Re: [R] R parser for If-else
D == Dani danicy...@gmail.com
on Tue, 24 Feb 2009 14:09:36 -0800 writes:
D Hi list,
D I don't know if somebody has spent a lot of time debugging strange
D problems with if else positioning - the parser seems to recognize only
D the syntax bellow - this is the only way of making these pieces of
D code to work.
D As far as i'm concerned, no examples were available (it would be so
D awesome to have them in the introductory manual!)
D #Try to change the placement of the keywords and you are dead!
[dead?]
Oh dear...
Note this has nothing to do with if( ) .. else ..
but indeed with how things are parsed.
I think this is FAQ (or should become one):
?if [the help page you really should read before spending too
much time or even post to R-help]
has the following section
Note that it is a common mistake to forget to put braces ('{ .. }')
around your statements, e.g., after 'if(..)' or 'for()'.
In particular, you should not have a newline between '}' and
'else' to avoid a syntax error in entering a 'if ... else'
construct at the keyboard or via 'source'. For that reason, one
(somewhat extreme) attitude of defensive programming is to always
use braces, e.g., for 'if' clauses.
Regards,
Martin Maechler, ETH Zurich
D Ex1:
D if (1==1){
D print('if')
D print('if again')
D }else
D print('else')
D Ex2:
D if (2==2) print('if') else print('else')
D Ex3:
D if (2==2){
D print('if')
D print('if again')
D }else
D {
D print('else')
D print('else2')
D }
D Ex4:
D if (2==2){
D print('if')
D print('if again')
D }else print('else')
D cheers,
D -
D Daniela
D __
D R-help@r-project.org mailing list
D https://stat.ethz.ch/mailman/listinfo/r-help
D PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
D and provide commented, minimal, self-contained, reproducible code.
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Re: [R] biplot.princomp - changing score labels
On Tue, 24 Feb 2009, Axel Strauß wrote: OK, the one thing I figured out: Is should be like: biplot(test.pca, cex=c(2,1), col=c(red,green)... to change size, colours etc separately. But I still don't know how change lables of observations to symbols properly. That's not part of the design of the function, so just make a copy and edit to meet your fancies. The designer of biplot.princomp. Tipps? Thanks again, Axel Dear R helpers, When producing a PCA biplot, vectors of environmental variables (as red arrows with labels) and scores of the observations (black labels (observation names)) are plotted by default. How can I change the graphical output? Let's say I would like that the scores are plottet only as symbols and not text. The only solution I found was this post in the help archive http://tolstoy.newcastle.edu.au/R/e2/help/06/12/7298.html suggesting cheating like: biplot(test.pca, xlabs=c(0,0,0,0,0,0... and using letters instead of symbols. This works somehow, but I am still not able the change e.g. the colour or size of only the scores. Whatever I try to do with col=..., cex=... and so on changes either all labels in the plot or none. Can someone tell me what is the trick to only modify either the environmental variables or the scores? Also e.g. the type of the arrow? Thanks in advance, Axel -- Brian D. Ripley, rip...@stats.ox.ac.uk 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] Using package ROCR
I am trying to use package ROCR to analyze classification accuracy, unfortunately there are some problems right at the beginning. Question 1) When I try to run demo I am getting the following error message library(ROCR) demo(ROCR) if(dev.cur() = 1) [TRUNCATED] Error in get(getOption(device)) : wrong first argument When I issue the command dev.cur() it returns null device 1 It seems something is wrong with my R-environment ? Could somebody provide a hint, what is wrong. Question 2) When I run an example commands from the manual library(ROCR) data(ROCR.simple) pred - prediction( ROCR.simple$predictions, ROCR.simple$labels ) perf - performance( pred, tpr, fpr ) plot( perf ) the plot command issues the following error message Error in as.double(y) : cannot coerce type 'S4' to vector of type 'double' How this could be fixed ? Thanks for the support -- View this message in context: http://www.nabble.com/Using-package-ROCR-tp22198213p22198213.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] Statistic community?
Hi there, I'm very glad to use the R-help mailing list for R-related question but more and more often I face general statistical problems. Does anyone know by chance a community (mailinglist, forum, ...) where I can ask these kind of questions? I'm glad for any link or hint :-) Antje __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 parser for If-else
Martin Maechler wrote: I think this is FAQ (or should become one): ?if [the help page you really should read before spending too much time or even post to R-help] ?if won't parse completely, you need ?'if' ;) vQ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] learning R
David, Wacek: Just so everyone knows, I just looked and this is explained quite clearly in the R Language Reference manual, very similarly to what Wacek did below. On Wed, Feb 25, 2009 at 3:42 AM, Wacek Kusnierczyk wrote: David Winsemius wrote: On Feb 24, 2009, at 11:36 PM, Fuchs Ira wrote: I was wondering why the following doesn't work: a=c(1,2) names(a)=c(one,two) a one two 1 2 names(a[2]) [1] two names(a[2])=too names(a) [1] one two a one two 1 2 I must not be understanding some basic concept here. Why doesn't the 2nd name change to too? I cannot tell you why, perhaps you are not actually working with the names of a, but I can show you that: names(a)[2] - too a[2] too 2 a one too 1 2 And this is seen as well in the help page examples. The help page also says the following, which I cannot understand: It is possible to update just part of the names attribute via the general rules: see the examples. This works because the expression there is evaluated as z - names-(z, [-(names(z), 3, c2)). the following: names(a[2]) = 'foo' has (partially) a functional flavour, in that you assign to the names of a *copy* of a part of a, while names(a)[2] = 'foo' does not have the flavour, in that you assign to the names of a; it seems, according to the man page you quote, to be equivalent to: a = 'names-'(a, '[-.'(names(a), 2, 'foo')) which proceeds as follows: tmp1 = names(a) # get a copy of the names of a, no effect on a tmp2 = '[-'(tmp1, 2, 'foo') # get a copy of tmp1 with the second element replaced with 'foo' # no effect on either a or tmp1 tmp3 = 'names-'(a, tmp2) # get a copy of a with its names replaced with tmp2 # no effect on either a, tmp1, or tmp2 a = tmp3 # backassign the result to a vQ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] learning R
Hi r-help-boun...@r-project.org napsal dne 25.02.2009 06:18:04: Hi Ira: For your first question, under the hood of R, names- is actually a function so , when you do that, you need to say names(a)[2] rather than names(a[2]). why this is is tricky and I wouldn't do it justice if i tried to explain it. it's best if you do ?names- at an R prompt and read that. For the second one, you can rbind x with anything that of length one and the recycling concept in R will add the extra now but maybe there's a better way that someone else will hopefully send. #== a=c(1,2) names(a)=c(one,two) names(a[2]) names(a)[2]-too names(a) #=== x=c(1,2,3) y=c(3,4,5) x - matrix(x,nrow=1) print(x) x - rbind(x,NA) x[2,] - y print(x) I can not resist to point out difference between matrices and data frames. For those who work with R are obvious but for newcomer using rbind or especially cbind with matrices or data frames can lead to nasty surprise when adding non numeric column to numeric matrix or values to data frame which have different type. See appropriate help page for rbind. Regards Petr On Tue, Feb 24, 2009 at 11:36 PM, Fuchs Ira wrote: I was wondering why the following doesn't work: a=c(1,2) names(a)=c(one,two) a one two 1 2 names(a[2]) [1] two names(a[2])=too names(a) [1] one two a one two 1 2 I must not be understanding some basic concept here. Why doesn't the 2nd name change to too? also unrelated: if I have two vectors and I want to combine them to form a matrix ,is cbind (or rbind) the most direct way to do this? e.g. x=c(1,2,3) y=c(3,4,5) z=rbind(x,y) alternatively: is there a way to make a matrix with dim=2,3 and then to replace the 2nd row with y something like this (which doesn't work but perhaps there is another way to do the equivalent?) attr(x,dim)=c(2,3) x[2,]=y __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] biplot.princomp - changing score labels
Prof Brian Ripley schrieb: On Tue, 24 Feb 2009, Axel Strauß wrote: OK, the one thing I figured out: Is should be like: biplot(test.pca, cex=c(2,1), col=c(red,green)... to change size, colours etc separately. But I still don't know how change lables of observations to symbols properly. That's not part of the design of the function, so just make a copy and edit to meet your fancies. The designer of biplot.princomp. The idea behind my question was actually not a styling one but to provide additional information in the graph. My observations have different species richness and I wanted to adopt symbol size to the number of species to show the change of species richness along the PCs. Anyway, thanks for the comment - and for designing biplot.princomp. Axel __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 interest group at Stellenbosch University formed: r...@sun
Hi I know this only affects a small number of subscribers, so I apologize to the Non Stellenbosch University subscribers for the noise. Two weeks ago, four R users met and discussed the possibility of forming an interest group of R users at SUN. The interest group (r...@sun) has the aim of: • Promote the use of R at SUN (Stellenbosch University); • Organize Hons stats courses using R; • Lobby for local R mirror; • Request R books for library; • Regular (monthly?) meetings to discuss R problems; aspects; new pack- ages; ...; • Special interest Group (r...@sun) seminars / workshops discussing special usages of R in more detail (genetics, GIS, SQL, ...); and • Offer seminars on R for departmental seminars et al. Our first official meeting will take place: WHEN: Wednesday, 4th of March at 14:00 WHERE: Ex Forestry Library, Paul Sauer Gebou Everybody is invited to attend. Please distribute this information as widely as possible. We have created a mailing list, r...@sympa.sun.ac.za You can subscribe to the mailing list either via the web interface https://sympa.sun.ac.za/wws/info/r or sending an email to sy...@sympa.sun.ac.za with subscribe r YourName in the body of the email. Please feel free to contact me if you have further questions me (Rainer Krug) rai...@krugs.de or, the easier solution, subscribe to the mailing list and post your question there. Hope to see you there, Rainer -- Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany) Centre of Excellence for Invasion Biology Natural Sciences Building Office Suite 2039 Stellenbosch University Main Campus, Merriman Avenue Stellenbosch South Africa Cell: +27 - (0)83 9479 042 Fax:+27 - (0)86 516 2782 Fax:+49 - (0)721 151 334 888 email: rai...@krugs.de Skype: RMkrug Google: r.m.k...@gmail.com I attach the Agenda for the meeting. Hope to see you all there, Rainer AgendaR@SUN_20090304.pdf Description: Adobe PDF document __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 : multiple regressions on columns
Hello and thanks for your reply, but as you said, this is not really what I'm trying to do. My purpose is not one of variable selection within a model with multiple predictors, but simply fitting a large number of models with only one predictor. I was just hoping there would be a solution as simple as the one given in my example which gives the results of many regression models of the type Yi~x where i spans all the colums in a matrix and x is one predictor. My objective being the fitting of many regression models of the type y~Xi where i spans all the columns in a matrix and y is one dependent variable. Best regards, David Gouache ARVALIS - Institut du végétal Station de La Minière 78280 Guyancourt Tel: 01.30.12.96.22 / Port: 06.86.08.94.32 -Message d'origine- De : Greg Snow [mailto:greg.s...@imail.org] Envoyé : mardi 24 février 2009 18:22 À : GOUACHE David; r-h...@stat.math.ethz.ch Objet : RE: multiple regressions on columns The add1 function might be what you want, there is also addterm in the MASS package and the leaps package can do some things along this line (plus more). But before doing this, you may want to ask yourself what question you are really trying to answer, then explore if this answers that question or not. -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r- project.org] On Behalf Of GOUACHE David Sent: Tuesday, February 24, 2009 10:13 AM To: r-h...@stat.math.ethz.ch Subject: [R] multiple regressions on columns R-helpers, A quick question regarding my wanting to run multiple regressions without writing a loop. Looking at a previous discussion : http://tolstoy.newcastle.edu.au/R/e2/help/07/02/9740.html my objective is to do the opposite, i.e. instead of having the same independent variable and testing it against multiple dependent variables, my goal is to test multiple independent variables against the same dependent variable. Using the iris dataset: iris4 - as.matrix(iris[,-c(1,5)]) summary(lm(iris4 ~ Sepal.Length, iris)) what I would have liked is to do the following : summary(lm(Sepal.Length ~ iris4, iris)) and obtain the results from 3 separate regressions, as above, instead of one multiple regression... Any clues ? Tanks in advance David Gouache ARVALIS - Institut du végétal Station de La Minière 78280 Guyancourt Tel: 01.30.12.96.22 / Port: 06.86.08.94.32 __ 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. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] learning R
markle...@verizon.net wrote: David, Wacek: Just so everyone knows, I just looked and this is explained quite clearly in the R Language Reference manual, very similarly to what Wacek did below. thanks, that's good, because i made it up following the page quoted by david, and if i'm flamed for nonsense, the langref has to be flamed too. vQ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] An error in fitting a non linear regression
Hi r-help-boun...@r-project.org napsal dne 24.02.2009 12:41:50: Hi Peter, You are totally right and it was a miscalculating and misunderstanding from me. Regarding the R-squared calculation of non linear model (question 2), is there any way to do that? I am not an expert statistician, Douglas Bates is so see his answer to similar question few years ago http://tolstoy.newcastle.edu.au/R/help/02b/0482.html Regards Petr Regards Saeed Petr Pikal wrote: Hi r-help-boun...@r-project.org napsal dne 24.02.2009 11:31:22: Hi, Thank you for the reply and suggestions. I have two questions? 1) If I want to use log, it seems that I have to take log from both sides of the model which will lead to lm(log(q)~log(-depth)). What is tehdifference between this syntax and lm(log(q) ~ I(-depth))? If you have y = a*exp(-b*x) then log of this equation is log(y) = log(a) - b * x at least I was told that by my teacher back at school some decades ago that log(exp(x)) = x. You can prove it by log(exp(whatever)) interactively in R Regards Petr 2) How can I calculate the R-squared of a fitted non linear model? Regards Saeed Christian Ritz-3 wrote: Hi Saeed, one approach is to try out several initial value combinations for a and b. It often helps to find initial values of the same order of magnitude and of the same sign as the final estimates. To get such initial values, you could linearize the model: lm(log(q) ~ I(-depth)) and supply the estimated coefficients from the linear regression as starting values: nreg - nls(q ~ a*exp(-b*depth), start = list(a = 0.76168, b = -0.08484)) summary(nreg) Christian __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- View this message in context: http://www.nabble.com/An-error-in-fitting-a-non- linear-regression-tp22118160p22179525.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. -- View this message in context: http://www.nabble.com/An-error-in-fitting-a-non- linear-regression-tp22118160p22180225.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] Odp: RE : multiple regressions on columns
Hi If you do not insist on matrix and use data frame instead lapply(iris4,function(x) lm(iris$Sepal.Length~x)) can do it Regards Petr r-help-boun...@r-project.org napsal dne 25.02.2009 09:56:25: Hello and thanks for your reply, but as you said, this is not really what I'm trying to do. My purpose is not one of variable selection within a model with multiple predictors, but simply fitting a large number of models with only one predictor. I was just hoping there would be a solution as simple as the one given in my example which gives the results of many regression models of the type Yi~x where i spans all the colums in a matrix and x is one predictor. My objective being the fitting of many regression models of the type y~Xi where i spans all the columns in a matrix and y is one dependent variable. Best regards, David Gouache ARVALIS - Institut du végétal Station de La Minière 78280 Guyancourt Tel: 01.30.12.96.22 / Port: 06.86.08.94.32 -Message d'origine- De : Greg Snow [mailto:greg.s...@imail.org] Envoyé : mardi 24 février 2009 18:22 À : GOUACHE David; r-h...@stat.math.ethz.ch Objet : RE: multiple regressions on columns The add1 function might be what you want, there is also addterm in the MASS package and the leaps package can do some things along this line (plus more). But before doing this, you may want to ask yourself what question you are really trying to answer, then explore if this answers that question or not. -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r- project.org] On Behalf Of GOUACHE David Sent: Tuesday, February 24, 2009 10:13 AM To: r-h...@stat.math.ethz.ch Subject: [R] multiple regressions on columns R-helpers, A quick question regarding my wanting to run multiple regressions without writing a loop. Looking at a previous discussion : http://tolstoy.newcastle.edu.au/R/e2/help/07/02/9740.html my objective is to do the opposite, i.e. instead of having the same independent variable and testing it against multiple dependent variables, my goal is to test multiple independent variables against the same dependent variable. Using the iris dataset: iris4 - as.matrix(iris[,-c(1,5)]) summary(lm(iris4 ~ Sepal.Length, iris)) what I would have liked is to do the following : summary(lm(Sepal.Length ~ iris4, iris)) and obtain the results from 3 separate regressions, as above, instead of one multiple regression... Any clues ? Tanks in advance David Gouache ARVALIS - Institut du végétal Station de La Minière 78280 Guyancourt Tel: 01.30.12.96.22 / Port: 06.86.08.94.32 __ 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. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R parser for If-else
WK == Wacek Kusnierczyk waclaw.marcin.kusnierc...@idi.ntnu.no on Wed, 25 Feb 2009 09:46:19 +0100 writes: WK Martin Maechler wrote: I think this is FAQ (or should become one): ?if [the help page you really should read before spending too much time or even post to R-help] WK ?if WK won't parse completely, you need WK ?'if' this depends on your GUI for R : In ESS (Emacs speaks statistics), ?if does work [but other non-standard versions of calling '?' do not; so I'm not claiming superiority of ESS here (but in general, of course, I do :-) ] Martin __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] [R-pkgs] leaps and biglm
New versions of leaps and biglm are percolating through CRAN. The new version of biglm fixes a bug in sandwich standard errors with weights, and adds predict(), deviance() and AIC() methods [based on code from Christophe Dutang]. The new version of leaps adds a regsubsets() method for biglm objects, so that the subset selection algorithms can be run efficiently on large data sets. -thomas Thomas Lumley Assoc. Professor, Biostatistics tlum...@u.washington.eduUniversity of Washington, Seattle ___ R-packages mailing list r-packa...@r-project.org https://stat.ethz.ch/mailman/listinfo/r-packages __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] learning R
