[R] Clash between alr3 and AlgDesign. (Was: Re: Second subsequent calls to function fails. Please help debug.)
Thanks, Duncan, I started a new session under the suspicion that packages were clashing. # # RUN 1 # require(faraway) # Loading required package: faraway data(oatvar) ov.lm - lm(yield ~ variety + block, oatvar) require(alr3) # Loading required package: alr3 out - tukey.nonadd.test(ov.lm) # # RUN 1 OK # RUN 2 # require(HH) #Loading required package: HH #Loading required package: lattice # #Attaching package: 'lattice' # # # The following object(s) are masked from package:faraway : # #melanoma # #Loading required package: grid #Loading required package: multcomp #Loading required package: mvtnorm # #Attaching package: 'HH' # # # The following object(s) are masked from package:alr3 : # #residual.plots # # # The following object(s) are masked from package:faraway : # #vif, #vif.default, #vif.lm # out - tukey.nonadd.test(ov.lm) # # RUN 2 OK # RUN 3 # require(crossdes) #Loading required package: crossdes #Loading required package: AlgDesign #Loading required package: gtools # #Attaching package: 'gtools' # # # The following object(s) are masked from package:faraway : # #logit # #Loading required package: MASS #Loading required package: grDevices out - tukey.nonadd.test(ov.lm) #Error in parse(text = x) : # unexpected symbol in yield ~ variety + block + preds(yield+variety +block+preds.sq)sq # # RUN 3 FAILS # # # CHECKING FOR INTERACTION AMONG PACKAGES # require(MASS) #Loading required package: MASS #Loading required package: grDevices out - tukey.nonadd.test(ov.lm) require(gtools) #Loading required package: gtools # #Attaching package: 'gtools' # # # The following object(s) are masked from package:faraway : # #logit # # out - tukey.nonadd.test(ov.lm) # # alr3 pays well with MASS, grDevices, gtools # require(AlgDesign) #Loading required package: AlgDesign out - tukey.nonadd.test(ov.lm) #Error in parse(text = x) : # unexpected symbol in yield ~ variety + block + preds(yield+variety +block+preds.sq)sq require(crossdes) #Loading required package: crossdes out - tukey.nonadd.test(ov.lm) #Error in parse(text = x) : # unexpected symbol in yield ~ variety + block + preds(yield+variety +block+preds.sq)sq # # BAD INTERACTION BETWEEN alr3 and AlgDesign # What now? _ Professor Michael Kubovy University of Virginia Department of Psychology USPS: P.O.Box 400400Charlottesville, VA 22904-4400 Parcels:Room 102Gilmer Hall McCormick RoadCharlottesville, VA 22903 Office:B011+1-434-982-4729 Lab:B019+1-434-982-4751 Fax:+1-434-982-4766 WWW:http://www.people.virginia.edu/~mk9y/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Journal for R
Hi the list I made up a new statistical procedure. I will publish it in a medical journal, but there will be only the way of using it, no calculation or algorithme detail. So is there a journal (I mean scientific journal) with selection commity to submit an article describing the detail of a package? Christophe __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Defining reference category for a cph model summary inside of a for loop
Wells, Brian wrote:
Dr. Harrell,
Thanks for you help.
I tried:
print(summary(f,parse(text=paste(i,'=1st Quartile', sep=''
Same result. No error, the reference category simply doesn't change.
That's good, because the default in summary is to compare the outer
quartiles for a continuous variable. And as I said before the string
'1st Quartile' has no special meaning for R or Design.
Get what you are trying to do to work without parse (and you'll need
eval() with parse) first. When you want total control over a setting,
say getting a hazard ratio for the .2 to the .8 quantile, do something like
summary(f, age=quantile(age,c(.2,.8),na.rm=TRUE))
Frank
Brian
-Original Message-
From: Frank E Harrell Jr [mailto:[EMAIL PROTECTED]
Sent: Friday, March 28, 2008 8:34 PM
To: Wells, Brian
Cc: r-help@r-project.org
Subject: Re: [R] Defining reference category for a cph model summary
inside of a for loop
Wells, Brian wrote:
I have the following code.
f - cph(formula = Surv(TimeToDeath, Dead == Yes)
~1,data=single.dat, x=T, y=T, surv=T)
for(i in c('A', 'B', 'C', 'D', 'E', 'F')){
f -update(f,as.formula(paste('Surv(TimeToDeath, Dead ==
Yes)~',i,sep='')))
print(summary(f, paste(i,=1st Quartile, sep='')))
There is no error message generated in R, but R ignores the reference
category defined with paste in the summary function for the cph model.
The output uses the 1st Quartile as the reference category to
calculate hazards for some of the variables defined by i, but not all
of
them.
Your code is confusing. What is to the right of ~ in a formula is a
predictor variable name, not a value. If your variables are named A, B,
C, ... you are OK.
'1st Quartile' has no special meaning to R or Design, and you can't pass
a character string as a second argument to summary and expect it to
work.
You will need parse(text=paste(...)) to create an appropriate
expression.
But Design gives you inter-quartile range hazard ratios by default
anyway.
Beware of getting hazard ratios that are not adjusted for other
variables needed in the model.
Frank Harrell
Any help would be greatly appreciated.
thanks
Brian J. Wells, MD, MS
Research Associate
Quantitative Health Sciences
Cleveland Clinic
--
Frank E Harrell Jr Professor and Chair School of Medicine
Department of Biostatistics Vanderbilt University
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Re: [R] Journal for R
On Sun, 2008-03-30 at 15:01 +0200, Christophe Genolini wrote: Hi the list I made up a new statistical procedure. I will publish it in a medical journal, but there will be only the way of using it, no calculation or algorithme detail. So is there a journal (I mean scientific journal) with selection commity to submit an article describing the detail of a package? There may be others, perhaps dedicated to a particular area of study (e.g. Computers and Geosciences, and Ecological Modelling might be appropriate places for the broad area of environmetrics), but the Journal of Statistical Software is an obvious choice for what you describe. www.jstatsoft.org HTH G Christophe __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ UK. WC1E 6BT. [w] http://www.freshwaters.org.uk %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Clash between alr3 and AlgDesign. (Was: Re: Second subsequent calls to function fails. Please help debug.)
On 30/03/2008 8:43 AM, Michael Kubovy wrote: Thanks, Duncan, I started a new session under the suspicion that packages were clashing. ... # # BAD INTERACTION BETWEEN alr3 and AlgDesign # What now? There's not much you can do; this is up to the package authors to fix. Some advice for them: alr3, crossdes, faraway, and HH don't use a namespace. This makes them very vulnerable to this sort of interaction, because they don't get to choose where the functions they use come from. They should add one. In my opinion, all packages should have namespaces, and I'd like to create a default one if the author doesn't. (The default would be: import what is listed in the Depends clause, export everything.) I don't think this will happen for 2.7.0, though package.skeleton might start creating one. Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Journal for R
Gavin Simpson wrote: On Sun, 2008-03-30 at 15:01 +0200, Christophe Genolini wrote: Hi the list I made up a new statistical procedure. I will publish it in a medical journal, but there will be only the way of using it, no calculation or algorithme detail. So is there a journal (I mean scientific journal) with selection commity to submit an article describing the detail of a package? There may be others, perhaps dedicated to a particular area of study (e.g. Computers and Geosciences, and Ecological Modelling might be appropriate places for the broad area of environmetrics), but the Journal of Statistical Software is an obvious choice for what you describe. www.jstatsoft.org HTH G Also, let me remind you and others that R News is also peer reviewed (although not yet indexed). It specifically includes solicits short to medium length articles of the following kinds * Changes in R: new features of the latest release * Changes on CRAN: new add-on packages, manuals, binary distributions, mirrors,... * Add-on packages: short introductions to or reviews of R extension packages * Programmer's Niche: nifty hints for programming in R (or S) * Hints for newcomers: Explaining sides of R that might not be so obvious from reading the manuals and FAQs. * Applications: Examples of analyzing data with R Lengthier papers are probably better placed in the JSS, JCGS (J.Computational and Graphical Statistics), or CSDA (Computational Statistics and Data Analysis), depending on contents. For in-depth descriptions of packages, JSS has become quite popular in recent years -pd (Current associate editor for R News, past AE for JSS) -- 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.
