[R] Extract values from data frame in R
Using R, I would like to find out which Samples (S1, S2, S3, S4, S5) fulfill the following criteria:contain minimally one value (x, y or z) bigger than 4. Any ideas? Thanks, Alex. data Sample xy z 1S1 -0.35.32.5 2S20.40.2 -1.2 3S31.2 -0.63.2 4S44.30.75.7 5S52.44.32.3 [[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] Extract values from data frame in R
On 08/09/2010 01:16 AM, Alexander Eggel wrote: Using R, I would like to find out which Samples (S1, S2, S3, S4, S5) fulfill the following criteria:contain minimally one value (x, y or z) bigger than 4. Any ideas? Thanks, Alex. data Sample xy z 1S1 -0.35.32.5 2S20.40.2 -1.2 3S31.2 -0.63.2 4S44.30.75.7 5S52.44.32.3 Untested: Sample[apply(Sample[-1], 1, function(x) any(x) 4)), Sample] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Extract values from data frame in R
On Aug 9, 2010, at 2:16 AM, Alexander Eggel wrote: Using R, I would like to find out which Samples (S1, S2, S3, S4, S5) fulfill the following criteria:contain minimally one value (x, y or z) bigger than 4. Any ideas? Thanks, Alex. data Sample xy z 1S1 -0.35.32.5 2S20.40.2 -1.2 3S31.2 -0.63.2 4S44.30.75.7 5S52.44.32.3 data$Sample[apply(data[, -1], 1, function(xyz) any(xyz 4))] [1] S1 S4 S5 David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Problem with installing a package in R!
gagea wrote: Dear friends, I am having problem with installing some packages in R in Ubuntu like ISwR. Bellow is the outcome. Anybody can help me to solve this problem. Thanks a lot and sorry if it is very simple question. install.packages(ISwr) ...ISwR..., I presume. Loading Tcl/Tk interface ... done trying URL 'http://probability.ca/cran/src/contrib/ISwR_2.0-5.tar.gz' Content type 'application/x-gzip' length 157441 bytes (153 Kb) opened URL == downloaded 153 Kb ERROR: failed to lock directory ‘/home/ubuntu/R/i486-pc-linux-gnu-library/2.9’ for modifying Try removing ‘/home/ubuntu/R/i486-pc-linux-gnu-library/2.9/00LOCK’ Did you try rm -rf /home/ubuntu/R/i486-pc-linux-gnu-library/2.9/00LOCK ? The lock dir is there to prevent two processes from messing with the same files at the same time, but can remain if an installation terminates prematurely. Do you have the appropriate permissions? It ia not clear to me whether that is supposed to be a user-level library or a system one. Is your user name ubuntu? (And is ubuntu really still shipping 2.9.x?) -- Peter Dalgaard Center for Statistics, Copenhagen Business School Phone: (+45)38153501 Email: pd@cbs.dk Priv: pda...@gmail.com __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Good Book To Work Through This Summer
Hello, I think that good introduction for application oriented people is book of Peter Dalgaard, Introductory Statistics with R http://www.springer.com/statistics/computanional+statistics/book/978-0-387-79053-4 This book is good for mastering basics of R. Book I like the one of John Fox, An R and S-PLUS Companion to Applied Regression http://socserv.socsci.mcmaster.ca/jfox/Books/Companion/index.html But there are dozens of books on this topic. Best regards, Ondrej Vozar. On 9 August 2010 06:38, TGS cran.questi...@gmail.com wrote: Dear R users, I'm hoping to get a few suggestions about which books are good to follow along and learn R. I'm hoping to spend the summer going through a good R book as it is applied in linear regression. Thanks! __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[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] Odp: Pausing script to allow user input from keyboard.
Hi
you are right. From ?scan default value for imput value is double, so you
need to specify that it shall be character. I just showed possible
solution not a solution which can be used in all imaginable cases.
Regards
Petr
r-help-boun...@r-project.org napsal dne 07.08.2010 05:20:56:
I'm having problems with your method Petr. I seem to get an additional
prompt.
Example...
f - function() {
cat(\n, Enter a string:, \n)
s - scan(n=1)
cat(\n, You entered, s, \n)
}
Running f() produces...
Enter a string:
1: blah
1:
Error in scan(file, what, nmax, sep, dec, quote, skip, nlines,
na.strings, :
scan() expected 'a real', got 'blah'
Changing the code to
scan(n=1, what=character)
Fixes the problem but your post implies that this is not necessary.
Could it be GUI specific ? I am running R 2.11.1 with the Mac OSX GUI
1.34 Leopard build 64-bit (5589)
Michael
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/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] metafor and meta-analysis at arm-level
Dear Angelo, This is (currently) not possible. Best, -- Wolfgang Viechtbauerhttp://www.wvbauer.com/ Department of Methodology and StatisticsTel: +31 (0)43 388-2277 School for Public Health and Primary Care Office Location: Maastricht University, P.O. Box 616 Room B2.01 (second floor) 6200 MD Maastricht, The Netherlands Debyeplein 1 (Randwyck) Original Message From: Angelo Franchini [mailto:angelo.franch...@bristol.ac.uk] Sent: Sunday, August 08, 2010 13:09 To: Viechtbauer Wolfgang (STAT) Cc: r-help@r-project.org Subject: RE: [R] metafor and meta-analysis at arm-level Dear Wolfgang, Is there any way for rma to add random effects only to each treatment arm, but not to the control one? Many thanks, Angelo On Thu, August 5, 2010 6:21 pm, Viechtbauer Wolfgang (STAT) wrote: Dear Angelo, rma(yi=o, sei=se, mods=~s+t-1, method=REML) is *a* way to run the arm-based pairwise meta-analysis. Whether it is the *correct* way is a question I cannot answer. lme(o~s+t-1, random=~t-1 | s, weights=(~ se^2)) is a different model. First of all, it adds a random effect only to each treatment arm within each study, while the rma model above gives a random effect to each observation. Moreover, the lme model assumes that the sampling variances are only known up to a proportionality constant, while the rma model assumes that they are known exactly. Similarly, lm(formula = o ~ s + t - 1, weights = 1/se.o^2) assumes that the sampling variances are only known up to a proportionality constant, while rma (with method=FE) assumes that they are known exactly. For the same reason will rma(yi=e, sei=se, method=REML) lme(e~1, random=~1 | s, weights=(~ se.e^2)) and rma(yi=e, sei=se.e, method=FE) lm(e~1, weights = 1/se.e^2) not give you the same results. Best, -- Wolfgang Viechtbauerhttp://www.wvbauer.com/ Department of Methodology and StatisticsTel: +31 (0)43 388-2277 School for Public Health and Primary Care Office Location: Maastricht University, P.O. Box 616 Room B2.01 (second floor) 6200 MD Maastricht, The Netherlands Debyeplein 1 (Randwyck) Original Message From: Angelo Franchini [mailto:angelo.franch...