Re: [R] Feed list of vectors to vioplot()?
Hm, now I have trouble using additional vioplot parameters.
mu-2
si-0.6
bimodal-c(rnorm(1000,-mu,si),rnorm(1000,mu,si))
uniform-runif(2000,-4,4)
normal-rnorm(2000,0,3)
mylist - list(bimodal,uniform,normal)
# Easy
do.call(vioplot,mylist)
# Works
do.call(vioplot,c(mylist,col=white))
# Does not
# vioplot expects names as a plain vector, not in the
# form names=c(One,Two,Three) ...
names - c(One,Two,Three)
do.call(vioplot,c(mylist,col=white,names))
Any help on how to do this?
Thanks, Joh
Johannes Graumann wrote:
Off-list it was pointed out to me that the trivial solution to this would
look like this:
myfunction2 - function(x, ...){
mylist - list(x, ...)
# plenty of lapply stuff
do.call(vioplot,mylist)
}
Thanks for everybodies patience,
Joh
Johannes Graumann wrote:
posted mailed
Thanks for the very appropriate scolding.
Here's my example (based on ?vioplot):
mu-2
si-0.6
bimodal-c(rnorm(1000,-mu,si),rnorm(1000,mu,si))
uniform-runif(2000,-4,4)
normal-rnorm(2000,0,3)
# Working just fine
myfunction1 - function(x, ...){vioplot(x,...)}
myfunction1(bimodal,uniform,normal)
# What I (believe to) need
myfunction2 - function(x, ...){
mylist - list(x, ...)
# plenty of lapply stuff
vioplot(mylist)
}
myfunction2(bimodal,uniform,normal)
-- Error in min(data) : invalid 'type' (list) of argument
I'm at a loss on how to disentangle mylist - unlist just gives me one
big vector back rather than the 3 I want to have back ...
Thanks for your patience, Joh
jim holtman wrote:
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html and provide commented,
minimal, self-contained, reproducible code.
It is hard to provide a solution if we do not understand the problem
to be solved. Sample data would be helpful along with an
understanding of what you would expect for output.
On Wed, Apr 23, 2008 at 10:11 AM, Johannes Graumann
[EMAIL PROTECTED] wrote:
Johannes Graumann wrote:
Hi,
I have a list of vectors and am trying to coerce them into something
that vioplot will take as groups of data to be plotted independently.
Can someone nudge me into the right direction?
Thanks, Joh
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I'll try less impolite and with more info ...
I'm writing a function that contains this:
# function(x, ... , morestuff){}
which is gathered into a list like so:
# mylist - list(x, ...)
down the line I'd like to output all elements from mylist in seperate
vioplots in a single coordiante system. Now I have a hell of a time
with that because vioplot does not accept a list as input but only a
succession of vectors ... how can I now force my list into that form so
a can say
# vioplot(magicfunction(mylist))
and get a violin plot for each list-member?
Thanks for any hint,
Joh
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Re: [R] mysterious (to me) automatic loading of package s when R starts up
Duncan Mackay duncan.mackay at flinders.edu.au writes: I have recently noticed that in one of my work areas, a number of packages are automatically loaded without my explicitly requesting them to be loaded (see below). This only happens in one particular workspace (located in a folder). I suspect (without any real evidence) that this may be related to my creating plots using the ggplot2 package earlier in this workspace. Loading required package: proto Loading required package: grid Loading required package: reshape [Previously saved workspace restored] Whenever you see the last line, there is an .Rdata-file in you startup directory. Delete it, and use rgui.exe --no-restore --no-save to start R (assuming Windows) to avoid the automatic loading/saving (which I find confusing). Dieter __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] filled contour plots (link)
Fernando De Sales fhds2000 at yahoo.com writes: I have moved the figure to the link below. thank Try again. Better than providing the link for the picture, make the example self-running by providing a fake data set that shows the problem. Dieter __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Factor to numeric
Hello! I have a problem whith a data.frame. I want to make a subset where some of the variables have values within ceartain limits. The variables are proportions like 1,00, 0,54, 0,00 etc. I don't get it right as R take the variables for factors. ekobsub1 - subset(ekob, PAP0,25 PAP0,6 CAP0,1 CAP0,6 FAP0,1) Error in `[.data.frame`(x, r, vars, drop = drop) : object CAP not found In addition: Warning message: In Ops.factor(PAP, 0) : not meaningful for factors ekobn-as.numeric(as.character(ekob[[PAP]])) Warning message: NAs introduced by coercion Thanks! /Jojje _ [[elided Hotmail spam]] px?sc_cmp2=JS_INT_SEMSN_NLPCV [[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] Factor to numeric
The decimal point in R is always '.', never ','. On Thu, 24 Apr 2008, Jojje Andersson wrote: Hello! I have a problem whith a data.frame. I want to make a subset where some of the variables have values within ceartain limits. The variables are proportions like 1,00, 0,54, 0,00 etc. I don't get it right as R take the variables for factors. ekobsub1 - subset(ekob, PAP0,25 PAP0,6 CAP0,1 CAP0,6 FAP0,1) Error in `[.data.frame`(x, r, vars, drop = drop) : object CAP not found In addition: Warning message: In Ops.factor(PAP, 0) : not meaningful for factors ekobn-as.numeric(as.character(ekob[[PAP]])) Warning message: NAs introduced by coercion Thanks! /Jojje _ [[elided Hotmail spam]] px?sc_cmp2=JS_INT_SEMSN_NLPCV [[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. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] looping problem
Dear r-expert,
I would like to generate 30 sets of random numbers from uniform distribution
(0,1). Each set of random numbers should have 90 data. Here is my code:
rand.no - function(n,itr)
{ for (i in 1:itr)
{rand.1 - runif(n,0,1)
if (i ==1) rand.2 - rand.1
else rand.2 - cbind(rand.2,rand.1)
}
rand.2
}
Question: The code is okay is just that it give me 31 sets instead of 30 sets.
Can anybody any adjustment to my code.
Your help is really appreciated.
Thank you.
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Re: [R] looping problem
Roslina Zakaria wrote:
Dear r-expert,
I would like to generate 30 sets of random numbers from uniform distribution
(0,1). Each set of random numbers should have 90 data. Here is my code:
rand.no - function(n,itr)
{ for (i in 1:itr)
{rand.1 - runif(n,0,1)
if (i ==1) rand.2 - rand.1
else rand.2 - cbind(rand.2,rand.1)
}
rand.2
}
Question: The code is okay is just that it give me 31 sets instead of 30
sets.
Works for me as expected, but really, why don't you simply say:
rand.no - function(n,itr){
matrix(runif(n*itr, 0, 1), nrow=n, ncol=itr)
}
which does the same, just much quicker...
Uwe Ligges
Can anybody any adjustment to my code.
Your help is really appreciated.
Thank you.
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know-it-all with Yahoo! Mobile. Try it now.
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Re: [R] select rows from data based on a vector of char strings
or using the %in% operator... ?%in% data[data$label %in% flist,] regards, Sean Applejus wrote: Hi, You are right the == doesn't work, but there's a workaround using regular expressions: flist-fun|food grep(flist, data$label) will give you the vector [2 4] which are the numbers of the rows of interest! Dirkheld wrote: Hi, I have loaded a dataset in R : data = label freq1 freq2 news 54 35 fun 37 21 milk19 7 food 3 3 etc And I have a vector flist-c(fun,food) Now I want to use the vector 'flist' for selecting these values from 'data' so that I get the following dataset : label freq1 freq2 fun 37 21 food 3 3 When I do 'data$label==flist[1]' I get 'F T F F', so it works for one item in the char vector flist. But, when I do 'data$label==flist' I get 'F F F F' while I expected 'F T F T'. It seems that I can't perform this action with a vector of charstrings? Is there an other way to do so? -- View this message in context: http://www.nabble.com/select-rows-from-data-based-on-a-vector-of-char-strings-tp16832735p16848199.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] significant variables in GPLS ?
There is little theory about significance and testing for PLSR (and, I would guess, GPLSR). Many practicioners use Jackknife variance estimates as a basis for significance tests. Note, however, that these variance estimates are known to be biased (in general), and their distribution is (to my knowledge) not known. Any significance deduced from them should therefore be regarede as merely indicators. -- Bjørn-Helge Mevik __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] bug in file.path?
Hello, This is what i get in R-2.7.0 (with the completely internal file.path()): setwd(c:/jml/Valoración F1/04 BA/) filename - Valoración F1 PAG.mdb file.path(getwd(), filename) [1] c:/jml/Valoración F1/04 BA/Valoración F1 PAG.mdb - worng file.path(c:/jml/Valoración F1/04 BA, filename) [1] c:/jml/Valoración F1/04 BA/Valoración F1 PAG.mdb - ok file.path(paste(getwd()), filename) [1] c:/jml/Valoración F1/04 BA/Valoración F1 PAG.mdb - ok With the older file.path() all of these return c:/jml/Valoración F1/04 BA/Valoración F1 PAG.mdb -- Session info --- R version 2.7.0 (2008-04-22) i386-pc-mingw32 locale: LC_COLLATE=Spanish_Spain.1252;LC_CTYPE=Spanish_Spain.1252;LC_MONETARY=Spanish_Spain.1252;LC_NUMERIC=C;LC_TIME=Spanish_Spain.1252 attached base packages: [1] stats graphics grDevices datasets utils methods base other attached packages: [1] RODBC_1.2-3 Is this a bug in the new file.path() or can I change something to make this work as before? Thanks. Javier. [[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] bug in file.path?
Javier Muñoz wrote: Hello, This is what i get in R-2.7.0 (with the completely internal file.path()): setwd(c:/jml/Valoraci�n F1/04 BA/) filename - Valoraci�n F1 PAG.mdb file.path(getwd(), filename) [1] c:/jml/Valoración F1/04 BA/Valoraci�n F1 PAG.mdb - worng file.path(c:/jml/Valoraci�n F1/04 BA, filename) [1] c:/jml/Valoraci�n F1/04 BA/Valoraci�n F1 PAG.mdb - ok file.path(paste(getwd()), filename) [1] c:/jml/Valoraci�n F1/04 BA/Valoraci�n F1 PAG.mdb - ok With the older file.path() all of these return c:/jml/Valoraci�n F1/04 BA/Valoraci�n F1 PAG.mdb -- Session info --- R version 2.7.0 (2008-04-22) i386-pc-mingw32 locale: LC_COLLATE=Spanish_Spain.1252;LC_CTYPE=Spanish_Spain.1252;LC_MONETARY=Spanish_Spain.1252;LC_NUMERIC=C;LC_TIME=Spanish_Spain.1252 attached base packages: [1] stats graphics grDevices datasets utils methods base other attached packages: [1] RODBC_1.2-3 Is this a bug in the new file.path() or can I change something to make this work as before? This could well be related to the PATH issue reported yesterday by Erik Joergensen, so please check whether R-patched fixes the issue (and please make a habit of checking our prereleases...). (Email encodings again: I assume that you see something weird in the one place where I see the accented o in valoración, whereas you see the accented o in all the places where I see a reverse-video question mark) -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] bug in file.path?
See my reply to Erik Jørgensen yesterday. Can you please send that again with a marked encoding, so we have a chance of reading it? Or attach it as a plain text file and tell us what encoding the file is in? Yes, there probably is a bug here but we do need to be able to reproduce it. On Thu, 24 Apr 2008, Javier Muñoz wrote: Hello, This is what i get in R-2.7.0 (with the completely internal file.path()): setwd(c:/jml/Valoraci?n F1/04 BA/) filename - Valoraci?n F1 PAG.mdb file.path(getwd(), filename) [1] c:/jml/Valoraci??n F1/04 BA/Valoraci?n F1 PAG.mdb - worng file.path(c:/jml/Valoraci?n F1/04 BA, filename) [1] c:/jml/Valoraci?n F1/04 BA/Valoraci?n F1 PAG.mdb - ok file.path(paste(getwd()), filename) [1] c:/jml/Valoraci?n F1/04 BA/Valoraci?n F1 PAG.mdb - ok With the older file.path() all of these return c:/jml/Valoraci?n F1/04 BA/Valoraci?n F1 PAG.mdb -- Session info --- R version 2.7.0 (2008-04-22) i386-pc-mingw32 locale: LC_COLLATE=Spanish_Spain.1252;LC_CTYPE=Spanish_Spain.1252;LC_MONETARY=Spanish_Spain.1252;LC_NUMERIC=C;LC_TIME=Spanish_Spain.1252 attached base packages: [1] stats graphics grDevices datasets utils methods base other attached packages: [1] RODBC_1.2-3 Is this a bug in the new file.path() or can I change something to make this work as before? Thanks. Javier. [[alternative HTML version deleted]] -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595__ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] changing format of a float value to another
hello How can I change a vector's float value from (1.085714e-01) format to a simpler format (like 0.1xxx). regards -- Ahmet Temiz Jeo. Müh. Afet İşleri Gen. Md.lüğü Deprem Ar. D. Ahmet Temiz Geo. Eng. General Dir. of Disaster Affairs -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] bug in file.path?
Sorry, this is the same test with R-patched (same results as well). setwd(c:/jml/Valoración F1/04 BA/) filename - Valoración F1 PAG.mdb file.path(getwd(), filename) [1] c:/jml/Valoración F1/04 BA/Valoración F1 PAG.mdb - wrong file.path(c:/jml/Valoración F1/04 BA, filename) [1] c:/jml/Valoración F1/04 BA/Valoración F1 PAG.mdb - ok file.path(paste(getwd()), filename) [1] c:/jml/Valoración F1/04 BA/Valoración F1 PAG.mdb -ok getwd() [1] c:/jml/Valoración F1/04 BA R version 2.7.0 Patched (2008-04-23 r45466) i386-pc-mingw32 locale: LC_COLLATE=Spanish_Spain.1252;LC_CTYPE=Spanish_Spain.1252;LC_MONETARY=Spanish_Spain.1252;LC_NUMERIC=C;LC_TIME=Spanish_Spain.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] RODBC_1.2-3 -- Thanks again. 2008/4/24, Prof Brian Ripley [EMAIL PROTECTED]: See my reply to Erik Jørgensen yesterday. Can you please send that again with a marked encoding, so we have a chance of reading it? Or attach it as a plain text file and tell us what encoding the file is in? Yes, there probably is a bug here but we do need to be able to reproduce it. On Thu, 24 Apr 2008, Javier Muñoz wrote: Hello, This is what i get in R-2.7.0 (with the completely internal file.path()): setwd(c:/jml/Valoraci?n F1/04 BA/) filename - Valoraci?n F1 PAG.mdb file.path(getwd(), filename) [1] c:/jml/Valoraci??n F1/04 BA/Valoraci?n F1 PAG.mdb - worng file.path(c:/jml/Valoraci?n F1/04 BA, filename) [1] c:/jml/Valoraci?n F1/04 BA/Valoraci?n F1 PAG.mdb - ok file.path(paste(getwd()), filename) [1] c:/jml/Valoraci?n F1/04 BA/Valoraci?n F1 PAG.mdb - ok With the older file.path() all of these return c:/jml/Valoraci?n F1/04 BA/Valoraci?n F1 PAG.mdb -- Session info --- R version 2.7.0 (2008-04-22) i386-pc-mingw32 locale: LC_COLLATE=Spanish_Spain.1252;LC_CTYPE=Spanish_Spain.1252;LC_MONETARY=Spanish_Spain.1252;LC_NUMERIC=C;LC_TIME=Spanish_Spain.1252 attached base packages: [1] stats graphics grDevices datasets utils methods base other attached packages: [1] RODBC_1.2-3 Is this a bug in the new file.path() or can I change something to make this work as before? Thanks. Javier. [[alternative HTML version deleted]] -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] bug in file.path?