a quick follow-up: e = new.env() e$a = 1 names(e) # NULL names(e) = 'a' # error in names(e) = foo : names() applied to a non-vector this is surprising. names(e) 'works', there is no complaint, but when names- is used, the error is about the use of names, not names-. btw. ?names says: Description: Functions to get or set the names of an object. Usage: names(x) names(x) - value Arguments: x: an R object. and there is no clarification in the rest of the page that x cannot be an environment, or that it has to be a vector. furthermore: p = pairlist(a=1) names(p) # a names(p) = 'b' # fine is.vector(p) # FALSE which is incoherent with the above error message, in that p is *not* a vector. vQ Wacek Kusnierczyk wrote: the following: names(a[2]) = 'foo' has (partially) a functional flavour, in that you assign to the names of a *copy* of a part of a, while names(a)[2] = 'foo' does not have the flavour, in that you assign to the names of a; it seems, according to the man page you quote, to be equivalent to: a = 'names-'(a, '[-.'(names(a), 2, 'foo')) which proceeds as follows: tmp1 = names(a) # get a copy of the names of a, no effect on a tmp2 = '[-'(tmp1, 2, 'foo') # get a copy of tmp1 with the second element replaced with 'foo' # no effect on either a or tmp1 tmp3 = 'names-'(a, tmp2) # get a copy of a with its names replaced with tmp2 # no effect on either a, tmp1, or tmp2 a = tmp3 # backassign the result to a __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Odp: Error in var(x, na.rm = na.rm) : no complete element pairs
Hi r-help-boun...@r-project.org napsal dne 22.02.2009 12:11:46: Hello all, I'm trying to calculate the standar desviation with sd(x,na.rm=TRUE) and I don't know why I have this error Error in var(x, na.rm = na.rm) : no complete element pairs when I try to calculate it, I have been looking for information about this error but nothing. Why it happens?. What can I do to fix it?. Thanks so much from Spain AFAIK nobody answered your question yet. Nor do I as I was not able to reproduce your error message and without it it is rather difficult to reveal what caused it. I suspect that x is not a vector but only you have means for checking it. Regards Petr Carlos Morales Diego __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] learning R
On Wed, 25 Feb 2009 09:57:36 +0100 Wacek Kusnierczyk waclaw.marcin.kusnierc...@idi.ntnu.no wrote: markle...@verizon.net wrote: David, Wacek: Just so everyone knows, I just looked and this is explained quite clearly in the R Language Reference manual, very similarly to what Wacek did below. thanks, that's good, because i made it up following the page quoted by david, and if i'm flamed for nonsense, the langref has to be flamed too. Actually, no. :) I do not remember the details, but I once tried to use the R Language Definition (I presume this is what we are talking about) to support my argument about some issue I had at that time. It was pointed out to me that the R Language Definition is a draft, hence not authoritative; and it seems its status of being a draft has not changed since. Cheers, Berwin __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] learning R
Berwin A Turlach wrote: On Wed, 25 Feb 2009 09:57:36 +0100 Wacek Kusnierczyk waclaw.marcin.kusnierc...@idi.ntnu.no wrote: markle...@verizon.net wrote: David, Wacek: Just so everyone knows, I just looked and this is explained quite clearly in the R Language Reference manual, very similarly to what Wacek did below. thanks, that's good, because i made it up following the page quoted by david, and if i'm flamed for nonsense, the langref has to be flamed too. Actually, no. :) I do not remember the details, but I once tried to use the R Language Definition (I presume this is what we are talking about) to support my argument about some issue I had at that time. It was pointed out to me that the R Language Definition is a draft, hence not authoritative; and it seems its status of being a draft has not changed since. ok, thanks for the explanation. i'll add the note 'draft version' to all my messages, so that i can always fall back on the explanation that they are not my final opinions. vQ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] learning R
Hi Wacek: Somewhere I remember reading that environments have functionality like lists EXCEPT for the names part. IIRC, I think that I read this in the R Language Reference manual also. On Wed, Feb 25, 2009 at 4:32 AM, Wacek Kusnierczyk wrote: a quick follow-up: e = new.env() e$a = 1 names(e) # NULL names(e) = 'a' # error in names(e) = foo : names() applied to a non-vector this is surprising. names(e) 'works', there is no complaint, but when names- is used, the error is about the use of names, not names-. btw. ?names says: Description: Functions to get or set the names of an object. Usage: names(x) names(x) - value Arguments: x: an R object. and there is no clarification in the rest of the page that x cannot be an environment, or that it has to be a vector. furthermore: p = pairlist(a=1) names(p) # a names(p) = 'b' # fine is.vector(p) # FALSE which is incoherent with the above error message, in that p is *not* a vector. vQ Wacek Kusnierczyk wrote: the following: names(a[2]) = 'foo' has (partially) a functional flavour, in that you assign to the names of a *copy* of a part of a, while names(a)[2] = 'foo' does not have the flavour, in that you assign to the names of a; it seems, according to the man page you quote, to be equivalent to: a = 'names-'(a, '[-.'(names(a), 2, 'foo')) which proceeds as follows: tmp1 = names(a) # get a copy of the names of a, no effect on a tmp2 = '[-'(tmp1, 2, 'foo') # get a copy of tmp1 with the second element replaced with 'foo' # no effect on either a or tmp1 tmp3 = 'names-'(a, tmp2) # get a copy of a with its names replaced with tmp2 # no effect on either a, tmp1, or tmp2 a = tmp3 # backassign the result to a __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 : RE : multiple regressions on columns
of course ! that was so obvious I didn't see it... thanks very much and sorry for the bother David Gouache ARVALIS - Institut du végétal Station de La Minière 78280 Guyancourt Tel: 01.30.12.96.22 / Port: 06.86.08.94.32 -Message d'origine- De : Petr PIKAL [mailto:petr.pi...@precheza.cz] Envoyé : mercredi 25 février 2009 10:09 À : GOUACHE David Cc : r-h...@stat.math.ethz.ch Objet : Odp: [R] RE : multiple regressions on columns Hi If you do not insist on matrix and use data frame instead lapply(iris4,function(x) lm(iris$Sepal.Length~x)) can do it Regards Petr r-help-boun...@r-project.org napsal dne 25.02.2009 09:56:25: Hello and thanks for your reply, but as you said, this is not really what I'm trying to do. My purpose is not one of variable selection within a model with multiple predictors, but simply fitting a large number of models with only one predictor. I was just hoping there would be a solution as simple as the one given in my example which gives the results of many regression models of the type Yi~x where i spans all the colums in a matrix and x is one predictor. My objective being the fitting of many regression models of the type y~Xi where i spans all the columns in a matrix and y is one dependent variable. Best regards, David Gouache ARVALIS - Institut du végétal Station de La Minière 78280 Guyancourt Tel: 01.30.12.96.22 / Port: 06.86.08.94.32 -Message d'origine- De : Greg Snow [mailto:greg.s...@imail.org] Envoyé : mardi 24 février 2009 18:22 À : GOUACHE David; r-h...@stat.math.ethz.ch Objet : RE: multiple regressions on columns The add1 function might be what you want, there is also addterm in the MASS package and the leaps package can do some things along this line (plus more). But before doing this, you may want to ask yourself what question you are really trying to answer, then explore if this answers that question or not. -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r- project.org] On Behalf Of GOUACHE David Sent: Tuesday, February 24, 2009 10:13 AM To: r-h...@stat.math.ethz.ch Subject: [R] multiple regressions on columns R-helpers, A quick question regarding my wanting to run multiple regressions without writing a loop. Looking at a previous discussion : http://tolstoy.newcastle.edu.au/R/e2/help/07/02/9740.html my objective is to do the opposite, i.e. instead of having the same independent variable and testing it against multiple dependent variables, my goal is to test multiple independent variables against the same dependent variable. Using the iris dataset: iris4 - as.matrix(iris[,-c(1,5)]) summary(lm(iris4 ~ Sepal.Length, iris)) what I would have liked is to do the following : summary(lm(Sepal.Length ~ iris4, iris)) and obtain the results from 3 separate regressions, as above, instead of one multiple regression... Any clues ? Tanks in advance David Gouache ARVALIS - Institut du végétal Station de La Minière 78280 Guyancourt Tel: 01.30.12.96.22 / Port: 06.86.08.94.32 __ 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. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] learning R
Thanks Berwin. You're correct in that I meant the R Language Definition. Well, it may be a draft but I read it for the first time a few months ago and it was very enlightening so, whether it's a draft or not, I highly recommend it. ( but not for total beginners. The R-intro is better for a more gentle introduction ). On Wed, Feb 25, 2009 at 4:34 AM, Berwin A Turlach wrote: On Wed, 25 Feb 2009 09:57:36 +0100 Wacek Kusnierczyk waclaw.marcin.kusnierc...@idi.ntnu.no wrote: markle...@verizon.net wrote: David, Wacek: Just so everyone knows, I just looked and this is explained quite clearly in the R Language Reference manual, very similarly to what Wacek did below. thanks, that's good, because i made it up following the page quoted by david, and if i'm flamed for nonsense, the langref has to be flamed too. Actually, no. :) I do not remember the details, but I once tried to use the R Language Definition (I presume this is what we are talking about) to support my argument about some issue I had at that time. It was pointed out to me that the R Language Definition is a draft, hence not authoritative; and it seems its status of being a draft has not changed since. Cheers, Berwin __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] leaps question
On Wed, 25 Feb 2009, Evelina Naryvska wrote: Colleagues, please help me with the simple question. How can I find R2 and p while doing best subsets regression? Also how can I see B and p for coefficients? You can't see coefficients or their p-values, because these are not computed. The subset selection algorithm does not actually fit all the models, it only works out what the residual sum of squares would be for the models. That is why it is fast. You have to actually fit the best models separately to get the coefficients, residuals, tests, and everything else. The summary() method for regsubsets objects returns an object that includes the other things you want. names(summary(a)) [1] which rsqrssadjr2 cp bicoutmat obj rsq is the r^2, rss is the residual sum of squares, adjr2 is the adjusted r^2, cp is Mallows' Cp, bic is the Schwartz Information Criterion. If you believed F-test p-values after subset selection you could compute them from the residual sum of squares. I wouldn't advise it. You could complain to the author of the package about the documentation. He seems to have forgotten to document summary.regsubsets(). -thomas Thomas Lumley Assoc. Professor, Biostatistics tlum...@u.washington.eduUniversity of Washington, Seattle __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Statistic community?
When discussions do burst out on the allstat list, people are usually pointed to one of the following alternatives: http://groups.google.com/group/MedStats http://datashaping.ning.com/forum HTH Heather Peters Gj (PSYCHOLOGY) wrote: Hey Antje list, Antje wrote: I'm very glad to use the R-help mailing list for R-related question but more and more often I face general statistical problems. Does anyone know by chance a community (mailinglist, forum, ...) where I can ask these kind of questions? I myself have recently started lurking at the Allstat and Stat-L lists. Stat-L does not seem very active, and my impression of Allstat is that it's mostly used for distributing information about conferences and vacancies. In addition, Allstat does not encourage discussion on-list - their rules ask you to reply to people in person. I myself prefer on-list discussions, as I frequently learn from these (just by lurking). So you could also try out these two lists - and if you find anything else, I would love to hear about them :-) Kind regards, Gjalt-Jorn --- Gjalt-Jorn Peters Work Social Psychology, faculty of Psychology Neuroscience, Maastricht 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-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 very large matrix
Dear friends, I have to use a very large matrix. Something of the sort of matrix(8,8,n) where n is something numeric of the sort 0.xx I have not found a way of doing it. I keep getting the error Error in matrix(nrow = 8, ncol = 8, 0.2) : too many elements specified Any suggestions? I have searched the mailing list, but to no avail. Best, -- Corrado Topi Global Climate Change Biodiversity Indicators Area 18,Department of Biology University of York, York, YO10 5YW, UK Phone: + 44 (0) 1904 328645, E-mail: ct...@york.ac.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] Inference for R Spam
Dieter Menne wrote: And, since my son asked me and I am basketball ignorant: Why are basketball scores mostly much too close to equality? The arguments (loose power when leading) Characteristic of the game. Possession of the ball changes rapidly and the probability of scoring is much higher given possession than in a game like soccer. The difference between winning and losing is largely a matter of not missing the frequent opportunities to score, whereas in soccer the difference is the ability to penetrate a much more effective defense. To see a similar thing within a sport, compare a tennis match between two power servers with one between two volley experts. Jim __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Using very large matrix
I have to use a very large matrix. Something of the sort of matrix(8,8,n) where n is something numeric of the sort 0.xx I have not found a way of doing it. I keep getting the error Error in matrix(nrow = 8, ncol = 8, 0.2) : too many elements specified Any suggestions? I have searched the mailing list, but to no avail. A 8x8 matrix has 6.4 billion cells. If you assume 4 byte (32bit) for a double precision floating point number that's an impressive 25.6 Gb. Certainly does not fit into RAM on my machine. cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik Technische Universität München Wissenschaftszentrum Weihenstephan 85350 Freising, Germany http://mips.gsf.de/staff/pagel __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Using very large matrix
Philipp Pagel wrote: I have to use a very large matrix. Something of the sort of matrix(8,8,n) where n is something numeric of the sort 0.xx I have not found a way of doing it. I keep getting the error Error in matrix(nrow = 8, ncol = 8, 0.2) : too many elements specified Any suggestions? I have searched the mailing list, but to no avail. A 8x8 matrix has 6.4 billion cells. If you assume 4 byte (32bit) for a double precision floating point number that's an impressive 25.6 Gb. Certainly does not fit into RAM on my machine. Doubles are 8 bytes, and R can't handle vectors that large, even if you have the memory. (Indices are limited to 32 bit values even in 64 bit R.) 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] Using very large matrix
On Wed, Feb 25, 2009 at 06:37:53AM -0500, Duncan Murdoch wrote: Philipp Pagel wrote: A 8x8 matrix has 6.4 billion cells. If you assume 4 byte (32bit) for a double precision floating point number that's an impressive 25.6 Gb. Certainly does not fit into RAM on my machine. Doubles are 8 bytes, Oops - of course. Even worse... cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik Technische Universität München Wissenschaftszentrum Weihenstephan 85350 Freising, Germany http://mips.gsf.de/staff/pagel __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Have a function like the _n_ in R ? (Automatic count function )
Have the counter function in R ? if we use the software SAS /*** SAS Code **/ data tmp(drop= i); retain seed x 0; do i = 1 to 5; call ranuni(seed,x); output; end; run; data new; counter=_n_; * this keyword _n_ ; set tmp; run; /* _n_ (Automatic variables) are created automatically by the DATA step or by DATA step statements. */ /*** Output counter seed x 1 5840432880.27197 2 9359029630.43581 3 3018795230.14057 4 7532125980.35074 5 1607264573 0.74844 / Have a function like the _n_ in R ? -- Nash - morri...@ibms.sinica.edu.tw __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Have a function like the _n_ in R ? (Automatic count function)
temp=data.frame(a=c(4,3,2,6),b=c(7,4,2,4))
temp
a b
1 4 7
2 3 4
3 2 2
4 6 4
temp$counter=1:nrow(temp)
temp
a b counter
1 4 7 1
2 3 4 2
3 2 2 3
4 6 4 4
Shubha Karanth | Amba Research
Ph +91 80 3980 8031 | Mob +91 94 4886 4510
Bangalore * Colombo * London * New York * San José * Singapore *
www.ambaresearch.com
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of Nash
Sent: Wednesday, February 25, 2009 5:55 PM
To: r-help
Subject: [R] Have a function like the _n_ in R ? (Automatic count function)
Have the counter function in R ?
if we use the software SAS
/*** SAS Code **/
data tmp(drop= i);
retain seed x 0;
do i = 1 to 5;
call ranuni(seed,x);
output;
end;
run;
data new;
counter=_n_; * this keyword _n_ ;
set tmp;
run;
/*
_n_ (Automatic variables)
are created automatically by the DATA step or by DATA step statements.
*/
/*** Output
counter seed x
1 5840432880.27197
2 9359029630.43581
3 3018795230.14057
4 7532125980.35074
5 1607264573 0.74844
/
Have a function like the _n_ in R ?
--
Nash - morri...@ibms.sinica.edu.tw
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Re: [R] Have a function like the _n_ in R ? (Automatic count function )
I think you can use seq function: seq(5) On Wed, Feb 25, 2009 at 9:25 AM, Nash morri...@ibms.sinica.edu.tw wrote: Have the counter function in R ? if we use the software SAS /*** SAS Code **/ data tmp(drop= i); retain seed x 0; do i = 1 to 5; call ranuni(seed,x); output; end; run; data new; counter=_n_; * this keyword _n_ ; set tmp; run; /* _n_ (Automatic variables) are created automatically by the DATA step or by DATA step statements. */ /*** Output counter seed x 1 5840432880.27197 2 9359029630.43581 3 3018795230.14057 4 7532125980.35074 5 1607264573 0.74844 / Have a function like the _n_ in R ? -- Nash - morri...@ibms.sinica.edu.tw __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] coxph: competing endpoints multiple time-dependent covariate
Dear R users: Analysis of the impact of a time-dependent covariate (GVHD or use of steroid after bone marrow transplantation) on two competing endpoints (invasive fungal infection and death) is frequently encountered in the setting of BMT data. Coxph package can be used as the following: for the analysis of GVHD: gvhd - coxph(Surv(start,stop,status = =1) ~ GVHD, data=bmt.data) and the data should be edited as the following: patient start stop status(IFI) GVHD 1 0 15 0 0 1 15 35 1 1 2 0 12 0 0 2 12 20 2 1 3 0 30 2 0 4 0 1000 0 5 0 25 0 0 5 25 1000 1 similarly, for steroid: steroid - coxph(Surv(start,stop,status = =1) ~ steroid, data=bmt.data) and the data was edited as the following: patient start stop status(IFI) steroid 1 0 16 0 0 1 16 35 1 1 2 0 13 0 0 2 13 20 2 1 3 0 14 0 0 3 14 30 2 1 4 0 1000 0 5 0 21 0 0 5 21 1000 1 I wonder how can I analyze the two risk factors (GVHD and steroid) concurrently? And how to edit the data. How can I manage it if a third baseline risk factor(age for example) was included? Thanks Yours sincerely Ping Zhang Feb 24 2009 [[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] error in dat
Prof Brian Ripley wrote:
On Mon, 16 Jun 2008, Wacek Kusnierczyk wrote:
Paul Adams wrote:
Hello everyone,
I have the following code which keeps giving me an error.