@bristol.ac.uk] Sent: Wednesday, August 04, 2010 16:26 To: Viechtbauer Wolfgang (STAT) Cc: 'Angelo Franchini'; r-help@r-project.org Subject: RE: [R] metafor and meta-analysis at arm-level Hello Wolfgang. I'd appreciate if you could help me check whether I am doing the proper thing to do an arm-level meta-analysis with metafor and what differences there might be in trying to do the same with lme and lm. I am following the arm based model described in section 3.2 of the Salanti's paper that you mentioned in your previous e-mail, namely: theta = B*eta + X*mu + W*beta where: theta = vector of parameter for outcomes in treatment arms (theta_ij for study i, treat. arm j) eta= vector of parameter for outcomes in control arms (eta_i for study i) mu = vector of effects (treat. vs cont.) (mu_ij for study i, treat. arm j) beta = vector of random effects (beta_ij for study i, treat. arm j) In my specific case with a pairwise meta-analysis, I had my data arranged as in columns for the following variables: s t o se with s as study/trial identifier t as 0/1 for control/treatment arm o as observed outcome in control or treatment arm se as standard error of that outcome measure I then ran metafor as: rma(yi=o, sei=se, mods=~s+t-1, method=REML) for random effects, and REML replaced by FE for fixed effects. Is that the correct way to run the arm-based pairwise meta-analysis? Shouldn't I be able to obtain similar results with LME for random-effects by using the command: lme(o~s+t-1, random=~t-1 | s, weights=(~ se^2)) and for fixed-effects with: lm(formula = o ~ s + t - 1, weights = 1/se.o^2) For the trial-based pairwise meta-analysis I used: data arranged as: s e se with: s study e effect se standard error and commands: rma(yi=e, sei=se, method=REML) or lme(e~1, random=~1 | s, weights=(~ se.e^2)) for random-effects, while for fixed-effects: rma(yi=e, sei=se.e, method=FE) lm(e~1, weights = 1/se.e^2) Does that make sense? Many thanks for any comment/advice on this matter. Best regards, Angelo __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] recurrent events
Hello, I have a cohort with approx 1,200 patients at the ages of 30-65 that had their first myocardial infarction during 1992: · They were in a follow up until 2005. · About 400 of them died during this period of time (right censored) · Each one of them had up to 4 mi recurrent events. I am using the semi-parametric model in order to assess the relationship of predictors to rate of occurrence allowing for multiple events per subject. The exposure variable (ESHKOL) is the socio-economic of the neighborhood while adjusting for additional variables such as age, sex, etc. In addition each patient has geo- statics -code for his neighborhood (stat_unit). I ran an Andersen Gill model: Ag-coxph(Surv(TStart,TStop,Status)~ ESHKOL+VAR1+ VAR2+cluster(id),data=recmi) My questions are: · I would like to check the unique effect of the stat_unit variable. How can I write it in code? · In your opinion does the AG model is the best model for this type of data? Or should I use models that consider the order of the events such as PWP or WLW? Thank you, Avi. [[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] recurrent events
Hello, I have a cohort with approx 1,200 patients at the ages of 30-65 that had their first myocardial infarction during 1992: • They were in a follow up until 2005. • About 400 of them died during this period of time (right censored) • Each one of them had up to 4 mi recurrent events. I am using the semi-parametric model in order to assess the relationship of predictors to rate of occurrence allowing for multiple events per subject. The exposure variable (ESHKOL) is the socio-economic of the neighborhood while adjusting for additional variables such as age, sex, etc. In addition each patient has geo- statics -code for his neighborhood (stat_unit). I ran an Andersen Gill model: Ag-coxph(Surv(TStart,TStop,Status)~ ESHKOL+VAR1+ VAR2+cluster(id),data=recmi) My questions are: • I would like to check the unique effect of the stat_unit variable. How can I write it in code? • In your opinion does the AG model is the best model for this type of data? Or should I use models that consider the order of the events such as PWP or WLW? Thank you, Avi. -- View this message in context: http://r.789695.n4.nabble.com/recurrent-events-tp2318296p2318296.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] Smart Indexing
Hi all, Suppose that I've two data frames, a and b say, both containing a column 'id'. While data frame 'a' contains multiple rows sharing the same id, data frame 'b' contains just one entry per id (i.e. a 1 to n relationship). For the ease of modeling I now want to generate a new data frame c, which is basically a copy of data frame 'a' augmented by the values of b. If I have a - data.frame(id = rep(1:3, each=3), val=rnorm(9)) b - data.frame(id=1:3, set1=LETTERS[1:3], set2=5:7) the resulting data frame should look like: c - data.frame(id = rep(1:3, each=3), val = a$val, set1=rep(LETTERS[1:3], each=3), set2 = rep(5:7, each = 3)) While this task is just an application of some 'rep's and 'c's for structured data frames, it is somehow cumbersome (and error prone) to construct 'c' explicitly for less structured data. Thus, I was thinking of making use of R's smart indexing possibilities to generate an index vector, i.e.: ind - c(1, 1, 1, 2, 2, 2, 3, 3, 3) c.prime - cbind(a, b[ind,-1]) rownames(c.prime) - NULL all.equal(c.prime , c) # TRUE The way I generate the index vector ind for the moment is tmp - seq_along(b$id) names(tmp) - b$id ind - tmp[a$id] However, I think that there should be a smarter way of doing that without the need of defining a temporary variable. Some combination of match, which, %in% maybe? Any hints? While writing these lines, I think ind - pmatch(a$id, b$id, duplicates=T) could do the job? Or do I run into troubles regarding the partial matching involved in pmatch? BTW, is there a way to prevent R of assigning [row|col]names? In the example above I had to remove the rownames generated by rbind explicitly, is there an one-liner? Thanks for your input + BR Thorn __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Smart Indexing
