh
On Mon, Nov 14, 2011 at 8:48 AM, Martyn Byng martyn.b...@nag.co.uk wrote:
Hi,
I've just downloaded and installed R 2.14.0 using the windows binary on
a 64bit windows machine running windows 7.
Rterm / RGui work as expected, as does
R CMD --help
and
R CMD BATCH --help
however
R CMD check --help
returns no information and I seem to be unable to check a package.
Various other options also seem to not be working as expected, i.e.
R CMD REMOVE aa
(where aa is just a garbage name) appears to do nothing (whereas the
same command on a 32bit windows machine returns with a message that
package aa does not exist.)
Just invoking R on the command line appears to do nothing on 64 bit
windows as opposed to starting a command line version of R (ala Rterm)
on 32 bit windows.
Any pointers as to what I've done wrong during the installation would be
appreciated.
Cheers
Martyn
sessionInfo()
R version 2.14.0 (2011-10-31)
Platform: x86_64-pc-mingw32/x64 (64-bit)
locale:
[1] LC_COLLATE=English_United Kingdom.1252
[2] LC_CTYPE=English_United Kingdom.1252
[3] LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United Kingdom.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
The Numerical Algorithms Group Ltd is a company registered in England
and Wales with company number 1249803. The registered office is:
Wilkinson House, Jordan Hill Road, Oxford OX2 8DR, United Kingdom.
This e-mail has been scanned for all viruses by Star. Th...{{dropped:4}}
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Joshua Wiley
Ph.D. Student, Health Psychology
Programmer Analyst II, ATS Statistical Consulting Group
University of California, Los Angeles
https://joshuawiley.com/
This e-mail has been scanned for all viruses by Star.
The Numerical Algorithms Group Ltd is a company registered in England
and Wales with company number 1249803. The registered office is:
Wilkinson House, Jordan Hill Road, Oxford OX2 8DR, United Kingdom.
This e-mail has been scanned for all viruses by Star. The service is
powered by MessageLabs.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/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] Plot 2 different fields with image.plot()
Dear R users, Is it possible to plot 2 different fields with image.plot(). For example at first a digitale elevation model and overlying another data field, where NA values are transparent, so that the digitale elevation model is still visble at this areas. Maybe there is another plotting option than image.plot where it's possible? Thanks. Chris -- View this message in context: http://r.789695.n4.nabble.com/Plot-2-different-fields-with-image-plot-tp4040413p4040413.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] unable to get R CMD to work as expected on a 64 bit windows machine
Hi Martyn,
I would not expect you to need directories besides Rversion\bin\x64.
That is all I normally have in my path...perhaps because I do a
complete install?
I do not really know how or why it works, so I do not have any great
insight---just my experience. Perhaps someone else will chime in with
more definitive advice.
Best,
Josh
On Mon, Nov 14, 2011 at 9:06 AM, Martyn Byng martyn.b...@nag.co.uk wrote:
Hi Josh,
Thanks for that, which directory needs to be in the path?
There is a file called R.exe in
C:\Program Files\R\R-2.14.0\bin
C:\Program Files\R\R-2.14.0\bin\x64
and
C:\Program Files\R\R-2.14.0\bin\i386
I currently have
C:\Program Files\R\R-2.14.0\bin\x64
in the path (which is, I'm guessing why R CMD --help works), do I need the
others in the path as well, and if so, in what order?
Cheers
Martyn
-Original Message-
From: Joshua Wiley [mailto:jwiley.ps...@gmail.com]
Sent: 14 November 2011 16:57
To: Martyn Byng
Cc: r-help@r-project.org
Subject: Re: [R] unable to get R CMD to work as expected on a 64 bit
windows machine
Hi Martyn,
My guess is that you need to add the directory where R is located to
your Windows PATH variable. It sounds like Windows just doesn't know
where to find R.
HTH,
Josh
On Mon, Nov 14, 2011 at 8:48 AM, Martyn Byng martyn.b...@nag.co.uk wrote:
Hi,
I've just downloaded and installed R 2.14.0 using the windows binary on
a 64bit windows machine running windows 7.
Rterm / RGui work as expected, as does
R CMD --help
and
R CMD BATCH --help
however
R CMD check --help
returns no information and I seem to be unable to check a package.
Various other options also seem to not be working as expected, i.e.
R CMD REMOVE aa
(where aa is just a garbage name) appears to do nothing (whereas the
same command on a 32bit windows machine returns with a message that
package aa does not exist.)