The code is:
dat-read.table(file=C:\\Documents and Settings\\Owner\\My
Documents\\eisen.txt,header=T,row.names=1,blank.lines.skip=F,na..strings=NA)
dimnames(dat)((1)) -as.character(dat(,1))
dat-dat(,-1)
dat-as.data.frame(dat)
file.show(file=C:\\Documents and Settings\\Owner\\My
Documents\\eisen.txt)
ann-read.table(file=C:\\Documents and Settings\\Owner\\My
Documents\\eisenClasses.txt,header=T)
file.show(file=C:\\Documents and Settings\\Owner\\My
Documents\\eisenClasses.txt)
cl-as.character(ann[,2])
dat-dat[,cl]
gc-cl(1:19)
act-cl(20:39)
x-as.numeric(dat(2000,gc))
y-as.numeric(dat(2000,act))
x-x(!is..na(x))
y-y(!is.na(y))
xy.list-list(x,y)
boxplot(xy.list,col=c(red,blue),main=Gene 2000)
The error is: error in eval .with.vis(expr, envir, enclos) :
could not find function dat
you misuse the syntax, check the docs. with 'dat(...)' r tries to apply
dat, but dat is a data frame, and is thus not applicable. what you want
is dat[...].
you can argue that the error message is misleading; unless you defined
one, r cannot find a function named 'dat', but it does find your data
frame, and it should complain about its non-applicability.
It is this explanation which is misleading. R (not r) looks for a
function named 'dat': it does not find the data frame when looking for
a function. To be explicit, when R encounters foo() it looks in the
current environment for a function named 'foo' and ignores all other
objects named 'foo' even if they are higher on the search path. This
was not the behaviour of Blue-Book S, but it has been the behvaviour
of S and R for many years.
are you sure it is not your explanation that is misleading? as far as i
can see, bindings for function objects are made in environments in just
the same way as for other kinds of objects.
when r looks for a function named 'foo', it checks, starting from the
current environment, for bindings for the name 'foo'; when it finds
one, it examines the corresponding value for its being a function
(roughly), and either successfully returns the value, or proceeds with
the enclosing environment. this is what can be seen in the sources
(simplified):
// starting at line 1223 in src/main/envir.c as of r48000
while (rho != R_EmptyEnv) {
...
vl = findVarInFrame3(rho, symbol, TRUE);
if (vl != R_UnboundValue) {
...
if (TYPEOF(vl) == CLOSXP || TYPEOF(vl) == BUILTINSXP ||
TYPEOF(vl) == SPECIALSXP)
return (vl);
...
}
...
}
clearly, appropriately named values *are* found and examined even if
they're not functions. this is also acknowledged in the following comment:
// starting at line 1208 in src/main/envir.c as of r48000
findFun
Search for a function in an environment This is a specially modified
version of findVar which ignores values its finds if they are not
functions.
note the 'finds'.
back to the original issue, your it does not find the data frame when
looking for a function. is *wrong*. r *does* find the data frame; r
ignores it because it is not a function, but it ignores it only *after*
the data frame has been *found* and *examined*. it searches further,
finds no function named 'dat', and complains.
to a naive user, the error message discussed above may be misleading.
if it said, e.g., that none of the objects named 'dat' is a function, it
might be easier for the user to find out what's wrong.
vQ
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Re: [R] how to NULL multiple variables of a df efficiently?
Wacek Kusnierczyk wrote: as above, this works as well: df[, vars] = list(NULL) and this, simplest of them all, works too: df[vars] = list(NULL) That's actually a curious anomaly/design-flaw/whatever... The usual rule is that you can treat data frames as lists, but aq - as.list(head(airquality)) aq[2:4] - list(NULL) aq $Ozone [1] 41 36 12 18 NA 28 $Solar.R NULL $Wind NULL $Temp NULL $Month [1] 5 5 5 5 5 5 $Day [1] 1 2 3 4 5 6 aq[2:4] - NULL aq $Ozone [1] 41 36 12 18 NA 28 $Month [1] 5 5 5 5 5 5 $Day [1] 1 2 3 4 5 6 #- whereas aq - head(airquality) aq[2:4] - NULL Error in `[-.data.frame`(`*tmp*`, 2:4, value = NULL) : replacement has 0 items, need 18 aq[2:4] - list(NULL) aq Ozone Month Day 141 5 1 236 5 2 312 5 3 418 5 4 5NA 5 5 628 5 6 It is not too strange that assigning list(NULL) differs since you can't have NULL columns in a data frame. It's more odd that assigning NULL to a set of variables fails to delete them. Not sure what the rationale (if any) for that might be. -- 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 ~~ - (p.dalga...@biostat.ku.dk) 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] Statistic community?
You might also try... http://groups.google.com/group/sci.stat.consult http://groups.google.com/group/sci.stat.edu http://groups.google.com/group/sci.stat.math Although I can't swear these don't overlap with some already mentioned. HTH Keith J Heather Turner heather.tur...@warwick.ac.uk wrote in message news:49a52167.10...@warwick.ac.uk... When discussions do burst out on the allstat list, people are usually pointed to one of the following alternatives: http://groups.google.com/group/MedStats http://datashaping.ning.com/forum HTH Heather Peters Gj (PSYCHOLOGY) wrote: Hey Antje list, Antje wrote: I'm very glad to use the R-help mailing list for R-related question but more and more often I face general statistical problems. Does anyone know by chance a community (mailinglist, forum, ...) where I can ask these kind of questions? I myself have recently started lurking at the Allstat and Stat-L lists. Stat-L does not seem very active, and my impression of Allstat is that it's mostly used for distributing information about conferences and vacancies. In addition, Allstat does not encourage discussion on-list - their rules ask you to reply to people in person. I myself prefer on-list discussions, as I frequently learn from these (just by lurking). So you could also try out these two lists - and if you find anything else, I would love to hear about them :-) Kind regards, Gjalt-Jorn --- Gjalt-Jorn Peters Work Social Psychology, faculty of Psychology Neuroscience, Maastricht 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] how to label the branches of a tree
When I execute that code, I get labels both on the branching points
and at the leaves of the tree. So I guess my reply is cannot
reproduce or do not understand. They are however not properly
positioned and the edges and bottoms of some of the labels are cut
off, but that did not sound like your question.
Using Mac OS X 10.5.6 and the ATT binary of R2.8.1. ‘rpart’ version
3.1-42.
--
David Winsemius
Note: your mailer is putting single quotes inside the enclosing angle
brackets so my mailer does not recognize the r-help address as a valid
address. Since this is the first time I have encountered this
construction, I wonder if your mailer is adhering to standards in its
reply-to functions.
On Feb 25, 2009, at 1:19 AM, Utkarsh Singhal wrote:
Hi,
I am using rpart package to fit classification trees.
library(rpart)
fit - rpart(Kyphosis ~ Age + Number + Start, data=kyphosis)
plot(fit,uniform=T)
text(fit, use.n=TRUE)
But I am unable to label the branches (not the nodes) of the tree.
Can somebody help me out in this?
Thank you,
Regards
Utkarsh Singhal | Amba Research
Ph +91 80 3980 8017 | Mob +91 99 0295 8815
Bangalore * Colombo * London * New York * San José * Singapore * www.ambaresearch.com
mailto:utkar...@ambaresearch.com
This e-mail may contain confidential and/or privileged i...{{dropped:
13}}
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Re: [R] Leave one out Cross validation (LOO)
Alex Roy wrote: Dear Frank, Thanks for your comments. But in my situation, I do not have any future data and I want to calculate Mean Square Error for prediction on future data. So, is it not it a good idea to go for LOO? thanks Alex With resampling you should be able to estimate any parameter including sigma. The Design package's validate.ols function can estimate sigma using the bootstrap or c-v, penalizing for backward stepdown variable selection, although I have found some counter-intuitive estimates of sigma using Efron's optimism bootstrap. Frank On Tue, Feb 24, 2009 at 7:15 PM, Frank E Harrell Jr f.harr...@vanderbilt.edu mailto:f.harr...@vanderbilt.edu wrote: Alex Roy wrote: Dear R user, I am working with LOO. Can any one who is working with leave one out cross validation (LOO) could send me the code? Thanks in advance Alex I don't think that LOO adequately penalizes for model uncertainty. I recommend the bootstrap or 50 repeats of 10-fold cross-validation. See for example the validate and calibrate functions in the R Design package. Frank -- __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] statistical significance of accuracy increase in classification
Monica, I have a few thoughts. - (I believe) it is usually better to put confidence in these metrics instead of relying on p-values. The intervals will allow you to make inferential statements and give you a way of characterizing the uncertainty in the estimates. You've seen how to do this with accuracy. For Kappa, there is probably an analytical formula for a CI, but I don;t know that it is in R. I would use the bootstrap (bia the boot or bootstrap package) to get intervals for kappa. - It sounds like some of the models were generated outside of R. I think that the sampling uncertainty can be large. In other words, if you were to do another training/test split, you would get different results so the CI for accuracy or kappa on a single test set don't really reflect this sampling noise. If you were doing models in R, I would suggest that you do many training/test splits and look at the distributions of those metrics. Max __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Have a function like the _n_ in R ? (Automatic count function )
The _n_ construct in SAS is most analogous to that of row names in R, accessible (and modifiable) via the row.names() function: DF - structure(list(Month = structure(c(2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 3L, 3L, 3L, 3L, 3L), .Label = c(Aug, July, Sept), class = factor), Week = 27:39, Estpassage = c(665L, 2232L, 9241L, 28464L, 41049L, 82216L, 230411L, 358541L, 747839L, 459682L, 609567L, 979475L, 837189L), MedFL = c(34L, 35L, 35L, 35L, 35L, 35L, 35L, 35L, 35L, 36L, 36L, 36L, 36L)), .Names = c(Month, Week, Estpassage, MedFL), class = data.frame, row.names = c(NA, -13L)) DF$counter - row.names(DF) DF Month Week Estpassage MedFL counter 1 July 2766534 1 2 July 28 223235 2 3 July 29 924135 3 4 July 30 2846435 4 5Aug 31 4104935 5 6Aug 32 8221635 6 7Aug 33 23041135 7 8Aug 34 35854135 8 9 Sept 35 74783935 9 10 Sept 36 45968236 10 11 Sept 37 60956736 11 12 Sept 38 97947536 12 13 Sept 39 83718936 13 Row names, however, not guaranteed to be integer, although if not specified at time of creation a dataframe will have its row names set to an ascending series of integer type. Another function that would provide similar utility for vectors might be seq_along().\, but in the case of dataframes, it may confuse the beginning R user because it will return a column oriented ascending sequence. seq_along(DF) [1] 1 2 3 4 5 -- David Winsemius On Feb 25, 2009, at 7:25 AM, Nash wrote: Have the counter function in R ? if we use the software SAS /*** SAS Code **/ data tmp(drop= i); retain seed x 0; do i = 1 to 5; call ranuni(seed,x); output; end; run; data new; counter=_n_; * this keyword _n_ ; set tmp; run; /* _n_ (Automatic variables) are created automatically by the DATA step or by DATA step statements. */ /*** Output counter seed x 1 5840432880.27197 2 9359029630.43581 3 3018795230.14057 4 7532125980.35074 5 1607264573 0.74844 / Have a function like the _n_ in R ? -- Nash - morri...@ibms.sinica.edu.tw __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] how to label the branches of a tree
On Wed, 25 Feb 2009, David Winsemius wrote: When I execute that code, I get labels both on the branching points and at the leaves of the tree. So I guess my reply is cannot reproduce or do not understand. They are however not properly positioned and the edges and bottoms of some of the labels are cut off, but that did not sound like your question. Try par(xpd), as mentioned in the help (?text.rpart): that also mentions a lot more ways to control the plot's appearance. Using Mac OS X 10.5.6 and the ATT binary of R2.8.1. ‘rpart’ version 3.1-42. The graphics device matters too. -- David Winsemius Note: your mailer is putting single quotes inside the enclosing angle brackets so my mailer does not recognize the r-help address as a valid address. Since this is the first time I have encountered this construction, I wonder if your mailer is adhering to standards in its reply-to functions. On Feb 25, 2009, at 1:19 AM, Utkarsh Singhal wrote: Hi, I am using rpart package to fit classification trees. library(rpart) fit - rpart(Kyphosis ~ Age + Number + Start, data=kyphosis) plot(fit,uniform=T) text(fit, use.n=TRUE) But I am unable to label the branches (not the nodes) of the tree. Can somebody help me out in this? Thank you, Regards Utkarsh Singhal | Amba Research -- Brian D. Ripley, rip...@stats.ox.ac.uk 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] read multiplan or sylk files in R
Hello, This may sound crazy, but I have a large number of Multiplan data files I'm in the process of recuperating, and I'm hoping to avoid having to open them one by one to convert them into a modern, directly usable format. So I was wondering if someone somewhere had encountered this and maybe had a way to read Multiplan files in R, or, at least, a way to read SYLK files directly in R. Any help appreciated. Thanks. David Gouache ARVALIS - Institut du végétal Station de La Minière 78280 Guyancourt Tel: 01.30.12.96.22 / Port: 06.86.08.94.32 __ 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] Have a function like the _n_ in R ? (Automatic count function )
And for completeness here's a function that returns the next integer
on each call.
n - (function(){
i - 0
function() {
i - i + 1
i
}
})()
n()
[1] 1
n()
[1] 2
n()
[1] 3
n()
[1] 4
n()
[1] 5
n()
[1] 6
;)
Hadley
On Wed, Feb 25, 2009 at 8:27 AM, David Winsemius dwinsem...@comcast.net wrote:
The _n_ construct in SAS is most analogous to that of row names in R,
accessible (and modifiable) via the row.names() function:
DF - structure(list(Month = structure(c(2L, 2L, 2L, 2L, 1L, 1L, 1L,
1L, 3L, 3L, 3L, 3L, 3L), .Label = c(Aug, July, Sept), class =
factor),
Week = 27:39, Estpassage = c(665L, 2232L, 9241L, 28464L,
41049L, 82216L, 230411L, 358541L, 747839L, 459682L, 609567L,
979475L, 837189L), MedFL = c(34L, 35L, 35L, 35L, 35L, 35L,
35L, 35L, 35L, 36L, 36L, 36L, 36L)), .Names = c(Month,
Week, Estpassage, MedFL), class = data.frame, row.names = c(NA,
-13L))
DF$counter - row.names(DF)
DF
Month Week Estpassage MedFL counter
1 July 27 665 34 1
2 July 28 2232 35 2
3 July 29 9241 35 3
4 July 30 28464 35 4
5 Aug 31 41049 35 5
6 Aug 32 82216 35 6
7 Aug 33 230411 35 7
8 Aug 34 358541 35 8
9 Sept 35 747839 35 9
10 Sept 36 459682 36 10
11 Sept 37 609567 36 11
12 Sept 38 979475 36 12
13 Sept 39 837189 36 13
Row names, however, not guaranteed to be integer, although if not specified
at time of creation a dataframe will have its row names set to an ascending
series of integer type. Another function that would provide similar utility
for vectors might be seq_along().\, but in the case of dataframes, it may
confuse the beginning R user because it will return a column oriented
ascending sequence.
seq_along(DF)
[1] 1 2 3 4 5
--
David Winsemius
On Feb 25, 2009, at 7:25 AM, Nash wrote:
Have the counter function in R ?
if we use the software SAS
/*** SAS Code **/
data tmp(drop= i);
retain seed x 0;
do i = 1 to 5;
call ranuni(seed,x);
output;
end;
run;
data new;
counter=_n_; * this keyword _n_ ;
set tmp;
run;
/*
_n_ (Automatic variables)
are created automatically by the DATA step or by DATA step statements.
*/
/*** Output
counter seed x
1 584043288 0.27197
2 935902963 0.43581
3 301879523 0.14057
4 753212598 0.35074
5 1607264573 0.74844
/
Have a function like the _n_ in R ?