I think you just need merge(), e.g. a - data.frame(id = rep(1:3, each=3), val = rnorm(9)) b - data.frame(id = 1:3, set1 = LETTERS[1:3], set2 = 5:7) merge(a, b, by = id) I hope it helps. Best, Dimitris On 8/9/2010 11:01 AM, Thaler, Thorn, LAUSANNE, Applied Mathematics wrote: Hi all, Suppose that I've two data frames, a and b say, both containing a column 'id'. While data frame 'a' contains multiple rows sharing the same id, data frame 'b' contains just one entry per id (i.e. a 1 to n relationship). For the ease of modeling I now want to generate a new data frame c, which is basically a copy of data frame 'a' augmented by the values of b. If I have a- data.frame(id = rep(1:3, each=3), val=rnorm(9)) b- data.frame(id=1:3, set1=LETTERS[1:3], set2=5:7) the resulting data frame should look like: c- data.frame(id = rep(1:3, each=3), val = a$val, set1=rep(LETTERS[1:3], each=3), set2 = rep(5:7, each = 3)) While this task is just an application of some 'rep's and 'c's for structured data frames, it is somehow cumbersome (and error prone) to construct 'c' explicitly for less structured data. Thus, I was thinking of making use of R's smart indexing possibilities to generate an index vector, i.e.: ind- c(1, 1, 1, 2, 2, 2, 3, 3, 3) c.prime- cbind(a, b[ind,-1]) rownames(c.prime)- NULL all.equal(c.prime , c) # TRUE The way I generate the index vector ind for the moment is tmp- seq_along(b$id) names(tmp)- b$id ind- tmp[a$id] However, I think that there should be a smarter way of doing that without the need of defining a temporary variable. Some combination of match, which, %in% maybe? Any hints? While writing these lines, I think ind- pmatch(a$id, b$id, duplicates=T) could do the job? Or do I run into troubles regarding the partial matching involved in pmatch? BTW, is there a way to prevent R of assigning [row|col]names? In the example above I had to remove the rownames generated by rbind explicitly, is there an one-liner? Thanks for your input + BR Thorn __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Dimitris Rizopoulos Assistant Professor Department of Biostatistics Erasmus University Medical Center Address: PO Box 2040, 3000 CA Rotterdam, the Netherlands Tel: +31/(0)10/7043478 Fax: +31/(0)10/7043014 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Smart Indexing
Thanks, that does the trick. Again a new command learned. Thanks. However, any hints regarding the rownames issue? BR Thorn -Original Message- From: Dimitris Rizopoulos [mailto:d.rizopou...@erasmusmc.nl] Sent: lundi 9 août 2010 11:07 To: Thaler,Thorn,LAUSANNE,Applied Mathematics Cc: r-help@r-project.org Subject: Re: [R] Smart Indexing I think you just need merge(), e.g. a - data.frame(id = rep(1:3, each=3), val = rnorm(9)) b - data.frame(id = 1:3, set1 = LETTERS[1:3], set2 = 5:7) merge(a, b, by = id) I hope it helps. Best, Dimitris On 8/9/2010 11:01 AM, Thaler, Thorn, LAUSANNE, Applied Mathematics wrote: Hi all, Suppose that I've two data frames, a and b say, both containing a column 'id'. While data frame 'a' contains multiple rows sharing the same id, data frame 'b' contains just one entry per id (i.e. a 1 to n relationship). For the ease of modeling I now want to generate a new data frame c, which is basically a copy of data frame 'a' augmented by the values of b. If I have a- data.frame(id = rep(1:3, each=3), val=rnorm(9)) b- data.frame(id=1:3, set1=LETTERS[1:3], set2=5:7) the resulting data frame should look like: c- data.frame(id = rep(1:3, each=3), val = a$val, set1=rep(LETTERS[1:3], each=3), set2 = rep(5:7, each = 3)) While this task is just an application of some 'rep's and 'c's for structured data frames, it is somehow cumbersome (and error prone) to construct 'c' explicitly for less structured data. Thus, I was thinking of making use of R's smart indexing possibilities to generate an index vector, i.e.: ind- c(1, 1, 1, 2, 2, 2, 3, 3, 3) c.prime- cbind(a, b[ind,-1]) rownames(c.prime)- NULL all.equal(c.prime , c) # TRUE The way I generate the index vector ind for the moment is tmp- seq_along(b$id) names(tmp)- b$id ind- tmp[a$id] However, I think that there should be a smarter way of doing that without the need of defining a temporary variable. Some combination of match, which, %in% maybe? Any hints? While writing these lines, I think ind- pmatch(a$id, b$id, duplicates=T) could do the job? Or do I run into troubles regarding the partial matching involved in pmatch? BTW, is there a way to prevent R of assigning [row|col]names? In the example above I had to remove the rownames generated by rbind explicitly, is there an one-liner? Thanks for your input + BR Thorn __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting- guide.html and provide commented, minimal, self-contained, reproducible code. -- Dimitris Rizopoulos Assistant Professor Department of Biostatistics Erasmus University Medical Center Address: PO Box 2040, 3000 CA Rotterdam, the Netherlands Tel: +31/(0)10/7043478 Fax: +31/(0)10/7043014 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] (no subject)
Hi there, I have been trying to use the pvclust package but have been having some difficulties. This is the first time I have used R so I am sure the mistake I am making is a basic one. The data I have is a distance matrix and I have been using the command; fit - pvclust(cluster, nboot=1000, method.dist=euclidean) to try and perform hierarchical clustering with bootstrapped p-values, but I get the error message; Error in t.default(x) : argument is not a matrix. I guess there is a problem with the way the data is laid out, do you know how the data should be displayed in order to get the command to work (the data I am using I have pasted below), I have tried various methods of organising it! V1 V2 V3V4 1 0. 0.03162278 0.05830952 0.1315295 2 0.03162278 0. 0.0600 0.1627882 3 0.05830952 0.0600 0. 0.1627882 4 0.13152946 0.16278821 0.16278821 0.000 Any help you could give me would be greatly appreciated. Kind Regards, Hannah [[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] Results with name of dataset
I generate and save a dataset
For example
exampledata-runif(10)
library(R.utils);
saveObject(exampledata, file=exampledata_9810.RData);
exampledata_9810- loadObject(exampledata_9810.RData);
I use ex function to make alot of calculations using sink to export results
(in this simply example only summary of dataset)
ex-function(data){
sink(paste(data,'Example.txt'))
print(summary(data))
}
ex(data=exampledata_9810)
Function ex works fine BUT I don't want the file of results to have the name
data Example but
exampledata_9810 Example
How can I do this?