[R] tests Rin Rout
Hi the list,
Some rumour (!) say that is it possible to prepare some tests for
checking our code using .Rin and .Rout. It seems to be a very good
practice, but I did not manage to find information on it.
So does someone know how it works ? What are we suppose to write in Rin ?
More precisely :
- I have a package myPack.r in directories ~/myR/myPack/R/
- I create the directory ~/myR/myPack/tests
myPack.r is :
`f1` - function(x){cat(\nXXX F1 = ,x,XXX\n)}
`f2` - function(x){cat(\nXXX F2 = ,f1(x^2),XXX\n)}
What am I suppose to do to test it? Create myPack.Rin, but what in it?
Thanks for your help.
Christophe
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[R] convert weekly time series data to monthly
I have weekly time series data with year, month, day, and price variables. The input data set for the weekly series takes the following form: Year month day price 19908 20 119.1 19908 27 124.5 19909 3 124.2 19909 10 125.2 19909 17 126.6 19909 24 127.2 199010 1 132.1 199010 8 133.3 199010 15 133.9 199010 22 134.5 199010 29 133.9 .. ... ... ... ... ... 20083 3 313.7 20083 10 320 20083 17 325.7 20083 24 322.4 I would like to collapse the data into monthly averages to merge with a monthly series. The input data set for the monthly series takes the following form: M-Y YearMonth Change Aug-199019908 -226.871 Sep-199019909 -896.333 Oct-1990199010 111.419 Nov-1990199011 -364.2 Dec-1990199012 -527.645 Jan-199119911 -70.935 Feb-199119912 231.214 Mar-199119913 -239 ... ... . .. The merged data set should be of class(ts). I can perform the conversions outside of R and then import but I would rather perform all conversions within R. I have looked through the zoo and Rmetrics packages but without success. Any help will be appreciated. Thanks, Richard Saba Department of Economics Auburn University Email: [EMAIL PROTECTED] Phone: 334 844-2922 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Clash between alr3 and AlgDesign. (Was: Re: Second subsequent calls to function fails. Please help debug.)
On Sun, Mar 30, 2008 at 9:43 AM, Duncan Murdoch [EMAIL PROTECTED] wrote: In my opinion, all packages should have namespaces, and I'd like to create a default one if the author doesn't. (The default would be: import what is listed in the Depends clause, export everything.) I don't think this will happen for 2.7.0, though package.skeleton might start creating one. Namespaces are such a pain when you don't really need them though. Its nice just to be able to source a new version of a function and have it immediately work with the package. Particularly for packages that are changing or for which there is substantial code changes in the devel version this is very convenient and namespaces interefere with that. Although its possible to have namespace problems as discussed in this thread I have found that it rarely actually happens and certainly not enough to impose it. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] convert weekly time series data to monthly
If I understand:
x.new - cbind('M.Y'=paste(month.abb[x$month], x$Year, sep=-), x[-3])
aggregate(list(Change=x.new$price),
list(M.Y=x.new[,M.Y], Year=x.new$Year,
Month=x.new$month), FUN=mean)
On 30/03/2008, Richard Saba [EMAIL PROTECTED] wrote:
I have weekly time series data with year, month, day, and price variables.
The input data set for the weekly series takes the following form:
Year month day price
1990 8 20 119.1
1990 8 27 124.5
1990 9 3 124.2
1990 9 10 125.2
1990 9 17 126.6
1990 9 24 127.2
1990 10 1 132.1
1990 10 8 133.3
1990 10 15 133.9
1990 10 22 134.5
1990 10 29 133.9
..... ... ...
... ...
2008 3 3 313.7
2008 3 10 320
2008 3 17 325.7
2008 3 24 322.4
I would like to collapse the data into monthly averages to merge with a
monthly series. The input data set for the monthly series takes the
following form:
M-Y YearMonth Change
Aug-1990 19908 -226.871
Sep-1990 19909 -896.333
Oct-1990 199010 111.419
Nov-1990 199011 -364.2
Dec-1990 199012 -527.645
Jan-1991 19911 -70.935
Feb-1991 19912 231.214
Mar-1991 19913 -239
... ... . ..
The merged data set should be of class(ts).
I can perform the conversions outside of R and then import but I would
rather perform all conversions within R. I have looked through the zoo and
Rmetrics packages but without success.
Any help will be appreciated.
Thanks,
Richard Saba
Department of Economics
Auburn University
Email: [EMAIL PROTECTED]
Phone: 334 844-2922
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Re: [R] convert weekly time series data to monthly
Do you mean merge them into a two column series of price for one column and change for another column? That is what I will assume since the result was not illustrated. Suggest you read the help files and the three vignettes in the zoo package. Also R News 4/1 has info on dates. If you were looking for OHLC representations then see the xts package which in turn uses zoo and read its documentation in addition to the above. library(zoo) # ensure you are using zoo 1.5.0 or later price.Lines - Year month day price 19908 20 119.1 19908 27 124.5 19909 3 124.2 19909 10 125.2 19909 17 126.6 19909 24 127.2 199010 1 132.1 199010 8 133.3 199010 15 133.9 199010 22 134.5 199010 29 133.9 20083 3 313.7 20083 10 320 20083 17 325.7 20083 24 322.4 price.DF - read.table(textConnection(price.Lines), header = TRUE) price - with(price.DF, zoo(price, as.Date(paste(Year, month, day, sep = - change.Lines - M-Y YearMonth Change Aug-199019908 -226.871 Sep-199019909 -896.333 Oct-1990199010 111.419 Nov-1990199011 -364.2 Dec-1990199012 -527.645 Jan-199119911 -70.935 Feb-199119912 231.214 Mar-199119913 -239 change - read.zoo(textConnection(change.Lines), header = TRUE, FUN = as.yearmon, format = %b-%Y, colClasses = c(character, NULL, NULL, numeric)) # convert change series to Date using last of month as the date time(change) - as.Date(time(change), frac = 1) merge(price, change) On Sun, Mar 30, 2008 at 11:24 AM, Richard Saba [EMAIL PROTECTED] wrote: I have weekly time series data with year, month, day, and price variables. The input data set for the weekly series takes the following form: Year month day price 19908 20 119.1 19908 27 124.5 19909 3 124.2 19909 10 125.2 19909 17 126.6 19909 24 127.2 199010 1 132.1 199010 8 133.3 199010 15 133.9 199010 22 134.5 199010 29 133.9 .. ... ... ... ... ... 20083 3 313.7 20083 10 320 20083 17 325.7 20083 24 322.4 I would like to collapse the data into monthly averages to merge with a monthly series. The input data set for the monthly series takes the following form: M-Y YearMonth Change Aug-199019908 -226.871 Sep-199019909 -896.333 Oct-1990199010 111.419 Nov-1990199011 -364.2 Dec-1990199012 -527.645 Jan-199119911 -70.935 Feb-199119912 231.214 Mar-199119913 -239 ... ... . .. The merged data set should be of class(ts). I can perform the conversions outside of R and then import but I would rather perform all conversions within R. I have looked through the zoo and Rmetrics packages but without success. Any help will be appreciated. Thanks, Richard Saba Department of Economics Auburn University Email: [EMAIL PROTECTED] Phone: 334 844-2922 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Quick question: Does this graph have a name?