I can read that version, thanks. The issue is probably that getwd() and filename are in different encodings, and file.path() was not expecting that. You need R-patched = r45490 for that fix. On Thu, 24 Apr 2008, Javier Muñoz wrote: Sorry, this is the same test with R-patched (same results as well). setwd(c:/jml/Valoración F1/04 BA/) filename - Valoración F1 PAG.mdb file.path(getwd(), filename) [1] c:/jml/Valoración F1/04 BA/Valoración F1 PAG.mdb - wrong file.path(c:/jml/Valoración F1/04 BA, filename) [1] c:/jml/Valoración F1/04 BA/Valoración F1 PAG.mdb - ok file.path(paste(getwd()), filename) [1] c:/jml/Valoración F1/04 BA/Valoración F1 PAG.mdb -ok getwd() [1] c:/jml/Valoración F1/04 BA R version 2.7.0 Patched (2008-04-23 r45466) i386-pc-mingw32 locale: LC_COLLATE=Spanish_Spain.1252;LC_CTYPE=Spanish_Spain.1252;LC_MONETARY=Spanish_Spain.1252;LC_NUMERIC=C;LC_TIME=Spanish_Spain.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] RODBC_1.2-3 -- Thanks again. 2008/4/24, Prof Brian Ripley [EMAIL PROTECTED]: See my reply to Erik Jørgensen yesterday. Can you please send that again with a marked encoding, so we have a chance of reading it? Or attach it as a plain text file and tell us what encoding the file is in? Yes, there probably is a bug here but we do need to be able to reproduce it. On Thu, 24 Apr 2008, Javier Muñoz wrote: Hello, This is what i get in R-2.7.0 (with the completely internal file.path()): setwd(c:/jml/Valoraci?n F1/04 BA/) filename - Valoraci?n F1 PAG.mdb file.path(getwd(), filename) [1] c:/jml/Valoraci??n F1/04 BA/Valoraci?n F1 PAG.mdb - worng file.path(c:/jml/Valoraci?n F1/04 BA, filename) [1] c:/jml/Valoraci?n F1/04 BA/Valoraci?n F1 PAG.mdb - ok file.path(paste(getwd()), filename) [1] c:/jml/Valoraci?n F1/04 BA/Valoraci?n F1 PAG.mdb - ok With the older file.path() all of these return c:/jml/Valoraci?n F1/04 BA/Valoraci?n F1 PAG.mdb -- Session info --- R version 2.7.0 (2008-04-22) i386-pc-mingw32 locale: LC_COLLATE=Spanish_Spain.1252;LC_CTYPE=Spanish_Spain.1252;LC_MONETARY=Spanish_Spain.1252;LC_NUMERIC=C;LC_TIME=Spanish_Spain.1252 attached base packages: [1] stats graphics grDevices datasets utils methods base other attached packages: [1] RODBC_1.2-3 Is this a bug in the new file.path() or can I change something to make this work as before? Thanks. Javier. [[alternative HTML version deleted]] -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595__ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Minimise a parameter of a given function f, with f 0
On Wed, Apr 23, 2008 at 8:51 PM, Kevin Lu [EMAIL PROTECTED] wrote: I need to find the minimum value of the parameter, s, such that the function f(s,t) 0 (where -Inf t Inf) I've looked into optim, constrOptim and others but they don't seem to do this. Des anyone have some suggestions? In order to allow us to help you, please send us a minimal example. Paul __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] changing format of a float value to another
Try this: x - 1.085714e-01 format(as.numeric(x), scientific = F) On Thu, Apr 24, 2008 at 7:28 AM, orkun [EMAIL PROTECTED] wrote: hello How can I change a vector's float value from (1.085714e-01) format to a simpler format (like 0.1xxx). regards -- Ahmet Temiz Jeo. Müh. Afet Ýþleri Gen. Md.lüðü Deprem Ar. D. Ahmet Temiz Geo. Eng. General Dir. of Disaster Affairs -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Memory usage
Hello, I have aggregate a data.frame from 16MB (Object size). After some minutes I get the error message cannot allocate vector of size 64.5MB. My computer has a physical memory of 4GB under Windows Vista. I have test the same command on another computer with the same OS and 2GB RAM. In nearly 2sec I get the result without problems. Thanks buch-read.delim(Y2006_1.csv,sep=;,as.is=TRUE,header=TRUE,dec=,) ana01-aggregate(buch[,c(VALUELW,LZLW,SZLW)],by=data.frame(buch$PRODGRP,buch$LAND1,buch$KUNDE1),sum) __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] changing format of a float value to another
?sprintf x - 1.085714e-01 sprintf(%.4f, as.numeric(x)) [1] 0.1086 On Thu, Apr 24, 2008 at 6:28 AM, orkun [EMAIL PROTECTED] wrote: hello How can I change a vector's float value from (1.085714e-01) format to a simpler format (like 0.1xxx). regards -- Ahmet Temiz Jeo. Müh. Afet İşleri Gen. Md.lüğü Deprem Ar. D. Ahmet Temiz Geo. Eng. General Dir. of Disaster Affairs -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 Cincinnati, OH +1 513 646 9390 What is the problem you are trying to solve? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] BB - a new package for solving nonlinear system of equations and for optimization with simple constraints
Dear Dr. Vardhan, From where can we download this package and its details. Thanks HAve a nice day. On Wed, 23 Apr 2008 16:39:50 -0400 Ravi Varadhan wrote: Hi, We (Paul Gilbert and I) have just released a new R package on CRAN called BB (stands for Barzilai-Borwein) that provides functionality for solving large-scale (and small-scale) nonlinear system of equations. Until now, R didn't have any functionality for solving nonlinear systems. We hope that this package fills that need. We also have an implementation of the spectral projected gradient method for the optimization of (smooth) nonlinear objective functions, subject to simple constraints that can be defined as a projection mapping. This function, spg(), is suited for large-s! cale optimization. It generally performs better than the conjugate-gradient methods in optim, and complements the low-memory BFGS method for constraints that can be defined by the user as projection mapping. Best regards, Ravi. --- Ravi Varadhan, Ph.D. Assistant Professor, The Center on Aging and Health Division of Geriatric Medicine and Gerontology Johns Hopkins University Ph: (410) 502-2619 Fax: (410) 614-9625 Email: [EMAIL PROTECTED] Webpage: http://www.jhsph.edu/agingandhealth/People/Faculty/Varadhan.html ---! - g t; [[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] Feed list of vectors to vioplot()?
Dirty solution: switched off x-axis plotting via 'par' and added it the
personalized way with 'axis'.
Joh
Johannes Graumann wrote:
Hm, now I have trouble using additional vioplot parameters.
mu-2
si-0.6
bimodal-c(rnorm(1000,-mu,si),rnorm(1000,mu,si))
uniform-runif(2000,-4,4)
normal-rnorm(2000,0,3)
mylist - list(bimodal,uniform,normal)
# Easy
do.call(vioplot,mylist)
# Works
do.call(vioplot,c(mylist,col=white))
# Does not
# vioplot expects names as a plain vector, not in the
# form names=c(One,Two,Three) ...
names - c(One,Two,Three)
do.call(vioplot,c(mylist,col=white,names))
Any help on how to do this?
Thanks, Joh
Johannes Graumann wrote:
Off-list it was pointed out to me that the trivial solution to this would
look like this:
myfunction2 - function(x, ...){
mylist - list(x, ...)
# plenty of lapply stuff
do.call(vioplot,mylist)
}
Thanks for everybodies patience,
Joh
Johannes Graumann wrote:
posted mailed
Thanks for the very appropriate scolding.
Here's my example (based on ?vioplot):
mu-2
si-0.6
bimodal-c(rnorm(1000,-mu,si),rnorm(1000,mu,si))
uniform-runif(2000,-4,4)
normal-rnorm(2000,0,3)
# Working just fine
myfunction1 - function(x, ...){vioplot(x,...)}
myfunction1(bimodal,uniform,normal)
# What I (believe to) need
myfunction2 - function(x, ...){
mylist - list(x, ...)
# plenty of lapply stuff
vioplot(mylist)
}
myfunction2(bimodal,uniform,normal)
-- Error in min(data) : invalid 'type' (list) of argument
I'm at a loss on how to disentangle mylist - unlist just gives me one
big vector back rather than the 3 I want to have back ...
Thanks for your patience, Joh
jim holtman wrote:
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html and provide commented,
minimal, self-contained, reproducible code.
It is hard to provide a solution if we do not understand the problem
to be solved. Sample data would be helpful along with an
understanding of what you would expect for output.
On Wed, Apr 23, 2008 at 10:11 AM, Johannes Graumann
[EMAIL PROTECTED] wrote:
Johannes Graumann wrote:
Hi,
I have a list of vectors and am trying to coerce them into something
that vioplot will take as groups of data to be plotted
independently. Can someone nudge me into the right direction?
Thanks, Joh
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PLEASE do read the posting guide
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I'll try less impolite and with more info ...
I'm writing a function that contains this:
# function(x, ... , morestuff){}
which is gathered into a list like so:
# mylist - list(x, ...)
down the line I'd like to output all elements from mylist in
seperate vioplots in a single coordiante system. Now I have a hell of
a time with that because vioplot does not accept a list as input but
only a succession of vectors ... how can I now force my list into that
form so a can say
# vioplot(magicfunction(mylist))
and get a violin plot for each list-member?
Thanks for any hint,
Joh
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Re: [R] Can I get rid of this for loop using apply?
Great suggestions. I tested the code on an example and the run time was reduced from 1 min 12 sec to 3 sec. Also, I like the suggestion to look at the quantiles. I will see what insight it provides in terms of detecting masked interactions. I have a couple questions about your code. First, why not use xs - seq(min(x1), max(x1), length = 100) instead of xs - with(m, seq(min(x1), max(x1), length = 100)) ? Second, what is the function geom_line()? I couldn't find it. Thanks, Mike On 4/23/08, hadley wickham [EMAIL PROTECTED] wrote: On Wed, Apr 23, 2008 at 8:33 PM, hadley wickham [EMAIL PROTECTED] wrote: Sure, I am creating a partial dependence plot (reference Friedman's stochastic gradient paper from, I want to say, 2001). The idea is to find the relationship between one of the predictors, say x1, and y by creating the following plot: take a random sample of actual data points, hold other predictors fixed (x2-xp), vary x1 across its range, create a string of Put your code doesn't have a random component - you're trying to calculate everything combination of the new x_n and the existing data? Is that right? And why are you using so many different values of the x variable? 100's should be sufficient to get a smooth curve, not thousands. I'd also think about displaying not just the mean, but a selection of quantiles as well: Here's one approach: model - lm(y ~ poly(x1, 2) + x2, data = m) xs - with(m, seq(min(x1), max(x1), length = 100)) library(reshape) newdf - expand.grid.df(data.frame(x1 = xs), m[, c(x2), drop=F]) predictions - predict(model, newdata = newdf) avg_pred - tapply(predictions, newdf$x1, mean) low_pred - tapply(predictions, newdf$x1, quantile, 0.25) high_pred - tapply(predictions, newdf$x1, quantile, 0.75) library(ggplot) qplot(xs, avg_pred, min = low_pred, max = high_pred, geom=ribbon) + geom_line() But following your code, it's exhaustive, not random. This should be a little faster because all the predictions are done in one go. Hadley -- http://had.co.nz/ [[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] Passing Inf from R to C using .C(myLibC...
On 4/24/2008 9:01 AM, Ardia David wrote: Dear all, How can I pass '-Inf' and 'Inf' values from R to C code using the function '.C(...)'. When running my code, I get an error since C does not recognize -Inf and Inf values. Of course, I could use instead a very low (or high) number, but I was wondering whether a more elegant solution exists. Thanks for your help. C doesn't have any problem, but many C functions do, so .C by default prevents you from doing this. However, if you know that it is safe, use the NAOK arg to .C and special values will get through. (The name NAOK may not suggest it also means Inf is okay, but the docs do clearly say that.) Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Extracting factor columns from a data frame
Hi All,
I have attempted to extract only the factor columns from an
existing data set inside a loop without success . I tried the transform
function which worked, but not inside the loop (attempts with cbind did
not work either - inside a loop). Here is my function:
getcatcolumns-function(x)
{
# ignore type checking for data frames etc
res - data.frame()
for(i in 1:length(x))
{
if (class(x[,i]) ==factor) res - transform(res, colname =
x[,i]) # append the factor column to the new data frame (res)
}
return(res)
}
The error I get is: arguments imply differing number of rows: 0, 5000
All help appreciated.
Regards,
Serge Merzliakov
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[R] logit newbie question...
Hi, I'm new to the glm and logit world... and I'm reading some lecture notes and examples. I would like to try and generate the same result in R.. but I don't seem to be able to find the proper way to specify the formula let's say i have Desire Using Drugs Not Using Drugs Yes 219 753 No 288 347 Desire is my explanatory and Drugs Using is my response... How can I specify the null model? Namely logit(pi) = n where mle should give n to be logit((219+288)/(753+347)) Also, if I want a one factor model logit(pi1) = n logit(pi2) = n + alpha where mle should give me n to be logit(219 / 972) and alpha be logit(288/635) - logit(219/972) Thanks! -- View this message in context: http://www.nabble.com/logit-newbie-question...-tp16850195p16850195.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] permutation of the rows of a matrix that minimizes the distance to another matrix
Hi! I have 2 matrices of numbers m1 and m2 with the same number of columns and rows. I would like to compute m2', the permutation of the rows of m2 such that the distance (e.g., sum(m1-m2') or sum((m1-m2')^2)) is minimized. Do you know of any function/algorithm to obtain such a permutation? Best regards, Carlos __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 for HP Integrity Superdome...