Thanks for your help
Evgenia
--
View this message in context:
http://r.789695.n4.nabble.com/Results-with-name-of-dataset-tp2318328p2318328.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] (no subject)
Hi Hannah, First, don't forget to add a subject to your email! Second, the best way to share data is to copy/paste the output from the dput() function into the email. I have never used pvclust, but the error tells you that your object cluster is not a matrix. What does str(cluster) return? You may think it's a matrix, but depending on how you've created it, it might be a data.frame or something else. str() is a very useful function. HTH, Ivan Le 8/9/2010 11:22, Holt, Hannah Rebecca a écrit : Hi there, I have been trying to use the pvclust package but have been having some difficulties. This is the first time I have used R so I am sure the mistake I am making is a basic one. The data I have is a distance matrix and I have been using the command; fit- pvclust(cluster, nboot=1000, method.dist=euclidean) to try and perform hierarchical clustering with bootstrapped p-values, but I get the error message; Error in t.default(x) : argument is not a matrix. I guess there is a problem with the way the data is laid out, do you know how the data should be displayed in order to get the command to work (the data I am using I have pasted below), I have tried various methods of organising it! V1 V2 V3V4 1 0. 0.03162278 0.05830952 0.1315295 2 0.03162278 0. 0.0600 0.1627882 3 0.05830952 0.0600 0. 0.1627882 4 0.13152946 0.16278821 0.16278821 0.000 Any help you could give me would be greatly appreciated. Kind Regards, Hannah [[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. -- Ivan CALANDRA PhD Student University of Hamburg Biozentrum Grindel und Zoologisches Museum Abt. Säugetiere Martin-Luther-King-Platz 3 D-20146 Hamburg, GERMANY +49(0)40 42838 6231 ivan.calan...@uni-hamburg.de ** http://www.for771.uni-bonn.de http://webapp5.rrz.uni-hamburg.de/mammals/eng/mitarbeiter.php [[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] Results with name of dataset
On 9 August 2010 19:30, Evgenia ev...@aueb.gr wrote:
Function ex works fine BUT I don't want the file of results to have the name
data Example but
exampledata_9810 Example
How can I do this?
Do you mean that you want the filename to be based on the name of the
object passed to the function ? If so, try this...
ex-function(data) {
sink(paste(deparse(substitute(data)), ' Example.txt'))
print(summary(data))
}
Michael
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/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] permanova on MICE object
Hi everyone! I have data consisting of several response variables and several explanatory variables. I wish to do a permanova on this using the vegan library and the adonis() function. However, my data had several missing values in it. In order to 'fix' this I used the mice() function from the mice library to make 5 imputations for all the missing values. To do analysis on the 5 datasets with different imputed values, the mice library includes the with.mids() function in which you can call the mice object and calculate a model for all the 5 datasets. The results from these analysis can later on be pooled with the pool() function from the mice library. The problem I have is that I am not sure how to include a permanova (with the adonis() function) as an expression in the with.mids() function. In order to use the mice() function and calculate multiple imputations I needed one dataframe with all of my response and explanatory variables. In order to use the adonis() function (I think) I need a separate dataframe with my response variables and a separate dataframe with my explanatory variables. Does anyone know how to use the output from a multiple imputation by chained equations (mice) to do a permanova? I hope my question is clear, and if anyone has any ideas or suggestions, your help would be greatly appreciated. Thanks! -- View this message in context: http://r.789695.n4.nabble.com/permanova-on-MICE-object-tp2318342p2318342.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] [OT] R on Atlas library
I don't know about the specific function (a simple, stand-alone reproducible example is always helpful, see the posting guide for details), but ATLAS certainly uses all my cores on a test like this: s - 7500 # Adjust for your hardware a - matrix(rnorm(s*s), ncol = s, nrow = s) b - crossprod(a) # Uses all cores here. My configuration of R with ATLAS on Linux (Fedora) is described at http://www.cybaea.net/Blogs/Data/Faster-R-through-better-BLAS.html Maybe your distribution has single-threaded ATLAS and you forgot to rebuild it with enable_native_atlas 1 or the equivalent for your platform? Allan On 06/08/10 15:12, Matthias Gondan wrote: Dear List, I am aware this is slightly off-topic, but I am sure there are people who already had the problem and who perhaps solved it. I am running long-lasting model fits using constrOptim command. At work there is a linux computer (Quad Core, debian) on which I already have compiled R and Atlas, in the hope that things will go faster on that machine. Atlas offers the possibility to be compiled for multiple cores, I used that option, but without success. Performance meter (top) for Linux shows 25% CPU usage, and there is no loss of performance if I run 4 instances of R doing heavy matrix multiplications. Performance drops when a 5th instance of R is doing the same job, so I assume my attempt was not successful. I am sure I did something wrong. Is there anybody who sucessfully runs R with Atlas and all processors? A short description of the necessary steps would be helpful. Searching around the internet was not very encourageing. Some people wrote that it is not so simple to have Atlas fully exploit a multicore computer. I hope this is not too unspecific. Best wishes, Matthias __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] About R base
Yes, there are differences between R on Windows and R on Linux. You probably want this document: http://cran.r-project.org/bin/windows/base/rw-FAQ.html Hope this helps a little. Allan On 06/08/10 16:47, Stephen Liu wrote: Hi folks, I have R x64 2.11.1 installed on Win 7 64 bit which is running as VM (guest) on Oracle VirtualBox. Is there any difference between it and R on Linux? I can install another R on Debian 5.04, also running as VM. TIA B.R. Stephen L __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Fwd: RE: pvclust function