Just invoking R on the command line appears to do nothing on 64 bit
windows as opposed to starting a command line version of R (ala Rterm)
on 32 bit windows.
Any pointers as to what I've done wrong during the installation would be
appreciated.
Cheers
Martyn
sessionInfo()
R version 2.14.0 (2011-10-31)
Platform: x86_64-pc-mingw32/x64 (64-bit)
locale:
[1] LC_COLLATE=English_United Kingdom.1252
[2] LC_CTYPE=English_United Kingdom.1252
[3] LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United Kingdom.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
The Numerical Algorithms Group Ltd is a company registered in England
and Wales with company number 1249803. The registered office is:
Wilkinson House, Jordan Hill Road, Oxford OX2 8DR, United Kingdom.
This e-mail has been scanned for all viruses by Star. Th...{{dropped:4}}
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Joshua Wiley
Ph.D. Student, Health Psychology
Programmer Analyst II, ATS Statistical Consulting Group
University of California, Los Angeles
https://joshuawiley.com/
This e-mail has been scanned for all viruses by Star.
The Numerical Algorithms Group Ltd is a company registered in England
and Wales with company number 1249803. The registered office is:
Wilkinson House, Jordan Hill Road, Oxford OX2 8DR, United Kingdom.
This e-mail has been scanned for all viruses by Star. The service is
powered by MessageLabs.
--
Joshua Wiley
Ph.D. Student, Health Psychology
Programmer Analyst II, ATS Statistical Consulting Group
University of California, Los Angeles
https://joshuawiley.com/
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Plot 2 different fields with image.plot()
On Nov 14, 2011, at 1:16 PM, Chris82 wrote: Dear R users, Is it possible to plot 2 different fields with image.plot(). There is an add parameter described on the helop page. Have you tried? For example at first a digitale elevation model and overlying another data field, where NA values are transparent, so that the digitale elevation model is still visble at this areas. Maybe there is another plotting option than image.plot where it's possible? -- David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] unable to get R CMD to work as expected on a 64 bit windows machine
Hi,
Thanks for the help.
I have now sorted out the issue.
Somehow the text C:\Progra~1\R\R-2.14.0\bin\x64\R had got added to the end of
an environment variable called comspec.
Removing the extraneous text solved the problem - so the only mystery now is
how I managed to paste the text into the environment variable - time to go home
I think :)
Cheers
Martyn
-Original Message-
From: Joshua Wiley [mailto:jwiley.ps...@gmail.com]
Sent: 14 November 2011 18:17
To: Martyn Byng
Cc: r-help@r-project.org
Subject: Re: [R] unable to get R CMD to work as expected on a 64 bit windows
machine
Hi Martyn,
I would not expect you to need directories besides Rversion\bin\x64.
That is all I normally have in my path...perhaps because I do a
complete install?
I do not really know how or why it works, so I do not have any great
insight---just my experience. Perhaps someone else will chime in with
more definitive advice.
Best,
Josh
On Mon, Nov 14, 2011 at 9:06 AM, Martyn Byng martyn.b...@nag.co.uk wrote:
Hi Josh,
Thanks for that, which directory needs to be in the path?
There is a file called R.exe in
C:\Program Files\R\R-2.14.0\bin
C:\Program Files\R\R-2.14.0\bin\x64
and
C:\Program Files\R\R-2.14.0\bin\i386
I currently have
C:\Program Files\R\R-2.14.0\bin\x64
in the path (which is, I'm guessing why R CMD --help works), do I need the
others in the path as well, and if so, in what order?
Cheers
Martyn
-Original Message-
From: Joshua Wiley [mailto:jwiley.ps...@gmail.com]
Sent: 14 November 2011 16:57
To: Martyn Byng
Cc: r-help@r-project.org
Subject: Re: [R] unable to get R CMD to work as expected on a 64 bit
windows machine
Hi Martyn,
My guess is that you need to add the directory where R is located to
your Windows PATH variable. It sounds like Windows just doesn't know
where to find R.
HTH,
Josh
On Mon, Nov 14, 2011 at 8:48 AM, Martyn Byng martyn.b...@nag.co.uk wrote:
Hi,
I've just downloaded and installed R 2.14.0 using the windows binary on
a 64bit windows machine running windows 7.
Rterm / RGui work as expected, as does
R CMD --help
and
R CMD BATCH --help
however
R CMD check --help
returns no information and I seem to be unable to check a package.