Hi, We just installed a HP Integrity Superdome (an Itanium-based SMP machine with 64 cores + 128 GB memory, running Red Hat AS 4 update 6) at our National Center for High Performance Computing. I would like to run R on it and use the hardware optimally. What is the best way? Is there a parallel (openMP ?) version of R. Or can one 'make it' using (if available) optimized parallel libraries? Any advise.suggestion will be appreciated. H. Nüzhet Dalfes Professor, Istanbul Technical University Eurasia Institute of Earth Sciences +90 (532) 206-1308 [EMAIL PROTECTED] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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-help Digest, Vol 62, Issue 24
---begin included message Hi, i need to use pspline. In this pspline function coxph.wtest was used. When I try to make some change to this function by pulling out the pspline function, it turns out R gave me an error msg, saying coxph.wtest cannot be found. Even if i dont change anything in pspline and just rename it and run the function, it did not work out. Can any one help me with this? is there anyway to get the coxph.wtest function? thank you --- end included message Your question is not completely clear to me, but I will guess that you have pulled out some code from coxph and tried to run it separately. If so, you are running into the name space problem: not all functions within the survival package are visible outside of the package. (Those for which the authors assumed that no one would call the function themselves.) A quick solution is to make your own local copy coxph.wtest - survival:::coxph.wtest It will now be visible to you. Terry T. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Documentation General Comments
Agree that terseness is good, but I also agree with other posters that better cross referencing or maybe an index of synonyms would be good. So far, the best suggestion is the pdf at this link (http://www.medepi.net/epir/epir_chap02.pdf). Is there a way to pop at least part of this into the R-base help page? Are there legal or copyright issues? If I had known this from the start, it would have been much better. A good analogy is that old cartoon of the blind guys trying to figure out what an elephant is. The guys feeling at the front get a much different impression than the guys poking at the back side. I felt like that using R data structures, had to blindly poke around trying different things, 90% of which did not work, yeilding only error messages, but now knowing the underlying organisation it is going much more smoothly. Ideally this kind of basic info would be in the core R docuemtation, you should not have to search this hard to get it! -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Bert Gunter Sent: Tuesday, April 22, 2008 10:29 AM To: r-help@r-project.org Subject: Re: [R] Documentation General Comments FWIW: I consider the documentation of Core R to be one of its great strengths: it is terse (read: to the point), detailed, and accurate. I find it eminently useful and helpful. Indeed, it was why I made the decision some years ago to switch from S-Plus to R (I readily acknowledge that S-Plus may have improved its docs since then -- haven't looked at it in years). While I understand that it may not suit everyone -- learning styles differ, after all -- may I at least say that there is one user out here who is appreciative of the hard work and care that has gone into the documentation. Far FAR better than anything I could do! -- Bert Gunter Genentech -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Greg Snow Sent: Tuesday, April 22, 2008 8:16 AM To: Beck, Kenneth (STP); r-help@r-project.org Subject: Re: [R] Documentation General Comments This is a case of you can't please everyone. A while back there was some complaint that Introduction to R spent to much time on talking about the different types of variables, just the opposite complaint of yours. There are several other sources of documentation (look under the books link on the R homepage or the contributed documentation link on any CRAN site, also browse through the newsletter). For more in depth information on variable types and object oriented programming in R you may want to invest in a copy of S Programming by Venables and Ripley. If you have specific questions (about data types, or other) then tell us what you have read and what you still do not understand and you are more likely to get a useful answer. (also read the posting guide that is referenced at the bottom of almost all posts to the list). -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare [EMAIL PROTECTED] (801) 408-8111 -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Beck, Kenneth (STP) Sent: Monday, April 21, 2008 3:56 PM To: r-help@r-project.org Subject: [R] Documentation General Comments I realize the R developers are probably overwhelmed and have little time for this, but the documentation really needs some serious reorganizaton. A good through description of basic variable types would help a lot, e.g. the difference between lists, arrays, matrices and frames. And, it appears there is some object-orientation to R, but it is not complete. I can't, for instance find a metafile method for a recordedplot type, using either the variable direclty or the replayPlot() method. I am sorry to post this, but I am really having trouble sorting out certain methods in R. The basic tutorial Introduction to R is so basic, it hardly helps at all, then digging through documentation is really an exercise in frustration. The SimpleR is also so basic it is of little help other than to just get started. I occasionally find answers in the mailing list. See my later post on recordPlot for a good example. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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,
Re: [R] Extracting factor columns from a data frame
Try this:
dat - data.frame(x = gl(4, 5), y = gl(5, 4), z = rnorm(20))
res - dat[sapply(dat, is.factor)]
On Thu, Apr 24, 2008 at 9:14 AM, Serge Merzliakov [EMAIL PROTECTED]
wrote:
Hi All,
I have attempted to extract only the factor columns from an
existing data set inside a loop without success . I tried the transform
function which worked, but not inside the loop (attempts with cbind did
not work either - inside a loop). Here is my function:
getcatcolumns-function(x)
{
# ignore type checking for data frames etc
res - data.frame()
for(i in 1:length(x))
{
if (class(x[,i]) ==factor) res - transform(res, colname =
x[,i]) # append the factor column to the new data frame (res)
}
return(res)
}
The error I get is: arguments imply differing number of rows: 0, 5000
All help appreciated.
Regards,
Serge Merzliakov
__
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PLEASE do read the posting guide
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and provide commented, minimal, self-contained, reproducible code.
--
Henrique Dallazuanna
Curitiba-Paraná-Brasil
25° 25' 40 S 49° 16' 22 O
[[alternative HTML version deleted]]
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Re: [R] Can I get rid of this for loop using apply?
Great suggestions. I tested the code on an example and the run time was reduced from 1 min 12 sec to 3 sec. Also, I like the suggestion to look at the quantiles. I will see what insight it provides in terms of detecting masked interactions. Well that's a decent speed up :) I have a couple questions about your code. First, why not use xs - seq(min(x1), max(x1), length = 100) instead of xs - with(m, seq(min(x1), max(x1), length = 100)) ? No real reason, just to make it a bit easier when you generalise to other data sets / models Second, what is the function geom_line()? I couldn't find it. It's in ggplot2 - http://had.co.nz/ggplot2/geom_line.html - ?geom_line should find it too though (provided you have version 0.6 of ggplot2) Hadley -- http://had.co.nz/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Name of objects in a list
Hi useRs,
I am trying to compare several distance matrices obtained from subsets
of variables from the same experiment. I put all the subsets in a list
and then calculated the distance matrices with lapply. In order to do a
mantel test between them I wrote a function the returns a list with the
output of single tests. I would like to include the name of the tests,
so I know what each element of the result list is. My code is as follows:
land - list(s1536 = s1536, s384L = s384L, s96L = s96L, s384c = s384c,
s96c = s96c, s384r = s384r, s96r = s96r)
library(analogue)
ldis - lapply(land, function(x) as.dist(distance(x, method = mixed)))
mantel.list - function(x, ...) {
require(ade4)
for (i in 2:length(x)) {
x1 - x[[i - 1]]
x2 - x[[i]]
y[[i]] - mantel.rtest(x1, x2)
}
return(y)
}
lmantel - mantel.list(ldis)
str(ldis)
List of 7
$ s1536:Class 'dist' atomic [1:15400] 0.357 0.260 0.341 0.342 0.267 ...
.. ..- attr(*, Labels)= chr [1:176] CS301 CS302 CS303 CS304 ...
.. ..- attr(*, Size)= int 176
.. ..- attr(*, call)= language as.dist.default(m = distance(x,
method = mixed))
.. ..- attr(*, Diag)= logi FALSE
.. ..- attr(*, Upper)= logi FALSE
$ s384L:Class 'dist' atomic [1:15400] 0.497 0.243 0.453 0.440 0.277 ...
.. ..- attr(*, Labels)= chr [1:176] CS301 CS302 CS303 CS304 ...
.. ..- attr(*, Size)= int 176
.. ..- attr(*, call)= language as.dist.default(m = distance(x,
method = mixed))
.. ..- attr(*, Diag)= logi FALSE
.. ..- attr(*, Upper)= logi FALSE
(...)
str(lmantel)
List of 7
$ :List of 5
..$ sim : num [1:99] 0.007734 0.002429 -0.021489 -0.000181
0.021703 ...
..$ obs : num 0.785
..$ rep : int 99
..$ pvalue: num 0.01
..$ call : language mantelnoneuclid(m1 = m1, m2 = m2, nrepet = nrepet)
..- attr(*, class)= chr rtest
$ :List of 5
..$ sim : num [1:99] 0.00749 0.02850 -0.01301 -0.01376 0.00883 ...
..$ obs : num 0.785
..$ rep : int 99
..$ pvalue: num 0.01
..$ call : language mantelnoneuclid(m1 = m1, m2 = m2, nrepet = nrepet)
..- attr(*, class)= chr rtest
(...)
I would like to get something like
str(lmantel)
List of 7
$ s1536_s384L
:List of 5
..$ sim : num [1:99] 0.007734 0.002429 -0.021489 -0.000181
0.021703 ...
..$ obs : num 0.785
..$ rep : int 99
..$ pvalue: num 0.01
..$ call : language mantelnoneuclid(m1 = m1, m2 = m2, nrepet = nrepet)
..- attr(*, class)= chr rtest
(...)
Thanks for your help.
Marc.
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[R] temporal dependence?
Hi, I'm not sure where to look for help with this problem. I don't even know the right search terms for it. First let me describe the analysis. I have land use data from satellite imagery (individual pixels or cells) for years 1985 and 1990. I am recoding development as 1 and non-development (forest, etc) as a zero. I am attempting to predict the probability of transition by cell over these 5 years from 0 to 1 as a function of several variables (slope, etc). I'm quite sure there will be spatial autocorrelation since development breeds new development. I know of ways to deal with this (autoregression, mixed models). I also expect a time dependency, if this is the correct term, for the following reason. Development that occurs in 1986 will affect future time periods and 1987 will also, etc. So, the dependent variables are not independent from each other either in space or time. I do not know from the data what year a particular cell was developed only that it occurred between 1985 and 1990. So, development will occur near other development that occurred prior to it, but I don't know the time ordering other than to say that development either occured before 1985 or between 1985 and 1990. I can think of a way to do this via simulation by starting at 1985 and assuming a basic relationship between development, past development, and other covariates (like slope). I would then apply this relationship to the landscape as of 1985 to assign probabilities of development. Next, I could develop some cells using a random number generator (creating a binary landscape that is a possible realization of the model) and repeat the process for 1986 and each year until 1990. I could do this many times and see the frequency with which each cell was developed and use this to estimate the likelihood. I could then adjust the functions in an attempt to maximize likelihood. This is very brute-force and I don't want to do it, if avoidable. Thanks for reading, Seth -- View this message in context: http://www.nabble.com/temporal-dependence--tp16850739p16850739.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] Documentation General Comments
On 4/24/2008 10:22 AM, Beck, Kenneth (STP) wrote: Agree that terseness is good, but I also agree with other posters that better cross referencing or maybe an index of synonyms would be good. So far, the best suggestion is the pdf at this link (http://www.medepi.net/epir/epir_chap02.pdf). Is there a way to pop at least part of this into the R-base help page? That's an easy question to answer: no. There is no way to just pop it in. Incorporating it would take a lot of thought and work. Are there legal or copyright issues? That's also easy: yes, there are. The authors of that chapter presumably have copyright in it (unless they've transferred it to someone else). Without their permission it would be illegal to pop it into R. If I had known this from the start, it would have been much better. A good analogy is that old cartoon of the blind guys trying to figure out what an elephant is. The guys feeling at the front get a much different impression than the guys poking at the back side. I felt like that using R data structures, had to blindly poke around trying different things, 90% of which did not work, yeilding only error messages, but now knowing the underlying organisation it is going much more smoothly. Ideally this kind of basic info would be in the core R docuemtation, you should not have to search this hard to get it! All of the (correct) information in that chapter is in the core documentation. They make a number of simplifications, which I think are appropriate for their audience, but you shouldn't believe everything you read there. The core documentation has to aim for a different target, because it needs to be correct. Duncan Murdoch -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Bert Gunter Sent: Tuesday, April 22, 2008 10:29 AM To: r-help@r-project.org Subject: Re: [R] Documentation General Comments FWIW: I consider the documentation of Core R to be one of its great strengths: it is terse (read: to the point), detailed, and accurate. I find it eminently useful and helpful. Indeed, it was why I made the decision some years ago to switch from S-Plus to R (I readily acknowledge that S-Plus may have improved its docs since then -- haven't looked at it in years). While I understand that it may not suit everyone -- learning styles differ, after all -- may I at least say that there is one user out here who is appreciative of the hard work and care that has gone into the documentation. Far FAR better than anything I could do! -- Bert Gunter Genentech -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Greg Snow Sent: Tuesday, April 22, 2008 8:16 AM To: Beck, Kenneth (STP); r-help@r-project.org Subject: Re: [R] Documentation General Comments This is a case of you can't please everyone. A while back there was some complaint that Introduction to R spent to much time on talking about the different types of variables, just the opposite complaint of yours. There are several other sources of documentation (look under the books link on the R homepage or the contributed documentation link on any CRAN site, also browse through the newsletter). For more in depth information on variable types and object oriented programming in R you may want to invest in a copy of S Programming by Venables and Ripley. If you have specific questions (about data types, or other) then tell us what you have read and what you still do not understand and you are more likely to get a useful answer. (also read the posting guide that is referenced at the bottom of almost all posts to the list). -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare [EMAIL PROTECTED] (801) 408-8111 -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Beck, Kenneth (STP) Sent: Monday, April 21, 2008 3:56 PM To: r-help@r-project.org Subject: [R] Documentation General Comments I realize the R developers are probably overwhelmed and have little time for this, but the documentation really needs some serious reorganizaton. A good through description of basic variable types would help a lot, e.g. the difference between lists, arrays, matrices and frames. And, it appears there is some object-orientation to R, but it is not complete. I can't, for instance find a metafile method for a recordedplot type, using either the variable direclty or the replayPlot() method. I am sorry to post this, but I am really having trouble sorting out certain methods in R. The basic tutorial Introduction to R is so basic, it hardly helps at all, then digging through documentation is really an exercise in frustration. The SimpleR is also so basic it is of little help other than to just get started. I occasionally find answers in the mailing list. See my later post on recordPlot for a good
[R] inverse F distribution in R?
Dear all, I'm looking for a function that calls the inverse F-distribution. Something equivalent to FINV in matlab or excel. Does anyone know if such a function already exists for R? (I haven't been able to find one.) Thanks for any leads. Best, Jennifer __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] inverse F distribution in R?
Hi Jennifer, Try ?qf or help.search(F distribution) HTH, Jorge On Thu, Apr 24, 2008 at 10:49 AM, Jennifer Balch [EMAIL PROTECTED] wrote: Dear all, I'm looking for a function that calls the inverse F-distribution. Something equivalent to FINV in matlab or excel. Does anyone know if such a function already exists for R? (I haven't been able to find one.) Thanks for any leads. Best, Jennifer __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] inverse F distribution in R?