--
Nash - morri...@ibms.sinica.edu.tw
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Re: [R] odfWeave problem Error in xmlEventParse
We should make this an FAQ (or find someone who knows how to correct the bug in XML). We've been working on that. It's hard to say what the problem is without the output of sessionInfo() and a reproducible example. Fredrik - if you can send me this off-list, I'll take a look (but it may take me a few days to get to it). -- Max __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] [R-pkgs] ggplot2 0.8.2
ggplot2 ggplot2 is a plotting system for R, based on the grammar of graphics, which tries to take the good parts of base and lattice graphics and avoid bad parts. It takes care of many of the fiddly details that make plotting a hassle (like drawing legends) as well as providing a powerful model of graphics that makes it easy to produce complex multi-layered graphics. Find out more at http://had.co.nz/ggplot2, and check out the nearly 500 examples of ggplot in use. If you're interested, you can also sign up to the ggplot2 mailing list at http://groups.google.com/group/ggplot2, or track development at http://github.com/hadley/ggplot2 ggplot2 0.8.2 (2008-02-23) New features * borders, fortify.map and map_data to make it easier to draw map borders and choropleth maps * cut_interval and cut_number utility functions to discretise continuous variables * stat_summary has reparameterised to make it easier to specify different summary functions. It now has four parameters: fun.y, fun.ymin and fun.ymax; and fun.data. See the documentation for stat_summary for more details Minor improvements * ggfluctuation: default to aspect ratio that produces squares * ggsave: filename now first parameter, not second * qplot: if sample aesthetic is used, stat automatically set to qq * scale_datetime: improved breaks calculation * scale_gradient: better default colour scheme from red to blue (thanks to Charlotte Wickham for providing the Munsell colours) * scale_size and scale_area: increased default size range * stats: all give useful error message if missing a required aesthetic * theme_set warns if missing needed theme elements * theme_text: now possible to right and left align text with hjust=0 and hjust=1 respectively Bug fixes * be explicit about plyr::is.discrete to avoid clash with Hmisc * facet_wrap: work around R bug so no longer crashers when ncol = 1 * geom_errorbar now works correctly with dashed lines * geom_path will now silently ignore lines with less than 2 points (instead of throwing a mysterious error as before) * geom_path now responds to the size aesthetic once more * geom_polygon etc now correctly displays linetype on legends * geom_step now works with multiple groups * geom_vline and geom_hline: fix bug when mapping intercept to variable in data frame * ggsave: path parameter correctly sets path * guides: fix broken legend from default stat aesthetics (e.g. for stat_sum) * scale_manual now works better with missing values * scale_manual: labels now correctly sets legend labels. * stat_density_2d: no longer passes unnecessary parameters to kde2d causing an error message (seen when setting aesthetics with qplot) * stat_pointrange: better relationship between point and line widths * stat_sum now correctly preserves other aesthetic columns (should be a bit faster too) Regards, Hadley -- http://had.co.nz/ ___ R-packages mailing list r-packa...@r-project.org https://stat.ethz.ch/mailman/listinfo/r-packages __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] statistical significance of accuracy increase in classification
Max, thanks for the reply. Yes, the models are done outside R (i will see what i can do to run some of them inside R in the future ) and the sampling is extremely skewed. But we use as truth or reference results from a field exercise where people actually went and gave detailed description of the locations visited. This was very much depended on accessibility of the site, which in majority is not. Unfortunately when results get reported to managers they do care about accuracy for example, but less about CI and even less about the skewed sampling unless i can prove that this gives unacceptable results. Do you know about any good reference that discusses kappa for classification and maybe CI for kappa??? Thanks again for your input, Monica Date: Wed, 25 Feb 2009 09:01:23 -0500 Subject: Re: [R] statistical significance of accuracy increase in classification From: mxk...@gmail.com To: pisican...@hotmail.com CC: r-help@r-project.org Monica, I have a few thoughts. - (I believe) it is usually better to put confidence in these metrics instead of relying on p-values. The intervals will allow you to make inferential statements and give you a way of characterizing the uncertainty in the estimates. You've seen how to do this with accuracy. For Kappa, there is probably an analytical formula for a CI, but I don;t know that it is in R. I would use the bootstrap (bia the boot or bootstrap package) to get intervals for kappa. - It sounds like some of the models were generated outside of R. I think that the sampling uncertainty can be large. In other words, if you were to do another training/test split, you would get different results so the CI for accuracy or kappa on a single test set don't really reflect this sampling noise. If you were doing models in R, I would suggest that you do many training/test splits and look at the distributions of those metrics. Max _ ore_022009 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Have a function like the _n_ in R ? (Automatic count function )
On Wed, Feb 25, 2009 at 8:41 AM, Wacek Kusnierczyk
waclaw.marcin.kusnierc...@idi.ntnu.no wrote:
hadley wickham wrote:
And for completeness here's a function that returns the next integer
on each call.
n - (function(){
i - 0
function() {
i - i + 1
i
}
})()
actually, you do not need the external function to have the functionality:
n = local({
i = 0
function() (i - i + 1)[1] })
n()
# 1
n()
# 2
Yes, I'm just using the function as a way of creating an environment.
The function method is a little more flexible if you want multiple
independent counters though.
Hadley
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[R] C-index for models fitted using start, stop in Surv?
Dear R-users, One can use the rcorr.cens function in Design to compute the C index when only the stop time is indicated (I think implicitely start=0 in that case). When the start and stop times are used in a Surv object, e.g. library(Design) S=with(heart, Surv(start,stop,event)) the object returned is no longer a single number vector, so none of the following ways to compare a model fit to S makes sense: rcorr.cens(-cph(S~ age+transplant+surgery, heart)$linear.predictors, with(heart, Surv(start,stop,event))) # C IndexDxy S.D. nmissing # 4.95e-01 -9.66e-03 7.15e-02 1.72e+02 0.00e+00 #this seems bad because it compares the fit to a different Surv than the one used to fit it (S, above) rcorr.cens(-cph(S~ age+transplant+surgery, heart)$linear.predictors, with(heart, Surv(stop-start,event))) # C IndexDxy S.D. nmissing # 6.02e-01 2.03e-01 7.54e-02 1.72e+02 0.00e+00 Is there some way I can compute the correlation for this type of survival time specification in R? If not, does anybody have some tips on how to go about computing it myself? Many Thanks Eleni Rapsomaniki Research Associate Strangeways Research Laboratory Department of Public Health and Primary Care University of Cambridge __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Have a function like the _n_ in R ? (Automatic count function )
On Wed, Feb 25, 2009 at 3:30 PM, hadley wickham h.wick...@gmail.com wrote:
And for completeness here's a function that returns the next integer
on each call.
n - (function(){
i - 0
function() {
i - i + 1
i
}
})()
n()
[1] 1
n()
[1] 2
n()
[1] 3
n()
[1] 4
n()
[1] 5
n()
[1] 6
;)
Hadley
*headache*!
I can't wrap my head around this one - too strange code!
Could someone please give a hint on what's going on?
How doesi- i+1 modify i permanently, seeing as i is defined as 0
to start with?
/Gustaf
--
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tel: +46(0)703 051 451
address:Essingetorget 40,112 66 Stockholm, SE
skype:gustaf_rydevik
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[R] Have any way to write a funtion into a list ?
Have any way to write a funtion into a list ? -- Nash - morri...@ibms.sinica.edu.tw __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Have any way to write a funtion into a list ?
On Wed, Feb 25, 2009 at 11:11:51PM +0800, Nash wrote:
Have any way to write a funtion into a list ?
You can do that the same way you would use with any other object:
foo - function(x){x^2}
foo(12)
[1] 144
a - list(foo, 12, 'as')
a
[[1]]
function(x){x^2}
[[2]]
[1] 12
[[3]]
[1] as
cu
Philipp
--
Dr. Philipp Pagel
Lehrstuhl für Genomorientierte Bioinformatik
Technische Universität München
Wissenschaftszentrum Weihenstephan
85350 Freising, Germany
http://mips.gsf.de/staff/pagel
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[R] How to make warning message colorful (or have sound)?
Dear R-helpers: I am new to R and wonder how to make a warning message colorful (if possible, having sound is also welcome). I did some research and failed to see options to allow this functionality. Is this a techical limitation so far, or I miss some information. Many thanks in advance. -sean [[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 label the branches of a tree
You may have to change/scale the sizes of the font by using cex and
then to keep all labels within the plotting window, use xpd=TRUE.
Like in
text(fit, use.n=TRUE, cex=0.8, xpd=TRUE)
Philip
--
A Smile costs Nothing But Rewards Everything
- Anonymous
Happiness is not perfected until it is shared
-Jane Porter
--- On Wed, 2/25/09, David Winsemius dwinsem...@comcast.net wrote:
From: David Winsemius dwinsem...@comcast.net
Subject: Re: [R] how to label the branches of a tree
To: Utkarsh Singhal utkar...@ambaresearch.com
Cc: R-help Forum r-help@r-project.org
Date: Wednesday, February 25, 2009, 7:28 AM
When I execute that code, I get labels both on the branching points and at the
leaves of the tree. So I guess my reply is cannot reproduce or
do not understand. They are however not properly positioned and the
edges and bottoms of some of the labels are cut off, but that did not sound like
your question.
Using Mac OS X 10.5.6 and the ATT binary of R2.8.1. rpart version 3.1-42.
--David Winsemius
Note: your mailer is putting single quotes inside the enclosing angle brackets
so my mailer does not recognize the r-help address as a valid address. Since
this is the first time I have encountered this construction, I wonder if your
mailer is adhering to standards in its reply-to functions.
On Feb 25, 2009, at 1:19 AM, Utkarsh Singhal wrote:
Hi,
I am using rpart package to fit classification trees.
library(rpart)
fit - rpart(Kyphosis ~ Age + Number + Start, data=kyphosis)
plot(fit,uniform=T)
text(fit, use.n=TRUE)
But I am unable to label the branches (not the nodes) of the tree. Can
somebody help me out in this?
Thank you,
Regards
Utkarsh Singhal | Amba Research
Ph +91 80 3980 8017 | Mob +91 99 0295 8815
Bangalore * Colombo * London * New York * San José * Singapore *
www.ambaresearch.com mailto:utkar...@ambaresearch.com
This e-mail may contain confidential and/or privileged i...{{dropped:13}}
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[[alternative HTML version deleted]]
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Re: [R] Have any way to write a funtion into a list ?
Nash wrote: Have any way to write a funtion into a list ? Sure: A - list(mean, var) A[[1]](1:2) # 1.5 A[[2]](1:2) # 0.5 Uwe Ligges -- Nash - morri...@ibms.sinica.edu.tw __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Have a function like the _n_ in R ? (Automatic count function )
On Wed, 25 Feb 2009, Gustaf Rydevik wrote:
On Wed, Feb 25, 2009 at 3:30 PM, hadley wickham h.wick...@gmail.com wrote:
And for completeness here's a function that returns the next integer
on each call.
n - (function(){
i - 0
function() {
i - i + 1
i
}
})()
n()
[1] 1
n()
[1] 2
n()
[1] 3
n()
[1] 4
n()
[1] 5
n()
[1] 6
;)
Hadley
*headache*!
I can't wrap my head around this one - too strange code!
Could someone please give a hint on what's going on?
How doesi- i+1 modify i permanently, seeing as i is defined as 0
to start with?
i is not _defined_ as zero. It is initially _assigned_ the value of zero
and is subsequently assigned other values.
As for the details of what goes here, see
An Introduction to R
Section 10.7 Scope
and study the open.acount() example there.
HTH,
Chuck
/Gustaf
--
Gustaf Rydevik, M.Sci.
tel: +46(0)703 051 451
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skype:gustaf_rydevik
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Charles C. Berry(858) 534-2098
Dept of Family/Preventive Medicine
E mailto:cbe...@tajo.ucsd.edu UC San Diego
http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego 92093-0901
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[R] Data Envelopment Analysis in R
How do I do a data envelopment analysis in R...provide me with the step by step procedure for that..thanks in advance... Arup -- View this message in context: http://www.nabble.com/Data-Envelopment-Analysis-in-R-tp22199360p22199360.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Using very large matrix
looks like you've run out of memory mate, because that sure is a big matrix, you'd probably need 64 bit OS/CPU/R and loads of RAM. see thread: http://www.nabble.com/Error-in-matrix:--too-many-elements-specified-td20457910.html I know there are some packages on cran which help with large datasets, but i haven't got around to using them myself (yet). from: http://cran.r-project.org/web/views/HighPerformanceComputing.html [quote start...] Large memory and out-of-memory data * The bigmemory package by Kane and Emerson permits storing large objects such as matrices in memory and uses external pointer objects to refer to them. This permits transparent access from R without bumping against R's internal memory limits. Several R processes on the same computer can also shared big memory objects. * A large number of database packages, and database-alike packages (such as sqldf by Grothendieck) are also of potential interest but not (yet?) reviewed here. [quote end.] Just for fun, i just tried (for the first time): library(bigmemory) big.matrix(nrow=8, ncol=8, type='double') but i ended up crashing out of R on my low spec windows XP uni laptop :D hope that helps a little, Tony Breyal On 25 Feb, 11:04, Corrado ct...@york.ac.uk wrote: Dear friends, I have to use a very large matrix. Something of the sort of matrix(8,8,n) where n is something numeric of the sort 0.xx I have not found a way of doing it. I keep getting the error Error in matrix(nrow = 8, ncol = 8, 0.2) : too many elements specified Any suggestions? I have searched the mailing list, but to no avail. Best, -- Corrado Topi Global Climate Change Biodiversity Indicators Area 18,Department of Biology University of York, York, YO10 5YW, UK Phone: + 44 (0) 1904 328645, E-mail: ct...@york.ac.uk __ r-h...@r-project.org mailing listhttps://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guidehttp://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] All the products of common factors
On Wed, Feb 25, 2009 at 9:25 AM, Fox, Gordon g...@cas.usf.edu wrote: The tricky part isn't finding the common factors -- we knew how to do that, though not in so concise a fashion as some of these suggestions. It was finding all their products without what I (as a recovered Fortran programmer) would call truly brute force. Several of these suggestions solve the problem nicely! Are you sure you are not confusing *prime factors* with *factors*? My understanding is that you are looking for all the factors of A which are also factors of B, i.e. the common factors of A and B. Why else would you be computing all those products? -s __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] How to get JRI to work from my NetBeans
Hi, I need your help. I have downloaded a precompiled JRI as part of rJava. I have included rJava as part of my R package libraries. Now I need to be able to work with some R functions from my Java apps. I'm using NetBeans on Windows. I have followed some instructions from http://www.rforge.net/JRI/ but i keep on getting errors when compiling my Java app as follows: run: Cannot find JRI native library! Please make sure that the JRI native library is in a directory listed in java.library.path. java.lang.UnsatisfiedLinkError: no jri in java.library.path at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1709) at java.lang.Runtime.loadLibrary0(Runtime.java:823) at java.lang.System.loadLibrary(System.java:1030) at org.rosuda.JRI.Rengine.clinit(Rengine.java:9) at rtest.main(rtest.java:61) Java Result: 1 BUILD SUCCESSFUL (total time: 0 seconds) Can anyone help me with detailed steps to solve the problem? Thanks. -- Yakub [[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] Linear Discriminant Analysis
Kindly let me know the process to carry out a Linear discriminant analysis...thanks in advance Arup -- View this message in context: http://www.nabble.com/Linear-Discriminant-Analysis-tp22199424p22199424.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] read and reshape time series table with empty items