Various other options also seem to not be working as expected, i.e.
R CMD REMOVE aa
(where aa is just a garbage name) appears to do nothing (whereas the
same command on a 32bit windows machine returns with a message that
package aa does not exist.)
Just invoking R on the command line appears to do nothing on 64 bit
windows as opposed to starting a command line version of R (ala Rterm)
on 32 bit windows.
Any pointers as to what I've done wrong during the installation would be
appreciated.
Cheers
Martyn
sessionInfo()
R version 2.14.0 (2011-10-31)
Platform: x86_64-pc-mingw32/x64 (64-bit)
locale:
[1] LC_COLLATE=English_United Kingdom.1252
[2] LC_CTYPE=English_United Kingdom.1252
[3] LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United Kingdom.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
The Numerical Algorithms Group Ltd is a company registered in England
and Wales with company number 1249803. The registered office is:
Wilkinson House, Jordan Hill Road, Oxford OX2 8DR, United Kingdom.
This e-mail has been scanned for all viruses by Star. Th...{{dropped:4}}
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Joshua Wiley
Ph.D. Student, Health Psychology
Programmer Analyst II, ATS Statistical Consulting Group
University of California, Los Angeles
https://joshuawiley.com/
This e-mail has been scanned for all viruses by Star.
The Numerical Algorithms Group Ltd is a company registered in England
and Wales with company number 1249803. The registered office is:
Wilkinson House, Jordan Hill Road, Oxford OX2 8DR, United Kingdom.
This e-mail has been scanned for all viruses by Star. The service is
powered by MessageLabs.
--
Joshua Wiley
Ph.D. Student, Health Psychology
Programmer Analyst II, ATS Statistical Consulting Group
University of California, Los Angeles
https://joshuawiley.com/
This e-mail has been scanned for all viruses by Star.
Re: [R] Very simple loop
Thank you all! It's working perfectly. I will have a look for an online guide. -- View this message in context: http://r.789695.n4.nabble.com/Very-simple-loop-tp4039895p4040291.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] Binary ARMA
http://r.789695.n4.nabble.com/file/n4040429/model.jpg
Hi All
I need some help about construct MLE logit for Binary Autogressive Moving
Average model.
Please see the model in the PDF attach file.
This is what i did.
y-c(0, 0, 1, 0, 0, 1, 1, 0, 0, 0, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1) # y
is a binary data
logitfun - function(beta,y,){
zeta1-beta[1]
zeta2-beta[2]
zeta3-beta[3]
ne-zeta1+zeta2*lag(y,-1)+zeta3*lag(y,-2)#
this is only AR(2)
mu - exp(ne)/(1.0+exp(ne))
sum( y * log! (mu) + (1-y)*log(1-mu) )
}
mle-optim(c(0,0,0),logitfun,y=y)
mle
summary(mle)
what i tring to do is to modified
ne-zeta1+zeta2*lag(y,-1)+zeta3*lag(y,-2)
How can i do ne with lag(y,-1) , lag(y,-2), (lag(y,-1)-lag(mu,-1)),
(lag(y,-2)-lag(mu,-2))
thanks
Napon H.
--
View this message in context:
http://r.789695.n4.nabble.com/Binary-ARMA-tp4040429p4040429.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] about R instalation
Hello, I would like to get help on the instalation of R. I have too few free space in my pc hard disk. So I wonder if it is possible to install R on an external removable hard drive. Can it be done? How should I proceed? Thank you for your help. best regards, Francisca A. S. dos Santos Bronner -- Francisca Ana Soares dos Santos 2000 - 2004: B.Sc. em Ciências Biológicas pela UFV (M.G., Brasil) 2005 - 2007: M.Sc. em Modelagem Computacional com ênfase em Bioinformática e Biologia Computacional pelo LNCC (R.J., Brasil) 2008 - 2010: Ph.D. em Biologia pela Universität Potsdam (Potsdam, Alemanha) URL: http://lattes.cnpq.br/9418134959504901 A grande diferença entre construção e criação é esta: que uma coisa construída só pode ser amada depois de ser construída; mas uma coisa criada é amada antes de existir. (Chesterton) [[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] string to list()
I can get an array of strings for the data that I want using 'paste()' as
follows:
paste('ma', 1:am$arma[2], '=', coef(am)[1:am$arma[2] + am$arma[1]], sep='')
This results in a vector of strings like:
[1] ma1=1.17760133668255 ma2=0.649795570407939 ma3=0.329456750858276
What I would like is
fixed.pars -
list(ma1=1.17760133668255,ma2=0.649795570407939,ma3=0.329456750858276)
Is there an 'R' guru that would be willing to suggest a good way of doing
this?