Jennifer Balch wrote: Dear all, I'm looking for a function that calls the inverse F-distribution. Something equivalent to FINV in matlab or excel. Does anyone know if such a function already exists for R? (I haven't been able to find one.) Thanks for any leads. I would guess that they are qf() or a variant thereof. I gather that _fpdf http://www.mathworks.com/access/helpdesk/help/toolbox/stats/fpdf.html__, fcdf http://www.mathworks.com/access/helpdesk/help/toolbox/stats/fcdf.html, finv http://www.mathworks.com/access/helpdesk/help/toolbox/stats/finv.html, frnd http://www.mathworks.com/access/helpdesk/help/toolbox/stats/frnd.html i_n matlab is df, pf, qf, and rf in R. We don't have an equivalent of fstat for mean and variance of the F distribution (this might actually be nice to have). Best, Jennifer __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Documentation General Comments
OK I've spent a lot of time with the core documentation, and I never found anything as simple as their table 2.1, which elucidated the difference between a vector, matrix and array first, then the higher level structures, frame and list. Maybe I'm not a good searcher, but believe me for every initial posting I submit to this group, I have spent hours trying to find the answer elsewhere. And, as you state, maybe I am now deluded by that presentation, maybe it is not this simple! Look at the help for data.frame. VERY terse explanation, with not a good comparison to the other data types. Then, look at the titles list. Where is a topic for data types Every other programming language I have used (C++, Pascal, SAS, Java) has a basic chapter in the documentation that goes over data types, what arrays are, higher level structures, etc. When I typed help.search(data type) I get the following: Help files with alias or concept or title matching 'data type' using fuzzy matching: character-class(methods) Classes Corresponding to Basic Data Types sqlTypeInfo(RODBC) Request Information about DataTypes in an ODBC Database Looking for the term character-class(methods) yields nothing. I don't think that is what I want! Given all this complaining, I actually have completed several nice project using R, it is an impressive package. Somehow, though, we need to make the documentation better. -Original Message- From: Duncan Murdoch [mailto:[EMAIL PROTECTED] Sent: Thursday, April 24, 2008 9:51 AM To: Beck, Kenneth (STP) Cc: Bert Gunter; r-help@r-project.org Subject: Re: [R] Documentation General Comments On 4/24/2008 10:22 AM, Beck, Kenneth (STP) wrote: Agree that terseness is good, but I also agree with other posters that better cross referencing or maybe an index of synonyms would be good. So far, the best suggestion is the pdf at this link (http://www.medepi.net/epir/epir_chap02.pdf). Is there a way to pop at least part of this into the R-base help page? That's an easy question to answer: no. There is no way to just pop it in. Incorporating it would take a lot of thought and work. Are there legal or copyright issues? That's also easy: yes, there are. The authors of that chapter presumably have copyright in it (unless they've transferred it to someone else). Without their permission it would be illegal to pop it into R. If I had known this from the start, it would have been much better. A good analogy is that old cartoon of the blind guys trying to figure out what an elephant is. The guys feeling at the front get a much different impression than the guys poking at the back side. I felt like that using R data structures, had to blindly poke around trying different things, 90% of which did not work, yeilding only error messages, but now knowing the underlying organisation it is going much more smoothly. Ideally this kind of basic info would be in the core R docuemtation, you should not have to search this hard to get it! All of the (correct) information in that chapter is in the core documentation. They make a number of simplifications, which I think are appropriate for their audience, but you shouldn't believe everything you read there. The core documentation has to aim for a different target, because it needs to be correct. Duncan Murdoch -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Bert Gunter Sent: Tuesday, April 22, 2008 10:29 AM To: r-help@r-project.org Subject: Re: [R] Documentation General Comments FWIW: I consider the documentation of Core R to be one of its great strengths: it is terse (read: to the point), detailed, and accurate. I find it eminently useful and helpful. Indeed, it was why I made the decision some years ago to switch from S-Plus to R (I readily acknowledge that S-Plus may have improved its docs since then -- haven't looked at it in years). While I understand that it may not suit everyone -- learning styles differ, after all -- may I at least say that there is one user out here who is appreciative of the hard work and care that has gone into the documentation. Far FAR better than anything I could do! -- Bert Gunter Genentech -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Greg Snow Sent: Tuesday, April 22, 2008 8:16 AM To: Beck, Kenneth (STP); r-help@r-project.org Subject: Re: [R] Documentation General Comments This is a case of you can't please everyone. A while back there was some complaint that Introduction to R spent to much time on talking about the different types of variables, just the opposite complaint of yours. There are several other sources of documentation (look under the books link on the R homepage or the contributed documentation link on any CRAN site, also browse through the newsletter). For more in depth information on
Re: [R] inverse F distribution in R?
just a comment to fstat... Using package distrEx one also has fstat functionality library(distrEx) E(Fd(df1 = 3, df2 = 3)) E(Fd(df1 = 4, df2 = 4)) E(Fd(df1 = 5, df2 = 5)) var(Fd(df1 = 5, df2 = 5)) for more functionals (skewness, kurtosis, IQR, ...) see for instance help(var, package = distrEx) Best Matthias Peter Dalgaard wrote: Jennifer Balch wrote: Dear all, I'm looking for a function that calls the inverse F-distribution. Something equivalent to FINV in matlab or excel. Does anyone know if such a function already exists for R? (I haven't been able to find one.) Thanks for any leads. I would guess that they are qf() or a variant thereof. I gather that _fpdf http://www.mathworks.com/access/helpdesk/help/toolbox/stats/fpdf.html__, fcdf http://www.mathworks.com/access/helpdesk/help/toolbox/stats/fcdf.html, finv http://www.mathworks.com/access/helpdesk/help/toolbox/stats/finv.html, frnd http://www.mathworks.com/access/helpdesk/help/toolbox/stats/frnd.html i_n matlab is df, pf, qf, and rf in R. We don't have an equivalent of fstat for mean and variance of the F distribution (this might actually be nice to have). Best, Jennifer __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Dr. Matthias Kohl www.stamats.de __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Documentation General Comments
Help files with alias or concept or title matching 'data type' using fuzzy matching: character-class(methods) Classes Corresponding to Basic Data Types sqlTypeInfo(RODBC) Request Information about DataTypes in an ODBC Database One small, but concrete improvement to the output from help.search would be to list the functions like: methods::character-class Classes Corresponding to Basic Data Types RODBC::sqlTypeInfo Request Information about DataTypes in an ODBC Database and then extend ? to correctly parse (e.g.) ?methods::character-class (although perhaps there a better display would be methods::character-class). This change would make function calling and accessing documentation a little more consistent. It would also be useful to list keywords in the help documentation, so that one could more easily figure out what other documentation might be related. Hadley Hadley -- http://had.co.nz/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Factor to numeric
Hello! Thanks! I changed the , to . in both datafile and code but the problem remains identical. Cheers! Jojje Date: Thu, 24 Apr 2008 09:16:38 +0100 From: [EMAIL PROTECTED] To: [EMAIL PROTECTED] CC: r-help@r-project.org Subject: Re: [R] Factor to numeric The decimal point in R is always '.', never ','. On Thu, 24 Apr 2008, Jojje Andersson wrote:Hello! I have a problem whith a data.frame. I want to make a subset where some of the variables have values within ceartain limits. The variables are proportions like 1,00, 0,54, 0,00 etc. I don't get it right as R take the variables for factors. ekobsub1 - subset(ekob, PAP0,25 PAP0,6 CAP0,1 CAP0,6 FAP0,1) Error in `[.data.frame`(x, r, vars, drop = drop) : object CAP not found In addition: Warning message: In Ops.factor(PAP, 0) : not meaningful for factors ekobn-as.numeric(as.character(ekob[[PAP]])) Warning message: NAs introduced by coercionThanks! /Jojje _ [[elide! d Hotmail spam]] px?sc_cmp2=JS_INT_SEMSN_NLPCV [[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. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UK Fax: +44 1865 272595 _ [[elided Hotmail spam]] [[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 needed: Plotting step by step.
On Thu, 24 Apr 2008, Atul Kulkarni wrote: Hi, Thanks for help. The ecdf has jumps of 1/n but I need jumps of 1. How do I do this? if I can See ?stepfun HTH, Chuck do this then I think Ic an plot the data properly. I am plotting epidemic simulation and want to plot my 2 processes Infection and Symptoms (after incubation) on the same chart to compare them. Atul. On Wed, Apr 23, 2008 at 12:35 PM, Charles C. Berry [EMAIL PROTECTED] wrote: Maybe like this? proc.1 - rexp(200,1) proc.2 - rexp(200,2) plot( ecdf( proc.1 ), xlim=range( proc.1, proc.2 ) ) plot( ecdf( proc.2 ), add=T, col.points='red' ) See ?ecdf ?plot.stepfun HTH, Chuck On Wed, 23 Apr 2008, Greg Snow wrote: Can you show us the code you used for the 5 to 10 points? (either generate some random data, or use a sample dataset). -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare [EMAIL PROTECTED] (801) 408-8111 -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Atul Kulkarni Sent: Wednesday, April 23, 2008 9:07 AM To: r-help@r-project.org Subject: [R] help needed: Plotting step by step. Hello, I have generated 2 Poisson processes and want to plot them on a single graph in a step by step manner in order to be able to compare them. I tried plot and biplot but it does not help, I could connect two points by hand for point graph if they were 5 or 10 I have more than 200 such point to be connected and Poisson cluster makes it difficult for me to even read them properly. Can anyone tell me which is the function that can plot a stepwise graph for me? I did google over the plot for step fun but did not understand much of it. A simpler help would be more useful to me, as I am not a expert either in Statistics or R. Regards, Atul. -- Atul S. Kulkarni Graduate Student, Department of Computer Science, University Of Minnesota, Duluth, MN 55812. www.d.umn.edu/~kulka053 http://www.d.umn.edu/%7Ekulka053 - Before you start some work, always ask yourself three questions - Why am I doing it, What the results might be and Will I be successful. Only when you think deeply and find satisfactory answers to these questions, go ahead. Chanakya quotes (Indian politician, strategist and writer, 350 BC-275 BC) [[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. Charles C. Berry(858) 534-2098 Dept of Family/Preventive Medicine E mailto:[EMAIL PROTECTED] UC San Diego http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego 92093-0901 -- Atul S. Kulkarni Graduate Student, Department of Computer Science, University Of Minnesota, Duluth, MN 55812. www.d.umn.edu/~kulka053 - Before you start some work, always ask yourself three questions - Why am I doing it, What the results might be and Will I be successful. Only when you think deeply and find satisfactory answers to these questions, go ahead. Chanakya quotes (Indian politician, strategist and writer, 350 BC-275 BC) Charles C. Berry(858) 534-2098 Dept of Family/Preventive Medicine E mailto:[EMAIL PROTECTED] UC San Diego http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego 92093-0901 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 needed: Plotting step by step.
Hi, Thanks for help. The ecdf has jumps of 1/n but I need jumps of 1. How do I do this? if I can do this then I think Ic an plot the data properly. I am plotting epidemic simulation and want to plot my 2 processes Infection and Symptoms (after incubation) on the same chart to compare them. Atul. On Wed, Apr 23, 2008 at 12:35 PM, Charles C. Berry [EMAIL PROTECTED] wrote: Maybe like this? proc.1 - rexp(200,1) proc.2 - rexp(200,2) plot( ecdf( proc.1 ), xlim=range( proc.1, proc.2 ) ) plot( ecdf( proc.2 ), add=T, col.points='red' ) See ?ecdf ?plot.stepfun HTH, Chuck On Wed, 23 Apr 2008, Greg Snow wrote: Can you show us the code you used for the 5 to 10 points? (either generate some random data, or use a sample dataset). -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare [EMAIL PROTECTED] (801) 408-8111 -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Atul Kulkarni Sent: Wednesday, April 23, 2008 9:07 AM To: r-help@r-project.org Subject: [R] help needed: Plotting step by step. Hello, I have generated 2 Poisson processes and want to plot them on a single graph in a step by step manner in order to be able to compare them. I tried plot and biplot but it does not help, I could connect two points by hand for point graph if they were 5 or 10 I have more than 200 such point to be connected and Poisson cluster makes it difficult for me to even read them properly. Can anyone tell me which is the function that can plot a stepwise graph for me? I did google over the plot for step fun but did not understand much of it. A simpler help would be more useful to me, as I am not a expert either in Statistics or R. Regards, Atul. -- Atul S. Kulkarni Graduate Student, Department of Computer Science, University Of Minnesota, Duluth, MN 55812. www.d.umn.edu/~kulka053 http://www.d.umn.edu/%7Ekulka053 - Before you start some work, always ask yourself three questions - Why am I doing it, What the results might be and Will I be successful. Only when you think deeply and find satisfactory answers to these questions, go ahead. Chanakya quotes (Indian politician, strategist and writer, 350 BC-275 BC) [[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. Charles C. Berry(858) 534-2098 Dept of Family/Preventive Medicine E mailto:[EMAIL PROTECTED] UC San Diego http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego 92093-0901 -- Atul S. Kulkarni Graduate Student, Department of Computer Science, University Of Minnesota, Duluth, MN 55812. www.d.umn.edu/~kulka053 - Before you start some work, always ask yourself three questions - Why am I doing it, What the results might be and Will I be successful. Only when you think deeply and find satisfactory answers to these questions, go ahead. Chanakya quotes (Indian politician, strategist and writer, 350 BC-275 BC) [[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] Factor to numeric
On Thu, 24 Apr 2008, Jojje Andersson wrote: Hello! Thanks! I changed the , to . in both datafile and code but the problem remains identical. Then we will need a reproducible example, as requested in the message footer. BTW, your example is a perfect illustration of the problem. Unless spaces are significant (and they are not in general in R nor in most computer languages) 1,00, 0,54, 0,00 looks just like 1, 00, 0, 54, 0, 00 and R's parser takes it as such. Cheers! Jojje __ Date: Thu, 24 Apr 2008 09:16:38 +0100 From: [EMAIL PROTECTED] To: [EMAIL PROTECTED] CC: r-help@r-project.org Subject: Re: [R] Factor to numeric The decimal point in R is always '.', never ','. On Thu, 24 Apr 2008, Jojje Andersson wrote: Hello! I have a problem whith a data.frame. I want to make a subset where some of the variables have values within ceartain limits. The variables are proportions like 1,00, 0,54, 0,00 etc. I don't get it right as R take the variables for factors. ekobsub1 - subset(ekob, PAP0,25 PAP0,6 CAP0,1 CAP0,6 FAP0,1) Error in `[.data.frame`(x, r, vars, drop = drop) : object CAP not found In addition: Warning message: In Ops.factor(PAP, 0) : not meaningful for factors ekobn-as.numeric(as.character(ekob[[PAP]])) Warning message: NAs introduced by coercion Thanks! /Jojje _ [[elided Hotmail spam]] px?sc_cmp2=JS_INT_SEMSN_NLPCV [[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. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UK Fax: +44 1865 272595 __ Tokbilliga solresor gratis reseguider! MSN Resor -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595__ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Factor to numeric
Hi Jojje, Try this: ekob=data.frame(PAP=seq(0,4,by=0.5),CAP=seq(1,5,by=0.5),FAP=seq(4,8,by=0.5)) attach(ekob) # Option 1 ekob[PAP1.5 PAP0.5 CAP1 CAP3 FAP4,] # Option 2 subset(ekob,PAP1.5 PAP0.5 CAP1 CAP3 FAP4) HTH, Jorge On Thu, Apr 24, 2008 at 11:31 AM, Jojje Andersson [EMAIL PROTECTED] wrote: Hello! Thanks! I changed the , to . in both datafile and code but the problem remains identical. Cheers! Jojje Date: Thu, 24 Apr 2008 09:16:38 +0100 From: [EMAIL PROTECTED] To: [EMAIL PROTECTED] CC: r-help@r-project.org Subject: Re: [R] Factor to numeric The decimal point in R is always '.', never ','. On Thu, 24 Apr 2008, Jojje Andersson wrote:Hello! I have a problem whith a data.frame. I want to make a subset where some of the variables have values within ceartain limits. The variables are proportions like 1,00, 0,54, 0,00 etc. I don't get it right as R take the variables for factors. ekobsub1 - subset(ekob, PAP0,25 PAP0,6 CAP0,1 CAP0,6 FAP0,1) Error in `[.data.frame`(x, r, vars, drop = drop) : object CAP not found In addition: Warning message: In Ops.factor(PAP, 0) : not meaningful for factors ekobn-as.numeric(as.character(ekob[[PAP]])) Warning message: NAs introduced by coercionThanks! /Jojje _ [[elide! d Hotmail spam]] px?sc_cmp2=JS_INT_SEMSN_NLPCV [[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. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ http://www.stats.ox.ac.uk/%7Eripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UK Fax: +44 1865 272595 _ [[elided Hotmail spam]] [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Documentation General Comments
Hmm,
KeBe == Beck, Kenneth (STP) [EMAIL PROTECTED]
on Thu, 24 Apr 2008 10:12:19 -0500 writes:
KeBe OK I've spent a lot of time with the core
KeBe documentation, and I never found anything as simple as
KeBe their table 2.1, which elucidated the difference
KeBe between a vector, matrix and array first, then the
KeBe higher level structures, frame and list. Maybe I'm
KeBe not a good searcher, but believe me for every initial
KeBe posting I submit to this group, I have spent hours
KeBe trying to find the answer elsewhere. And, as you
KeBe state, maybe I am now deluded by that presentation,
KeBe maybe it is not this simple!