You should reply to the list, not just me, and even more because I cannot really help you!! My guess (but I don't know this package, and even less this function) is that pvclust() is expecting a matrix as the first argument. However, cluster is no data, it is a function. Why, I don't know. Take a closer look at ?pvclust, especially the usage, arguments and examples parts. HTH, Ivan Message original Sujet: RE: pvclust function Date : Mon, 9 Aug 2010 10:52:30 +0100 De :Holt, Hannah Rebecca hh...@rvc.ac.uk Pour : ivan.calan...@uni-hamburg.de Sorry Ivan, Thanks for your tips the output from str(cluster) is; function (file, header = FALSE, sep = , quote = \', dec = ., row.names, col.names, as.is = !stringsAsFactors, na.strings = NA, colClasses = NA, nrows = -1, skip = 0, check.names = TRUE, fill = !blank.lines.skip, strip.white = FALSE, blank.lines.skip = TRUE, comment.char = #, allowEscapes = FALSE, flush = FALSE, stringsAsFactors = default.stringsAsFactors(), fileEncoding = , encoding = unknown) I am not sure how to interpret this! Kind Regards, Hannah -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Ivan Calandra Sent: 09 August 2010 10:40 To: r-help@r-project.org Subject: Re: [R] (no subject) Hi Hannah, First, don't forget to add a subject to your email! Second, the best way to share data is to copy/paste the output from the dput() function into the email. I have never used pvclust, but the error tells you that your object cluster is not a matrix. What does str(cluster) return? You may think it's a matrix, but depending on how you've created it, it might be a data.frame or something else. str() is a very useful function. HTH, Ivan Le 8/9/2010 11:22, Holt, Hannah Rebecca a écrit : Hi there, I have been trying to use the pvclust package but have been having some difficulties. This is the first time I have used R so I am sure the mistake I am making is a basic one. The data I have is a distance matrix and I have been using the command; fit- pvclust(cluster, nboot=1000, method.dist=euclidean) to try and perform hierarchical clustering with bootstrapped p-values, but I get the error message; Error in t.default(x) : argument is not a matrix. I guess there is a problem with the way the data is laid out, do you know how the data should be displayed in order to get the command to work (the data I am using I have pasted below), I have tried various methods of organising it! V1 V2 V3V4 1 0. 0.03162278 0.05830952 0.1315295 2 0.03162278 0. 0.0600 0.1627882 3 0.05830952 0.0600 0. 0.1627882 4 0.13152946 0.16278821 0.16278821 0.000 Any help you could give me would be greatly appreciated. Kind Regards, Hannah [[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. -- Ivan CALANDRA PhD Student University of Hamburg Biozentrum Grindel und Zoologisches Museum Abt. Säugetiere Martin-Luther-King-Platz 3 D-20146 Hamburg, GERMANY +49(0)40 42838 6231 ivan.calan...@uni-hamburg.de ** http://www.for771.uni-bonn.de http://webapp5.rrz.uni-hamburg.de/mammals/eng/mitarbeiter.php [[alternative HTML version deleted]] [[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] Does anybody know how to control the appearance of the end of the line in lattice?
Hi
see
http://finzi.psych.upenn.edu/Rhelp10/2010-April/234441.html
The following I think works - its a bit rough - needs improving but saves
closing the device.
xyplot(y2+y1~x,
data=Source,
par.settings = list(grid.pars = list(lineend = butt)),
#distribute.type=TRUE,
y1 = Source$y1,
y2=Source$y2,
panel = function(x,y1,y2,...){
panel.segments(x,y1, x,y2, gp = gpar(lineend=butt),
col=c(black), lwd =20)
}
)
Regards
Duncan
Duncan Mackay
Department of Agronomy and Soil Science
University of New England
ARMIDALE NSW 2351
Email home: mac...@northnet.com.au
At 06:23 9/08/2010, you wrote:
Hi
On 9/08/2010 7:49 a.m., George Chen wrote:
Hi All,
I am plotting vertical lines using xyplot in lattice and type=h.
It works well, but the problem is that the tops of the lines are convex
and the bottoms are concave.
Is there a way to flatten the tops and bottoms?
You want to control the graphical parameter called lineend, but I don't
think this is generally made available via trellis.par.set(). Also, trying
to set a default value via the 'grid.pars' argument, or via a viewport
with the 'draw.in' argument doesn't appear to work in this case (the
lineend may be hard coded in the internal code somewhere). The following
code (to be run AFTER your code) does the trick for your example ...
library(grid)
grid.gedit(segments, gp=gpar(lineend=butt), grep=TRUE)
... though I believe this will also make the ends of the tick marks on the
axes square (not obvious to the naked eye at the default size).
Paul
Here's my code:
Source-matrix(1:30,10,3)
colnames(Source)-c(x,y1,y2)
Source-data.frame(Source)
xyplot(y2+y1~x,
data=Source,
distribute.type=TRUE,
type=c(h,h),
col=c(black,white),
lwd=20)
graphics.off()
Thanks.
George Chen
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Dr Paul Murrell
Department of Statistics
The University of Auckland
Private Bag 92019
Auckland
New Zealand
64 9 3737599 x85392
p...@stat.auckland.ac.nz
http://www.stat.auckland.ac.nz/~paul/
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/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] memory use without running gc()
How about asking the operating system, e.g. ### Method 1 ## Setup cmd - paste(ps -o vsz, Sys.getpid()) ## In your logging routine z - system(cmd, intern = TRUE) cat(Virtual size: , z[2], \n, sep = ) ### Method 2 ## Setup file - paste(/proc, Sys.getpid(), stat, sep = /) what - vector(list, 44); what[[23]] - integer(0) ## In your logging routine vsz - scan(file, what = what, quiet = TRUE)[[23]]/1024 cat(Virtual size: , vsz, \n, sep = ) ### Time the methods library(rbenchmark) benchmark(scan = scan(file, what = what, quiet = TRUE)[[23]]/1024, system = system(cmd, intern = TRUE), columns = c(test, replications, elapsed, relative), order = relative) # test replications elapsed relative # 1 scan 100 0.015 1. # 2 system 100 2.408 160.5333 The scan method should be plenty fast. Change as appropriate if your definition of memory is different from virtual size. Hope this helps a little. Allan On 06/08/10 19:11, Johann Hibschman wrote: jim holtmanjholt...@gmail.com writes: ?memory.size Only works on Windows. I guess I should have specified; this is on Linux. Thanks, Johann __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] TM Package - installation
Hi All, I have been trying to do some text analytics in R using tm package. I have installed and loaded the package, along with dependencies (slam, rWeka,rjava). When I try to run a tm_map command, it gives me Error in .jnew(name) : java.lang.NoClassDefFoundError: weka/core/stemmers/SnowballStemmer error. Can someone please throw some light on this?. Am I missing out on something? - Regards Sujatha [[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] Logistic Regression in R (SAS -like output)