Thank you.
Kevin
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] about R instalation
I haven't personally used it, but I think this might work: http://sourceforge.net/projects/rportable/ Michael 2011/11/14 Francisca Soares dos Santos fsoaresan...@gmail.com: Hello, I would like to get help on the instalation of R. I have too few free space in my pc hard disk. So I wonder if it is possible to install R on an external removable hard drive. Can it be done? How should I proceed? Thank you for your help. best regards, Francisca A. S. dos Santos Bronner -- Francisca Ana Soares dos Santos 2000 - 2004: B.Sc. em Ciências Biológicas pela UFV (M.G., Brasil) 2005 - 2007: M.Sc. em Modelagem Computacional com ênfase em Bioinformática e Biologia Computacional pelo LNCC (R.J., Brasil) 2008 - 2010: Ph.D. em Biologia pela Universität Potsdam (Potsdam, Alemanha) URL: http://lattes.cnpq.br/9418134959504901 A grande diferença entre construção e criação é esta: que uma coisa construída só pode ser amada depois de ser construída; mas uma coisa criada é amada antes de existir. (Chesterton) [[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] Very simple loop
The one included in the standard R installation -- which can be accessed by typing help.start() at your prompt -- is quite good for beginners (and very conveniently located). If you tell us a bit more about yourself, we can help direct you to others as well: specifically, 1) Prior programming experience? 2) Experience with other statistical packages? 3) Is there a specific domain you will be working in? E.g., biomedical, time series/financial, simulation, etc. There exist specialized intros for many branches of stats 4) Level of statistical training: there are some books that provide an integrated intro to statistical methods and R so if you need to brush up your stats as well, you can do them both at once. Best of luck and welcome to the R-world -- it's quite a fun place, Michael On Mon, Nov 14, 2011 at 12:38 PM, Davg davidgrim...@hotmail.com wrote: Thank you all! It's working perfectly. I will have a look for an online guide. -- View this message in context: http://r.789695.n4.nabble.com/Very-simple-loop-tp4039895p4040291.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] string to list()
Do it in 2 steps:
z - as.list( coef(am)[1:am$arma[2] + am$arma[1]])
names(z) - paste(ma,seq_along(z), sep=)
-- Bert
On Mon, Nov 14, 2011 at 10:40 AM, Kevin Burton rkevinbur...@charter.netwrote:
I can get an array of strings for the data that I want using 'paste()' as
follows:
paste('ma', 1:am$arma[2], '=', coef(am)[1:am$arma[2] + am$arma[1]], sep='')
This results in a vector of strings like:
[1] ma1=1.17760133668255 ma2=0.649795570407939 ma3=0.329456750858276
What I would like is
fixed.pars -
list(ma1=1.17760133668255,ma2=0.649795570407939,ma3=0.329456750858276)
Is there an 'R' guru that would be willing to suggest a good way of doing
this?
Thank you.
Kevin
[[alternative HTML version deleted]]
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PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
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
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[R] Power analysis and sample size calculation for nonlinear regression
Is there a library that provides power calculation and sample size estimation for nonlinear regression? The task is easy for linear regression with the pwr package, but I can't find a method for nonlinear regression (estimated with the nls package). -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- Dr. Johannes W. Dietrich, M.D. -- Laboratory XU44, Endocrine Research -- Medical Hospital I, Bergmannsheil University Hospitals -- Ruhr University of Bochum -- Buerkle-de-la-Camp-Platz 1, D-44789 Bochum, NRW, Germany -- Phone: +49:234:302-6400, Fax: +49:234:302-6403 -- eMail: j.w.dietr...@medical-cybernetics.de -- WWW: http://medical-cybernetics.de -- WWW: http://www.bergmannsheil.de -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- [[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] about R instalation
See R Windows FAQ 2.6 On Monday, 14 November 2011, R. Michael Weylandt michael.weyla...@gmail.com wrote: I haven't personally used it, but I think this might work: http://sourceforge.net/projects/rportable/ Michael 2011/11/14 Francisca Soares dos Santos fsoaresan...@gmail.com: Hello, I would like to get help on the instalation of R.O I have too few free space in my pc hard disk. So I wonder if it is possible to install R on an external removable hard drive. Can it be done? How should I proceed? Thank you for your help. best regards, Francisca A. S. dos Santos Bronner -- Francisca Ana Soares dos Santos 2000 - 2004: B.Sc. em Ciências Biológicas pela UFV (M.G., Brasil) 2005 - 2007: M.Sc. em Modelagem Computacional com ênfase em Bioinformática e Biologia Computacional pelo LNCC (R.J., Brasil) 2008 - 2010: Ph.D. em Biologia pela Universität Potsdam (Potsdam, Alemanha) URL: http://lattes.cnpq.br/9418134959504901 A grande diferença entre construção e criação é esta: que uma coisa construída só pode ser amada depois de ser construída; mas uma coisa criada é amada antes de existir. (Chesterton) [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- John C Frain Economics Department Trinity College Dublin Dublin 2 Ireland www.tcd.ie/Economics/staff/frainj/home.html mailto:fra...@tcd.ie mailto:fra...@gmail.com [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R v2.13.2 - Cannot find Rcmd on path?