Well, I get the impression that you've never read the manual
Introduction to R
(or some good book such as Peter Dalgaard's)
but have directly jumped into reading help() pages ???
Maybe a good idea would be to improve the Introduction to R
rather than thinking of misusing the help() collection
{which is the reference manual, not the user manual !!}
by making it easy to understand (and consequently less precise) ??
Patches (well reflected ..) to the Introduction are quite
welcome, indeed.
The (development) source is always available
at https://svn.r-project.org/R/trunk/doc/manual/R-intro.texi
(and yes, the source does look a bit less user-friendly,
than its PDF output, e.g.
http://cran.r-project.org/doc/manuals/R-intro.pdf
or its daily updated HTML output at
http://stat.ethz.ch/R-manual/R-devel/doc/manual/R-intro.html
)
Regards,
Martin
KeBe Look at the help for data.frame. VERY terse
KeBe explanation, with not a good comparison to the other
KeBe data types. Then, look at the titles list. Where is a
KeBe topic for data types Every other programming
KeBe language I have used (C++, Pascal, SAS, Java) has a
KeBe basic chapter in the documentation that goes over data
KeBe types, what arrays are, higher level structures, etc.
KeBe When I typed help.search(data type) I get the
KeBe following:
KeBe Help files with alias or concept or title matching
KeBe 'data type' using fuzzy matching:
KeBe character-class(methods) Classes Corresponding to
KeBe Basic Data Types sqlTypeInfo(RODBC) Request
KeBe Information about DataTypes in an ODBC Database
KeBe Looking for the term character-class(methods) yields
KeBe nothing. I don't think that is what I want!
KeBe Given all this complaining, I actually have completed
KeBe several nice project using R, it is an impressive
KeBe package. Somehow, though, we need to make the
KeBe documentation better.
KeBe -Original Message- From: Duncan Murdoch
KeBe [mailto:[EMAIL PROTECTED] Sent: Thursday, April
KeBe 24, 2008 9:51 AM To: Beck, Kenneth (STP) Cc: Bert
KeBe Gunter; r-help@r-project.org Subject: Re: [R]
KeBe Documentation General Comments
KeBe On 4/24/2008 10:22 AM, Beck, Kenneth (STP) wrote:
Agree that terseness is good, but I also agree with other
posters that
better cross referencing or maybe an index of synonyms
would be good.
So far, the best suggestion is the pdf at this link
(http://www.medepi.net/epir/epir_chap02.pdf).
Is there a way to pop at least part of this into the
R-base help page?
KeBe That's an easy question to answer: no. There is no
KeBe way to just pop it in. Incorporating it would take a
KeBe lot of thought and work.
Are there legal or copyright issues?
KeBe That's also easy: yes, there are. The authors of that
KeBe chapter presumably have copyright in it (unless
KeBe they've transferred it to someone else). Without
KeBe their permission it would be illegal to pop it into R.
KeBe If I had known this from the start,
it would have been much better. A good analogy is that
old cartoon of the blind guys trying to figure out what
an elephant is. The guys feeling at the front get a much
different impression than the guys poking at the back
side. I felt like that using R data structures, had to
blindly poke around trying different things, 90% of which
did not work, yeilding only error messages, but now
knowing the underlying
organisation it is going much more smoothly. Ideally this
kind of basic info would be in the core R docuemtation,
you should not have to
search this hard to get it!
KeBe All of the (correct) information in that chapter is in
KeBe the core documentation. They make a number of
KeBe simplifications, which I think are appropriate for
KeBe their audience, but you shouldn't believe everything
KeBe you read there. The core documentation has to aim for
KeBe a different target, because it needs to be correct.
KeBe Duncan Murdoch
-Original Message- From:
[EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Bert
Gunter
Re: [R] Factor to numeric
If you have a variable that is supposed to be numeric, but R thinks it is a factor, then you may (probably) have something in your input that is not a number. You changed the commas to decimal points at Prof. Ripley's suggestion. You still have the same error message. Therefore, you probably still have something in your input that is not a number. try: unique(ekob$PAP) and see what you get Assuming you created this dataframe using read.table() (or read.delim(), etc.), I'd suggest you read the documentation for that function very carefully, and inspect your input data for non-numeric strings where there should be a numeric string. It would be helpful if you show what you tried, and the error message, from *after* you changed to decimal points. -Don At 5:31 PM +0200 4/24/08, Jojje Andersson wrote: Hello! Thanks! I changed the , to . in both datafile and code but the problem remains identical. Cheers! Jojje Date: Thu, 24 Apr 2008 09:16:38 +0100 From: [EMAIL PROTECTED] To: [EMAIL PROTECTED] CC: r-help@r-project.org Subject: Re: [R] Factor to numeric The decimal point in R is always '.', never ','. On Thu, 24 Apr 2008, Jojje Andersson wrote:Hello! I have a problem whith a data.frame. I want to make a subset where some of the variables have values within ceartain limits. The variables are proportions like 1,00, 0,54, 0,00 etc. I don't get it right as R take the variables for factors.ekobsub1 - subset(ekob, PAP0,25 PAP0,6 CAP0,1 CAP0,6 FAP0,1) Error in `[.data.frame`(x, r, vars, drop = drop) : object CAP not found In addition: Warning message: In Ops.factor(PAP, 0) : not meaningful for factors ekobn-as.numeric(as.character(ekob[[PAP]])) Warning message: NAs introduced by coercionThanks! /Jojje _ [[elide! d Hotmail spam]] px?sc_cmp2=JS_INT_SEMSN_NLPCV [[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. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UK Fax: +44 1865 272595 _ [[elided Hotmail spam]] [[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. -- -- Don MacQueen Environmental Protection Department Lawrence Livermore National Laboratory Livermore, CA, USA 925-423-1062 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Documentation General Comments
On 4/24/2008 12:08 PM, Martin Maechler wrote:
Hmm,
KeBe == Beck, Kenneth (STP) [EMAIL PROTECTED]
on Thu, 24 Apr 2008 10:12:19 -0500 writes:
KeBe OK I've spent a lot of time with the core
KeBe documentation, and I never found anything as simple as
KeBe their table 2.1, which elucidated the difference
KeBe between a vector, matrix and array first, then the
KeBe higher level structures, frame and list. Maybe I'm
KeBe not a good searcher, but believe me for every initial
KeBe posting I submit to this group, I have spent hours
KeBe trying to find the answer elsewhere. And, as you
KeBe state, maybe I am now deluded by that presentation,
KeBe maybe it is not this simple!
Well, I get the impression that you've never read the manual
Introduction to R
(or some good book such as Peter Dalgaard's)
but have directly jumped into reading help() pages ???
That's not correct. Kenneth started the thread (on Monday) saying:
The basic tutorial Introduction to R is so basic, it
hardly helps at all, then digging through documentation is really an
exercise in frustration.
Duncan Murdoch
Maybe a good idea would be to improve the Introduction to R
rather than thinking of misusing the help() collection
{which is the reference manual, not the user manual !!}
by making it easy to understand (and consequently less precise) ??
Patches (well reflected ..) to the Introduction are quite
welcome, indeed.
The (development) source is always available
at https://svn.r-project.org/R/trunk/doc/manual/R-intro.texi
(and yes, the source does look a bit less user-friendly,
than its PDF output, e.g.
http://cran.r-project.org/doc/manuals/R-intro.pdf
or its daily updated HTML output at
http://stat.ethz.ch/R-manual/R-devel/doc/manual/R-intro.html
)
Regards,
Martin
KeBe Look at the help for data.frame. VERY terse
KeBe explanation, with not a good comparison to the other
KeBe data types. Then, look at the titles list. Where is a
KeBe topic for data types Every other programming
KeBe language I have used (C++, Pascal, SAS, Java) has a
KeBe basic chapter in the documentation that goes over data
KeBe types, what arrays are, higher level structures, etc.
KeBe When I typed help.search(data type) I get the
KeBe following:
KeBe Help files with alias or concept or title matching
KeBe 'data type' using fuzzy matching:
KeBe character-class(methods) Classes Corresponding to
KeBe Basic Data Types sqlTypeInfo(RODBC) Request
KeBe Information about DataTypes in an ODBC Database
KeBe Looking for the term character-class(methods) yields
KeBe nothing. I don't think that is what I want!
KeBe Given all this complaining, I actually have completed
KeBe several nice project using R, it is an impressive
KeBe package. Somehow, though, we need to make the
KeBe documentation better.
KeBe -Original Message- From: Duncan Murdoch
KeBe [mailto:[EMAIL PROTECTED] Sent: Thursday, April
KeBe 24, 2008 9:51 AM To: Beck, Kenneth (STP) Cc: Bert
KeBe Gunter; r-help@r-project.org Subject: Re: [R]
KeBe Documentation General Comments
KeBe On 4/24/2008 10:22 AM, Beck, Kenneth (STP) wrote:
Agree that terseness is good, but I also agree with other
posters that
better cross referencing or maybe an index of synonyms
would be good.
So far, the best suggestion is the pdf at this link
(http://www.medepi.net/epir/epir_chap02.pdf).
Is there a way to pop at least part of this into the
R-base help page?
KeBe That's an easy question to answer: no. There is no
KeBe way to just pop it in. Incorporating it would take a
KeBe lot of thought and work.
Are there legal or copyright issues?
KeBe That's also easy: yes, there are. The authors of that
KeBe chapter presumably have copyright in it (unless
KeBe they've transferred it to someone else). Without
KeBe their permission it would be illegal to pop it into R.
KeBe If I had known this from the start,
it would have been much better. A good analogy is that
old cartoon of the blind guys trying to figure out what
an elephant is. The guys feeling at the front get a much
different impression than the guys poking at the back
side. I felt like that using R data structures, had to
blindly poke around trying different things, 90% of which
did not work, yeilding only error messages, but now
knowing the underlying
organisation it is going much more smoothly. Ideally this
kind of basic info would be in the core R docuemtation,
you should not have to
search this hard to get it!
KeBe All of the (correct) information in that chapter is in
KeBe the core documentation. They make a number of
KeBe
Re: [R] Minimise a parameter of a given function f, with f 0
The function is f(s,t) = ( a1*t + a2*t^2 + ( a3*t + a4*t^2 )*d1*s^2*t^2 + (a5*t + a6*t^2)*d1^2*b^4*t^4 )*exp(-0.5*d1*s^2*t^2) + a8 where a1,a2,...,a8,d1 are some constants (can be positive or negative), which are computed from a given set of data. The objective is to find the minimum value of s 0.5, which satisfies f(s,t) 0 where t can be any value on the real line. It may be that such s does not exist for the given dataset If the conditions f(s,t)0 and s0.5 were not needed, then optim could be used to find the minimum values for both (s,t) with the range setting at -Inf and Inf. I suppose one way to do it (I haven't tried out) is to substitute the values of (s,t) found and see if they satisfy f(s,t)0, but it may be that s found is 0.5, and there is another one just 0.5 There are also other potential problems and computational disadvantages. 2008/4/24 Paul Smith [EMAIL PROTECTED]: On Wed, Apr 23, 2008 at 8:51 PM, Kevin Lu [EMAIL PROTECTED] wrote: I need to find the minimum value of the parameter, s, such that the function f(s,t) 0 (where -Inf t Inf) I've looked into optim, constrOptim and others but they don't seem to do this. Des anyone have some suggestions? In order to allow us to help you, please send us a minimal example. Paul __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] truncate row names
Hi, I would like to truncate row names. Is that possible? I ran a regression with the covariates in a matrix, and in the results the coefficients have the matrix name concatenated with the variable name: full.t.ag - Icens(lfirst_well, llast_well, lfirst_ill, formula=~ t.ag.X, breaks=t.ag.int, data=t.ag) full.t.ag$cov$coeff t.ag.Xnyearct.ag.Xhorset.ag.Xswine t.ag.Xpett.ag.Xother t.ag.Xpoultry t.ag.Xyr.horse -0.29497437 0.77857817-0.53315929-1.02745065 -0.17775268-0.08237047-0.36606818 I want these coefficients to have the t.ag.X removed from the names. ie. nyearchorse swine petother poultry yr.horse -0.29497437 0.77857817-0.53315929-1.02745065 -0.17775268-0.08237047-0.36606818 I have a lot of results, so going through and renaming every row is not a very appealing option. Is there another way? Is there a way to cut off the first 5 character positions in the row name? Or to force R to take the column names rather than concatenate the matrix and column names in the regression? Any help would be greatly appreciated. Thanks, Summer [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] truncate row names
Try: cof - full.t.ag$cov$coeff gsub(t.ag.X, , names(cof)) On Thu, Apr 24, 2008 at 1:47 PM, Summer Nitely [EMAIL PROTECTED] wrote: Hi, I would like to truncate row names. Is that possible? I ran a regression with the covariates in a matrix, and in the results the coefficients have the matrix name concatenated with the variable name: full.t.ag - Icens(lfirst_well, llast_well, lfirst_ill, formula=~ t.ag.X, breaks=t.ag.int, data=t.ag) full.t.ag$cov$coeff t.ag.Xnyearct.ag.Xhorset.ag.Xswine t.ag.Xpett.ag.Xother t.ag.Xpoultry t.ag.Xyr.horse -0.29497437 0.77857817-0.53315929-1.02745065 -0.17775268-0.08237047-0.36606818 I want these coefficients to have the t.ag.X removed from the names. ie. nyearchorse swine petother poultry yr.horse -0.29497437 0.77857817-0.53315929-1.02745065 -0.17775268-0.08237047-0.36606818 I have a lot of results, so going through and renaming every row is not a very appealing option. Is there another way? Is there a way to cut off the first 5 character positions in the row name? Or to force R to take the column names rather than concatenate the matrix and column names in the regression? Any help would be greatly appreciated. Thanks, Summer [[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. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O [[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 Newbie Question/Data Model
Given a data set and a set of predictors and a response in the data, we would like to find a model that fits the data set best. Suppose that we do not know what kind of model (linear, polynomial regression,... ) might be good, we are wondering if there is R-package(s) can auctomatically do this. Otherwise, can you direct me, or point out reference(s), basic steps to do this. Thanks. -james __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] alternatives to RColorBrewer?
I've found RColorBrewer useful for its qualitative palettes, but wished that it could generate more than 12 qualitative palettes (e.g. with Set3). Any suggestions for alternative color palette generators that can handle e.g. 18 distinctive colors? (I'm aware of using rainbow(), but this doesn't generate enough distinct colors when the number of palettes is large). Thanks, Andrew [[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] alternatives to RColorBrewer?