Thanks a lot for all your replies so far! I now share your feeling that this might not be the best way to show the data. Here's what the data is about: We have search engine queries (12,000 of them), which are grouped into semantic categories. (Some ask for a Person, some are about celebrity Gossip etc., you can see this on the x-axis.) Then we asked three subjects for each query, how they think the query should best be answered, we were mainly interested in the preferred length of the response (y-axis: With a phrase, a sentence, a text paragraph etc.) We want to show in this graph, 1) that users indeed think that queries from different semantic categories should be answered with responses of different lengths. (That a Yes/No answer basically.) 2) how the different length categories are distributed in the individual semantic categories. I hope this was somewhat clear..? Thanks! -- View this message in context: http://www.nabble.com/Quick-question%3A-Does-this-graph-have-a-name--tp16349649p16384250.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] Problem: using cor.test with by( )
Hello everyone, I'm a new R user switching from SAS and JMP. In the first few days, I have been trying to do a fairly simple task but yet found no success. I've checked the help archive as well as few R textbooks but didn't seem to find the answer. So, please help me if you can. Basically, I want to calculate the correlation between variable A and B for every subject in my study. (yep, that simple) What I did is this: by(data, id, function (x) cor.test(A,B, data=x)) The results gave me numbers of correlation for each subject. But, the problem is that, all these correlations are the same numbers and the sample size was always the entire database (including all subjects). I've also tried the lm function instead of the cor.test, and the by() function works fine. Can any of you tell me what I did wrong? Or could you tell me what is the best way to apply a function by subjects? Thank you! Best, Che-hsu (Joe) Chang, Sc.D., P.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.
Re: [R] Journal for R
As a medical researcher, I keep tabs on the journals Bioinformatics andd BMC Bioinformatics. If your package is for 'omics, those are good journals to look at. Mark On Sun, Mar 30, 2008 at 10:02 AM, Peter Dalgaard [EMAIL PROTECTED] wrote: Gavin Simpson wrote: On Sun, 2008-03-30 at 15:01 +0200, Christophe Genolini wrote: Hi the list I made up a new statistical procedure. I will publish it in a medical journal, but there will be only the way of using it, no calculation or algorithme detail. So is there a journal (I mean scientific journal) with selection commity to submit an article describing the detail of a package? There may be others, perhaps dedicated to a particular area of study (e.g. Computers and Geosciences, and Ecological Modelling might be appropriate places for the broad area of environmetrics), but the Journal of Statistical Software is an obvious choice for what you describe. www.jstatsoft.org HTH G Also, let me remind you and others that R News is also peer reviewed (although not yet indexed). It specifically includes solicits short to medium length articles of the following kinds * Changes in R: new features of the latest release * Changes on CRAN: new add-on packages, manuals, binary distributions, mirrors,... * Add-on packages: short introductions to or reviews of R extension packages * Programmer's Niche: nifty hints for programming in R (or S) * Hints for newcomers: Explaining sides of R that might not be so obvious from reading the manuals and FAQs. * Applications: Examples of analyzing data with R Lengthier papers are probably better placed in the JSS, JCGS (J.Computational and Graphical Statistics), or CSDA (Computational Statistics and Data Analysis), depending on contents. For in-depth descriptions of packages, JSS has become quite popular in recent years -pd (Current associate editor for R News, past AE for JSS) -- 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. -- Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, Mobile VoiceMail (317) 663-0513 Home (no voice mail please) ** [[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] Clash between alr3 and AlgDesign. (Was: Re: Second subsequent calls to function fails. Please help debug.)
Hi Duncan,
Yes, I came to realize that ifelse was not the way to go. Here is how
I dealt with it:
if(sum('AlgDesign' == (.packages())) 0) detach('package:AlgDesign')
It requires me (and my students) to learn only the (.packages())
construct (and avoid knowing anything about search(), match() or pos).
As a former student of mine (who has long since gone into business)
once said: I avoid learning experiences like the plague.
Thanks again,
Michael
On Mar 30, 2008, at 1:36 PM, Duncan Murdoch wrote:
On 30/03/2008 10:06 AM, Michael Kubovy wrote:
I've been trying to dynamically detach and attach things in my
Sweave, in order to circumvent the problem.
Here is my first attempt:
pkg - 'package:AlgDesign'
p - is.na(match(pkg, search()))
ifelse(p == FALSE, detach(pkg), NA)
You can't use detach this way. It is fine to say
detach(package:AlgDesign) or detach(AlgDesign), but the way detach
is written, you're attempting to detach something named pkg.
This rewrite of your code is untested, but I think it should work:
pkg - 'package:AlgDesign'
p - match(pkg, search())
if (!is.na(p)) detach(pos=p)
require(alr3)
I've also changed your ifelse() to if (), and not just because I
don't need an else clause: ifelse() is designed to do computations
on vectors, if() is designed for flow control. I think we want flow
control here.
Duncan Murdoch
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University of Virginia
Department of Psychology
USPS: P.O.Box 400400Charlottesville, VA 22904-4400
Parcels:Room 102Gilmer Hall
McCormick RoadCharlottesville, VA 22903
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] Clash between alr3 and AlgDesign. (Was: Re: Second subsequent calls to function fails. Please help debug.)
On 30/03/2008 11:31 AM, Gabor Grothendieck wrote: On Sun, Mar 30, 2008 at 9:43 AM, Duncan Murdoch [EMAIL PROTECTED] wrote: In my opinion, all packages should have namespaces, and I'd like to create a default one if the author doesn't. (The default would be: import what is listed in the Depends clause, export everything.) I don't think this will happen for 2.7.0, though package.skeleton might start creating one. Namespaces are such a pain when you don't really need them though. I would say there is no such case. Packages all import functions. Having the imports change because of unrelated code means that there is no way to write reliable code. Its nice just to be able to source a new version of a function and have it immediately work with the package. Particularly for packages that are changing or for which there is substantial code changes in the devel version this is very convenient and namespaces interefere with that. That sounds like a problem with the way we handle package code, making it too hard to reload a package that has had small changes made. We should make it easy to make a small change to a package and reload the modified version. Although its possible to have namespace problems as discussed in this thread I have found that it rarely actually happens and certainly not enough to impose it. I suspect it happens more than people realize, and that in some cases they just get the wrong answers, without any helpful error message to let them know about it. Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Clash between alr3 and AlgDesign. (Was: Re: Second subsequent calls to function fails. Please help debug.)
On 30/03/2008 10:06 AM, Michael Kubovy wrote:
I've been trying to dynamically detach and attach things in my Sweave,
in order to circumvent the problem.
Here is my first attempt:
pkg - 'package:AlgDesign'
p - is.na(match(pkg, search()))
ifelse(p == FALSE, detach(pkg), NA)
You can't use detach this way. It is fine to say
detach(package:AlgDesign) or detach(AlgDesign), but the way detach is
written, you're attempting to detach something named pkg.
This rewrite of your code is untested, but I think it should work:
pkg - 'package:AlgDesign'
p - match(pkg, search())
if (!is.na(p)) detach(pos=p)
require(alr3)
I've also changed your ifelse() to if (), and not just because I don't
need an else clause: ifelse() is designed to do computations on
vectors, if() is designed for flow control. I think we want flow
control here.
Duncan Murdoch
require(alr3)
My first two runs show that I've done something wrong:
Sweave('20080331.Rnw')
Writing to file 20080331.tex
Processing code chunks ...