Path manager has a nice feature. Thanks. While I can see that rcmd is in the path setting, it is still not recognized as an internal command. That is something really confuses me. Jixiang Wu On Mon, Nov 14, 2011 at 11:30 AM, Henrik Bengtsson h...@biostat.ucsf.eduwrote: FYI, you can use tools such as Path Manager 1.1.1 (GPL) on Windows: http://www.softpedia.com/get/System/System-Miscellaneous/Path-Manager.shtml to list, modify (add, remove, reorder, remove duplicates, normalize) your PATH environment variable. For each directory it identifies in PATH it will also let you know whether it is valid or not and list files that exist in that directory, iff valid. So, if you don't see Rcmd.exe where you expect it to be, you know you did something wrong when setting PATH. My $.02 /Henrik On Sun, Nov 13, 2011 at 9:50 PM, Yihui Xie x...@yihui.name wrote: Well, I just mean to give the user an option during installation -- like you did in Rtools. I have decided not to argue on this issue any more. Thanks a lot anyway! 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 Sun, Nov 13, 2011 at 4:20 PM, Duncan Murdoch murdoch.dun...@gmail.com wrote: On 11-11-13 1:15 PM, Yihui Xie wrote: I remember I was torn into pieces a few months back when I made a wishlist here that R adds its bin path to PATH on Windows during installation. People had tons of reasons of objection. Although I do not use these batchfiles (usually I do not actually use Windows), I see there is a motivation behind them: there needs to be an easy way for Windows users to use R in command line (e.g. R CMD build...). You may argue that it is easy to understand PATH and modify it manually, and I will say nothing but thank Windows again. Sorry this seems to be off-topic. I don't remember any rending and tearing, but I do remember objections to modifying the path during installation. I wouldn't want to write code to do that, because it's hard: - Most people don't want to put R first, because it may hide something important. - Putting it last won't work if an earlier version is already there. So you need to examine the path and correct it, an automatic change is unlikely to be successful. But if you want to write code to do that, just go ahead and do it. Put it in a package, even. Duncan Murdoch Regards, Yihui -- Yihui Xiexieyi...@gmail.com Phone: 515-294-2465 Web: http://yihui.name Department of Statistics, Iowa State University 2215 Snedecor Hall, Ames, IA __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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. [[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] Problem with edit()
Since installing R 2.14.0 on my Mac (a Mac Pro running 10.6.8) an issue has
arisen when using the vi editor in conjunction with the edit() command. More
specifically, commented lines disappear from edited functions when using
[functionname.R] - edit().
That is, if you have created a function called test.func as such:
function ()
{
# This is a test
ex _ 4
duh - seq(1, 10)
fuh - seq(11, 20)
plot(duh, fuh)
}
you will of course get an error message:
Error in edit(name, file, title, editor) :
unexpected input occurred on line 4
use a command like
x - edit()
to recover
When using the x - edit (or in this case, test.func - edit()), the comment
This is a test will disappear from the edited function.
Does anyone have any insight into this problem?
Thanks,
Jeff Freedman
_
Jeff Freedman
Lead Research Scientist
AWS Truepower, LLC
463 New Karner Road
Albany, NY 12205
phone: 518-213-0044 (x1049)
fax: 518-640-6897
[[alternative HTML version deleted]]
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and provide commented, minimal, self-contained, reproducible code.