Dear useR's, I have a problem to read data (daily precipitation). The data are formated in months by columns wich leads to empty items in months with less then 31 days. What i did was reading the file and try to reshape the object a- read.table(nds.txt, header=TRUE, sep=;, dec = ., na.string=NA) ar-reshape(a, timevar=month,varying=list(c(Jan,Febr,März,April,Mai,Juni,Juli,Aug,Sept,Okt,Nov,Dez)),direction=long) My problem is: months are rowed instead of years (78Jan,79Jan,...,79Dec,80Dec) empty items (like Feb30 and Feb31) are filled with NA My aim is toget a simple data frame ore time series with format: Date,value 1979/4/1;0.6 1979/4/2;0.0 ... 1980/4/1;1.2 1980/4/1;1.3 1980/4/1;0.0 The data I've got have been excel tables for each year. I transformed them to a text file that looks like: #Precipitation in mm like in nds.txt Jahr;Tag;Jan;Febr;März;April;Mai;Juni;Juli;Aug;Sept;Okt;Nov;Dez 1978;1;NA;NA;NA;0.0;5.5;0.0;11.8;0.0;2.4;6.4;0.0;0.0 1978;2;NA;NA;NA;0.0;0.5;0.0;2.0;2.0;0.0;9.0;0.0;0.0 1978;3;NA;NA;NA;0.3;0.0;3.0;3.2;0.4;0.0;24.7;0.0;0.0 1978;4;NA;NA;NA;0.7;0.0;0.0;24.4;1.1;0.0;8.6;0.0;0.0 1978;5;NA;NA;NA;11.8;2.2;0.0;17.0;0.0;0.0;0.0;0.0;0.0 1978;6;NA;NA;NA;0.5;0.5;0.0;4.5;4.4;10.6;0.0;0.0;0.0 1978;7;NA;NA;NA;0.0;6.5;0.0;0.5;29.0;9.4;0.0;0.0;0.0 1978;8;NA;NA;1.0;0.0;7.3;4.0;0.0;6.0;6.7;0.0;0.0;7.0 1978;9;NA;NA;4.0;0.3;2.0;3.5;2.7;0.4;2.9;0.0;0.0;0.0 1978;10;NA;NA;0.0;1.5;2.4;19.5;0.5;1.8;0.5;0.0;0.0;0.0 1978;11;NA;NA;3.8;9.0;2.8;0.0;4.0;0.0;0.0;0.0;0.0;0.0 1978;12;NA;NA;0.0;6.8;3.5;0.0;2.5;0.0;11.3;0.0;0.0;3.0 1978;13;NA;NA;1.3;2.8;5.4;3.8;2.3;3.4;0.5;0.0;0.0;1.0 1978;14;NA;NA;0.7;1.0;0.3;0.2;7.9;0.0;0.0;0.0;0.0;1.0 1978;15;NA;NA;3.7;2.7;4.8;0.0;4.2;0.0;0.0;0.0;0.0;0.0 1978;16;NA;NA;13.7;2.8;0.0;1.4;0.0;5.5;0.0;0.0;0.5;1.8 1978;17;NA;NA;0.0;1.5;3.8;2.3;0.0;2.3;0.0;3.5;0.0;0.0 1978;18;NA;NA;0.0;0.0;1.0;0.0;11.6;0.0;0.5;5.3;0.0;0.0 1978;19;NA;NA;1.0;0.0;7.0;0.0;1.1;0.0;0.0;0.0;0.0;4.0 1978;20;NA;NA;17.5;0.0;0.5;0.2;0.0;0.0;0.0;0.0;0.0;0.3 1978;21;NA;NA;1.0;1.5;4.5;0.0;2.6;0.0;0.0;0.0;0.0;0.7 1978;22;NA;NA;0.5;0.0;12.0;1.6;0.0;0.0;0.2;1.7;0.0;3.5 1978;23;NA;NA;4.0;0.5;5.8;5.8;0.0;0.0;13.0;3.7;0.0;1.3 1978;24;NA;NA;0.8;0.0;12.0;24.3;0.0;0.0;3.3;0.0;0.0;0.0 1978;25;NA;NA;0.0;0.0;0.0;4.4;0.0;0.0;0.0;0.0;0.0;0.0 1978;26;NA;NA;5.0;0.0;0.5;0.2;1.0;0.0;0.0;6.0;5.7;0.0 1978;27;NA;NA;2.2;6.0;0.0;1.3;9.8;0.0;2.3;3.0;2.9;0.0 1978;28;NA;NA;0.7;1.8;0.0;0.4;0.0;0.0;5.4;0.0;1.5;0.0 1978;29;NA;;0.0;0.5;0.5;0.0;0.0;4.0;3.5;0.0;0.0;3.5 1978;30;NA;;0.0;1.0;0.0;0.0;0.0;6.0;6.1;0.0;0.0;1.5 1978;31;NA;;0.0;;0.0;;0.0;1.5;;0.0;;0.9 1979;1;3.5;1.0;0.5;NA;NA;0.1;0.0;0.5;0.0;0.0;0.0;0.0 1979;2;0.3;0.0;0.0;NA;NA;0.7;2.7;0.5;0.0;0.0;1.6;0.0 1979;3;0.5;2.7;0.0;NA;NA;0.0;3.0;2.5;1.0;0.0;1.0;0.0 1979;4;0.0;0.9;0.3;NA;NA;0.0;0.9;3.0;0.1;0.0;0.0;0.0 1979;5;0.0;2.2;0.0;NA;NA;0.0;0.0;0.0;0.0;0.6;3.5;0.0 1979;6;0.0;1.0;0.0;NA;NA;0.1;0.0;0.4;0.0;1.7;11.5;0.0 1979;7;0.0;1.0;0.0;NA;NA;1.0;0.6;0.0;0.0;0.0;5.0;0.0 1979;8;0.0;0.7;0.3;NA;NA;1.8;6.5;7.5;6.8;0.0;3.5;0.0 1979;9;3.5;1.8;0.8;NA;NA;0.2;9.3;2.2;4.3;0.0;6.5;0.9 1979;10;0.0;1.2;18.8;NA;NA;1.0;11.0;7.0;0.2;0.0;9.0;2.0 1979;11;1.2;1.0;7.8;NA;NA;3.4;0.0;1.4;0.0;0.3;0.0;12.0 1979;12;0.8;0.5;1.8;NA;NA;1.0;7.0;2.3;0.0;0.0;0.3;2.5 1979;13;1.4;0.0;0.0;NA;NA;3.2;3.0;0.0;0.0;5.3;0.0;0.0 1979;14;0.0;0.0;NA;NA;NA;30.5;0.7;0.0;3.3;4.6;0.8;3.9 1979;15;0.0;13.5;NA;NA;NA;1.4;0.0;0.0;2.2;19.0;8.0;3.4 1979;16;0.5;1.5;NA;NA;NA;20.2;0.0;0.0;0.0;1.2;6.8;1.8 1979;17;0.5;5.5;NA;NA;NA;14.8;4.0;5.5;0.0;11.1;9.8;1.4 1979;18;0.0;3.5;NA;NA;NA;2.0;0.0;14.5;0.0;0.0;3.0;0.8 1979;19;0.0;0.0;NA;NA;NA;0.0;4.0;0.0;0.0;0.0;6.0;4.0 1979;20;0.0;0.0;NA;NA;NA;0.0;6.2;1.0;2.3;0.0;6.2;1.2 1979;21;0.0;0.0;NA;NA;NA;0.0;0.0;0.0;36.0;0.0;1.0;4.0 1979;22;0.0;0.0;NA;NA;NA;0.0;0.0;0.0;35.9;0.8;8.0;17.0 1979;23;2.3;0.0;NA;NA;NA;0.0;0.0;1.5;4.6;5.8;0.0;3.0 1979;24;0.0;0.0;NA;NA;NA;0.0;0.0;27.3;1.9;0.0;0.0;1.0 1979;25;0.5;0.0;NA;NA;NA;0.7;0.0;0.8;0.0;0.0;0.0;0.0 1979;26;4.0;0.0;NA;NA;0.0;2.0;0.0;2.1;0.0;0.0;0.0;0.0 1979;27;11.5;0.0;NA;NA;4.5;3.6;0.0;0.0;0.0;0.0;4.0;0.0 1979;28;3.0;2.0;NA;NA;0.0;1.1;1.0;0.5;0.0;3.6;0.0;0.0 1979;29;0.8;;NA;NA;0.0;0.0;5.0;0.0;0.0;0.6;0.0;0.0 1979;30;0.8;;NA;NA;0.0;0.0;5.4;0.0;0.0;1.8;0.0;0.0 1979;31;0.4;;NA;;1.7;;15.5;0.0;;0.4;;0.0 1980;1;NA;NA;NA;NA;NA;0.6;0.0;0.0;1.0;0.0;0.0;NA 1980;2;NA;NA;NA;NA;NA;0.5;0.0;0.0;0.0;1.5;0.0;NA 1980;3;NA;NA;NA;NA;NA;0.7;3.6;0.0;0.0;0.0;0.0;NA 1980;4;NA;NA;NA;NA;NA;17.2;0.0;6.5;0.0;0.0;2.2;NA 1980;5;NA;NA;NA;NA;NA;0.0;0.0;0.0;0.0;0.0;0.7;NA 1980;6;NA;NA;NA;NA;NA;0.5;0.0;0.0;6.4;0.0;NA;NA 1980;7;NA;NA;NA;NA;0.0;0.0;2.3;0.0;0.0;0.5;NA;NA 1980;8;NA;NA;NA;NA;2.3;2.3;2.8;10.5;0.0;10.5;NA;NA 1980;9;NA;NA;NA;NA;6.7;2.2;21.0;0.0;3.8;7.8;NA;NA 1980;10;NA;NA;NA;NA;0.9;2.7;3.5;0.0;2.2;2.3;NA;NA 1980;11;NA;NA;NA;NA;0.9;1.2;0.3;0.0;4.0;3.4;NA;NA 1980;12;NA;NA;NA;NA;0.0;0.0;0.0;5.0;0.0;1.5;NA;NA 1980;13;NA;NA;NA;NA;0.0;0.0;3.5;0.0;0.0;0.0;NA;NA 1980;14;NA;NA;NA;NA;8.3;0.0;0.0;0.0;0.0;0.0;NA;NA 1980;15;NA;NA;NA;NA;19.0;2.0;0.5;1.3;0.0;0.0;NA;NA
[R] survival::predict.coxph
Hi, if I got it right then the survival-time we expect for a subject is the integral over the specific survival-function of the subject from 0 to t_max. If I have a trained cox-model and want to make a prediction of the survival-time for a new subject I could use survfit(coxmodel, newdata=newSubject) to estimate a new survival-function which I have to integrate thereafter. Actually I thought predict(coxmodel, newSubject) would do this for me, but I´m confused which type I have to declare. If I understand the little pieces of documentation right then none of the available types is exactly the predicted survival-time. I think I have to use the mean survival-time of the baseline-function times exp(the result of type linear predictor). Am I right? Regards Bernhard __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] read multiplan or sylk files in R
According to the microsoft site http://support.microsoft.com/kb/323626;, SYLK files are ordinary text or csv files with a peculiar character in that the first two characters of the file are the uppercase letters. For example for a csv file, the first column may contain the variable identity written as ID. Excel would indicate this as a SYLK file. The way around this is to change the variable name to lower case id then you can save this file in any format that is readable to R. Have a great day. -- A Smile costs Nothing But Rewards Everything - Anonymous Happiness is not perfected until it is shared -Jane Porter --- On Wed, 2/25/09, GOUACHE David d.goua...@arvalisinstitutduvegetal.fr wrote: From: GOUACHE David d.goua...@arvalisinstitutduvegetal.fr Subject: [R] read multiplan or sylk files in R To: r-h...@stat.math.ethz.ch Date: Wednesday, February 25, 2009, 7:48 AM Hello, This may sound crazy, but I have a large number of Multiplan data files I'm in the process of recuperating, and I'm hoping to avoid having to open them one by one to convert them into a modern, directly usable format. So I was wondering if someone somewhere had encountered this and maybe had a way to read Multiplan files in R, or, at least, a way to read SYLK files directly in R. Any help appreciated. Thanks. David Gouache ARVALIS - Institut du végétal Station de La Minière 78280 Guyancourt Tel: 01.30.12.96.22 / Port: 06.86.08.94.32 __ 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. [[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 label the branches of a tree
Hi David,
May be I was not clear, but I want to label the branches itself and not the
branching points or the leaves.
Regards
Utkarsh
From: Philip Twumasi-Ankrah [mailto:nana_kwadwo_der...@yahoo.com]
Sent: Wednesday, February 25, 2009 9:07 PM
To: Utkarsh Singhal
Cc: R-help Forum
Subject: Re: [R] how to label the branches of a tree
You may have to change/scale the sizes of the font by using cex and then to
keep all labels within the plotting window, use xpd=TRUE. Like in
text(fit, use.n=TRUE, cex=0.8, xpd=TRUE)
Philip
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--- On Wed, 2/25/09, David Winsemius dwinsem...@comcast.net wrote:
From: David Winsemius dwinsem...@comcast.net
Subject: Re: [R] how to label the branches of a tree
To: Utkarsh Singhal utkar...@ambaresearch.com
Cc: R-help Forum r-help@r-project.org
Date: Wednesday, February 25, 2009, 7:28 AM
When I execute that code, I get labels both on the branching points and at the
leaves of the tree. So I guess my reply is cannot reproduce or
do not understand. They are however not properly positioned and the
edges and
bottoms of some of the labels are cut off, but that did not sound like
your question.
Using Mac OS X 10.5.6 and the ATT binary of R2.8.1. 'rpart' version 3.1-42.
--David Winsemius
Note: your mailer is putting single quotes inside the enclosing angle brackets
so my mailer does not recognize the r-help address as a valid address. Since
this is the first time I have encountered this construction, I wonder if your
mailer is adhering to standards in its reply-to functions.
On Feb 25, 2009, at 1:19 AM, Utkarsh Singhal wrote:
Hi,
I am using rpart package to fit classification trees.
library(rpart)
fit - rpart(Kyphosis ~ Age + Number + Start, data=kyphosis)
plot(fit,uniform=T)
text(fit, use.n=TRUE)
But I am unable to label the branches (not
the nodes) of the tree. Can
somebody help me out in this?
Thank you,
Regards
Utkarsh Singhal | Amba Research
Ph +91 80 3980 8017 | Mob +91 99 0295 8815
Bangalore * Colombo * London * New York * San José * Singapore *
www.ambaresearch.com mailto:utkar...@ambaresearch.com
This e-mail may contain confidential and/or privileged i...{{dropped:13}}
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Re: [R] Linear Discriminant Analysis
Dear Arup, See the lda function in the MASS package. In general, require(MASS) Loading required package: MASS ?lda HTH, Jorge On Wed, Feb 25, 2009 at 4:44 AM, Arup arup.pramani...@gmail.com wrote: Kindly let me know the process to carry out a Linear discriminant analysis...thanks in advance Arup -- View this message in context: http://www.nabble.com/Linear-Discriminant-Analysis-tp22199424p22199424.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.
[R] Similarity between clusters generated by hclust + cutree
Dear friends I have clustered some objects using the hclust algorithm, with method ward. I then cutree with 48 classes. distPredTurn-as.dist(resultMatrix) hctr-hclust(distPredTurn,ward) cutree(hctr,k=NC) I would like to estimate the similarity between each pair of the 48 clusters, for example as (1-distance or dissimilarity) between the centroids. Any clue on how I can do that? Regards -- Corrado Topi Global Climate Change Biodiversity Indicators Area 18,Department of Biology University of York, York, YO10 5YW, UK Phone: + 44 (0) 1904 328645, E-mail: ct...@york.ac.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] Linear Discriminant Analysis
Maybe as a starter RSiteSearch(linear discriminant analysis) R has tools to help you help yourself with this types of questions. -Christos -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Arup Sent: Wednesday, February 25, 2009 4:45 AM To: r-help@r-project.org Subject: [R] Linear Discriminant Analysis Kindly let me know the process to carry out a Linear discriminant analysis...thanks in advance Arup -- View this message in context: http://www.nabble.com/Linear-Discriminant-Analysis-tp22199424p 22199424.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] Have a function like the _n_ in R ? (Automatic count function )
hadley wickham wrote:
On Wed, Feb 25, 2009 at 8:41 AM, Wacek Kusnierczyk
waclaw.marcin.kusnierc...@idi.ntnu.no wrote:
hadley wickham wrote:
And for completeness here's a function that returns the next integer
on each call.
n - (function(){
i - 0
function() {
i - i + 1
i
}
})()
actually, you do not need the external function to have the functionality:
n = local({
i = 0
function() (i - i + 1)[1] })
n()
# 1
n()
# 2
Yes, I'm just using the function as a way of creating an environment.
The function method is a little more flexible if you want multiple
independent counters though.
not as it stands above, because you immediately apply your function and
lose grip of it -- so it's just as do-once a solution as that with
local. but clearly, to have multiple independent counters, you'd need
two nested functions, as in this generalized version:
make.counter =
function(value)
function(increment)
(value - value + increment)[1]
counters =
lapply(rep(0, 3), make.counter)
mapply(
function(counter, increment)
counter(increment),
counters, 1)
# 1 1 1
which is what you presumably had in mind, roughly.
vQ
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Re: [R] Help with Latex (Hmisc)
on 02/25/2009 07:52 AM Frank E Harrell Jr wrote: Dieter Menne wrote: Frank E Harrell Jr f.harrell at vanderbilt.edu writes: ... Word and pdf It depends on how you copy. By all means use Insert ... Picture ... from file and directly insert pdf. Please, tell me how you got this to work. Dieter On Word 2003 there was no pdf option but I just used Insert ... Picture ... From File ... encapsulated postscript. We need to check that Word did not convert this to bitmap though. That is still the case with Office 2007, that is, no PDF import. If you import an EPS file and there is no pre-existing preview image, a bitmapped preview image will be generated upon import. It is the bitmapped image that you will see visually on the display and this is the image that will be printed by default, as Office does not natively render EPS. As I recall, older versions of Office would just leave you with a box-like placeholder for the EPS image, with no other indication of the content. You need to print to a PS compatible printer in order for the EPS image to be used. The same general situation is in place for OO.org relative to EPS images. There is a beta version of an OO.org PDF import filter available here: http://extensions.services.openoffice.org/project/pdfimport however, my experience with it last fall was less than enthusiastic and it still has a ways to go. It looks like there have been no updates for a while. There are commercial applications available that can enable you to import a PDF file into Office and a Google search will yield many options. I have not tried any of them, so buyer beware. HTH, Marc Schwartz __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to get JRI to work from my NetBeans
Did you set a system property for java.libary.path that points to the native library as the error message instructs? I'm not familiar with NetBeans, but in Eclipse you can set the JVM properties in a dialog. Otherwise you can always pass it in via the command line: -Djava.library.path=path to the JRI library HTH, Brian -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Yakub Sebastian Sent: Wednesday, February 25, 2009 4:34 AM To: r-help@r-project.org Subject: [R] How to get JRI to work from my NetBeans Hi, I need your help. I have downloaded a precompiled JRI as part of rJava. I have included rJava as part of my R package libraries. Now I need to be able to work with some R functions from my Java apps. I'm using NetBeans on Windows. I have followed some instructions from http://www.rforge.net/JRI/ but i keep on getting errors when compiling my Java app as follows: run: Cannot find JRI native library! Please make sure that the JRI native library is in a directory listed in java.library.path. java.lang.UnsatisfiedLinkError: no jri in java.library.path at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1709) at java.lang.Runtime.loadLibrary0(Runtime.java:823) at java.lang.System.loadLibrary(System.java:1030) at org.rosuda.JRI.Rengine.clinit(Rengine.java:9) at rtest.main(rtest.java:61) Java Result: 1 BUILD SUCCESSFUL (total time: 0 seconds) Can anyone help me with detailed steps to solve the problem? Thanks. -- Yakub [[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. -- This message w/attachments (message) may be privileged, confidential or proprietary, and if you are not an intended recipient, please notify the sender, do not use or share it and delete it. Unless specifically indicated, this message is not an offer to sell or a solicitation of any investment products or other financial product or service, an official confirmation of any transaction, or an official statement of Merrill Lynch. Subject to applicable law, Merrill Lynch may monitor, review and retain e-communications (EC) traveling through its networks/systems. The laws of the country of each sender/recipient may impact the handling of EC, and EC may be archived, supervised and produced in countries other than the country in which you are located. This message cannot be guaranteed to be secure or error-free. References to Merrill Lynch are references to any company in the Merrill Lynch Co., Inc. group of companies, which are wholly-owned by Bank of America Corporation. Secu! rities and Insurance Products: * Are Not FDIC Insured * Are Not Bank Guaranteed * May Lose Value * Are Not a Bank Deposit * Are Not a Condition to Any Banking Service or Activity * Are Not Insured by Any Federal Government Agency. Attachments that are part of this E-communication may have additional important disclosures and disclaimers, which you should read. This message is subject to terms available at the following link: http://www.ml.com/e-communications_terms/. By messaging with Merrill Lynch you consent to the foregoing. -- __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Have a function like the _n_ in R ? (Automatic count function )
On Wed, Feb 25, 2009 at 4:43 PM, Charles C. Berry cbe...@tajo.ucsd.edu wrote:
On Wed, 25 Feb 2009, Gustaf Rydevik wrote:
On Wed, Feb 25, 2009 at 3:30 PM, hadley wickham h.wick...@gmail.com
wrote:
And for completeness here's a function that returns the next integer
on each call.
n - (function(){
i - 0
function() {
i - i + 1
i
}
})()
n()
[1] 1
n()
[1] 2
n()
[1] 3
n()
[1] 4
n()
[1] 5
n()
[1] 6
;)
Hadley
*headache*!
I can't wrap my head around this one - too strange code!
Could someone please give a hint on what's going on?
How doesi- i+1 modify i permanently, seeing as i is defined as 0
to start with?
i is not _defined_ as zero. It is initially _assigned_ the value of zero and
is subsequently assigned other values.
As for the details of what goes here, see
An Introduction to R
Section 10.7 Scope
and study the open.acount() example there.
HTH,
Chuck
Thank you - I think I finally understood how that code got parsed.
Does the text below describe things correctly?