1 : term hide (label=setup)
2 : echo term verbatim (label=oatvar)
3 : echo term verbatim (label=oatvar1)
4 : echo term verbatim (label=oat2wt)
5 : echo term verbatim (label=oat2wt)
6 : echo term verbatim (label=lm)
7 : echo term verbatim (label=diag)
8 : echo term verbatim (label=tukey)
9 : echo term verbatim (label=nonad)
10 : echo term verbatim (label=efficiency)
11 : echo term verbatim (label=wear)
12 : echo term verbatim (label=wearX)
13 : echo term verbatim (label=gyd)
Loading required package: crossdes
Loading required package: AlgDesign
14 : echo term verbatim (label=2wt)
15 : echo term verbatim (label=ablm)
16 : echo term verbatim (label=abaov)
17 : echo term verbatim (label=abTukey)
18 : echo term verbatim (label=effAb)
19 : echo term verbatim (label=rabbit)
20 : echo term verbatim (label=rabbit2)
21 : echo term verbatim (label=rabbit2wt)
You can now run LaTeX on '20080331.tex'
There were 42 warnings (use warnings() to see them)
Sweave('20080331.Rnw')
Writing to file 20080331.tex
Processing code chunks ...
1 : term hide (label=setup)
2 : echo term verbatim (label=oatvar)
3 : echo term verbatim (label=oatvar1)
4 : echo term verbatim (label=oat2wt)
5 : echo term verbatim (label=oat2wt)
6 : echo term verbatim (label=lm)
7 : echo term verbatim (label=diag)
8 : echo term verbatim (label=tukey)
Error: chunk 8 (label=tukey)
Error in detach(pkg) : invalid name
pkg
[1] package:AlgDesign
(1) I should learn how to fix the above code.
(2) In general, in preparing scripts, perhaps one should just ditch
all the loaded packages at the beginning of each run, so as to insure
that users won't get bitten by packages I had loaded but didn't do so
explicitly in the Sweave script, *and* it would solve the current
problem as well. Is there a straightforward way to do that?
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Re: [R] Problem: using cor.test with by( )
Che-hsu (Joe) Chang wrote: Hello everyone, I'm a new R user switching from SAS and JMP. In the first few days, I have been trying to do a fairly simple task but yet found no success. I've checked the help archive as well as few R textbooks but didn't seem to find the answer. So, please help me if you can. Basically, I want to calculate the correlation between variable A and B for every subject in my study. (yep, that simple) What I did is this: by(data, id, function (x) cor.test(A,B, data=x)) The results gave me numbers of correlation for each subject. But, the problem is that, all these correlations are the same numbers and the sample size was always the entire database (including all subjects). I've also tried the lm function instead of the cor.test, and the by() function works fine. Can any of you tell me what I did wrong? Or could you tell me what is the best way to apply a function by subjects? Thank you! Only the model formula interface to cor.test uses the data argument, so you need either cor.test(x$A,x$B) or cor.test(~A+B, data=x) Best, Che-hsu (Joe) Chang, Sc.D., P.T. -- 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] tests Rin Rout
On 30/03/2008 10:44 AM, Christophe Genolini wrote:
Hi the list,
Some rumour (!) say that is it possible to prepare some tests for
checking our code using .Rin and .Rout. It seems to be a very good
practice, but I did not manage to find information on it.
So does someone know how it works ? What are we suppose to write in Rin ?
See the paragraph in Writing R Extensions which explains this, near the
end of the section on Package Subdirectories (section 1.1.3 in the
version I'm looking at).
Rin would be fairly rarely needed: it is supposed to write a script to
perform the tests. Normally you write your script directly, in a .R file.
More precisely :
- I have a package myPack.r in directories ~/myR/myPack/R/
- I create the directory ~/myR/myPack/tests
myPack.r is :
`f1` - function(x){cat(\nXXX F1 = ,x,XXX\n)}
`f2` - function(x){cat(\nXXX F2 = ,f1(x^2),XXX\n)}
What am I suppose to do to test it? Create myPack.Rin, but what in it?
Create tests/myPack.R with those lines in it plus lines to actually run
the code. If the code generates errors, your test will fail. If you
want to see reports of changes to the output, also include
tests/myPack.Rout.save with the known correct versions of the output.
Duncan Murdoch
Thanks for your help.
Christophe
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Re: [R] Generating maps in R
Aleksandr Andreev aleksandr.andreev at duke.edu writes: Greetings! I am trying plot some data on a map in R. Here's the scenario. I have a variable called probworkinghealthy which contains a predicted probability of employment for every individual in my sample (about 100,000 observations). I have another variable, called a001ter, which contains the subject of residency in the Russian Federation (akin to a US state) for every individual in the sample. I have a shape file with the boundaries of all the subjects, called russia.shp. I can plot boxplots of the probability by Federal Subject using plot(probworkinghealthy ~ a001ter). I can also plot the map using plot(russia.shp) So what you need to do is to aggregate the input data frame for individuals, and assign the summary value, here mean, to the correct shapefile geometries. Probably most of what you need is in the maptools package. There is a question about the IDs used to identify the Federal Subject geometries in the shapefile. Assuming that they are named as in the individual data frame, something like: FS - readShapePoly(russia.shp, IDvar=a001ter) will associate the geometries in the SpatialPolygonsDataFrame with the correct ID - change the IDvar argument value to suit the shapefile. If you do not have IDs in the shapefile to match the unique values of a001ter, you will need to create them. From there, create a new data frame with row names matching the unique IDs: agg1 - tapply(probworkinghealthy, a001ter, mean) agg2 - data.frame(mean_probworkinghealthy=agg1, row.names=names(agg1)) and check row.names(agg2) and sapply(slot(FS, polygons), function(x) slot(x, ID)) for obvious blunders. Merge using: FS1 - spCbind(FS, agg2) (usually takes a number of tries to get the matching correct). The reason for the complications with IDs is that it is easy to merge data with geometries in the wrong order, and having to provide positive matching should help prevent this. Now, I would like to plot the mean probability of employment (i.e. mean(probworkinghealthy)) on a map of Russia using color coding all the Federal Subjects. Does anyone know how to do something like that? Then spplot(FS1, mean_probworkinghealthy) gives a map with default class intervals and colour palette. I suggest that you also consider assigning a coordinate reference system to the geometries as Russia has a large extent, and the correct interpretation of the geometry coordinates may matter. Roger PS. You could consider following up on the R-sig-geo list, or exploring information in the Spatial Task View, or in the list archives. Much appreciated, Aleks Andreev Duke University __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Definition of wrapper?
I think I more or less understand what a ³wrapper² is, but I¹d like to hear how more experienced R users define it, and especially I'd like to know if there is a formal definition. In my reading, it seems like there are a fairly wide range of meanings, but they are all conceptually similar. I've looked in a couple of the classic R texts, the extensions and developers' manuals, and R help archives, and didn't find a definition. Of course, I may have missed it. Thanks in advance. Bryan ** Bryan Hanson Professor of Chemistry Biochemistry DePauw University 602 S. College Avenue Greencastle, IN 46135 PHONE 765-658-4602 FAX 765-658-6084 [EMAIL PROTECTED] http://academic.depauw.edu/~hanson/deadpezsociety.html http://www.depauw.edu/acad/chemistry/ http://academic.depauw.edu/~hanson/UMP/index.html __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] tests Rin Rout
See the paragraph in Writing R Extensions which explains this Well, I saw it again and again (before asking on the r-help) but I do not understand. Same for the Kurt Hornik slides on the web. Create tests/myPack.R with those lines in it plus lines to actually run the code. Does it mean that each time I change the code, I will have to change it twice, once in R/ and once in tests/ If the code generates errors, your test will fail. If you want to see reports of changes to the output, also include tests/myPack.Rout.save with the known correct versions of the output. What should the Rout.save looks like ? I mean, what is the syntax of this file ? Christophe __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Definition of wrapper?