Hello useRs, I have a problem at hand which I'd think is fairly common amongst groups were R is being adopted for Analytics in place of SAS. Users would like to obtain results for logistic regression in R that they have become accustomed to in SAS. Towards this end, I was able to propose the Design package in R which contains many functions to extract the various metrics that SAS reports. If you have suggestions pertaining to other packages, or sample code that replicates some of the SAS outputs for logistic regression, I would be glad to hear of them. Some of the requirements are: - Stepwise variable selection for logistic regression - Choose base level for factor variables - The Hosmer-Lemeshow statistic - concordant and discordant - Tau C statistic Thank you for your suggestions. Regards, Harsh Singhal __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Different colour in each bar in lattice package
Hi, I try to plot bars with different colours in a barchart graphic. My idea is make that all X-Levels from trat var with different colour (grey scale). I search for a solution but dont find any. Any help? Thanks dados - structure(list(Medias = c(0.994169096209855, 0.99416342412449, 0.974683544303797, 0.954430379746835, 0.669047619047619, 0.8475569, 0.994163424124514, 0.99240506329114, 0.929113924050633, 0.70952380952381, 0.9473166, 0.9439193, 0.99746835443038, 0.99746835443038, 0.923809523809524, 0.862973760932945, 0.784046692606905, 0.645569620253165, 0.555035128805621, 0.470886075949367, 0.932944606413993, 0.809338521400778, 0.668354430379747, 0.608040201005025, 0.606060606060606), ICI = c(0.976994567793296, 0.98206380431608, 0.953595979983429, 0.928839427641527, 0.622608688475051, 1, 0.982063775957542, 0.976722631854148, 0.899246653813278, 0.664275771030459, 1, 1, 0.98225705686684, 0.98225705686684, 0.894238146710719, 0.802350976424288, 0.729009506353544, 0.575768730809864, 0.487173600236996, 0.401669070838163, 0.89054916155, 0.762545402476806, 0.607108256850681, 0.545852506856716, 0.546177521647536), ICS = c(0.998541256282513, 0.99811638878729, 0.986325619477418, 0.971104547021077, 0.712411667007983, 1, 0.998116391814118, 0.99754802608, 0.950613606532198, 0.750959759947381, 1, 1, 0.999643506018429, 0.999643506018429, 0.94561548964544, 0.90715403340414, 0.830504883009395, 0.70967681170475, 0.620904467505572, 0.541241164275512, 0.959662136271508, 0.848739648593426, 0.724387494422558, 0.666908727580774, 0.66291862672965), trat = structure(c(5L, 1L, 3L, 2L, 4L, 5L, 1L, 3L, 2L, 4L, 1L, 5L, 2L, 3L, 4L, 5L, 1L, 2L, 4L, 3L, 5L, 1L, 2L, 3L, 4L), .Label = c(O, P, Pl, T, TN), class = factor), Yvar = structure(c(2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 3L, 3L, 3L, 3L, 3L, 5L, 5L, 5L, 5L, 5L, 4L, 4L, 4L, 4L, 4L), .Label = c(0BG, 0BP, 0T, 1A, 1D), class = factor)), .Names = c(Medias, ICI, ICS, trat, Yvar), row.names = c(tratTN, tratO, tratPl, tratP, tratT, tratTN1, tratO1, tratPl1, tratP1, tratT1, tratO2, tratTN2, tratP2, tratPl2, tratT2, tratTN3, tratO3, tratP3, tratT3, tratPl3, tratTN4, tratO4, tratP4, tratPl4, tratT4), class = data.frame) library(lattice) dados$Yvar - as.factor(dados$Yvar) with(dados,barchart(Medias*100~trat|Yvar,col=gray50)) -- 10ª lei - Seu orientador espera que a sua produtividade seja baixa inicialmente e esteja acima da média após um ano. --Herman, I. P. 2007. Following the law. NATURE, Vol 445, p. 228. Prof. Ronaldo Reis Júnior | .''`. UNIMONTES/DBG/Lab. Ecologia Comportamental e Computacional | : :' : Campus Universitário Prof. Darcy Ribeiro, Vila Mauricéia | `. `'` CP: 126, CEP: 39401-089, Montes Claros - MG - Brasil | `- Fone: (38) 3229-8192 | ronaldo.r...@unimontes.br | http://www.ppgcb.unimontes.br/lecc | LinuxUser#: 205366 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] image plot but data not on grid.
qplot does (?) what I was looking for! At least it plots what I want to plot in the interactive modus. However, it seems not to work with Sweave. Thanks On 7 August 2010 16:15, Michael Bedward michael.bedw...@gmail.com wrote: If it's regular, but incomplete, that method will work. If it's irregular, then no image method will work without first interpolating a regular grid. Thanks Hadley. As I suspected, but ggplot2 is so very clever that I thought it was worth asking :) Michael __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Witold Eryk Wolski Heidmark str 5 D-28329 Bremen tel.: 04215261837 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] RExcel: Sctools not available
I have a problem with RExcel which I have now installed on top of R 2.11.0. The problem had been posted in 2009 on the forum by someone else, but no (useful) response had been uploaded. The issue is that whenever I am trying to start R from excel, or by clicking the[ RExcel2007 with RCommander] icon., I get the following messages boxes : SCTools not available then: there seems to be no R process connected to excel though both r and excel starts after I click the Icon!! Could you please help me with this issue? Thank you very much. [[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] Invalid plot type '1'
Stephen Liu satimis at yahoo.com writes: On R-Project The R Manuals http://www.r-project.org/ There are several manuals. Whether I should follow:- An Introduction to R http://www.r-project.org/ The Introduction to R is rather terse, but a reasonable starting point. The other manuals listed on that page are special-purpose manuals for installation administration, development, etc.. You can try the manuals listed in the contributed documentation section too. YouTube videos are OK, too ... The point that Erik was making was that if you have a question about a particular function, the help page for that function (in this case the results of ?plot or help(plot)) is the definitive documentation. Ben Bolker __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Different colour in each bar in lattice package