First, Hadley defines a function that returns another function, like this:
function(){
i - 0
function() {
i - i + 1
i
}
}
Since the returned function is defined in a local environment , R
returns the function together with that local environment, and lexical
scoping can work it's magic
Finally Hadley evaluates the above defined function-returning
function, and stores the returned function in n.
n-function(){
i - 0
function() {
i - i + 1
i
}
}()
*Phew*
That wasn't too difficult after all :-)
/Gustaf
--
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tel: +46(0)703 051 451
address:Essingetorget 40,112 66 Stockholm, SE
skype:gustaf_rydevik
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[R] : record which entry in one file doesn't appear in a different file
Hi dear list, If anybody could help me, it would be great! I have two files: File 1 is a list (one column and around 10 rows) File 2 is a list with all the names from file one and a few more (one column and more than 10 rows) What I want is to add a column in file 2 that says which name appeared in file 1 and which doesn't (yes and no would work as a code) It's very important to keep the order of the names in file 2. Thank you! Laura __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] : record which entry in one file doesn't appear in a different file
Hi Laura. Let's assume file 1 and 2 are vectors loaded in R named: vec1 and vec2, here is a short code (with dummy numbers) for a solution: vec1 - c(1,2,34,4,3,6,76) vec2 - c(1,2,34,76,24,62,1,4234,435,4333,4422,304,776) which.vec2.where.in.vec1 - vec2 %in% vec1 which.vec2.where.in.vec1.turned.into.yes.and.no-ifelse(which.vec2.where.in.vec1 , yes, no) cbind(vec2, which.vec2.where.in.vec1.turned.into.yes.and.no) Cheers, Tal On Wed, Feb 25, 2009 at 6:17 PM, Laura Rodriguez Murillo laura.lmuri...@gmail.com wrote: Hi dear list, If anybody could help me, it would be great! I have two files: File 1 is a list (one column and around 10 rows) File 2 is a list with all the names from file one and a few more (one column and more than 10 rows) What I want is to add a column in file 2 that says which name appeared in file 1 and which doesn't (yes and no would work as a code) It's very important to keep the order of the names in file 2. Thank you! Laura __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- -- My contact information: Tal Galili Phone number: 972-50-3373767 FaceBook: Tal Galili My Blogs: www.talgalili.com www.biostatistics.co.il [[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] Computing sd across an array with missing values
Dear help, suppose I have this array and want to compute sd aross rows and
columns.
p - array(c(1:5, rep(NA, times = 3)), dim = c(5, 5, 3))
apply(p, 1:2, sd) fails because sd requires at least 2 numbers to compute sd
apply(p, 1:2, sd, na.rm = TRUE) fails for the same reason
I crafted my own function that does what I want
sd_fun - function(i){
if(sum(!is.na(i))==0){
temp.sd - NA
}else{
temp.sd - sd(i, na.rm = TRUE)
}
return(temp.sd)
}
apply(p, 1:2, sd_fun)
This does what I want, but when I scale up to large arrays like
pp - array(c(1:5, rep(NA, times = 3)), dim = c(1000, 1000, 60))
the apply function takes a long time to run.
Is there a faster, more efficient way to do this?
Thanks in advance
Matt
--
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Assistant Professor
College of Marine and Earth Studies
University of Delaware
700 Pilottown Rd.
Lewes, DE, 19958
302-645-4079
http://www.ocean.udel.edu/people/profile.aspx?moliver
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[R] Anova Help?
I am conducting an experiment where students are put into 5 total groups (one is the control group). They are given a task and then I'm measuring if there are differences (A 5 X 1 between-subject design will be used for the experiment). I'm a little confused on the data explanation (or should I say how do I explain what is being analyzed versus just comparing values) Any help? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Anova Help?
Hi Dar. I am not sure I got your question - Are you asking what analysis to perform ? Or how to perform it ? Could you please give more details ? On Wed, Feb 25, 2009 at 5:52 PM, Dar darre...@aol.com wrote: I am conducting an experiment where students are put into 5 total groups (one is the control group). They are given a task and then I'm measuring if there are differences (A 5 X 1 between-subject design will be used for the experiment). I'm a little confused on the data explanation (or should I say how do I explain what is being analyzed versus just comparing values) Any help? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- -- My contact information: Tal Galili Phone number: 972-50-3373767 FaceBook: Tal Galili My Blogs: www.talgalili.com www.biostatistics.co.il [[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] : record which entry in one file doesn't appear in a different file
hey Laura, I hope this help f1 = c(a,b,c) f2 = c(b,a,c,d) match(f2,f1) f3 = match(f2,f1,0) ?match cbind(f2,f3) cbind(f2,f30) f4 = ifelse(f30,yes,no) cbind(f2,f4) data.frame(f2,f4) Patrizio 2009/2/25 Laura Rodriguez Murillo laura.lmuri...@gmail.com: Hi dear list, If anybody could help me, it would be great! I have two files: File 1 is a list (one column and around 10 rows) File 2 is a list with all the names from file one and a few more (one column and more than 10 rows) What I want is to add a column in file 2 that says which name appeared in file 1 and which doesn't (yes and no would work as a code) It's very important to keep the order of the names in file 2. Thank you! Laura __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Computing sd across an array with missing values
Dear Matt,
Here are two ways:
# Data
p - array(c(1:5, rep(NA, times = 3)), dim = c(5, 5, 3))
# First
res-apply(p,3,function(X)
c(scols=apply(X,2,sd,na.rm=TRUE),srows=apply(X,2,sd,na.rm=TRUE))
)
res
# Second
res2-apply(p,3,function(X)
list(scols=apply(X,2,sd,na.rm=TRUE),srows=apply(X,1,sd,na.rm=TRUE))
)
lapply(res2,function(x) do.call(rbind,x))
HTH,
Jorge
On Wed, Feb 25, 2009 at 10:53 AM, Matt Oliver moli...@udel.edu wrote:
Dear help, suppose I have this array and want to compute sd aross rows and
columns.
p - array(c(1:5, rep(NA, times = 3)), dim = c(5, 5, 3))
apply(p, 1:2, sd) fails because sd requires at least 2 numbers to compute
sd
apply(p, 1:2, sd, na.rm = TRUE) fails for the same reason
I crafted my own function that does what I want
sd_fun - function(i){
if(sum(!is.na(i))==0){
temp.sd - NA
}else{
temp.sd - sd(i, na.rm = TRUE)
}
return(temp.sd)
}
apply(p, 1:2, sd_fun)
This does what I want, but when I scale up to large arrays like
pp - array(c(1:5, rep(NA, times = 3)), dim = c(1000, 1000, 60))
the apply function takes a long time to run.
Is there a faster, more efficient way to do this?
Thanks in advance
Matt
--
Matthew J. Oliver
Assistant Professor
College of Marine and Earth Studies
University of Delaware
700 Pilottown Rd.
Lewes, DE, 19958
302-645-4079
http://www.ocean.udel.edu/people/profile.aspx?moliver
[[alternative HTML version deleted]]
__
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and provide commented, minimal, self-contained, reproducible code.
[[alternative HTML version deleted]]
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[R] Using gregexpr with multiple search elements
Dear list, I am trying to use gregexpr to see if entries in a dataframe have either of two possible values for a string. here's an example text-c(fat, rat, cat, dog, log, fish) If I just wanted to find if any one of the elements in text match the pattern at I would do gregexpr(\\at, text) which would match on the first three elements, you can do something like ifelse(gregexpr(\\at,text)-1, 1,0) to see if a particular entry in the data text is matched. My problem is I need to check if either of two patterns match in the data, an example that doesn't work is gregexpr(c(\\at, \\og), text) which is the basic form of what I'm looking to do, if this would work I would get a match for elements 1 through 5 of text, since either at or og occurs. If anyone might have an idea about this I would greatly appreciate it. Best, Corey Corey Sparks Assistant Professor Department of Demography and Organization Studies University of Texas at San Antonio One UTSA Circle San Antonio, TX 78249 210 458 6858 corey.spa...@utsa.edu __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] survival::survfit,plot.survfit
I am confused when trying the function survfit. my question is: what does the survival curve given by plot.survfit mean? is it the survival curve with different covariates at different points? or just the baseline survival curve? for example, I run the following code and get the survival curve library(survival) fit-coxph(Surv(futime,fustat)~resid.ds+rx+ecog.ps,data=ovarian) plot(survfit(fit,type=breslow)) summary(survfit(fit,type=breslow)) for the first two failure points, we have s(59|x1)=0.971, s(115|x2)=0.942 how can we guarantee that s(59|x1) is always greater than s(115|x2)? since s(59|x1)=s_0(59)^exp(\beta'x1) and s(115|x2)=s_0(115)^exp(\beta'x2), we can manipulate covariates to make s(59|x1) s(115|x2), right? do I miss anything? thanks in advance Jeff -- View this message in context: http://www.nabble.com/survival%3A%3Asurvfit%2Cplot.survfit-tp22206954p22206954.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Using gregexpr with multiple search elements
gregexpr(\\at|\\og, text) -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Corey Sparks Sent: Wednesday, February 25, 2009 11:50 AM To: R Help Subject: [R] Using gregexpr with multiple search elements Dear list, I am trying to use gregexpr to see if entries in a dataframe have either of two possible values for a string. here's an example text-c(fat, rat, cat, dog, log, fish) If I just wanted to find if any one of the elements in text match the pattern at I would do gregexpr(\\at, text) which would match on the first three elements, you can do something like ifelse(gregexpr(\\at,text)-1, 1,0) to see if a particular entry in the data text is matched. My problem is I need to check if either of two patterns match in the data, an example that doesn't work is gregexpr(c(\\at, \\og), text) which is the basic form of what I'm looking to do, if this would work I would get a match for elements 1 through 5 of text, since either at or og occurs. If anyone might have an idea about this I would greatly appreciate it. Best, Corey Corey Sparks Assistant Professor Department of Demography and Organization Studies University of Texas at San Antonio One UTSA Circle San Antonio, TX 78249 210 458 6858 corey.spa...@utsa.edu __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] All the products of common factors
Sorry - I didn't express myself very clearly. Yes, we're looking for common factors of A and B. One way to get there is by my initial approach: find the prime factors of each, select those that are in common, and then take pairwise products. My initial question was about the last step only. But your approach to the whole problem sidesteps that. It's more elegant, as well as faster, than the way I thought of the problem. Gordon Stavros Macrakis wrote: On Wed, Feb 25, 2009 at 9:25 AM, Fox, Gordon g...@cas.usf.edu wrote: The tricky part isn't finding the common factors -- we knew how to do that, though not in so concise a fashion as some of these suggestions. It was finding all their products without what I (as a recovered Fortran programmer) would call truly brute force. Several of these suggestions solve the problem nicely! Are you sure you are not confusing *prime factors* with *factors*? My understanding is that you are looking for all the factors of A which are also factors of B, i.e. the common factors of A and B. Why else would you be computing all those products? -s -- Dr. Gordon A. Fox Voice: (813)974-7352 Fax: (813)974-3263 Dept. of Integrative Biology ((for US mail:)SCA 110) ((for FedEx etc:)NES 107) Univ. of South Florida 4202 E. Fowler Ave. Tampa, FL 33620, USA http://foxlab.cas.usf.edu Trying is the first step towards failure. -- Homer Simpson [[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] Computing sd across an array with missing values
Hi Mark,
There is a typo in the first way. My apologies. It should be:
# First
res-apply(p,3,function(X)
c(scols=apply(X,2,sd,na.rm=TRUE),srows=apply(X,1,sd,na.rm=TRUE))
)
res
HTH,
Jorge
On Wed, Feb 25, 2009 at 11:42 AM, Jorge Ivan Velez jorgeivanve...@gmail.com
wrote:
Dear Matt,
Here are two ways:
# Data
p - array(c(1:5, rep(NA, times = 3)), dim = c(5, 5, 3))
# First
res-apply(p,3,function(X)
c(scols=apply(X,2,sd,na.rm=TRUE),srows=apply(X,2,sd,na.rm=TRUE))
)
res
# Second
res2-apply(p,3,function(X)
list(scols=apply(X,2,sd,na.rm=TRUE),srows=apply(X,1,sd,na.rm=TRUE))
)
lapply(res2,function(x) do.call(rbind,x))
HTH,
Jorge
On Wed, Feb 25, 2009 at 10:53 AM, Matt Oliver moli...@udel.edu wrote:
Dear help, suppose I have this array and want to compute sd aross rows and
columns.
p - array(c(1:5, rep(NA, times = 3)), dim = c(5, 5, 3))
apply(p, 1:2, sd) fails because sd requires at least 2 numbers to compute
sd
apply(p, 1:2, sd, na.rm = TRUE) fails for the same reason
I crafted my own function that does what I want
sd_fun - function(i){
if(sum(!is.na(i))==0){
temp.sd - NA
}else{
temp.sd - sd(i, na.rm = TRUE)
}
return(temp.sd)
}
apply(p, 1:2, sd_fun)
This does what I want, but when I scale up to large arrays like
pp - array(c(1:5, rep(NA, times = 3)), dim = c(1000, 1000, 60))
the apply function takes a long time to run.
Is there a faster, more efficient way to do this?
Thanks in advance
Matt
--
Matthew J. Oliver
Assistant Professor
College of Marine and Earth Studies
University of Delaware
700 Pilottown Rd.
Lewes, DE, 19958
302-645-4079
http://www.ocean.udel.edu/people/profile.aspx?moliver
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[R] vertically aligned X axis labels disappear off R Graphics window
Hi guys, I'm evaluating R for basic data exploration. I produce a bar plot of the data, with the x axis labels aligned vertically. However, the start of labels longer than about 10 characters are cut off by the bottom of the graphics window. I'd appreciate your help in properly spacing the space around a plot reserved for labels so that this problem can be avoided. Thanks, Richie [[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] C-index for models fitted using start, stop in Surv?
Eleni Rapsomaniki wrote: Dear R-users, One can use the rcorr.cens function in Design to compute the C index when only the stop time is indicated (I think implicitely start=0 in that case). When the start and stop times are used in a Surv object, e.g. library(Design) S=with(heart, Surv(start,stop,event)) the object returned is no longer a single number vector, so none of the following ways to compare a model fit to S makes sense: rcorr.cens(-cph(S~ age+transplant+surgery, heart)$linear.predictors, with(heart, Surv(start,stop,event))) # C IndexDxy S.D. nmissing # 4.95e-01 -9.66e-03 7.15e-02 1.72e+02 0.00e+00 #this seems bad because it compares the fit to a different Surv than the one used to fit it (S, above) rcorr.cens(-cph(S~ age+transplant+surgery, heart)$linear.predictors, with(heart, Surv(stop-start,event))) # C IndexDxy S.D. nmissing # 6.02e-01 2.03e-01 7.54e-02 1.72e+02 0.00e+00 Is there some way I can compute the correlation for this type of survival time specification in R? If not, does anybody have some tips on how to go about computing it myself? Many Thanks Eleni Rapsomaniki Research Associate Strangeways Research Laboratory Department of Public Health and Primary Care University of Cambridge rcorr.cens is not meant for that. Frank -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt 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] how to label the branches of a tree
How do you want the labels to appear? Each branch will be the logical
conjunction of the criteria for *all* of the upstream splits. Perhaps
you can get direction by looking at the code of text.rpart:
getAnywhere(text.rpart)
Any split would need to add an Split-N yes or an Split-N No to
any lower branch.
--
David Winsemius
On Feb 25, 2009, at 10:44 AM, Utkarsh Singhal wrote:
Hi David,
May be I was not clear, but I want to label the branches itself and
not the branching points or the leaves.
Regards
Utkarsh
From: Philip Twumasi-Ankrah [mailto:nana_kwadwo_der...@yahoo.com]
Sent: Wednesday, February 25, 2009 9:07 PM
To: Utkarsh Singhal
Cc: R-help Forum
Subject: Re: [R] how to label the branches of a tree
You may have to change/scale the sizes of the font by using cex
and then to keep all labels within the plotting window, use
xpd=TRUE. Like in
text(fit, use.n=TRUE, cex=0.8, xpd=TRUE)
Philip
--
A Smile costs Nothing But Rewards Everything
-
Anonymous
Happiness is not perfected until it is shared
-Jane
Porter
--- On Wed, 2/25/09, David Winsemius dwinsem...@comcast.net wrote:
From: David Winsemius dwinsem...@comcast.net
Subject: Re: [R] how to label the branches of a tree
To: Utkarsh Singhal utkar...@ambaresearch.com
Cc: R-help Forum r-help@r-project.org
Date: Wednesday, February 25, 2009, 7:28 AM
When I execute that code, I get labels both on the branching points
and at the
leaves of the tree. So I guess my reply is cannot reproduce or
do not understand. They are however not properly positioned and the
edges and
bottoms of some of the labels are cut off, but that did not sound
like
your question.
Using Mac OS X 10.5.6 and the ATT binary of R2.8.1. ‘rpart’ version
3.1-42.
--David Winsemius
Note: your mailer is putting single quotes inside the enclosing
angle brackets
so my mailer does not recognize the r-help address as a valid
address. Since
this is the first time I have encountered this construction, I
wonder if your
mailer is adhering to standards in its reply-to functions.
On Feb 25, 2009, at 1:19 AM, Utkarsh Singhal wrote:
Hi,
I am using rpart package to fit classification trees.
library(rpart)
fit - rpart(Kyphosis ~ Age + Number + Start, data=kyphosis)
plot(fit,uniform=T)
text(fit, use.n=TRUE)
But I am unable to label the branches (not
the nodes) of the tree. Can
somebody help me out in this?
Thank you,
Regards
Utkarsh Singhal | Amba Research
Ph +91 80 3980 8017 | Mob +91 99 0295 8815
Bangalore * Colombo * London * New York * San José * Singapore *
www.ambaresearch.com mailto:utkar...@ambaresearch.com
This e-mail may contain confidential and/or privileged i...
{{dropped:13}}
__
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PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
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list
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and provide commented, minimal, self-contained, reproducible code.