On Mar 30, 2008, at 2:51 PM, Bryan Hanson wrote: I think I more or less understand what a “wrapper” is, but I’d like to hear how more experienced R users define it, and especially I'd like to know if there is a formal definition. In my reading, it seems like there are a fairly wide range of meanings, but they are all conceptually similar. I've looked in a couple of the classic R texts, the extensions and developers' manuals, and R help archives, and didn't find a definition. Of course, I may have missed it. Thanks in advance. Bryan This is a general programming question, likely. This might offer a starting point: http://en.wikipedia.org/wiki/Wrapper_pattern Greetings from Hanover, IN ** Bryan Hanson Professor of Chemistry Biochemistry DePauw University Haris Skiadas Department of Mathematics and Computer Science Hanover College __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Describing discriminant function
hello, I have two 2-d normal multivariate distributions mapped out on a scatter plot. I now need a line that equates the two discriminant functions, ie. g1(x) = g2(x). This should be a quadratic. How can I solve this in R? Thanks -- View this message in context: http://www.nabble.com/Describing-discriminant-function-tp16385838p16385838.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] Definition of wrapper?
The wrapper wraps, i.e. calls, another function that does the real work but provides a different or more convenient (or more convenient for a specific purpose) interface to it or specific syntax. Often the wrapper has the same arguments but different defaults and sometimes that is referred to as a convenience wrapper. Sometimes its used in the sense of providing an R interface to a C function with essentially similar arguments. by is a wrapper to tapply which preprocesses the data in a way that makes it acceptable to tapply, read.csv and Map are wrappers to read.table and mapply which are the same but have different argument defaults, sprintf is a wrapper to the C function of the same name, %o% is a wrapper to outer. I don't think there is a formalized definition within R -- the above is based on current usage. On Sun, Mar 30, 2008 at 2:51 PM, Bryan Hanson [EMAIL PROTECTED] wrote: I think I more or less understand what a ³wrapper² is, but I¹d like to hear how more experienced R users define it, and especially I'd like to know if there is a formal definition. In my reading, it seems like there are a fairly wide range of meanings, but they are all conceptually similar. I've looked in a couple of the classic R texts, the extensions and developers' manuals, and R help archives, and didn't find a definition. Of course, I may have missed it. Thanks in advance. Bryan ** Bryan Hanson Professor of Chemistry Biochemistry DePauw University 602 S. College Avenue Greencastle, IN 46135 PHONE 765-658-4602 FAX 765-658-6084 [EMAIL PROTECTED] http://academic.depauw.edu/~hanson/deadpezsociety.html http://www.depauw.edu/acad/chemistry/ http://academic.depauw.edu/~hanson/UMP/index.html __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] tests Rin Rout
For questions like this about package development, you should ask on R-devel, but I'll continue the thread here for one more message. On 30/03/2008 2:54 PM, Christophe Genolini wrote: See the paragraph in Writing R Extensions which explains this Well, I saw it again and again (before asking on the r-help) but I do not understand. Same for the Kurt Hornik slides on the web. Generally I find it's good to look at examples that work. For examples of packages using tests, look at source packages on CRAN. Run the tests on them (using R CMD check), and see what gets produced. Create tests/myPack.R with those lines in it plus lines to actually run the code. Does it mean that each time I change the code, I will have to change it twice, once in R/ and once in tests/ There shouldn't be any duplication. Just put tests in the tests directory. That code will be run with your package loaded when you run R CMD check. If it fails, your package will fail the check. If the code generates errors, your test will fail. If you want to see reports of changes to the output, also include tests/myPack.Rout.save with the known correct versions of the output. What should the Rout.save looks like ? I mean, what is the syntax of this file ? It should just be a copy of the Rout file produced from a previous trusted run. R CMD check will ignore certain differences (like changes to the date or R version at the top of the file), but will report on others. 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] Plot for jump point
Hi,
My code is as the following,
ratio-seq(0,1,by=0.01)
payoff-NULL
for (i in 1:length(ratio) )
{
payoff1-100*(ratio[i]=0.7)+max(100*(1+(ratio[i]-1)*2),0)*(ratio[i]0.7)
payoff-c(payoff,payoff1)
}
plot(ratio,payoff, xlab='ST/S0', ylab='Payoff',type='l')
I have the discontinuous point at ratio=0.7. I do not want to have the line at
0.7, and would like a solid dot at payoff=100 and a hollow dot at payoff=40 at
the jump point 0.7. How would I do this?
Thanks,
Kate
[[alternative HTML version deleted]]
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Re: [R] Problem: using cor.test with by( )
On Sun, Mar 30, 2008 at 7:11 PM, Che-hsu (Joe) Chang [EMAIL PROTECTED] wrote: Basically, I want to calculate the correlation between variable A and B for every subject in my study. (yep, that simple) What I did is this: by(data, id, function (x) cor.test(A,B, data=x)) This recent thread [1] might prove of interest. Liviu [1] http://www.nabble.com/p-value-in-Spearman-rank-order-tt15738907.html __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] I need really help
Dear , Madam/Sir I'm student doing master in statistics, I'd like to know how i can set data in R and apply meta-analysis. i have tries many ways but I'm really stuck. i really appreciate if you can help me in this matter. Mohammed Owlowa - [[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] maximum of identical elements in a vector
Hi, the problem I have is seemingly very simple, but not simple enough for me to figure out. I just want to find the most (or least) frequent element in the vector. a=c(Alice,Alice,Alice,Alice,Bob,Bob) unique(a) length(which(a==Alice)) unique(a) shows me that the elements in my vector are Alice and Bob. The latter expression gives 4 as the frequency of Alice in vector a. To find the maximum frequency of the unique elements, however, it assumes that I know that Alice is the most (or least) frequent element. Therefore, how can find that Alice is the most frequent element in this vector? I assume there is an easier way than computationally intensive loops (for long vectors). Cheers, Daniel - cuncta stricte discussurus __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Plot for jump point
Try this:
ratio-seq(0,1,by=0.01)
payoff-NULL
for (i in 1:length(ratio) )
{
payoff1-100*(ratio[i]=0.7)+max(100*(1+(ratio[i]-1)*2),0)*(ratio[i]0.7)
payoff-c(payoff,payoff1)
}
payoff[70] - NA # force no line
plot(ratio,payoff, xlab='ST/S0', ylab='Payoff',type='l')
points(c(ratio[69], ratio[71]), c(payoff[69], payoff[71]), pch=c(1,16))
On Sun, Mar 30, 2008 at 4:17 PM, kate [EMAIL PROTECTED] wrote:
Hi,
My code is as the following,
ratio-seq(0,1,by=0.01)
payoff-NULL
for (i in 1:length(ratio) )
{
payoff1-100*(ratio[i]=0.7)+max(100*(1+(ratio[i]-1)*2),0)*(ratio[i]0.7)
payoff-c(payoff,payoff1)
}
plot(ratio,payoff, xlab='ST/S0', ylab='Payoff',type='l')
I have the discontinuous point at ratio=0.7. I do not want to have the line
at 0.7, and would like a solid dot at payoff=100 and a hollow dot at
payoff=40 at the jump point 0.7. How would I do this?
Thanks,
Kate
[[alternative HTML version deleted]]
__
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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?