Andrew Yee andrewjyee at gmail.com writes: I've found RColorBrewer useful for its qualitative palettes, but wished that it could generate more than 12 qualitative palettes (e.g. with Set3). Any suggestions for alternative color palette generators that can handle e.g. 18 distinctive colors? (I'm aware of using rainbow(), but this doesn't generate enough distinct colors when the number of palettes is large). Assume you want 40 colors, get a basic color palette from RcolorBrewer, and use colorRampPalette to interpolate # Brewer palette Paired 12 pal12 = c(#A6CEE3, #1F78B4, #B2DF8A, #33A02C, #FB9A99, #E31A1C, #FDBF6F, #FF7F00, #CAB2D6, #6A3D9A, #99, #B15928) colorRampPalette(pal12)(40) Dieter __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] alternatives to RColorBrewer?
On Thu, 24 Apr 2008, Andrew Yee wrote: I've found RColorBrewer useful for its qualitative palettes, but wished that it could generate more than 12 qualitative palettes (e.g. with Set3). Any suggestions for alternative color palette generators that can handle e.g. 18 distinctive colors? (I'm aware of using rainbow(), but this doesn't generate enough distinct colors when the number of palettes is large). Package vcd implements several palette generators in HCL space which are somewhat similar to the palettes in ColorBrewer but provide some more flexibility. The underlying ideas are explained here http://epub.wu-wien.ac.at/dyn/openURL?id=oai:epub.wu-wien.ac.at:epub-wu-01_c87 See also help(rainbow_hcl, package = vcd) which has a few more examples. However, I guess that it will be hard to select a qualitative palette with 18 distinct colors...I couldn't imagine a plot where it would be sufficiently easy for humans to decode that. But maybe you can combine that with some sequential or diverging palette or so? Best, Z Thanks, Andrew [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] re shaping long-form longitudinal data from sql query
hi, I'm a total noob who is having to ramp up to full speed very quickly due to an unfortunate abrupt staffing change at my job :) I have longitudinal data that looks like this: PID OBSDATEDaysAgo CleanValue NAME 1 1410164934000610 8/17/2004 13:03:3813456.2HGBA1C 2 1410164934000610 11/16/2004 10:39:5112547.1HGBA1C ...etc I'd like to end up with a wide-format table like: PID OBSDATE.1DaysAgo.1CleanValue.1 [...] OBSDATE.n DaysAgo.n CleanValue.n The problem: Every patient's on a different schedule, so there's no natural timevar value to reshape with. My solution involved creating another column for the timevar and looping through the dataframe to populate that column with correct values; however, it's a pretty big table and so the loop runs really slowly. I need to do this particular operation on quite a few datafiles on a regular basis, and my database keeps getting bigger - so I anticipate this solution won't be ideal in the future. Can anyone recommend a more efficient solution? -- View this message in context: http://www.nabble.com/reshaping-%22long-form%22-longitudinal-data-from-sql-query-tp16851308p16851308.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] extracting averages from smooth.ppp output on spatstat
I have used smooth.ppp in spatstat to create a smoothed surface plot based on randomly selected depths across a lake (as marks). I wonder if based on the smoothed surface plot if I can calculate the average depth for each 10x10 grid square across the lake. I can't see any obvious way of doing this and would appreciate some pointers. Many thanks, Graham [[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 with image.smooth
Hi all, I was wondering if anyone in here is familiar with the command image.smooth. How can set the arguments dx, dy and theta so my resulting matrix is not smoothed out too much? Thank you. [[elided Yahoo spam]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] alternatives to RColorBrewer?
Great, thanks, that was helpful. Andrew On Thu, Apr 24, 2008 at 2:15 PM, Achim Zeileis [EMAIL PROTECTED] wrote: On Thu, 24 Apr 2008, Andrew Yee wrote: I've found RColorBrewer useful for its qualitative palettes, but wished that it could generate more than 12 qualitative palettes (e.g. with Set3). Any suggestions for alternative color palette generators that can handle e.g. 18 distinctive colors? (I'm aware of using rainbow(), but this doesn't generate enough distinct colors when the number of palettes is large). Package vcd implements several palette generators in HCL space which are somewhat similar to the palettes in ColorBrewer but provide some more flexibility. The underlying ideas are explained here http://epub.wu-wien.ac.at/dyn/openURL?id=oai:epub.wu-wien.ac.at:epub-wu-01_c87 See also help(rainbow_hcl, package = vcd) which has a few more examples. However, I guess that it will be hard to select a qualitative palette with 18 distinct colors...I couldn't imagine a plot where it would be sufficiently easy for humans to decode that. But maybe you can combine that with some sequential or diverging palette or so? Best, Z Thanks, Andrew [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] alternatives to RColorBrewer?
Achim Zeileis Achim.Zeileis at wu-wien.ac.at writes: However, I guess that it will be hard to select a qualitative palette with 18 distinct colors...I couldn't imagine a plot where it would be sufficiently easy for humans to decode that. But maybe you can combine that with some sequential or diverging palette or so? I slightly disagree here. In many cases, in color-coded surface plots, you do not want to attribute the colors to, let's say, altitudes, but rather use the color transitions as contour lines without explicitly drawing contours. You could also use continuous colors, but it is amazing how this fails, while something like 25 colors looks good. Dieter __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] re shaping long-form longitudinal data from sql query
If DF is your data frame then create a time column like this: DF$time - ave(DF$DaysAgo, DF$PID, FUN = seq_along) and now use the reshape command on DF (or melt/cast from the reshape package). On Thu, Apr 24, 2008 at 2:13 PM, Tubin [EMAIL PROTECTED] wrote: hi, I'm a total noob who is having to ramp up to full speed very quickly due to an unfortunate abrupt staffing change at my job :) I have longitudinal data that looks like this: PID OBSDATEDaysAgo CleanValue NAME 1 1410164934000610 8/17/2004 13:03:3813456.2HGBA1C 2 1410164934000610 11/16/2004 10:39:5112547.1HGBA1C ...etc I'd like to end up with a wide-format table like: PID OBSDATE.1DaysAgo.1CleanValue.1 [...] OBSDATE.n DaysAgo.n CleanValue.n The problem: Every patient's on a different schedule, so there's no natural timevar value to reshape with. My solution involved creating another column for the timevar and looping through the dataframe to populate that column with correct values; however, it's a pretty big table and so the loop runs really slowly. I need to do this particular operation on quite a few datafiles on a regular basis, and my database keeps getting bigger - so I anticipate this solution won't be ideal in the future. Can anyone recommend a more efficient solution? -- View this message in context: http://www.nabble.com/reshaping-%22long-form%22-longitudinal-data-from-sql-query-tp16851308p16851308.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] a simple question of importing data
i just want to read data from Excel and i copied it and pasted into a txt file. then i want to use read.table to read it. but however i tried, it doesn't work. can someone help me? data is attached. thanks http://www.nabble.com/file/p16851853/weekly.txt weekly.txt -- View this message in context: http://www.nabble.com/a-simple-question-of-importing-data-tp16851853p16851853.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] R Newbie Question/Data Model
First off there are multiple definitions of best, you need to decide which best is best for you. Second, for reasonable definitions of best, deciding between, linear, polynomial, and ... Requires backgroud knowledge and real thought. R can fit many different models and give you numerical and graphical summaries of those models, but determining the best model requires at least 1 person, some actual knowledge, and some real thought. Basic steps: Take a bunch more statistics classes and/or hire a statistician. If you can come back with a bit more of an example of what you are trying to accomplish along with background, what you mean by best, and show what your thought process has been so far, then we may be able to direct you better. You should also read through the posting guide that is linked to at the bottom of most posts to the group. -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare [EMAIL PROTECTED] (801) 408-8111 -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of [EMAIL PROTECTED] Sent: Thursday, April 24, 2008 10:58 AM To: r-help@r-project.org Subject: [R] R Newbie Question/Data Model Given a data set and a set of predictors and a response in the data, we would like to find a model that fits the data set best. Suppose that we do not know what kind of model (linear, polynomial regression,... ) might be good, we are wondering if there is R-package(s) can auctomatically do this. Otherwise, can you direct me, or point out reference(s), basic steps to do this. Thanks. -james __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] a simple question of importing data
try: var - read.table(weekly.txt, sep=\t, header=TRUE) Charles On Thu, Apr 24, 2008 at 3:29 PM, tzsmile [EMAIL PROTECTED] wrote: i just want to read data from Excel and i copied it and pasted into a txt file. then i want to use read.table to read it. but however i tried, it doesn't work. can someone help me? data is attached. thanks http://www.nabble.com/file/p16851853/weekly.txt weekly.txt -- View this message in context: http://www.nabble.com/a-simple-question-of-importing-data-tp16851853p16851853.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] a simple question of importing data
-Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of tzsmile Sent: Thursday, April 24, 2008 12:30 PM To: r-help@r-project.org Subject: [R] a simple question of importing data i just want to read data from Excel and i copied it and pasted into a txt file. then i want to use read.table to read it. but however i tried, it doesn't work. can someone help me? data is attached. thanks http://www.nabble.com/file/p16851853/weekly.txt weekly.txt -- View this message in context: http://www.nabble.com/a-simple-question-of-importing-data-tp16 851853p16851853.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. Have you looked at the foreign package? It should help do what you want. Or you could use Excel to output a .csv and read that with read.table(). Hope this is helpful, Dan __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] a simple question of importing data
Try also, setwd(C:\\) yourdata=read.table(tzmile.txt,header=TRUE) attach(yourdata) yourdata[1:10,] warcode date weeklyrt 130001 16-Dec-05 -0.0043 230001 23-Dec-05 0.1313 330001 30-Dec-05 -0.0844 430001 6-Jan-06 0.0097 530001 13-Jan-06 -0.1009 630001 20-Jan-06 -0.0450 730001 25-Jan-06 -0.1700 830001 10-Feb-06 0.3060 930001 17-Feb-06 -0.0721 10 30001 24-Feb-06 0.2260 HTH, Jorge On Thu, Apr 24, 2008 at 3:53 PM, Charles Danko [EMAIL PROTECTED] wrote: try: var - read.table(weekly.txt, sep=\t, header=TRUE) Charles On Thu, Apr 24, 2008 at 3:29 PM, tzsmile [EMAIL PROTECTED] wrote: i just want to read data from Excel and i copied it and pasted into a txt file. then i want to use read.table to read it. but however i tried, it doesn't work. can someone help me? data is attached. thanks http://www.nabble.com/file/p16851853/weekly.txt weekly.txt -- View this message in context: http://www.nabble.com/a-simple-question-of-importing-data-tp16851853p16851853.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. [[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] a simple question of importing data
Or you could use the read.xls program in the gdata library that uses a perl script underneath. Charles Danko wrote: try: var - read.table(weekly.txt, sep=\t, header=TRUE) Charles On Thu, Apr 24, 2008 at 3:29 PM, tzsmile [EMAIL PROTECTED] wrote: i just want to read data from Excel and i copied it and pasted into a txt file. then i want to use read.table to read it. but however i tried, it doesn't work. can someone help me? data is attached. thanks http://www.nabble.com/file/p16851853/weekly.txt weekly.txt -- View this message in context: http://www.nabble.com/a-simple-question-of-importing-data-tp16851853p16851853.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. [[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] Obtaining correlation parameters for multiple rows
Hi, I would like to obtain correlation parameters (e.g., coefficients, p-value) for multiple samples in regard to a reference. I have my data in a table with the reference as the second row (first row are headers) and then each sample in a row. What I do so far is load up the data, get the reference sample and use apply and lm to do the regression: x - read.table(file.txt,header=TRUE) x - t(x) ref - x[,1] test - apply(x,2,function(z)lm(z~ref)) My problem is that while I can see the results in test and even obtain the F-statistic with summary for individual rows (i.e., summary(test[[1]]), I can't seem to be able to apply the summary to all rows or get only the coefficients from test so I can save them to a new file. Ideally, I would like to save a new table to a file withthe correlation coefficients and the F-statistic for each of my samples. Any suggestions would be extremely useful. Thanks. -- View this message in context: http://www.nabble.com/Obtaining-correlation-parameters-for-multiple-rows-tp16851980p16851980.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] alternatives to RColorBrewer?
On Thu, 24 Apr 2008, Dieter Menne wrote: Achim Zeileis Achim.Zeileis at wu-wien.ac.at writes: However, I guess that it will be hard to select a qualitative palette with 18 distinct colors...I couldn't imagine a plot where it would be sufficiently easy for humans to decode that. But maybe you can combine that with some sequential or diverging palette or so? I slightly disagree here. In many cases, in color-coded surface plots, you do not want to attribute the colors to, let's say, altitudes, but rather use the color transitions as contour lines without explicitly drawing contours. You could also use continuous colors, but it is amazing how this fails, while something like 25 colors looks good. I think it depends a lot on what you want to bring out in such a graphic. Qualitative palettes will convey the impression of different groups in the data so that distinction of various levels is easier but the impression of an underlying smooth curve is often lost. However, if you use a sequential palette, the smoothness is conveyed much better and it is easy to identify the peaks but much harder to compare other levels of your curve. (Re: my original comment. What I meant was that it would be challenging to decode some truly categorical data, i.e., without an underlying continuous scale, with 18 levels from a qualitative palette with 18 different colors.) Best, Z Dieter __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] system() function
Hi,
I am trying to run the command: R CMD INSTALL -l mypath mypackagename
from within R (Windows XP) using system() and get the following error:
ARGUMENT 'CMD INSTALL -l D:/R/JMB.LIBS jmb.test' __ignored__
Fatal error: you must specify '--save', '--no-save' or '--vanilla'
My function contains these 3 lines:
setwd(D:/R/R.pkgs) # path to files set using package.skeleton()
commands - shQuote(CMD INSTALL -l D:/R/JMB.LIBS jmb.test)
system(paste('R',commands))
Can anyone tell me where I have gone astray? I suspect the problem lies in
quoting the strings. The command (R CMD INSTALL etc.) runs OK if I run it in
a windows shell.
Thank you.
Jeff Breiwick
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and provide commented, minimal, self-contained, reproducible code.