This e-mail may contain confidential and/or privileged...{{dropped:12}}
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] multiple regressions on columns
Well add1 (and others) does fit the regressions you asked about if you give it the base model only including the intercept and the scope including the x variables of interest. Unfortunately it only returns certain statistics on those models, not the whole object, but if you were interested in the test of significance, then the F that you could ask to be returned would give that to you (you could also modify the function to return any additional information that you want/need). You did not specify what information from the fits you wanted, so add1 was a possibility if it matched with what you wanted. I have made a note to my future self asking future me to use the timetravel package to send a copy of the ESP package back in time to past me to help with answering posts. However, present me has not received it yet. Possibly near future me does something that results in far future me not wanting to cooperate, I guess I should stick to my diet a little better. It looks like you found the lapply solution, another option would be to stack the data and use the lmList function from the nlme package, or the by function, or ..., but if lapply works for you, it is probably not worth the effort to try the others. -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r- project.org] On Behalf Of GOUACHE David Sent: Wednesday, February 25, 2009 1:56 AM To: Greg Snow; r-h...@stat.math.ethz.ch Subject: [R] RE : multiple regressions on columns Hello and thanks for your reply, but as you said, this is not really what I'm trying to do. My purpose is not one of variable selection within a model with multiple predictors, but simply fitting a large number of models with only one predictor. I was just hoping there would be a solution as simple as the one given in my example which gives the results of many regression models of the type Yi~x where i spans all the colums in a matrix and x is one predictor. My objective being the fitting of many regression models of the type y~Xi where i spans all the columns in a matrix and y is one dependent variable. Best regards, David Gouache ARVALIS - Institut du végétal Station de La Minière 78280 Guyancourt Tel: 01.30.12.96.22 / Port: 06.86.08.94.32 -Message d'origine- De : Greg Snow [mailto:greg.s...@imail.org] Envoyé : mardi 24 février 2009 18:22 À : GOUACHE David; r-h...@stat.math.ethz.ch Objet : RE: multiple regressions on columns The add1 function might be what you want, there is also addterm in the MASS package and the leaps package can do some things along this line (plus more). But before doing this, you may want to ask yourself what question you are really trying to answer, then explore if this answers that question or not. -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r- project.org] On Behalf Of GOUACHE David Sent: Tuesday, February 24, 2009 10:13 AM To: r-h...@stat.math.ethz.ch Subject: [R] multiple regressions on columns R-helpers, A quick question regarding my wanting to run multiple regressions without writing a loop. Looking at a previous discussion : http://tolstoy.newcastle.edu.au/R/e2/help/07/02/9740.html my objective is to do the opposite, i.e. instead of having the same independent variable and testing it against multiple dependent variables, my goal is to test multiple independent variables against the same dependent variable. Using the iris dataset: iris4 - as.matrix(iris[,-c(1,5)]) summary(lm(iris4 ~ Sepal.Length, iris)) what I would have liked is to do the following : summary(lm(Sepal.Length ~ iris4, iris)) and obtain the results from 3 separate regressions, as above, instead of one multiple regression... Any clues ? Tanks in advance David Gouache ARVALIS - Institut du végétal Station de La Minière 78280 Guyancourt Tel: 01.30.12.96.22 / Port: 06.86.08.94.32 __ 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. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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
Re: [R] C-index for models fitted using start, stop in Surv?
rcorr.cens is not meant for that. Thank you for the clarification. On a second thought, I think (hope) a time-dependent AUC index should be more appropriate in this case, such as survivalROC. Many many thanks for all your help! Eleni Rapsomaniki Research Associate Tel: +44 (0) 1223 740273 Strangeways Research Laboratory Department of Public Health and Primary Care University of Cambridge -Original Message- From: Frank E Harrell Jr [mailto:f.harr...@vanderbilt.edu] Sent: 25 February 2009 17:50 To: Eleni Rapsomaniki Cc: r-help@r-project.org Subject: Re: [R] C-index for models fitted using start, stop in Surv? Eleni Rapsomaniki wrote: Dear R-users, One can use the rcorr.cens function in Design to compute the C index when only the stop time is indicated (I think implicitely start=0 in that case). When the start and stop times are used in a Surv object, e.g. library(Design) S=with(heart, Surv(start,stop,event)) the object returned is no longer a single number vector, so none of the following ways to compare a model fit to S makes sense: rcorr.cens(-cph(S~ age+transplant+surgery, heart)$linear.predictors, with(heart, Surv(start,stop,event))) # C IndexDxy S.D. n missing # 4.95e-01 -9.66e-03 7.15e-02 1.72e+02 0.00e+00 #this seems bad because it compares the fit to a different Surv than the one used to fit it (S, above) rcorr.cens(-cph(S~ age+transplant+surgery, heart)$linear.predictors, with(heart, Surv(stop-start,event))) # C IndexDxy S.D. n missing # 6.02e-01 2.03e-01 7.54e-02 1.72e+02 0.00e+00 Is there some way I can compute the correlation for this type of survival time specification in R? If not, does anybody have some tips on how to go about computing it myself? Many Thanks Eleni Rapsomaniki Research Associate Strangeways Research Laboratory Department of Public Health and Primary Care University of Cambridge rcorr.cens is not meant for that. Frank -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt 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] how to label the branches of a tree
Following Dr Ripley's advice I looked at the text.rpart documentation
a bit more thoroughly and after seeing The edges connecting the nodes
are labeled by left and right splits. I find that the fancy=TRUE
invocation does cause a labeling of what you appear to be calling
branches.
See if this minor modification of the rpart example code produces your
desired result:
library(rpart)
fit - rpart(Kyphosis ~ Age + Number + Start, data=kyphosis)
par(mfrow=c(1,1), xpd=NA) # otherwise on some devices the text is
clipped
plot(fit)
text(fit, use.n=TRUE, fancy=TRUE)
On my devices (Mac OS X 10.5.6, R 2.8.1, quartz) the boxes around
the leaf labels are a bit too low on the default screen device, and
sending the output to a pdf file does not correct that problem, but as
always the code is there for you to work with.
--
David Winsemius
sessionInfo()
R version 2.8.1 Patched (2009-01-07 r47515)
i386-apple-darwin9.6.0
locale:
en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] rpart_3.1-42
loaded via a namespace (and not attached):
[1] grid_2.8.1 lattice_0.17-20 tools_2.8.1
capabilities()
jpeg png tifftcltk X11 aqua http/ftp
sockets libxml fifo cledit
TRUE TRUEFALSE TRUE TRUE TRUE TRUE
TRUE TRUE TRUE TRUE
iconv NLS profmemcairo
TRUE TRUEFALSE TRUE
On Feb 25, 2009, at 1:01 PM, David Winsemius wrote:
How do you want the labels to appear? Each branch will be the
logical conjunction of the criteria for *all* of the upstream
splits. Perhaps you can get direction by looking at the code of
text.rpart:
getAnywhere(text.rpart)
Any split would need to add an Split-N yes or an Split-N No
to any lower branch.
--
David Winsemius
On Feb 25, 2009, at 10:44 AM, Utkarsh Singhal wrote:
Hi David,
May be I was not clear, but I want to label the branches itself and
not the branching points or the leaves.
Regards
Utkarsh
From: Philip Twumasi-Ankrah [mailto:nana_kwadwo_der...@yahoo.com]
Sent: Wednesday, February 25, 2009 9:07 PM
To: Utkarsh Singhal
Cc: R-help Forum
Subject: Re: [R] how to label the branches of a tree
You may have to change/scale the sizes of the font by using cex
and then to keep all labels within the plotting window, use
xpd=TRUE. Like in
text(fit, use.n=TRUE, cex=0.8, xpd=TRUE)
Philip
--
A Smile costs Nothing But Rewards Everything
-
Anonymous
Happiness is not perfected until it is shared
-Jane
Porter
--- On Wed, 2/25/09, David Winsemius dwinsem...@comcast.net wrote:
From: David Winsemius dwinsem...@comcast.net
Subject: Re: [R] how to label the branches of a tree
To: Utkarsh Singhal utkar...@ambaresearch.com
Cc: R-help Forum r-help@r-project.org
Date: Wednesday, February 25, 2009, 7:28 AM
When I execute that code, I get labels both on the branching points
and at the
leaves of the tree. So I guess my reply is cannot reproduce or
do not understand. They are however not properly positioned and
the
edges and
bottoms of some of the labels are cut off, but that did not sound
like
your question.
Using Mac OS X 10.5.6 and the ATT binary of R2.8.1. ‘rpart’ version
3.1-42.
--David Winsemius
Note: your mailer is putting single quotes inside the enclosing
angle brackets
so my mailer does not recognize the r-help address as a valid
address. Since
this is the first time I have encountered this construction, I
wonder if your
mailer is adhering to standards in its reply-to functions.
On Feb 25, 2009, at 1:19 AM, Utkarsh Singhal wrote:
Hi,
I am using rpart package to fit classification trees.
library(rpart)
fit - rpart(Kyphosis ~ Age + Number + Start, data=kyphosis)
plot(fit,uniform=T)
text(fit, use.n=TRUE)
But I am unable to label the branches (not
the nodes) of the tree. Can
somebody help me out in this?
Thank you,
Regards
Utkarsh Singhal | Amba Research
Ph +91 80 3980 8017 | Mob +91 99 0295 8815
Bangalore * Colombo * London * New York * San José * Singapore *
www.ambaresearch.com mailto:utkar...@ambaresearch.com
This e-mail may contain confidential and/or privileged i...
{{dropped:13}}
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/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
[R] monotonic GAM with more than one term
Hi, Does anyone know how to fit a GAM where one or more smooth terms are constrained to be monotonic, in the presence of by variables or other terms? I looked at the example in ?pcls but so far have not been able to adapt it to the case where there is more than one predictor. For example, require(mgcv) set.seed(0) n-100 # Generate data from a monotonic truth. x-runif(100)*4-1 x-sort(x) m - structure(rep(1:2,50), .Label=c(one,two), class=factor) f-as.integer(m) * exp(4*x)/(1+exp(4*x)) y-f+rnorm(100)*0.1 plot(x,y,xlim=c(min(x), max(x)*2)) dat-data.frame(x=x,m=m,y=y) # Show regular spline fit (and save fitted object) f.ug-gam(y~m+s(x,k=10,by=m,bs=cr)) bool - m==one yhat - fitted(f.ug) lines(x[bool],yhat[bool]) lines(x[!bool],yhat[!bool]) xx - seq(max(x), 2*max(x), length=100) mm - structure(rep(1:2,50), .Label=c(one,two), class=factor) yy - predict(f.ug, newdata=data.frame(m=mm,x=xx)) bool - mm==one lines(xx[bool],yy[bool], lty=2) # show effect of extrapolation lines(xx[!bool],yy[!bool], lty=2) # this is where I start running into trouble sm-smoothCon(s(x,k=10,by=m,bs=cr),dat,knots=NULL)[[1]] FF-mono.con(sm$xp); # get constraints G-list(y=y, w=rep(1, n), X=sm$X, C=matrix(0,0,0), S = sm$S, off = 0, sp=f.ug$sp, p=sm$xp, Ain = FF$A, bin = FF$b ) p-pcls(G) # fit spline (using s.p. from unconstrained fit) fv-Predict.matrix(sm,data.frame(x=x))%*%p # can we do this without calling smoothCon directly ? # also having trouble here. f.nofit-gam(y~m+s(x,k=10,by=m,bs=cr),fit=FALSE) FF2 - mono.con(f.nofit$smooth[[1]]$xp) stopifnot(identical(FF, FF2)) G2 - list(y = f.nofit$y, w = f.nofit$w, X = f.nofit$X, C = f.nofit$C, S = f.nofit$smooth[[1]]$S, off = f.nofit$off, sp = f.ug$sp, p = f.nofit$smooth[[1]]$xp, Ain = FF2$A, bin = FF2$b ) p2 - pcls(G2) fv2-Predict.matrix(f.nofit$smooth[[1]],data.frame(x=x))%*%p2 Many thanks -Ben __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] vertically aligned X axis labels disappear off R Graphics window
R User R User wrote: Hi guys, I'm evaluating R for basic data exploration. I produce a bar plot of the data, with the x axis labels aligned vertically. However, the start of labels longer than about 10 characters are cut off by the bottom of the graphics window. I'd appreciate your help in properly spacing the space around a plot reserved for labels so that this problem can be avoided. See ?par, particularly its argument mar. Uwe Ligges Thanks, Richie [[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] Anova Help?
I’m just setting up the experiment and need help explaining what the data analysis would be. Let me know of any questions….. what would be compared and how it would be measured. Is it a multi-way or 1-way anova? Thanks! A 5 X 1 between-subject design will be used for the experiment. Four tool groups (Group1, Group2, Group3, Group4) will be able to view one category of information that their groups are allowed to in their tools. The control group, however, will have no access to the experimental tool. Pre-survey has demographic and previous experience questionnaire. The independent variable is the exposure to the information. The independent variable has five levels: no information, appearance information, educational information, contact information, and personal information. The dependent variable will be (2 dependent variables) gathered through a questionnaire at the end of the study. Connectedness. This variable will be operationalized as the Connectedness score Learning. This variable will be operationalized as the Learning score Covariates: Frequency of using tool Duration of tool use Previous experience (three types of previous experience). On Feb 25, 11:35 am, Tal Galili tal.gal...@gmail.com wrote: Hi Dar. I am not sure I got your question - Are you asking what analysis to perform ? Or how to perform it ? Could you please give more details ? On Wed, Feb 25, 2009 at 5:52 PM, Dar darre...@aol.com wrote: I am conducting an experiment where students are put into 5 total groups (one is the control group). They are given a task and then I'm measuring if there are differences (A 5 X 1 between-subject design will be used for the experiment). I'm a little confused on the data explanation (or should I say how do I explain what is being analyzed versus just comparing values) Any help? __ r-h...@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- -- My contact information: Tal Galili Phone number: 972-50-3373767 FaceBook: Tal Galili My Blogs:www.talgalili.comwww.biostatistics.co.il [[alternative HTML version deleted]] __ r-h...@r-project.org mailing listhttps://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guidehttp://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] make check reg-tests-1.R error on solaris
R 2.5.1 compiled, passed the make check and has been successfully running for a couple years on a Sun Fire V490 running Solaris 9. I need a newer version of R, but can't get a newer version of R to pass the make check. I've tried 2.8.1, 2.7.2, 2.6.2 and 2.6.0. (2.5.1 still passes on this server) At this point I thought I'd try to compile it on another Sun server (Solaris 10), but it had the same problem. Configuring with no options didn't help. I commented out the failed test from the Makefile to see if it would pass the rest of the tests. It passes all the rest of the tests. Here is the failure error from make check. make[2]: Entering directory `/usr/local/src/R-2.8.1/tests' running regression tests make[3]: Entering directory `/usr/local/src/R-2.8.1/tests' running code in 'reg-tests-1.R' ...make[3]: *** [reg-tests-1.Rout] Error 1 make[3]: Leaving directory `/usr/local/src/R-2.8.1/tests' make[2]: *** [test-Reg] Error 2 make[2]: Leaving directory `/usr/local/src/R-2.8.1/tests' make[1]: *** [test-all-basics] Error 1 make[1]: Leaving directory `/usr/local/src/R-2.8.1/tests' make: *** [check] Error 2 bash-2.05# Here is output from reg-tests-1.Rout.fail. [1] 41c6167e dir1 dir2 dirs file275c23f2 [6] file33f963f2 moredirs file.create(file.path(dd, somefile)) [1] TRUE TRUE TRUE TRUE dir(., recursive=TRUE) [1] 41c6167e dir1/somefile dir2/somefile [4] dirs/somefile file275c23f2 file33f963f2 [7] moredirs/somefile stopifnot(unlink(dir?) == 1) # not an error Error: unlink(dir?) == 1 is not TRUE Execution halted rm: Cannot remove any directory in the path of the current working directory /tmp/RtmprBjF6W Looking through the archives I did find a couple other people with this error, both running Solaris 10. PR#10501 and PR#11738 have quite a lot of information about this error, but I don't see any resolution for them. This looks like it could possibly be enough of a problem that I haven't put 2.8.1 in production. Can you help me with a resolution or let me know if it is safe to ignore? I'd appreciate it. Thank you! Karen __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Gradient function for optim.