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Re: [R] maximum of identical elements in a vector
On 3/30/2008 5:35 PM, Daniel Malter wrote: Hi, the problem I have is seemingly very simple, but not simple enough for me to figure out. I just want to find the most (or least) frequent element in the vector. a=c(Alice,Alice,Alice,Alice,Bob,Bob) unique(a) length(which(a==Alice)) unique(a) shows me that the elements in my vector are Alice and Bob. The latter expression gives 4 as the frequency of Alice in vector a. To find the maximum frequency of the unique elements, however, it assumes that I know that Alice is the most (or least) frequent element. Therefore, how can find that Alice is the most frequent element in this vector? I assume there is an easier way than computationally intensive loops (for long vectors). names(which.max(table(a))) [1] Alice Cheers, Daniel - cuncta stricte discussurus __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Chuck Cleland, Ph.D. NDRI, Inc. (www.ndri.org) 71 West 23rd Street, 8th floor New York, NY 10010 tel: (212) 845-4495 (Tu, Th) tel: (732) 512-0171 (M, W, F) fax: (917) 438-0894 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] maximum of identical elements in a vector
On Sun, 2008-03-30 at 17:35 -0400, Daniel Malter wrote: Hi, the problem I have is seemingly very simple, but not simple enough for me to figure out. I just want to find the most (or least) frequent element in the vector. a=c(Alice,Alice,Alice,Alice,Bob,Bob) unique(a) length(which(a==Alice)) a - c(Alice,Alice,Alice,Alice,Bob,Bob) tab - table(a) tab a Alice Bob 4 2 which.max(tab) Alice 1 tab[which.max(tab)] Alice 4 HTH G unique(a) shows me that the elements in my vector are Alice and Bob. The latter expression gives 4 as the frequency of Alice in vector a. To find the maximum frequency of the unique elements, however, it assumes that I know that Alice is the most (or least) frequent element. Therefore, how can find that Alice is the most frequent element in this vector? I assume there is an easier way than computationally intensive loops (for long vectors). Cheers, Daniel - cuncta stricte discussurus __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ UK. WC1E 6BT. [w] http://www.freshwaters.org.uk %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] problem with white space
Here is one way of doing it. I would suggest that you read in the
data with readLines and then combine into one single string so that
you can use substring on it. Since you did not provide provide
commented, minimal, self-contained, reproducible code, I will take a
guess at that your data looks like:
# create some test data -- might be read in the readLines
sdata - sapply(1:10, function(x){ # 10 lines of strings with 50 characters
paste(sample(LETTERS, 50, TRUE), collapse='')
})
# put into one large string so you can do substring on it
sdata - paste(sdata, collapse='')
# now create 10 sample of size 20 and write in files (file1, file2, ... file10)
for (i in 1:10){
x - sample(nchar(sdata), 20)
writeLines(paste(substring(sdata, x, x), collapse=''),
con=paste(file, i, sep=''))
}
On Sun, Mar 30, 2008 at 3:41 PM, Suraaga Kulkarni
[EMAIL PROTECTED] wrote:
Hi,
I need to resample characters from a dataset that consists of an extremely
long string that is written over hundreds of thousands of lines, each of
length 50 characters. I am currently doing this by first inserting a space
after each character in the dataset and then using the following commands:
y - as.matrix(read.table(data.txt), stringsAsFactors=FALSE)
bstrap - sample(length(y), 10, TRUE)
write(y[bstrap], file=Rep1.txt, ncolumns=50, append=FALSE)
bstrap - sample(length(y), 10, TRUE)
write(y[bstrap], file=Rep2.txt, ncolumns=50, append=FALSE)
bstrap - sample(length(y), 10, TRUE)
.
.
.
and so on for 500 reps.
I think there should be a better way of doing this. My specific questions:
1. Is there a way to avoid inserting spaces between the characters before
calling the sample command (because I don't want spaces between the
resampled characters in the output either; see number 2 below)?
2. If I have no choice but to insert the spaces in my data before
resampling, is there a way to output the resampled data without spaces, but
simply as 50-character long strings one below the other)? I tried inserting
the following command: strip.white=TRUE in the write command line, but it
gave me an error as it did not understand the command.
3. Finally, since I have to get 500 such resampled reps from each dataset
(and there are over 20 such huge datasets) is there a way around having to
write a separate write command for each rep?
Any suggestions will be greatly appreciated.
Thanks,
S.
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+1 513 646 9390
What is the problem you are trying to solve?
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Re: [R] problem with white space
How long is it taking? Can you send me the code that you are using.
Another technique is to recode you characters into numbers and store
them as integers. You can then sample the values and reconstruct the
output. Here is a faster way:
# create some test data -- might be read in the readLines
# use 'raw' class for the data.
sdata - sapply(1:10, function(x){
charToRaw(paste(sample(LETTERS, 50, TRUE), collapse=))#
encode the character as a number
})
# now create 10 sample of size 20 and write in files
for (i in 1:10){
x - sample(sdata, 10, TRUE)
# convert back to characters
writeLines(rawToChar(x), con=paste(file, i, sep=''))
}
On Sun, Mar 30, 2008 at 6:06 PM, Suraaga Kulkarni
[EMAIL PROTECTED] wrote:
Jim,
Thanks very much. I am very new to R and am trying to understand your code.
It works perfectly on your sample data of course. I tried your code on my
data. While it works, it takes too much time to generate each replicate.
At present I'm outputting the replicates with only 2000 resampled
characters. I actually need to resample something like 1-5 million
characters. I work with the human genome, and need to generate 500
bootstrap replicates of a scaled down version (about 2%) of each chromosome
by means of resampling with replacement.
Sorry about the cryptic code but I thought my initial description of the
problem explained it. In any case, your guess was correct.
Let me see if I can rework your code to suit my purposes. In the meanwhile,
if you have any other suggestions, I'll be happy to hear them.
Thanks again for the prompt response.
S.
On Sun, Mar 30, 2008 at 6:15 PM, jim holtman [EMAIL PROTECTED] wrote:
Here is one way of doing it. I would suggest that you read in the
data with readLines and then combine into one single string so that
you can use substring on it. Since you did not provide provide
commented, minimal, self-contained, reproducible code, I will take a
guess at that your data looks like:
# create some test data -- might be read in the readLines
sdata - sapply(1:10, function(x){ # 10 lines of strings with 50
characters
paste(sample(LETTERS, 50, TRUE), collapse='')
})
# put into one large string so you can do substring on it
sdata - paste(sdata, collapse='')
# now create 10 sample of size 20 and write in files (file1, file2, ...
file10)
for (i in 1:10){
x - sample(nchar(sdata), 20)
writeLines(paste(substring(sdata, x, x), collapse=''),
con=paste(file, i, sep=''))
}
On Sun, Mar 30, 2008 at 3:41 PM, Suraaga Kulkarni
[EMAIL PROTECTED] wrote:
Hi,
I need to resample characters from a dataset that consists of an
extremely
long string that is written over hundreds of thousands of lines, each of
length 50 characters. I am currently doing this by first inserting a
space
after each character in the dataset and then using the following
commands:
y - as.matrix(read.table(data.txt), stringsAsFactors=FALSE)
bstrap - sample(length(y), 10, TRUE)
write(y[bstrap], file=Rep1.txt, ncolumns=50, append=FALSE)
bstrap - sample(length(y), 10, TRUE)
write(y[bstrap], file=Rep2.txt, ncolumns=50, append=FALSE)
bstrap - sample(length(y), 10, TRUE)
.
.
.
and so on for 500 reps.
I think there should be a better way of doing this. My specific
questions:
1. Is there a way to avoid inserting spaces between the characters
before
calling the sample command (because I don't want spaces between the
resampled characters in the output either; see number 2 below)?