[R] How to test for NULL?
x == NULL returns logical(0) instead of FALSE or TRUE as you might expect and I cannot find the right way to write this test in R. Thanks in advance for any hint, -- O.L. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 test for NULL?
is.null Olivier Lefevre wrote: x == NULL returns logical(0) instead of FALSE or TRUE as you might expect and I cannot find the right way to write this test in R. Thanks in advance for any hint, -- O.L. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Using image function to plot character values
Hello. I am a newbie to R. If I should be reading some FAQ or manual that could help answer my question please tell me and I will go there. Problem: I have a spreadsheet that contains a character code in each cell. The columns in the spreadsheet represent time and the rows represent people. I want to use the image function to display this information, but the image function requires numeric data. I know how to read in the spreadsheet into a data frame, but if I use data.matrix to convert data frame into a numeric matrix, each column gets converted separately, so that the same character code may get converted to a different numeric code depending on the column. How do I apply the character to numeric conversion so that each character gets converted to the same numeric value? A secondary problem is that after I do the conversion, I need to know what codes were converted to what numeric values. Example: In the example below, B gets converted to 2 in the first column, but gets converted to 1 in the second column. dv - read.csv( SourceFileName, header=TRUE) dv m1 m2 1 A B 2 B C 3 C D data.matrix(dv) m1 m2 [1,] 1 1 [2,] 2 2 [3,] 3 3 Thanks in advance, --eric __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] matrix from list
Another possibly simple thing that I cannot get right is how to extract the data part of a list as a matrix. The data were read from xls, with labels, and thus are of list mode, e.g., col1 col2 1 0.1 1.1 2 0.2 1.2 I want to extract from that just the numeric data part, i.e., (in this case) the same thing that matrix(c(0.1, 0.2, 1.1, 1.2), 2, 2) would return. I am grasping for a syntax like list[[1:2]] but that doesn't work and I can't find anything that does. Thanks, -- O.L. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] matrix from list
Hi Olivier, is this what you want? x=col1 col2 1 0.1 1.1 2 0.2 1.2 m=read.table(textConnection(x),header=TRUE) m1=matrix(unlist(m),ncol=2) m1 [,1] [,2] [1,] 0.1 1.1 [2,] 0.2 1.2 HTH, Jorge On Thu, Apr 24, 2008 at 6:02 PM, Olivier Lefevre [EMAIL PROTECTED] wrote: Another possibly simple thing that I cannot get right is how to extract the data part of a list as a matrix. The data were read from xls, with labels, and thus are of list mode, e.g., col1 col2 1 0.1 1.1 2 0.2 1.2 I want to extract from that just the numeric data part, i.e., (in this case) the same thing that matrix(c(0.1, 0.2, 1.1, 1.2), 2, 2) would return. I am grasping for a syntax like list[[1:2]] but that doesn't work and I can't find anything that does. Thanks, -- O.L. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to test for NULL?
chenxh007 wrote: is.null Thanks! That one is mentioned in the LRM under §2.1.6 (NULL), so I should have found it... -- O.L. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 test for NULL?
Dear Olivier, You can use is.null(). apropos(null) finds is.null(), and help.search(null) turns up ?NULL, which documents is.null(). I hope this helps, John -- John Fox, Professor Department of Sociology McMaster University Hamilton, Ontario, Canada web: socserv.mcmaster.ca/jfox -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] project.org] On Behalf Of Olivier Lefevre Sent: April-24-08 5:19 PM To: [EMAIL PROTECTED] Subject: [R] How to test for NULL? x == NULL returns logical(0) instead of FALSE or TRUE as you might expect and I cannot find the right way to write this test in R. Thanks in advance for any hint, -- O.L. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] matrix from list
Yes, unlist is the magic wand I was looking for. Thanks a million! Having said that, I find it rather arbitrary that you can write mat[1:4] but not list[[1:2]]; IMO there should be no need for a magic operator like unlist: list[[1:length(list)]] could do the job. -- O.L. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] why R doesn't recognize my file?
i want to read a txt file weekly. this file is in d:/my documents i tried the following a-read.table(d:/my documents/weekly, sep= , header=TRUE) but get the following error: Error in open.connection(file, r) : unable to open connection In addition: Warning message: cannot open file 'd:/my documents/weekly', reason 'No such file or directory' in: open.connection(file, r) why? -- View this message in context: http://www.nabble.com/why-R-doesn%27t-recognize-my-file--tp16852537p16852537.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] why R doesn't recognize my file?
Hi there, You need the extension txt. Try this: a-read.table(d:/my documents/weekly.txt, sep= , header=TRUE) HTH, Jorge On Thu, Apr 24, 2008 at 4:43 PM, tzsmile [EMAIL PROTECTED] wrote: i want to read a txt file weekly. this file is in d:/my documents i tried the following a-read.table(d:/my documents/weekly, sep= , header=TRUE) but get the following error: Error in open.connection(file, r) : unable to open connection In addition: Warning message: cannot open file 'd:/my documents/weekly', reason 'No such file or directory' in: open.connection(file, r) why? -- View this message in context: http://www.nabble.com/why-R-doesn%27t-recognize-my-file--tp16852537p16852537.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] why R doesn't recognize my file?
tzsmile wrote: i want to read a txt file weekly. this file is in d:/my documents i tried the following a-read.table(d:/my documents/weekly, sep= , header=TRUE) but get the following error: Error in open.connection(file, r) : unable to open connection In addition: Warning message: cannot open file 'd:/my documents/weekly', reason 'No such file or directory' in: open.connection(file, r) why? Perhaps it has a filename extension, which Microsoft in their infinite wisdom is suppressing? The easiest way to open a file in windows is to use file.choose() in place of a specification of the filename. It will return a correct filename, which read.table can use, i.e. read.table(file.choose(), header=TRUE) or f - file.choose() read.table(f, header=TRUE) Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Sum of random values
Hello, I have two random variables with their percentiles which correspond to their probability distribution function. My objective is to sum these two random variables. There exists any algorithm or procedure in R capable of converting the percentiles to a probability density function? is the fast Fourier transform function of R(fft) capable of doing the sum with a convolution? I'm just starting with this specific problem, so any help it will be very useful. Best regards, Ricardo Bessa _ [[elided Hotmail spam]] [[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 on read in a txt file
Dear list, Hello! I had a problem of reading in a txt file and need your help. The txt file, called A, comprises of 592 columns and 34179 rows. I need to note that for some cells of A , A[i,j], are blank. I used read.table() and got the warning message: A-read.table(file=A.txt,sep=\t) Warning message: In scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : number of items read is not a multiple of the number of columns dim(A) [1] 33623 592 However, as some rows were missed because the original number of rows is 34179, after read.table(), it was decreased to 33623. I have no idea whether it has anything to do with the warning message. Do you have any suggestions for this problem? Thanks much, Alex [[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] means and variances of several groups in the matrix
Hy Katie, There are many ways to do this. A simple one is to create a vector of the same length than your 'x' vector, containing a group label. group=rep(c(1,2,3),times=nr[1,]) Then you can use tapply to apply a function (in this case mean and variance) of the values of x within each group. means=tapply(x,group,mean) vars=tapply(x,group,var) means 1 2 3 -0.14711206 0.28314274 -0.07861427 vars 1 2 3 1.4584971 0.3611996 0.6300624 Julian kathie wrote: Dear R users, I have 32 observations in data x. After sorting this, I want to compute means and variances of 3 groups divided by nr. Actually, the number of groups is flexible. Any suggestion will be greatly appreciated. Kathryn Lord --- x=rnorm(32) y=sort(x) nr=matrix(c(12,11,10,10,10,11),2,3) nr [,1] [,2] [,3] [1,] 12 10 10- sum=32 [2,] 11 10 11- sum=32 For the 1st row in nr, index of y = (1,..,12, 13,...,23, 24,...32) I want to compute means and variances for 3 groups (1st group is 1 through 12; 2nd group is 13-23; 3rd group is 24-32) For the 2nd row in nr, index of y = (1,..,11, 12,...,22, 23,...32) also, I want to compute means and variances for 3 groups (1st group is 1 through 11; 2nd group is 12-22; 3rd group is 23-32) __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 on read in a txt file
It seems to indicate that you don't have 592 columns on all lines. Try the following to see how many columns are in each line: x - count.fields(A.txt, sep=\t) which(x != 592) # print out the lines that are not correct You might also try: read.table(a.txt, sep=\t, fill=TRUE) On Thu, Apr 24, 2008 at 8:32 PM, ss [EMAIL PROTECTED] wrote: Dear list, Hello! I had a problem of reading in a txt file and need your help. The txt file, called A, comprises of 592 columns and 34179 rows. I need to note that for some cells of A , A[i,j], are blank. I used read.table() and got the warning message: A-read.table(file=A.txt,sep=\t) Warning message: In scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : number of items read is not a multiple of the number of columns dim(A) [1] 33623 592 However, as some rows were missed because the original number of rows is 34179, after read.table(), it was decreased to 33623. I have no idea whether it has anything to do with the warning message. Do you have any suggestions for this problem? Thanks much, Alex [[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. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem you are trying to solve? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 on read in a txt file
Thanks Jim. I got this: A-read.table(a.txt, sep=\t, fill=TRUE) dim(A) [1] 33623 592 x - count.fields(a.txt, sep=\t) which(x != 592) # print out the lines that are not correct which(x != 592) # print out the lines that are not correct [1] 31279 31281 33625 Actually, I just need from the txt file to grab 83 columns whose column names have the pattern '_A01/Ratio'. For instance, I am listing the column names of the first 23 columns and I only need the columns ends with '_A01/Ratio'. So is there a way to get around reading in all the data first? Thanks, Alex Database ebi.ac.uk:Database:ensembl Database ebi.ac.uk:Database:locus Database ebi.ac.uk:Database:refseq Database ebi.ac.uk:Database:tigr_thc Database www.chem.agilent.com:Database:agp Reporter group Reporter identifier Reporter name Reporter sequence type MBA: US14702370_16012391010920_S01_A01/Log(Ratio) MBA: US14702370_16012391010920_S01_A01/Ratio MBA: US14702370_16012391010920_S01_A01/Fold Change MBA: US14702370_16012391010920_S01_A01/Log(Error) MBA: US14702370_16012391010920_S01_A01/P-Value MBA: US14702370_16012391010920_S01_A01/Intensity 1 MBA: US14702370_16012391010920_S01_A01/Intensity 2 MBA: US14702370_16012391010525_S01_A01/Log(Ratio) MBA: US14702370_16012391010525_S01_A01/Ratio MBA: US14702370_16012391010525_S01_A01/Fold Change MBA: US14702370_16012391010525_S01_A01/Log(Error) MBA: US14702370_16012391010525_S01_A01/P-Value MBA: US14702370_16012391010525_S01_A01/Intensity 1 MBA: US14702370_16012391010525_S01_A01/Intensity 2 On Thu, Apr 24, 2008 at 9:27 PM, jim holtman [EMAIL PROTECTED] wrote: It seems to indicate that you don't have 592 columns on all lines. Try the following to see how many columns are in each line: x - count.fields(A.txt, sep=\t) which(x != 592) # print out the lines that are not correct You might also try: read.table(a.txt, sep=\t, fill=TRUE) On Thu, Apr 24, 2008 at 8:32 PM, ss [EMAIL PROTECTED] wrote: Dear list, Hello! I had a problem of reading in a txt file and need your help. The txt file, called A, comprises of 592 columns and 34179 rows. I need to note that for some cells of A , A[i,j], are blank. I used read.table() and got the warning message: A-read.table(file=A.txt,sep=\t) Warning message: In scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : number of items read is not a multiple of the number of columns dim(A) [1] 33623 592 However, as some rows were missed because the original number of rows is 34179, after read.table(), it was decreased to 33623. I have no idea whether it has anything to do with the warning message. Do you have any suggestions for this problem? Thanks much, Alex [[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. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem you are trying to solve? [[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] Differentiate alphanumeric vs numeric strings
The following will return the indices or the values of character strings that are all numeric: x - c(12345, 123AS23, A123, 398457) grep(^[[:digit:]]*$, x) # index [1] 1 4 grep(^[[:digit:]]*$, x, value=TRUE) # values [1] 12345 398457 On Thu, Apr 24, 2008 at 10:39 PM, Farrel Buchinsky [EMAIL PROTECTED] wrote: I have a bunch of tables in a Microsoft Access database. An updated database is sent to me every week containing a new table. I know that is inefficient and weird but welcome to my life. I want to read the tables whose names are something such as 040207 but not the ones that have alphanumeric names such as everyone. Using RODBC I am easily able to create a character vector of the names of the tables. Is there a function that can differentiate values consisting only of digits (numerics) as opposed to ones that contain letters (and perhaps digts as well)? I am sure there is. What is it and where should I have found it? -- Farrel Buchinsky GrandCentral Tel: (412) 567-7870 [[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. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem you are trying to solve? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Differentiate alphanumeric vs numeric strings
This has the disadvantage of producing a warning when it finds non-numerics and also there are situations like 1E1 which it will regard as numeric so using a regexp is probably preferred but it is simple: !is.na(as.numeric(x)) On Thu, Apr 24, 2008 at 10:39 PM, Farrel Buchinsky [EMAIL PROTECTED] wrote: I have a bunch of tables in a Microsoft Access database. An updated database is sent to me every week containing a new table. I know that is inefficient and weird but welcome to my life. I want to read the tables whose names are something such as 040207 but not the ones that have alphanumeric names such as everyone. Using RODBC I am easily able to create a character vector of the names of the tables. Is there a function that can differentiate values consisting only of digits (numerics) as opposed to ones that contain letters (and perhaps digts as well)? I am sure there is. What is it and where should I have found it? -- Farrel Buchinsky GrandCentral Tel: (412) 567-7870 [[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] Documentation General Comments
I just read through this thread and I didn't see the R Language
Definition mentioned. As with An Introduction to R it can be accessed
-- at least in my Windows GUI -- via the menu bar: Help - Manuals (in
PDF). If An Introduction to R is too basic, then the Language
Definition should be a good place to look for more details on R
objects (Ch 2). However An Introduction to R does include
authoritative introductions to the data types mentioned by the
original poster: factors (Ch4), arrays and matrices (Ch 5), and lists
and data frames (Ch 6).
That said, I agree that learning efficiency could be improved by
augmenting the manuals with tables similar to the table 2.1 that was
referenced earlier in the thread (aside: are functions, or even lists,
really Data Objects?). Of course, as pointed out by Duncan, we are
collaborators not consumers, so if I think there should be more tables
in the documents then the onus is on me to try to get my ideas
incorporated (see
http://wiki.r-project.org/rwiki/doku.php?id=misc:rpatch ).
Kingsford Jones
On Thu, Apr 24, 2008 at 9:37 AM, Duncan Murdoch [EMAIL PROTECTED] wrote:
On 4/24/2008 12:08 PM, Martin Maechler wrote:
Hmm,
KeBe == Beck, Kenneth (STP) [EMAIL PROTECTED]
on Thu, 24 Apr 2008 10:12:19 -0500 writes:
KeBe OK I've spent a lot of time with the core
KeBe documentation, and I never found anything as simple as
KeBe their table 2.1, which elucidated the difference
KeBe between a vector, matrix and array first, then the
KeBe higher level structures, frame and list. Maybe I'm
KeBe not a good searcher, but believe me for every initial
KeBe posting I submit to this group, I have spent hours
KeBe trying to find the answer elsewhere. And, as you
KeBe state, maybe I am now deluded by that presentation,
KeBe maybe it is not this simple!
Well, I get the impression that you've never read the manual
Introduction to R
(or some good book such as Peter Dalgaard's)
but have directly jumped into reading help() pages ???
That's not correct. Kenneth started the thread (on Monday) saying:
The basic tutorial Introduction to R is so basic, it
hardly helps at all, then digging through documentation is really an
exercise in frustration.
Duncan Murdoch
Maybe a good idea would be to improve the Introduction to R
rather than thinking of misusing the help() collection
{which is the reference manual, not the user manual !!}
by making it easy to understand (and consequently less precise) ??
Patches (well reflected ..) to the Introduction are quite
welcome, indeed.
The (development) source is always available
at https://svn.r-project.org/R/trunk/doc/manual/R-intro.texi
(and yes, the source does look a bit less user-friendly,
than its PDF output, e.g.
http://cran.r-project.org/doc/manuals/R-intro.pdf
or its daily updated HTML output at
http://stat.ethz.ch/R-manual/R-devel/doc/manual/R-intro.html
)
Regards,
Martin
KeBe Look at the help for data.frame. VERY terse
KeBe explanation, with not a good comparison to the other
KeBe data types. Then, look at the titles list. Where is a
KeBe topic for data types Every other programming
KeBe language I have used (C++, Pascal, SAS, Java) has a
KeBe basic chapter in the documentation that goes over data
KeBe types, what arrays are, higher level structures, etc.