I have read that when the gradient function is not supplied (is null) then first order differencing is used to find the differential. I was trying to track down this for my own information but I run into .Internal(optim.). I was not sure where to look next to see the function that is automatically supplied for the gradient. Thank you. Kevin __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] run latent class analysis with R
poLCA is designed to work this way. There's a complete user's guide and manual on the project website at http://userwww.service.emory.edu/~dlinzer/poLCA/ http://userwww.service.emory.edu/~dlinzer/poLCA/ Thanks, Drew == Drew Linzer Assistant Professor Department of Political Science Emory University 102 Tarbutton dlin...@emory.edu http://userwww.service.emory.edu/~dlinzer 404-727-0697 Wen Gu wrote: What's the best approach to running latent class analysis with R? I've downloaded both randomLCA and poLCA packages, but I am interesting in running a standard LCA with individual records (not frequency table) as input data. Wen Gu John Jay College of Criminal Justice445 West 59 StreetNew York, NY 10029 w...@gc.cuny.edu _ 50F681DAD532637!7540.entry?ocid=TXT_TAGLM_WL_t2_ugc_post_022009 [[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. -- View this message in context: http://www.nabble.com/run-latent-class-analysis-with-R-tp22197424p22209341.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] biplot.princomp - changing score labels
Perhaps this may help you. Regards data(iris3) ir - rbind(iris3[ , , 1], iris3[ , , 2], iris3[ , , 3]) ir.pca - princomp(ir) biplot(ir.pca) # Rehacer Biplot # Calcular Factor para re-escalar scores y eigenvectores lambda - ir.pca$sdev[1:2] * sqrt(ir.pca$n.obs) scores - t( t(ir.pca$scores[ , c(1, 2)]) / lambda ) variables - t( t(ir.pca$loadings[ , c(1, 2)]) * lambda ) x11() plot(scores, type=p, xlim=c(-0.22, 0.24), ylim=c(-0.2, 0.2), pch=c(rep(16, 50), rep(21, 50), rep(14, 50)), col=c(rep(red, 50), rep(blue, 50), rep(green, 50))) abline(v=0, h=0, lty=3) par(new=TRUE) plot(variables, type=n, xaxt=n, yaxt=n, xlim=c(-22, 24), ylim=c(-20, 20)) arrows(0, 0, variables[ , 1], variables[ , 2], len=0.1, col=red) text(2*variables, rownames(variables), col=red, xpd=TRUE) axis(3); axis(4) On 25 Feb 2009 at 9:52, Axel Strauß wrote: Date sent: Wed, 25 Feb 2009 09:52:54 +0100 From: Axel Strauß a.stra...@tu-bs.de To: R-help@r-project.org Subject:Re: [R] biplot.princomp - changing score labels Prof Brian Ripley schrieb: On Tue, 24 Feb 2009, Axel Strauß wrote: OK, the one thing I figured out: Is should be like: biplot(test.pca, cex=c(2,1), col=c(red,green)... to change size, colours etc separately. But I still don't know how change lables of observations to symbols properly. That's not part of the design of the function, so just make a copy and edit to meet your fancies. The designer of biplot.princomp. The idea behind my question was actually not a styling one but to provide additional information in the graph. My observations have different species richness and I wanted to adopt symbol size to the number of species to show the change of species richness along the PCs. Anyway, thanks for the comment - and for designing biplot.princomp. Axel -- Héctor Villalobos hvill...@ipn.mx CICIMAR - IPN A.P. 592. Col. Centro La Paz, Baja California Sur, MÉXICO. 23000 Tels. (+52 612) 122 53 44; 123 46 58; 123 47 34 ext. 82425 Fax. (+52 612) 122 53 22 [[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] biplot.princomp - changing score labels
have you thought about extracting the data and using this in ggplot? On Wed, Feb 25, 2009 at 3:52 AM, Axel Strauß a.stra...@tu-bs.de wrote: Prof Brian Ripley schrieb: On Tue, 24 Feb 2009, Axel Strauß wrote: OK, the one thing I figured out: Is should be like: biplot(test.pca, cex=c(2,1), col=c(red,green)... to change size, colours etc separately. But I still don't know how change lables of observations to symbols properly. That's not part of the design of the function, so just make a copy and edit to meet your fancies. The designer of biplot.princomp. The idea behind my question was actually not a styling one but to provide additional information in the graph. My observations have different species richness and I wanted to adopt symbol size to the number of species to show the change of species richness along the PCs. Anyway, thanks for the comment - and for designing biplot.princomp. Axel __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Stephen Sefick Let's not spend our time and resources thinking about things that are so little or so large that all they really do for us is puff us up and make us feel like gods. We are mammals, and have not exhausted the annoying little problems of being mammals. -K. Mullis __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] read and reshape time series table with empty items
Try this: Lines - 'Jahr;Tag;Jan;Febr;März;April;Mai;Juni;Juli;Aug;Sept;Okt;Nov;Dez 1978;1;NA;NA;NA;0.0;5.5;0.0;11.8;0.0;2.4;6.4;0.0;0.0 1978;2;NA;NA;NA;0.0;0.5;0.0;2.0;2.0;0.0;9.0;0.0;0.0 1978;3;NA;NA;NA;0.3;0.0;3.0;3.2;0.4;0.0;24.7;0.0;0.0 1978;4;NA;NA;NA;0.7;0.0;0.0;24.4;1.1;0.0;8.6;0.0;0.0 1978;5;NA;NA;NA;11.8;2.2;0.0;17.0;0.0;0.0;0.0;0.0;0.0 1978;6;NA;NA;NA;0.5;0.5;0.0;4.5;4.4;10.6;0.0;0.0;0.0 1978;7;NA;NA;NA;0.0;6.5;0.0;0.5;29.0;9.4;0.0;0.0;0.0 1978;8;NA;NA;1.0;0.0;7.3;4.0;0.0;6.0;6.7;0.0;0.0;7.0 1978;9;NA;NA;4.0;0.3;2.0;3.5;2.7;0.4;2.9;0.0;0.0;0.0 1978;10;NA;NA;0.0;1.5;2.4;19.5;0.5;1.8;0.5;0.0;0.0;0.0 1978;11;NA;NA;3.8;9.0;2.8;0.0;4.0;0.0;0.0;0.0;0.0;0.0 1978;12;NA;NA;0.0;6.8;3.5;0.0;2.5;0.0;11.3;0.0;0.0;3.0 1978;13;NA;NA;1.3;2.8;5.4;3.8;2.3;3.4;0.5;0.0;0.0;1.0 1978;14;NA;NA;0.7;1.0;0.3;0.2;7.9;0.0;0.0;0.0;0.0;1.0 1978;15;NA;NA;3.7;2.7;4.8;0.0;4.2;0.0;0.0;0.0;0.0;0.0 1978;16;NA;NA;13.7;2.8;0.0;1.4;0.0;5.5;0.0;0.0;0.5;1.8 1978;17;NA;NA;0.0;1.5;3.8;2.3;0.0;2.3;0.0;3.5;0.0;0.0 1978;18;NA;NA;0.0;0.0;1.0;0.0;11.6;0.0;0.5;5.3;0.0;0.0 1978;19;NA;NA;1.0;0.0;7.0;0.0;1.1;0.0;0.0;0.0;0.0;4.0 1978;20;NA;NA;17.5;0.0;0.5;0.2;0.0;0.0;0.0;0.0;0.0;0.3 1978;21;NA;NA;1.0;1.5;4.5;0.0;2.6;0.0;0.0;0.0;0.0;0.7 1978;22;NA;NA;0.5;0.0;12.0;1.6;0.0;0.0;0.2;1.7;0.0;3.5 1978;23;NA;NA;4.0;0.5;5.8;5.8;0.0;0.0;13.0;3.7;0.0;1.3 1978;24;NA;NA;0.8;0.0;12.0;24.3;0.0;0.0;3.3;0.0;0.0;0.0 1978;25;NA;NA;0.0;0.0;0.0;4.4;0.0;0.0;0.0;0.0;0.0;0.0 1978;26;NA;NA;5.0;0.0;0.5;0.2;1.0;0.0;0.0;6.0;5.7;0.0 1978;27;NA;NA;2.2;6.0;0.0;1.3;9.8;0.0;2.3;3.0;2.9;0.0 1978;28;NA;NA;0.7;1.8;0.0;0.4;0.0;0.0;5.4;0.0;1.5;0.0 1978;29;NA;;0.0;0.5;0.5;0.0;0.0;4.0;3.5;0.0;0.0;3.5 1978;30;NA;;0.0;1.0;0.0;0.0;0.0;6.0;6.1;0.0;0.0;1.5 1978;31;NA;;0.0;;0.0;;0.0;1.5;;0.0;;0.9 1979;1;3.5;1.0;0.5;NA;NA;0.1;0.0;0.5;0.0;0.0;0.0;0.0 1979;2;0.3;0.0;0.0;NA;NA;0.7;2.7;0.5;0.0;0.0;1.6;0.0 1979;3;0.5;2.7;0.0;NA;NA;0.0;3.0;2.5;1.0;0.0;1.0;0.0 1979;4;0.0;0.9;0.3;NA;NA;0.0;0.9;3.0;0.1;0.0;0.0;0.0 1979;5;0.0;2.2;0.0;NA;NA;0.0;0.0;0.0;0.0;0.6;3.5;0.0 1979;6;0.0;1.0;0.0;NA;NA;0.1;0.0;0.4;0.0;1.7;11.5;0.0 1979;7;0.0;1.0;0.0;NA;NA;1.0;0.6;0.0;0.0;0.0;5.0;0.0 1979;8;0.0;0.7;0.3;NA;NA;1.8;6.5;7.5;6.8;0.0;3.5;0.0 1979;9;3.5;1.8;0.8;NA;NA;0.2;9.3;2.2;4.3;0.0;6.5;0.9 1979;10;0.0;1.2;18.8;NA;NA;1.0;11.0;7.0;0.2;0.0;9.0;2.0 1979;11;1.2;1.0;7.8;NA;NA;3.4;0.0;1.4;0.0;0.3;0.0;12.0 1979;12;0.8;0.5;1.8;NA;NA;1.0;7.0;2.3;0.0;0.0;0.3;2.5 1979;13;1.4;0.0;0.0;NA;NA;3.2;3.0;0.0;0.0;5.3;0.0;0.0 1979;14;0.0;0.0;NA;NA;NA;30.5;0.7;0.0;3.3;4.6;0.8;3.9 1979;15;0.0;13.5;NA;NA;NA;1.4;0.0;0.0;2.2;19.0;8.0;3.4 1979;16;0.5;1.5;NA;NA;NA;20.2;0.0;0.0;0.0;1.2;6.8;1.8 1979;17;0.5;5.5;NA;NA;NA;14.8;4.0;5.5;0.0;11.1;9.8;1.4 1979;18;0.0;3.5;NA;NA;NA;2.0;0.0;14.5;0.0;0.0;3.0;0.8 1979;19;0.0;0.0;NA;NA;NA;0.0;4.0;0.0;0.0;0.0;6.0;4.0 1979;20;0.0;0.0;NA;NA;NA;0.0;6.2;1.0;2.3;0.0;6.2;1.2 1979;21;0.0;0.0;NA;NA;NA;0.0;0.0;0.0;36.0;0.0;1.0;4.0 1979;22;0.0;0.0;NA;NA;NA;0.0;0.0;0.0;35.9;0.8;8.0;17.0 1979;23;2.3;0.0;NA;NA;NA;0.0;0.0;1.5;4.6;5.8;0.0;3.0 1979;24;0.0;0.0;NA;NA;NA;0.0;0.0;27.3;1.9;0.0;0.0;1.0 1979;25;0.5;0.0;NA;NA;NA;0.7;0.0;0.8;0.0;0.0;0.0;0.0 1979;26;4.0;0.0;NA;NA;0.0;2.0;0.0;2.1;0.0;0.0;0.0;0.0 1979;27;11.5;0.0;NA;NA;4.5;3.6;0.0;0.0;0.0;0.0;4.0;0.0 1979;28;3.0;2.0;NA;NA;0.0;1.1;1.0;0.5;0.0;3.6;0.0;0.0 1979;29;0.8;;NA;NA;0.0;0.0;5.0;0.0;0.0;0.6;0.0;0.0 1979;30;0.8;;NA;NA;0.0;0.0;5.4;0.0;0.0;1.8;0.0;0.0 1979;31;0.4;;NA;;1.7;;15.5;0.0;;0.4;;0.0 1980;1;NA;NA;NA;NA;NA;0.6;0.0;0.0;1.0;0.0;0.0;NA 1980;2;NA;NA;NA;NA;NA;0.5;0.0;0.0;0.0;1.5;0.0;NA 1980;3;NA;NA;NA;NA;NA;0.7;3.6;0.0;0.0;0.0;0.0;NA 1980;4;NA;NA;NA;NA;NA;17.2;0.0;6.5;0.0;0.0;2.2;NA 1980;5;NA;NA;NA;NA;NA;0.0;0.0;0.0;0.0;0.0;0.7;NA 1980;6;NA;NA;NA;NA;NA;0.5;0.0;0.0;6.4;0.0;NA;NA 1980;7;NA;NA;NA;NA;0.0;0.0;2.3;0.0;0.0;0.5;NA;NA 1980;8;NA;NA;NA;NA;2.3;2.3;2.8;10.5;0.0;10.5;NA;NA 1980;9;NA;NA;NA;NA;6.7;2.2;21.0;0.0;3.8;7.8;NA;NA 1980;10;NA;NA;NA;NA;0.9;2.7;3.5;0.0;2.2;2.3;NA;NA 1980;11;NA;NA;NA;NA;0.9;1.2;0.3;0.0;4.0;3.4;NA;NA 1980;12;NA;NA;NA;NA;0.0;0.0;0.0;5.0;0.0;1.5;NA;NA 1980;13;NA;NA;NA;NA;0.0;0.0;3.5;0.0;0.0;0.0;NA;NA 1980;14;NA;NA;NA;NA;8.3;0.0;0.0;0.0;0.0;0.0;NA;NA 1980;15;NA;NA;NA;NA;19.0;2.0;0.5;1.3;0.0;0.0;NA;NA 1980;16;NA;NA;NA;NA;2.3;0.5;0.0;6.7;0.0;6.5;NA;NA 1980;17;NA;NA;NA;NA;2.4;23.3;0.0;4.4;0.0;50.5;NA;NA 1980;18;NA;NA;NA;NA;0.5;1.2;0.0;0.0;0.0;6.5;NA;NA 1980;19;NA;NA;NA;NA;0.0;0.0;0.0;0.0;0.0;1.5;NA;NA 1980;20;NA;NA;NA;NA;0.0;0.5;9.5;2.2;0.0;0.0;NA;NA 1980;21;NA;NA;NA;NA;1.2;8.5;14.0;4.3;0.0;0.0;NA;NA 1980;22;NA;NA;NA;NA;0.4;11.0;0.0;0.5;0.0;0.0;NA;NA 1980;23;NA;NA;NA;NA;0.5;5.0;0.0;0.2;8.3;0.0;NA;NA 1980;24;NA;NA;NA;NA;0.2;5.5;0.0;0.0;0.0;2.0;NA;NA 1980;25;NA;NA;NA;NA;0.5;0.7;0.0;0.0;0.0;19.0;NA;NA 1980;26;NA;NA;NA;NA;0.0;0.3;0.0;0.0;0.0;0.5;NA;NA 1980;27;NA;NA;NA;NA;0.0;9.0;0.0;0.0;0.0;0.0;NA;NA 1980;28;NA;NA;NA;NA;2.1;0.0;0.0;2.1;0.0;0.0;NA;NA 1980;29;NA;NA;NA;NA;1.9;0.0;6.9;2.0;0.0;0.0;NA;NA 1980;30;NA;;NA;NA;0.9;0.0;1.6;2.8;0.0;0.0;NA;NA 1980;31;NA;;NA;;1.1;;0.0;2.2;;0.0;;NA' # DF - read.csv2(myfile, as.is = TRUE) DF -
[R] make check reg-tests-1.R error on solaris
R 2.5.1 compiled, passed the make check and has been successfully running for a couple years on a Sun Fire V490 running Solaris 9. I need a newer version of R, but can't get a newer version of R to pass the make check. I've tried 2.8.1, 2.7.2, 2.6.2 and 2.6.0. (2.5.1 still passes on this server) At this point I thought I'd try to compile it on another Sun server (Solaris 10), but it had the same problem. Configuring with no options didn't help. I commented out the failed test from the Makefile to see if it would pass the rest of the tests. It passes all the rest of the tests. Here is the failure error from make check. make[2]: Entering directory `/usr/local/src/R-2.8.1/tests' running regression tests make[3]: Entering directory `/usr/local/src/R-2.8.1/tests' running code in 'reg-tests-1.R' ...make[3]: *** [reg-tests-1.Rout] Error 1 make[3]: Leaving directory `/usr/local/src/R-2.8.1/tests' make[2]: *** [test-Reg] Error 2 make[2]: Leaving directory `/usr/local/src/R-2.8.1/tests' make[1]: *** [test-all-basics] Error 1 make[1]: Leaving directory `/usr/local/src/R-2.8.1/tests' make: *** [check] Error 2 bash-2.05# Here is output from reg-tests-1.Rout.fail. [1] 41c6167e dir1 dir2 dirs file275c23f2 [6] file33f963f2 moredirs file.create(file.path(dd, somefile)) [1] TRUE TRUE TRUE TRUE dir(., recursive=TRUE) [1] 41c6167e dir1/somefile dir2/somefile [4] dirs/somefile file275c23f2 file33f963f2 [7] moredirs/somefile stopifnot(unlink(dir?) == 1) # not an error Error: unlink(dir?) == 1 is not TRUE Execution halted rm: Cannot remove any directory in the path of the current working directory /tmp/RtmprBjF6W Looking through the archives I did find a couple other people with this error, both running Solaris 10. PR#10501 and PR#11738 have quite a lot of information about this error, but I don't see any resolution for them. This looks like it could possibly be enough of a problem that I haven't put 2.8.1 in production. Can you help me with a resolution or let me know if it is safe to ignore? I'd appreciate it. Thank you! Karen [[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, joint scaling test, quantitative genetic analysis sensitivity to model violations
Hi all,This is really a stats question as much as an R question. I'm trying to do a joint scaling test (JST - see below) on some very oddly-distributed data and was wondering if anyone can suggest a good way of dealing with model violations and/or using R to evaluate how sensitive the model is to violations of the normality assumption. Here's a quick explanation of the analysis, the goal of which is to describe variation in phenotype z (time to metamorphosis, for example) between a series of hybrid crosses between two parental species. i used a mixed effects framework to fit a standard quantitative genetic model: z(i) = mu(0) + b(S)S(i) + b(H)H(i) + b(SS)S^2(i) + b(HH)H^2(i) + b(SH)S(i)H(i) + block +error where S(i) is the ancestry index (proportional to the expected fraction of parent 2 alleles in individual i based on its cross type), H(i) is the heterozygosity index (proportional to the expected fraction of loci with one allele from parent 1 and one allele from parent 2), b(i) are the regression coefficients and mu(0) is the mean phenotype of the F2 generation of hybrids (reference generation). Non-genetic components of variation are partitioned into individual (error) and block terms. Regression coefficients represent additive (b(S)), dominance (b(H)) and epistatic (b(SS), b(HH), b(SH)) effects of genetic differences between parental lineages. I fit a series, starting with the additive effect only and adding dominance and epistatic effects up to the full model and use AIC to choose the best model. The problem I'm facing is that there is a great deal of heterogeneity in the distributions of hybrid cross type (6 types total). the full model does well in modeling means (which are actually similar across distributions), but can't capture the heterogeneity of distributions if i assume a consistent error function. Any suggestions on ways of dealing with this problem, or at least ways of evaluating model sensitivity to these kinds of violations would be very welcome. thanks, mo [[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.