2. If I have no choice but to insert the spaces in my data before
resampling, is there a way to output the resampled data without spaces,
but
simply as 50-character long strings one below the other)? I tried
inserting
the following command: strip.white=TRUE in the write command line, but
it
gave me an error as it did not understand the command.
3. Finally, since I have to get 500 such resampled reps from each
dataset
(and there are over 20 such huge datasets) is there a way around having
to
write a separate write command for each rep?
Any suggestions will be greatly appreciated.
Thanks,
S.
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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?
--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem you are trying to solve?
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PLEASE do read the posting guide
Re: [R] Generating maps in R
Roger Bivand Roger.Bivand at nhh.no writes: Merge using: FS1 - spCbind(FS, agg2) This call fails, because: Error in spCbind(FS, agg2) : different numbers of rows The reason is because I have data in a001ter for 79 Federal Subjects, but russia.shp contains 193 labeled objects (93 Federal Subjects plus 100 Arctic Ocean Islands and other things). Is there a way I can merge without an equal number of rows, labeling the data for the Arctic islands as missing? Thanks, Aleks Andreev Duke University 2008/3/29, Aleksandr Andreev [EMAIL PROTECTED]: Greetings! I am trying plot some data on a map in R. Here's the scenario. I have a variable called probworkinghealthy which contains a predicted probability of employment for every individual in my sample (about 100,000 observations). I have another variable, called a001ter, which contains the subject of residency in the Russian Federation (akin to a US state) for every individual in the sample. I have a shape file with the boundaries of all the subjects, called russia.shp. I can plot boxplots of the probability by Federal Subject using plot(probworkinghealthy ~ a001ter). I can also plot the map using plot(russia.shp) Now, I would like to plot the mean probability of employment (i.e. mean(probworkinghealthy)) on a map of Russia using color coding all the Federal Subjects. Does anyone know how to do something like that? Much appreciated, Aleks Andreev Duke University __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] maximum of identical elements in a vector
Thanks to all who responded so quickly. - cuncta stricte discussurus - -Ursprüngliche Nachricht- Von: Chuck Cleland [mailto:[EMAIL PROTECTED] Gesendet: Sunday, March 30, 2008 5:45 PM An: Daniel Malter Cc: [EMAIL PROTECTED] Betreff: Re: [R] maximum of identical elements in a vector On 3/30/2008 5:35 PM, Daniel Malter wrote: Hi, the problem I have is seemingly very simple, but not simple enough for me to figure out. I just want to find the most (or least) frequent element in the vector. a=c(Alice,Alice,Alice,Alice,Bob,Bob) unique(a) length(which(a==Alice)) unique(a) shows me that the elements in my vector are Alice and Bob. The latter expression gives 4 as the frequency of Alice in vector a. To find the maximum frequency of the unique elements, however, it assumes that I know that Alice is the most (or least) frequent element. Therefore, how can find that Alice is the most frequent element in this vector? I assume there is an easier way than computationally intensive loops (for long vectors). names(which.max(table(a))) [1] Alice Cheers, Daniel - cuncta stricte discussurus __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Chuck Cleland, Ph.D. NDRI, Inc. (www.ndri.org) 71 West 23rd Street, 8th floor New York, NY 10010 tel: (212) 845-4495 (Tu, Th) tel: (732) 512-0171 (M, W, F) fax: (917) 438-0894 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Finding a mean value of a variable holding a dummy variable fixed
I have time-series data on approval ratings of British Prime Ministers. The prime ministers dating from MacMillan onward till today are coded as dummy variables and the approval ratings are entered for each month. I want to know the mean value of the approval rating of each Prime Minister in the dataset and the approval rating during his/her first month and last month as PM. What R code should I enter for these data? In other words, I want hold the dummy corresponding to each Prime Minister fixed at value one and know the first rating that PM has, the last rating s/he has, and the mean rating s/he has. Thanks. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Finding a mean value of a variable holding a dummy variablefixed
The mean problem can be solved with president=c(Johnson,Johnson,Johnson,Johnson,Johnson,Johnson,Nix on,Nixon,Nixon,Nixon,Nixon,Nixon) approval=seq(1:12) tapply(approval,president,mean) For the other, I will try to come back. But I am sure somebody will be faster than I. Cheers, Daniel - cuncta stricte discussurus - -Ursprüngliche Nachricht- Von: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Im Auftrag von Alexander Ovodenko Gesendet: Sunday, March 30, 2008 9:47 PM An: r-help@r-project.org Betreff: [R] Finding a mean value of a variable holding a dummy variablefixed I have time-series data on approval ratings of British Prime Ministers. The prime ministers dating from MacMillan onward till today are coded as dummy variables and the approval ratings are entered for each month. I want to know the mean value of the approval rating of each Prime Minister in the dataset and the approval rating during his/her first month and last month as PM. What R code should I enter for these data? In other words, I want hold the dummy corresponding to each Prime Minister fixed at value one and know the first rating that PM has, the last rating s/he has, and the mean rating s/he has. Thanks. [[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] Finding a mean value of a variable holding a dummy variablefixed
I found a solution. It's probably not the easiest one, but it works. It assumes that your data frame is ordered from earliest to latest record for each president, but it can be easily adjusted if you want to make it dependent on a third column. The final vector index gives you the line indices for the first record for each president. If you replace min by max you get the last instead of the first record. You can then find the values by ##Sample data president=c(Johnson,Johnson,Johnson,Johnson,Johnson,Johnson,Nix on,Nixon,Nixon,Nixon,Nixon,Nixon) approval=c(3,4,5,6,7,8,6,5,4,3,2,1) tapply(approval,president,mean) ##Find index for first row of each president; assumes ascending order of observations; change min to max to find last record index=NULL for(i in 1:length(unique(president))) index[i]=min(which((president==unique(president)[i])==TRUE)) index ##Generate table with first approvals first.approval=data.frame(cbind(index,president[index],approval[index])) names(first.approval)=c(Index,President,Approval) first.approval Cheers, Daniel - cuncta stricte discussurus - -Ursprüngliche Nachricht- Von: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Im Auftrag von Alexander Ovodenko Gesendet: Sunday, March 30, 2008 9:47 PM An: r-help@r-project.org Betreff: [R] Finding a mean value of a variable holding a dummy variablefixed I have time-series data on approval ratings of British Prime Ministers. The prime ministers dating from MacMillan onward till today are coded as dummy variables and the approval ratings are entered for each month. I want to know the mean value of the approval rating of each Prime Minister in the dataset and the approval rating during his/her first month and last month as PM. What R code should I enter for these data? In other words, I want hold the dummy corresponding to each Prime Minister fixed at value one and know the first rating that PM has, the last rating s/he has, and the mean rating s/he has. Thanks. [[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] Finding a mean value of a variable holding a dummyvariablefixed