KeBe When I typed help.search(data type) I get the
KeBe following:
KeBe Help files with alias or concept or title matching
KeBe 'data type' using fuzzy matching:
KeBe character-class(methods) Classes Corresponding to
KeBe Basic Data Types sqlTypeInfo(RODBC) Request
KeBe Information about DataTypes in an ODBC Database
KeBe Looking for the term character-class(methods) yields
KeBe nothing. I don't think that is what I want!
KeBe Given all this complaining, I actually have completed
KeBe several nice project using R, it is an impressive
KeBe package. Somehow, though, we need to make the
KeBe documentation better.
KeBe -Original Message- From: Duncan Murdoch
KeBe [mailto:[EMAIL PROTECTED] Sent: Thursday, April
KeBe 24, 2008 9:51 AM To: Beck, Kenneth (STP) Cc: Bert
KeBe Gunter; r-help@r-project.org Subject: Re: [R]
KeBe Documentation General Comments
KeBe On 4/24/2008 10:22 AM, Beck, Kenneth (STP) wrote:
Agree that terseness is good, but I also agree with other
posters that
better cross referencing or maybe an index of synonyms
would be good.
So far, the best suggestion is the pdf at this link
(http://www.medepi.net/epir/epir_chap02.pdf).
Is there a way to pop at least part of this into the
R-base help page?
[R] make check errors with R 2.7.0
I installed R-2.7.0 from the tar.gz file. It's the end of make check
that my question is about.
make[3]: Entering directory `/usr/local/R-2.7.0/tests'
make[3]: `reg-tests-1.Rout' is up to date.
make[3]: `reg-tests-2.Rout' is up to date.
running code in 'reg-IO.R' ... OK
comparing 'reg-IO.Rout' to './reg-IO.Rout.save' ...44c44
In readLines(testIO.R) : incomplete final line found on 'testIO.R'
---
In readLines(testIO.R) : incomplete final line found on 'testIO.R'
88c88
In readLines(testIO.R) : incomplete final line found on 'testIO.R'
---
In readLines(testIO.R) : incomplete final line found on 'testIO.R'
111c111
In readLines(testIO.R) : incomplete final line found on 'testIO.R'
---
In readLines(testIO.R) : incomplete final line found on 'testIO.R'
134c134
In readLines(testIO.R) : incomplete final line found on 'testIO.R'
---
In readLines(testIO.R) : incomplete final line found on 'testIO.R'
make[3]: *** [reg-IO.Rout] Error 1
make[3]: Leaving directory `/usr/local/R-2.7.0/tests'
make[2]: *** [test-Reg] Error 2
make[2]: Leaving directory `/usr/local/R-2.7.0/tests'
make[1]: *** [test-all-basics] Error 1
make[1]: Leaving directory `/usr/local/R-2.7.0/tests'
make: *** [check] Error 2
When I look at testIO.R, it seems indeed to be designed to have a
missing CR at the end. Is this simply testing to see if it is found,
or does the fact that it exits with Error 2 mean that it's not going
onto other tests? It did seem to be rather a lot shorter than I
remember other installations.
I did not have any difficulty in installing the lme4 package and its
dependencies which might indicate that the installation has been
successful.
Do I have any cause for concern?
--
~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.
___Patrick Connolly
{~._.~} Great minds discuss ideas
_( Y )_Middle minds discuss events
(:_~*~_:)Small minds discuss people
(_)-(_) . Anon
~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/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] Documentation General Comments
Dear Colleagues,
It seems to me that the issue is not whether the information we seek
is in the documentation. I, for one, am amazed at the quality of the
documentation of R and of contributed materials. For me the issue is
one of finding the information in an efficient way out of the
mountains of information in the official and unofficial documentation
of R. Part of this is on the head of the seeker of information to
generate keywords that will lead a search engine to find what we are
looking for. But part of it is on the heads of contributors to insure
that relevant keywords are associated with relevant content in a way
that the search engine will find it and rank order it in a sensible
way.
Take RSiteSearch(), for example. Are we as a user and contributor
group familiar with the scoring scheme that Namazu uses to score and
order the information it finds? I refer you to:
http://www.namazu.org/doc/tips.html for this information. For
example, if Namazu finds a keyword in a meta name =keywords
content=... tag the score is bumped by 32 points. Finding a
keyword in a title tag is worth 16 points, etc. Also on the
referenced url page we are essentially told not to use more than two
words in the search. It seems to me that knowing these things alone
will help authors increase the quality of searches and seekers to more
easily find what they are looking for.
My thanks to all the contributors who have made R a terrific system.
Regards,
Larry
On Thu, Apr 24, 2008 at 8:55 PM, Kingsford Jones
[EMAIL PROTECTED] wrote:
I just read through this thread and I didn't see the R Language
Definition mentioned. As with An Introduction to R it can be accessed
-- at least in my Windows GUI -- via the menu bar: Help - Manuals (in
PDF). If An Introduction to R is too basic, then the Language
Definition should be a good place to look for more details on R
objects (Ch 2). However An Introduction to R does include
authoritative introductions to the data types mentioned by the
original poster: factors (Ch4), arrays and matrices (Ch 5), and lists
and data frames (Ch 6).
That said, I agree that learning efficiency could be improved by
augmenting the manuals with tables similar to the table 2.1 that was
referenced earlier in the thread (aside: are functions, or even lists,
really Data Objects?). Of course, as pointed out by Duncan, we are
collaborators not consumers, so if I think there should be more tables
in the documents then the onus is on me to try to get my ideas
incorporated (see
http://wiki.r-project.org/rwiki/doku.php?id=misc:rpatch ).
Kingsford Jones
On Thu, Apr 24, 2008 at 9:37 AM, Duncan Murdoch [EMAIL PROTECTED] wrote:
On 4/24/2008 12:08 PM, Martin Maechler wrote:
Hmm,
KeBe == Beck, Kenneth (STP) [EMAIL PROTECTED]
on Thu, 24 Apr 2008 10:12:19 -0500 writes:
KeBe OK I've spent a lot of time with the core
KeBe documentation, and I never found anything as simple as
KeBe their table 2.1, which elucidated the difference
KeBe between a vector, matrix and array first, then the
KeBe higher level structures, frame and list. Maybe I'm
KeBe not a good searcher, but believe me for every initial
KeBe posting I submit to this group, I have spent hours
KeBe trying to find the answer elsewhere. And, as you
KeBe state, maybe I am now deluded by that presentation,
KeBe maybe it is not this simple!
Well, I get the impression that you've never read the manual
Introduction to R
(or some good book such as Peter Dalgaard's)
but have directly jumped into reading help() pages ???
That's not correct. Kenneth started the thread (on Monday) saying:
The basic tutorial Introduction to R is so basic, it
hardly helps at all, then digging through documentation is really an
exercise in frustration.
Duncan Murdoch
Maybe a good idea would be to improve the Introduction to R
rather than thinking of misusing the help() collection
{which is the reference manual, not the user manual !!}
by making it easy to understand (and consequently less precise) ??
Patches (well reflected ..) to the Introduction are quite
welcome, indeed.
The (development) source is always available
at https://svn.r-project.org/R/trunk/doc/manual/R-intro.texi
(and yes, the source does look a bit less user-friendly,
than its PDF output, e.g.
http://cran.r-project.org/doc/manuals/R-intro.pdf
or its daily updated HTML output at
http://stat.ethz.ch/R-manual/R-devel/doc/manual/R-intro.html
)
Regards,
Martin
KeBe Look at the help for data.frame. VERY terse
KeBe explanation, with not a good comparison to the other
KeBe data types. Then, look at the titles list. Where is a
KeBe topic for data
Re: [R] Obtaining correlation parameters for multiple rows
Hi,
I'm sure it could be better but try this:
# F statistics based on lm
FSTAT=function(y,x) summary(lm(y~x))$f[1]
# Correlation and p-value
CORR=function(y,x){
tc=cor.test(x,y,method=spearman,alternative=two.sided)
temp=matrix(c(tc$estimate,tc$p.value),ncol=2)
colnames(temp)=c('rho','pvalue')
temp
}
# 1000 variables and 100 samples
set.seed(124)
X=matrix(rnorm(1000*100),ncol=100)
# Correlation coefficient, p-value and F statistics
corr=t(apply(X[-1,],1,CORR,x=X[1,])) # Your reference is X[1,]
fs=apply(X[-1,],1,FSTAT,x=X[1,]) # Your reference is X[1,]
# Report
temp=data.frame(fstats=fs,rho=corr[,1],pvalue=corr[,2])
rownames(temp)=paste(X,2:nrow(X),sep=)
dim(temp)
[1] 999 3
temp[1:10,]
fstats rho pvalue
X2 1.421307790 -0.05038104 0.61807912
X3 0.051423768 -0.04614461 0.64795111
X4 0.128000634 0.01795380 0.85902211
X5 0.990235820 -0.06540654 0.51730942
X6 5.569006085 0.24232823 0.01532172
X7 0.001862766 -0.01436544 0.88703532
X8 1.025363077 -0.10628263 0.29206908
X9 0.679794149 0.06509451 0.51927479
X10 1.296034903 0.09492949 0.34686211
X11 0.126636867 0.05137714 0.61110106
HTH,
Jorge
On Thu, Apr 24, 2008 at 3:40 PM, jpnitya [EMAIL PROTECTED]
wrote:
Hi,
I would like to obtain correlation parameters (e.g., coefficients, p-value)
for multiple samples in regard to a reference. I have my data in a table
with the reference as the second row (first row are headers) and then each
sample in a row. What I do so far is load up the data, get the reference
sample and use apply and lm to do the regression:
x - read.table(file.txt,header=TRUE)
x - t(x)
ref - x[,1]
test - apply(x,2,function(z)lm(z~ref))
My problem is that while I can see the results in test and even obtain the
F-statistic with summary for individual rows (i.e., summary(test[[1]]), I
can't seem to be able to apply the summary to all rows or get only the
coefficients from test so I can save them to a new file. Ideally, I would
like to save a new table to a file withthe correlation coefficients and the
F-statistic for each of my samples.
Any suggestions would be extremely useful.
Thanks.
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[R] force glm estimates to be nonnegative
Is there a way to force certain formula parameters to be nonnegative? What I want to do is to estimate student capacity over time, namely by capacity ~ Student + Student:Day I add this formula to a glm call and obtain negative learning slope estimates (Student:Day) in some cases. However, I don't want to allow for that. In such a case, glm should solve capacity ~ Student and I will set the slope to zero. Is there an option to constrain a parameter set to nonnegative values? Many thanks in advance! Michele Itten, BS. Carnegie Mellon __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] system() function
You don't want shQuote - that makes it a single argument.
Shells strip quotes, but system() does not use a shell on Windows -- you
could use shell() not system(), but that would be overkill here.
On Thu, 24 Apr 2008, Jeff Breiwick wrote:
Hi,
I am trying to run the command: R CMD INSTALL -l mypath mypackagename
from within R (Windows XP) using system() and get the following error:
ARGUMENT 'CMD INSTALL -l D:/R/JMB.LIBS jmb.test' __ignored__
Fatal error: you must specify '--save', '--no-save' or '--vanilla'
My function contains these 3 lines:
setwd(D:/R/R.pkgs) # path to files set using package.skeleton()
commands - shQuote(CMD INSTALL -l D:/R/JMB.LIBS jmb.test)
system(paste('R',commands))
Can anyone tell me where I have gone astray? I suspect the problem lies in
quoting the strings. The command (R CMD INSTALL etc.) runs OK if I run it in
a windows shell.
Thank you.
Jeff Breiwick
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--
Brian D. Ripley, [EMAIL PROTECTED]
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595
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Re: [R] force glm estimates to be nonnegative
On Fri, 25 Apr 2008, Michele Christina Itten wrote: Is there a way to force certain formula parameters to be nonnegative? What I want to do is to estimate student capacity over time, namely by capacity ~ Student + Student:Day I add this formula to a glm call and obtain negative learning slope estimates (Student:Day) in some cases. However, I don't want to allow for that. In such a case, glm should solve capacity ~ Student and I will set the slope to zero. Is there an option to constrain a parameter set to nonnegative values? Not in glm(). Easily if you fit the model by optim(), and there is example code for binomial GLMs in MASS chapter 16 (and the scripts in its package). Many thanks in advance! Michele Itten, BS. Carnegie Mellon __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] make check errors with R 2.7.0
Note that the problem is not that you got the message, but an apparent
whitespace issue in the output. That's clearer in this version: note that
the output for reg-IO.Rout.save is shifted left one column. But I don't
trust email to transmit these things faithfully (especially after the last
two days of encoding issues).
So the problem is most likely either the way reg-IO.Rout.save got unpacked
or your 'diff' function.
You don't mention an OS, but my recollection is that you usually use
Linux. I *have* seen an error in this test on Cygwin, where the issue was
the unpacking by tar.
If this is Linux, it has been tested successfully many times by others,
and I don't recall any change to that test since 2.6.2 (and nor do the SVN
logs).
On Fri, 25 Apr 2008, Patrick Connolly wrote:
I installed R-2.7.0 from the tar.gz file. It's the end of make check
that my question is about.
make[3]: Entering directory `/usr/local/R-2.7.0/tests'
make[3]: `reg-tests-1.Rout' is up to date.
make[3]: `reg-tests-2.Rout' is up to date.
running code in 'reg-IO.R' ... OK
comparing 'reg-IO.Rout' to './reg-IO.Rout.save' ...44c44
In readLines(testIO.R) : incomplete final line found on 'testIO.R'
---
In readLines(testIO.R) : incomplete final line found on 'testIO.R'
88c88
In readLines(testIO.R) : incomplete final line found on 'testIO.R'
---
In readLines(testIO.R) : incomplete final line found on 'testIO.R'
111c111
In readLines(testIO.R) : incomplete final line found on 'testIO.R'
---
In readLines(testIO.R) : incomplete final line found on 'testIO.R'
134c134
In readLines(testIO.R) : incomplete final line found on 'testIO.R'
---
In readLines(testIO.R) : incomplete final line found on 'testIO.R'
make[3]: *** [reg-IO.Rout] Error 1
make[3]: Leaving directory `/usr/local/R-2.7.0/tests'
make[2]: *** [test-Reg] Error 2
make[2]: Leaving directory `/usr/local/R-2.7.0/tests'
make[1]: *** [test-all-basics] Error 1
make[1]: Leaving directory `/usr/local/R-2.7.0/tests'
make: *** [check] Error 2
When I look at testIO.R, it seems indeed to be designed to have a
missing CR at the end. Is this simply testing to see if it is found,
or does the fact that it exits with Error 2 mean that it's not going
onto other tests? It did seem to be rather a lot shorter than I
remember other installations.
That's a late test, but it did terminate with an error.
I did not have any difficulty in installing the lme4 package and its
dependencies which might indicate that the installation has been
successful.
Do I have any cause for concern?
Some, but with your toolset.
--
~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.
___Patrick Connolly
{~._.~}Great minds discuss ideas
_( Y )_ Middle minds discuss events
(:_~*~_:) Small minds discuss people
(_)-(_) . Anon
~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.
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and provide commented, minimal, self-contained, reproducible code.
--
Brian D. Ripley, [EMAIL PROTECTED]
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595
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