[R] reliability analysis
hello all R experts, how do I calculate the reliability between the two groups using the ICCs? -- Sincerely, Supreet kaur, Biomedical research engineer, Nationwide Childrens Hospital, Columbus, OH (614)355-3509 [[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] rearrange set of items randomly
If you don't want to go with the simple method mentioned by David and Ted, or you just want some more theory, you can check out: http://en.wikipedia.org/wiki/Fisher%E2%80%93Yates_shuffle and implement that. -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-bounces@r- project.org] On Behalf Of flokke Sent: Monday, November 07, 2011 2:09 PM To: r-help@r-project.org Subject: [R] rearrange set of items randomly Dear all, I hope that this question is not too weird, I will try to explain it as good as I can. I have to write a function for a school project and one limitation is that I may not use the in built function sample() At one point in the function I would like to resample/rearrange the items of my sample (so I would want to use sample, but I am not allowed to do so), so I have to come up with sth else that does the same as the in built function sample() The only thing that sample() does is rearranging the items of a sample, so I searched the internet for a function that does that to be able to use it, but I cannot find anything that could help me. Can maybe someone help me with this? I would be very grateful, Cheers, Maria -- View this message in context: http://r.789695.n4.nabble.com/rearrange- set-of-items-randomly-tp4013723p4013723.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] Adding units to levelplot's colorkey
How to add units (e.g. cm) to the color key of a lattice levelplot? The plots looks fantastic, but it would be nice to indicate somewhere near the end of the color key that the values associated with its colors are in centimeters or some other physical units. The only thing I find is the possibility to specify the labels so that one explicitly includes the units. That leaves little flexibility for positioning where this information appears. Is there a better way? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Power analysis and sample size calculation for nonlinear regression
May I suggest you consult your local statistician. For reasons that (s)he can answer, your request makes little sense. Hint: Nonlinear regression is much different than linear regression: The design matrix -- and hence the variance of estimators -- is a function of the parameters being estimated. (But there may well be packages that are relevant -- the issue is your ability to use them properly) Cheers, Bert On Mon, Nov 14, 2011 at 10:52 AM, Johannes W. Dietrich johannes.dietr...@ruhr-uni-bochum.de wrote: Is there a library that provides power calculation and sample size estimation for nonlinear regression? The task is easy for linear regression with the pwr package, but I can't find a method for nonlinear regression (estimated with the nls package). -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- Dr. Johannes W. Dietrich, M.D. -- Laboratory XU44, Endocrine Research -- Medical Hospital I, Bergmannsheil University Hospitals -- Ruhr University of Bochum -- Buerkle-de-la-Camp-Platz 1, D-44789 Bochum, NRW, Germany -- Phone: +49:234:302-6400, Fax: +49:234:302-6403 -- eMail: j.w.dietr...@medical-cybernetics.de -- WWW: http://medical-cybernetics.de -- WWW: http://www.bergmannsheil.de -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- [[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. -- 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 [[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] max min values within dataframe
Groupwise data summarization is a very common task, and it is worth learning the various ways to do it in R. Josh showed you one way to use aggregate() from the base package and Michael showed you one way of using the plyr package to do the same; another way would be ddply(df, .(Patient, Region), summarise, max = max(Score), min = min(Score)) to save on writing an explicit function. Similarly, if you have a version of R = 2.11.0, the aggregate() function now has a nice formula interface, so Josh's code could also be written as aggregate(Score ~ Patient + Region, data = df, FUN = range) with a subsequent renaming of the variables as shown. Other packages that could perform this task with ease include the doBy package, the data.table package, the remix package, the Hmisc package and, if you are comfortable with SQL, the sqldf package. For relative novices, the doBy package is a very nice place to start because it comes with a well written vignette and the function names correspond well with the tasks they perform (e.g., summaryBy(), transformBy()). The plyr and data.table packages are more general and more powerful in terms of the types of tasks to which each is suited. Unlike aggregate() and doBy:::summaryBy(), these packages can process multivariable functions. As noted above, if you have an SQL background, sqldf operates on R data objects as though they were SQL tables, which is advantageous in complex data extraction tasks. Package remix is useful if you want to organize results into a tabular form that is reminiscent of SAS. HTH, Dennis On Mon, Nov 14, 2011 at 8:10 AM, B Laura gm.spam2...