Here is another way, starting with similar dummy data: PMData - data.frame(PM = c(Thatcher, Thatcher, Thatcher, Thatcher, Thatcher, Thatcher,Major, Major, Major, Major, Major, Major), approval = c(3, 4, 5, 6, 7, 8, 6, 5, 4, 3, 2, 1)) PMData - transform(PMData, Month = 1:nrow(PMData)) ## add the time variable PM_average - with(PMData, tapply(approval, PM, mean)) PM_span - with(PMData, sapply(tapply(Month, PM, range), function(x) structure(approval[Month[x]], names = c(First, Last rbind(mean = PM_average, PM_span) Major Thatcher mean3.5 5.5 First 6.0 3.0 Last1.0 8.0 (I don't recall any Prime Minister called Johnson or Nixon, by the way...) Bill Venables CSIRO Laboratories PO Box 120, Cleveland, 4163 AUSTRALIA Office Phone (email preferred): +61 7 3826 7251 Fax (if absolutely necessary): +61 7 3826 7304 Mobile: +61 4 8819 4402 Home Phone: +61 7 3286 7700 mailto:[EMAIL PROTECTED] http://www.cmis.csiro.au/bill.venables/ -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Daniel Malter Sent: Monday, 31 March 2008 1:22 PM To: 'Alexander Ovodenko'; r-help@r-project.org Subject: Re: [R] Finding a mean value of a variable holding a dummyvariablefixed I found a solution. It's probably not the easiest one, but it works. It assumes that your data frame is ordered from earliest to latest record for each president, but it can be easily adjusted if you want to make it dependent on a third column. The final vector index gives you the line indices for the first record for each president. If you replace min by max you get the last instead of the first record. You can then find the values by ##Sample data president=c(Johnson,Johnson,Johnson,Johnson,Johnson,Johnson,Nix on,Nixon,Nixon,Nixon,Nixon,Nixon) approval=c(3,4,5,6,7,8,6,5,4,3,2,1) tapply(approval,president,mean) ##Find index for first row of each president; assumes ascending order of observations; change min to max to find last record index=NULL for(i in 1:length(unique(president))) index[i]=min(which((president==unique(president)[i])==TRUE)) index ##Generate table with first approvals first.approval=data.frame(cbind(index,president[index],approval[index])) names(first.approval)=c(Index,President,Approval) first.approval Cheers, Daniel - cuncta stricte discussurus - -Ursprüngliche Nachricht- Von: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Im Auftrag von Alexander Ovodenko Gesendet: Sunday, March 30, 2008 9:47 PM An: r-help@r-project.org Betreff: [R] Finding a mean value of a variable holding a dummy variablefixed I have time-series data on approval ratings of British Prime Ministers. The prime ministers dating from MacMillan onward till today are coded as dummy variables and the approval ratings are entered for each month. I want to know the mean value of the approval rating of each Prime Minister in the dataset and the approval rating during his/her first month and last month as PM. What R code should I enter for these data? In other words, I want hold the dummy corresponding to each Prime Minister fixed at value one and know the first rating that PM has, the last rating s/he has, and the mean rating s/he has. Thanks. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Find the index for min of a matrix
Hi, My example is as the following, W-matrix(c(2,4,2,8,1,3),ncol=3) which(W==min(W)) I would like to find the index for min of the matrix W, i.e. (1, 3) instead of 5 as the output. What command could I use? Thanks, Kate [[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] APPLY as alternate to FOR loop?
Dear list,
Below I've written a clunky for loop that counts NA's in a row, replacing all
with NA if there are
more than 3 missing values, or keeping the values if 4 or more are present.
This is sample code from a very large
dataframe I'm trying to clean up.
I know there are many simpler more elegant solutions to this little problem.
Would someone be willing to show me how to create a function that I can APPLY
to
each row rather than looping? I've tried and can't get it.
Thank you,
Zack
# Count NA's in each row. IF
3 NA's in a row, make all
NA###
## test dataframe ###x1 - c(1,NA,NA,NA,NA,1,2,2)x2 -
c(1,NA,NA,NA,NA,1,2,1)x3 - c(1,NA,1,1,1,1,1,5)x4 - c(1,NA,NA,NA,NA,NA,NA,5)x
- rbind(x1,x2,x3,x4)test - rowSums(is.na(x)) ## count numer of NA's
in rowx - cbind(x, test) ## add row NA count to datax -
data.frame(x) ## make dataframe
# FOR LOOP to apply across all rows of dataframe -- for(i in 1:nrow(x))
{if(x[i,9] 4) {x[i,1:7] - NA} else { x[i,1:7] - x[i,1:7]i = i+1}}
#
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[R] multivariate histogram
Dear Everyone, 1. I have an n-dimension data. 2. I could get the shape of pdf of each one from each of their histograms. 3.?Now I would like to get the joint pdf of the all the dimensions of X. How do we do #3 above? Regards, Joh [[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] APPLY as alternate to FOR loop?
As far as I know there is no function called 'APPLY'
There is one called 'apply', but why are you determined to use it here?
It is essentially concealed looping.
Here is an alternative way of solving your problem:
___
x - rbind(x1 = c(1, NA, NA, NA, NA, 1, 2, 2),
x2 = c(1, NA, NA, NA, NA, 1, 2, 1),
x3 = c(1, NA, 1, 1, 1, 1, 1, 5),
x4 = c(1, NA, NA, NA, NA, NA, NA, 5))
badRows - which(rowSums(is.na(x)) 3)
is.na(x[as.matrix(expand.grid(badRows, 1:ncol(x)))]) - TRUE
___
x
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
x1 NA NA NA NA NA NA NA NA
x2 NA NA NA NA NA NA NA NA
x31 NA111115
x4 NA NA NA NA NA NA NA NA
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
On Behalf Of zack holden
Sent: Monday, 31 March 2008 2:32 PM
To: r-help@r-project.org
Subject: [R] APPLY as alternate to FOR loop?
Dear list,
Below I've written a clunky for loop that counts NA's in a row,
replacing all with NA if there are
more than 3 missing values, or keeping the values if 4 or more are
present. This is sample code from a very large
dataframe I'm trying to clean up.
I know there are many simpler more elegant solutions to this little
problem.
Would someone be willing to show me how to create a function that I can
APPLY to
each row rather than looping? I've tried and can't get it.
Thank you,
Zack
# Count NA's in each
row. IF 3 NA's in a row, make all
NA###
## test dataframe ###x1 - c(1,NA,NA,NA,NA,1,2,2)x2 -
c(1,NA,NA,NA,NA,1,2,1)x3 - c(1,NA,1,1,1,1,1,5)x4 -
c(1,NA,NA,NA,NA,NA,NA,5)x - rbind(x1,x2,x3,x4)test - rowSums(is.na(x))
## count numer of NA's in rowx - cbind(x, test) ## add
row NA count to datax - data.frame(x) ## make
dataframe
# FOR LOOP to apply across all rows of dataframe -- for(i in 1:nrow(x))
{if(x[i,9] 4) {x[i,1:7] - NA} else { x[i,1:7] - x[i,1:7]i = i+1}}
#
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[R] WinXP exhibits sluggish graphics window movement mouse tracking (repainting?) over windows graphics devices
I just noticed when using 2.6.1, 2.6.2 (2008-02-08), 2.6.2pat (2008-02-21 r44582), and 2.6.2pat (2008-03-24 r44975) on my poor old Celeron D330 (2.6 GHz; 3.5 years old) running Windows XP, that the mouse cursor appears to be redrawn more sluggishly when the pointer is over R windows graphics devices than over the R console window or other applications' windows. The slowdown seems to start only after I plotting something in the window (running windows() to open the device does not cause any slowdown), but the behavior starts after a plot(rnorm(100)). The slowdown seems to depend on the area of the R graphics window that is visible. The slowdown also occurs when moving the plot window. For example, if the graphics window is frontmost, and I want to move it until it is mostly offscreen, then the movement is jerky. However, once the window is mostly offscreen, dragging it back onto the screen is smooth and fast. (When I drag windows, I only see the frame, not the contents.) This seems to affect SDI and MDI modes. The Windows task manager confirms that when the plot window is frontmost, Rgui.exe takes most of the CPU time. My graphics card is based on an ATI Radeon 7000, with 32 MB of RAM. I am surprised that I never noticed this before. Nobody else seems to have reported it to the r-help list. Is this problem restricted to my system? (My work machine is much newer, and I do not notice the problem there.) -- 607-351-4838 / [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.