Try this: with(dados,barchart(Medias * 100 ~ trat | Yvar, col = grey(seq(0, 1, l = nlevels(trat) On Mon, Aug 9, 2010 at 8:18 AM, Ronaldo Reis Junior chrys...@gmail.comwrote: Hi, I try to plot bars with different colours in a barchart graphic. My idea is make that all X-Levels from trat var with different colour (grey scale). I search for a solution but dont find any. Any help? Thanks dados - structure(list(Medias = c(0.994169096209855, 0.99416342412449, 0.974683544303797, 0.954430379746835, 0.669047619047619, 0.8475569, 0.994163424124514, 0.99240506329114, 0.929113924050633, 0.70952380952381, 0.9473166, 0.9439193, 0.99746835443038, 0.99746835443038, 0.923809523809524, 0.862973760932945, 0.784046692606905, 0.645569620253165, 0.555035128805621, 0.470886075949367, 0.932944606413993, 0.809338521400778, 0.668354430379747, 0.608040201005025, 0.606060606060606), ICI = c(0.976994567793296, 0.98206380431608, 0.953595979983429, 0.928839427641527, 0.622608688475051, 1, 0.982063775957542, 0.976722631854148, 0.899246653813278, 0.664275771030459, 1, 1, 0.98225705686684, 0.98225705686684, 0.894238146710719, 0.802350976424288, 0.729009506353544, 0.575768730809864, 0.487173600236996, 0.401669070838163, 0.89054916155, 0.762545402476806, 0.607108256850681, 0.545852506856716, 0.546177521647536), ICS = c(0.998541256282513, 0.99811638878729, 0.986325619477418, 0.971104547021077, 0.712411667007983, 1, 0.998116391814118, 0.99754802608, 0.950613606532198, 0.750959759947381, 1, 1, 0.999643506018429, 0.999643506018429, 0.94561548964544, 0.90715403340414, 0.830504883009395, 0.70967681170475, 0.620904467505572, 0.541241164275512, 0.959662136271508, 0.848739648593426, 0.724387494422558, 0.666908727580774, 0.66291862672965), trat = structure(c(5L, 1L, 3L, 2L, 4L, 5L, 1L, 3L, 2L, 4L, 1L, 5L, 2L, 3L, 4L, 5L, 1L, 2L, 4L, 3L, 5L, 1L, 2L, 3L, 4L), .Label = c(O, P, Pl, T, TN), class = factor), Yvar = structure(c(2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 3L, 3L, 3L, 3L, 3L, 5L, 5L, 5L, 5L, 5L, 4L, 4L, 4L, 4L, 4L), .Label = c(0BG, 0BP, 0T, 1A, 1D), class = factor)), .Names = c(Medias, ICI, ICS, trat, Yvar), row.names = c(tratTN, tratO, tratPl, tratP, tratT, tratTN1, tratO1, tratPl1, tratP1, tratT1, tratO2, tratTN2, tratP2, tratPl2, tratT2, tratTN3, tratO3, tratP3, tratT3, tratPl3, tratTN4, tratO4, tratP4, tratPl4, tratT4), class = data.frame) library(lattice) dados$Yvar - as.factor(dados$Yvar) with(dados,barchart(Medias*100~trat|Yvar,col=gray50)) -- 10ª lei - Seu orientador espera que a sua produtividade seja baixa inicialmente e esteja acima da média após um ano. --Herman, I. P. 2007. Following the law. NATURE, Vol 445, p. 228. Prof. Ronaldo Reis Júnior | .''`. UNIMONTES/DBG/Lab. Ecologia Comportamental e Computacional | : :' : Campus Universitário Prof. Darcy Ribeiro, Vila Mauricéia | `. `'` CP: 126, CEP: 39401-089, Montes Claros - MG - Brasil | `- Fone: (38) 3229-8192 | ronaldo.r...@unimontes.br | http://www.ppgcb.unimontes.br/lecc | LinuxUser#: 205366 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- 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] error (code 12)
Hi, I am runing R on my mac and I get this error: R(206,0xa01ad720) malloc: *** mmap(size=402048) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug R(206,0xa01ad720) malloc: *** mmap(size=402048) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug Is there any an easy way to overcome this error? Any help or information would be great, thanks I am using Mac OS X 10.5.8. Khazaei __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] ESS question. How to get rid of ess-smart-underscore?
Hi, ESS replaces _ by -. How can I switch off this feature? I need to be able to type the underscore Thanks Eryk -- Witold Eryk Wolski Heidmark str 5 D-28329 Bremen tel.: 04215261837 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] ESS question. How to get rid of ess-smart-underscore?
On Aug 9, 2010, at 7:26 AM, W Eryk Wolski wrote: Hi, ESS replaces _ by -. How can I switch off this feature? I need to be able to type the underscore Thanks Eryk Eryk, If you type the underscore key twice, you get an underscore character rather than the assignment operator. You can disable the behavior by putting: (ess-toggle-underscore nil) in your .emacs file. Also, as you may be aware, there is a dedicated ESS help list at: https://stat.ethz.ch/mailman/listinfo/ess-help 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] ESS question. How to get rid of ess-smart-underscore?
W Eryk Wolski wrote: Hi, ESS replaces _ by -. How can I switch off this feature? I need to be able to type the underscore Thanks Eryk Pressing the underscore a second time gives you the underscore. -- Kevin E. Thorpe Biostatistician/Trialist, Knowledge Translation Program Assistant Professor, Dalla Lana School of Public Health University of Toronto email: kevin.tho...@utoronto.ca Tel: 416.864.5776 Fax: 416.864.3016 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Difference Between R: wilcox.test and STATA: signrank
This is my first post to the mailing list and I guess it's a pretty stupid question but I can't figure it out. I hope this is the right forum for these kind of questions. Before I started using R I was using STATA to run a Wilcoxon signed-rank test on two variables. See data below: https://spreadsheets.google.com/pub?key=0ApodAA2GAEP_dDZkdzZHSFBqX1JHOWJBX1dMQUZCVkEhl=enoutput=html%20%20https://spreadsheets.google.com/pub?key=0ApodAA2GAEP_dDZkdzZHSFBqX1JHOWJBX1dMQUZCVkEhl=enoutput=html STATA Output: . signrank x=y Wilcoxon signed-rank test sign | obs sum ranksexpected -+- positive | 413101 2330.5 negative | 181560 2330.5 zero | 4912251225 -+- all | 10858865886 unadjusted variance 106438.50 adjustment for ties -282.38 adjustment for zeros -10106.25 -- adjusted variance 96049.88 Ho: transfer_2_a = transfer_2_b z = 2.486 Prob |z| = *0.0129* When running a Wilcoxon signed-rank test wilcox.test(datablatt$x, datablatt$y) Wilcoxon rank sum test with continuity correction data: datablatt$x and datablatt$y W = 7059.5, p-value = *0.09197* alternative hypothesis: true location shift is not equal to 0 As you can see the p Values are different (one with H0 rejection and the other one not). I tested whether it could be that the STATA one isn't paired but this doesn't seem to be the problem. I'm dumbfound what could lead to such a difference. I couldn't find any seetings I have missed but I somehow I guess I'm using the function in the wrong way... Any ideas? Thanks a lot in advance! [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] 3d data plot
Hello! E.g. I have a file like sample.csv: condition1;condition2;myVar 0.902443929;0.879344831;0.963357725 0.91014254;0.717720763;0.953787867 0.899773581;0.871760835;1.031798755 0.892074969;0.863043345;1.080447426 0.847759139;0.894642857;1.080521187 0.847179086;0.89650009;1.111348011 0.849229318;0.912751303;1.154026236 (... some thousands of measurements, like (p,V,T) - just other types of physical quantities) (wherever a data misses, it's sign is -999) I can read it into a data frame like: mes - read.csv(sample.csv, sep=;, na.strings=-999) But what shall I do afterwards? I've tried to understand persp, but that doesn't really seem to be the solution. Maybe it would help if you could tell me just which example to check more carefully on the mentioned page. I've tried to search for one, but failed unfortunatelly. -- View this message in context: http://r.789695.n4.nabble.com/3d-data-plot-tp2306540p2318397.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] coef(summary) and plyr