@gmail.com wrote: dear R-team I need to find the min, max values for each patient from dataset and keep the output of it as a dataframe with the following columns - Patient nr - Region (remains same per patient) - Min score - Max score Patient Region Score Time 1 1 X 19 28 2 1 X 20 126 3 1 X 22 100 4 1 X 25 191 5 2 Y 12 1 6 2 Y 12 2 7 2 Y 25 4 8 2 Y 26 7 9 3 X 6 1 10 3 X 6 4 11 3 X 21 31 12 3 X 22 68 13 3 X 23 31 14 3 X 24 38 15 3 X 21 15 16 3 X 22 24 17 3 X 23 15 18 3 X 24 243 19 3 X 25 77 20 4 Y 6 5 21 4 Y 22 28 22 4 Y 23 75 23 4 Y 24 19 24 5 Y 23 3 25 5 Y 24 1 26 5 Y 23 33 27 5 Y 24 13 28 5 Y 25 42 29 5 Y 26 21 30 5 Y 27 4 31 6 Y 24 4 32 6 Y 32 8 So far I could find the min and max values for each patient, but the output of it is not (yet) what I need. Patient.nr = unique(Patient) aggregate(Score, list(Patient), max) Group.1 x 1 1 25 2 2 26 3 3 25 4 4 24 5 5 27 6 6 32 aggregate(Score, list(Patient), min) Group.1 x 1 1 19 2 2 12 3 3 6 4 4 6 5 5 23 6 6 24 I would like to do same but writing this new information (min, max values) in a dataframe with following columns - Patient nr - Region (remains same per patient) - Min score - Max score Can anybody help me with this? Thanks Laura [[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] Problem with edit()
There is a difference between parsed functions and .R files. What you see when
you type the name of a function alone on the R command line is a text
representation of the parsed function that is ready to run in RAM. That has
none of the comments or whitespace from the function as you wrote it. The
parsed version is what the edit function allows you to modify. This is why we
use .R files.
FWIW I never use the edit function. I use a separate window for editing the
code I want to keep, and either copy/paste the bits I want to execute (with or
without the use of macros to facilitate that) into the R command line, or use
the source function to pull in a set of functions all at once.
---
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.
Jeff Freedman jfreed...@awstruepower.com wrote:
Since installing R 2.14.0 on my Mac (a Mac Pro running 10.6.8) an issue
has arisen when using the vi editor in conjunction with the edit()
command. More specifically, commented lines disappear from edited
functions when using [functionname.R] - edit().
That is, if you have created a function called �test.func� as such:
function ()
{
# This is a test
ex _ 4
duh - seq(1, 10)
fuh - seq(11, 20)
plot(duh, fuh)
}
you will of course get an error message:
Error in edit(name, file, title, editor) :
unexpected input occurred on line 4
use a command like
x - edit()
to recover
When using the �x - edit� (or in this case, test.func - edit()), the
comment �This is a test� will disappear from the edited function.
Does anyone have any insight into this problem?
Thanks,
Jeff Freedman
_
Jeff Freedman
Lead Research Scientist
AWS Truepower, LLC
463 New Karner Road
Albany, NY 12205
phone: 518-213-0044 (x1049)
fax: 518-640-6897
[[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] Upgrade R?
I have had similar problems. I have several installations of R and now I have no control over which one opens when I try opening a RData file. The RGUI is registered more than once, but they all have the exact same appearance in the choose programs menu. It's become particularly annoying now that new versions of R seem to be published with ever increasing frequency. On Mon, Nov 14, 2011 at 10:11 AM, Kevin Burton rkevinbur...@charter.netwrote: I am also using statConn so I will let you know if I hear anything new. -Original Message- From: Cem Girit [mailto:gi...@comcast.net] Sent: Monday, November 14, 2011 8:52 AM To: 'Kevin Burton' Cc: r-help@r-project.org Subject: RE: [R] Upgrade R? Hello Kevin, Thank you. I will delete the folder and run an application called CCleaner (free). That will remove all the broken registry entries. There should be a problem free update path for R installation. As you rightfully mentioned the R- manual is not clear about package update issues. I received many helpful suggestions on the update path but some of the them were contradictory in the order of steps to be taken. I am also using statConn (DCOM) interface for programming. So my problems are multifold. I will compile the answers I received on the R version update issue and publish them so that that the experts could put them into more effective use. Sincerely, Cem -Original Message- From: Kevin Burton [mailto:rkevinbur...@charter.net] Sent: Sunday, November 13, 2011 4:11 PM To: 'Cem Girit' Subject: RE: [R] Upgrade R? I don't know if it was correct but I just removed the directory and then searched and removed all instances in the registry that referred to 2.13.1 (in my case searching for this seemed to only return references to 'R'). I have since been given some links that address specific registry entries but I haven't had any problem yet with my 'slash and burn' approach. It removed it from the 'Install/Uninstall' list with windows so it seems to have be removed and the disk space that 2.13.2 took up has been reclaimed. Hope this helps. Let me know if you find any more definitive answers. Thanks. Kevin -Original Message- From: Cem Girit [mailto:gi...@comcast.net] Sent: Saturday, November 12, 2011 6:33 PM To: 'Kevin Burton' Subject: RE: [R] Upgrade R? Hello Kevin, I am getting the same error utCompiledCode... since I installed R2.14 while R2.13 existed. How did you get rid of R2.13 eventually? Did you just delete it? If so, how did you clean the registry? Thank you, Cem -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Kevin Burton Sent: Thursday, November 10, 2011 11:54 AM To: 'jose Bartolomei'; 'R Help' Subject: Re: [R] Upgrade R? The problem with this documentation is two-fold. One it seems to concentrate on building from source which I don't need. Two it doesn't address the upgade. I have a number of packages and so I need to do what has been suggested and install the latest version *first*. Then copy the libraries (packages). Then uninstall the previous version. It is on this last step that I am stuck on right now. The last link on uninstalling R manually was what I needed. Thank you. Kevin From: jose Bartolomei [mailto:surfpr...@hotmail.com] Sent: Thursday, November 10, 2011 10:19 AM To: rkevinbur...@charter.net; R Help Subject: RE: [R] Upgrade R? Hi, Don't know if this will help you but... In my short experience and following the guidelines you should first uninstall R. http://cran.r-project.org/doc/manuals/R-admin.html#Installing-R-under-Window s Unistall it from the Windows control panel. The old R version libraries file will be kept on machine. For example : C:\Program Files\R\R-2.13.0\library Then install the new version via: http://cran.r-project.org/doc/manuals/R-admin.html#Installing-R-under-Window s You can copy/paste libraries from the old version R library file to the new one. C:\Program Files\R\R-2.14.0\library There is too an function named: ?update.packagee If above was what you did, then there is a post on Uninstalling R manually: http://learnserver.csd.univie.ac.at/rcomwiki/doku.php?id=wiki:uninstalling_r _manually Regards, Jose From: rkevinbur...@charter.net To: r-help@r-project.org Date: Thu, 10 Nov 2011 09:07:20 -0600 Subject: Re: [R] Upgrade R? Since apparently there is no one familiar with this error message let me rephrase the question. Is there a 'manual' process to fully remove a version of 'R' from my machine? This is a Window PC running Windows 7. Thank you. Kevin From: Kevin Burton [mailto:rkevinbur...@charter.net] Sent: Monday, November 07, 2011 2:23 PM To: 'r-help@r-project.org' Subject: Upgrade R? I am trying to upgrade to R 2.14 from R 2.13.1 I have compied all the
[R] JSS Special Volumes for 2011
So far in 2011 JSS has published 4 (four !) special volumes. If you have additional suggestions for special volumes, let us know. Also, submit your JSS-adapted package vignettes. If you like what you see, friend us at http://www.facebook.com/jstatsoft Tabelow and Whitcher, Guest Editors Volume 44: Magnetic Resonance Imaging in R http://www.jstatsoft.org/v44 Altman, Fox, Jackman and Zeileis , Guest Editors Volume 42: Political Methodology http://www.jstatsoft.org/v42 Commandeur, Koopman, and Ooms, Guest Editors Volume 41: Statistical Software for State Space Methods http://www.jstatsoft.org/v41 Putter, Guest Editor Volume 38: Competing Risks and Multi-State Models http://www.jstatsoft.org/v38 Additional regular volumes, of course, at http://www.jstatsoft.org. === Jan de Leeuw; Distinguished Professor and Chair, UCLA Department of Statistics; Editor: Journal of Multivariate Analysis, Journal of Statistical Software; US mail: 8125 Math Sciences Bldg, Box 951554, Los Angeles, CA 90095-1554 phone (310)-825-9550; fax (310)-206-5658; email: dele...@stat.ucla.edu .mac: jdeleeuw ++ aim: deleeuwjan ++ skype: j_deleeuw homepages: http://gifi.stat.ucla.edu ++ http://www.cuddyvalley.org - No matter where you go, there you are. --- Buckaroo Banzai http://gifi.stat.ucla.edu/sounds/nomatter.au __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