Dear all, I´m having trouble getting a list of regression variables back into a dataframe. mydf - data.frame(x1=rnorm(100), x2=rnorm(100), x3=rnorm(100)) mydf$fac-factor(sample((0:2),replace=T,100)) mydf$y- mydf$x1+0.01+mydf$x2*3-mydf$x3*19+rnorm(100) dlply(mydf,.(fac),function(df) lm(y~x1+x2+x3,data=df))-dl here I´d like to use ldply(dl,coef(summary)) or something similar but I cant figure it out... Best, M __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Logistic Regression in R (SAS -like output)
Frank E Harrell Jr Professor and ChairmanSchool of Medicine Department of Biostatistics Vanderbilt University On Mon, 9 Aug 2010, Harsh wrote: Hello useRs, I have a problem at hand which I'd think is fairly common amongst groups were R is being adopted for Analytics in place of SAS. Users would like to obtain results for logistic regression in R that they have become accustomed to in SAS. Towards this end, I was able to propose the Design package in R which contains many functions to extract the various metrics that SAS reports. The replacement for Design, rms, has some new indexes. If you have suggestions pertaining to other packages, or sample code that replicates some of the SAS outputs for logistic regression, I would be glad to hear of them. Some of the requirements are: - Stepwise variable selection for logistic regression an invalid procedure - Choose base level for factor variables not relevant - get what you need from predicted values and differences in predicted values or contrasts - this automatically takes care of reference cells - The Hosmer-Lemeshow statistic obsolete: low power and sensitive to choice of binning - concordant and discordant see Hmisc's rcorr.cens - Tau C statistic Those are two different statistics. tau and C are obtained by lrm in rms/Design. Frank Thank you for your suggestions. Regards, Harsh Singhal __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] error (code 12)
On Aug 9, 2010, at 8:23 AM, khaz...@ceremade.dauphine.fr wrote: Hi, I am runing R on my mac and I get this error: R(206,0xa01ad720) malloc: *** mmap(size=402048) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug R(206,0xa01ad720) malloc: *** mmap(size=402048) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug Is there any an easy way to overcome this error? Please read the Posting Guide. You have not offered any information that would allow anyone to replicate or investigate your system- generated error. ?sessionInfo Any help or information would be great, thanks I am using Mac OS X 10.5.8. Same as I. Probably should be reposted (after read the R-Mac Faq _and_ you supply the missing information that render this question basically unanswerable) on R-MAC-SIG. If this is happening on startuop then pay particular attention to 12.16. -- David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Good Book To Work Through This Summer
There are some book-length documents (downloadable for free) at the contributed documentation section of the R project website here: http://cran.r-project.org/other-docs.html In particular, the book “Practical Regression and Anova using R” by Julian Faraway looks to have the content you want, though I haven't read it myself. There are other high quality authors in the list also. -Matt On Mon, 2010-08-09 at 03:20 -0400, Ondrej Vozar wrote: Hello, I think that good introduction for application oriented people is book of Peter Dalgaard, Introductory Statistics with R http://www.springer.com/statistics/computanional+statistics/book/978-0-387-79053-4 This book is good for mastering basics of R. Book I like the one of John Fox, An R and S-PLUS Companion to Applied Regression http://socserv.socsci.mcmaster.ca/jfox/Books/Companion/index.html But there are dozens of books on this topic. Best regards, Ondrej Vozar. On 9 August 2010 06:38, TGS cran.questi...@gmail.com wrote: Dear R users, I'm hoping to get a few suggestions about which books are good to follow along and learn R. I'm hoping to spend the summer going through a good R book as it is applied in linear regression. Thanks! __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[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. -- Matthew S. Shotwell Graduate Student Division of Biostatistics and Epidemiology Medical University of South Carolina __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Bootstrap
You should bootstrap the two groups separately. The bootstrap sample you get do not follow the same order as the original sample, so the first 62 observations are coming from both groups. What you bootstrapped is essentially the difference between the pooled mean and itself, which would no doubt come up as 0. -- View this message in context: http://r.789695.n4.nabble.com/Bootstrap-tp2317776p2318480.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] Difference Between R: wilcox.test and STATA: signrank
Hi, Look at the output of the test made in R and you can see it is a Wilcoxon rank sum test and not a Wilcoxon signed rank test. If there are ties, I know I prefer wilcox.exact from the exactRankTests. Alain On 09-Aug-10 12:43, Capasia wrote: This is my first post to the mailing list and I guess it's a pretty stupid question but I can't figure it out. I hope this is the right forum for these kind of questions. Before I started using R I was using STATA to run a Wilcoxon signed-rank test on two variables. See data below: https://spreadsheets.google.com/pub?key=0ApodAA2GAEP_dDZkdzZHSFBqX1JHOWJBX1dMQUZCVkEhl=enoutput=html%20%20https://spreadsheets.google.com/pub?key=0ApodAA2GAEP_dDZkdzZHSFBqX1JHOWJBX1dMQUZCVkEhl=enoutput=html STATA Output: . signrank x=y Wilcoxon signed-rank test sign | obs sum ranksexpected -+- positive | 413101 2330.5 negative | 181560 2330.5 zero | 4912251225 -+- all | 10858865886 unadjusted variance 106438.50 adjustment for ties -282.38 adjustment for zeros -10106.25 -- adjusted variance 96049.88 Ho: transfer_2_a = transfer_2_b z = 2.486 Prob |z| = *0.0129* When running a Wilcoxon signed-rank test wilcox.test(datablatt$x, datablatt$y) Wilcoxon rank sum test with continuity correction data: datablatt$x and datablatt$y W = 7059.5, p-value = *0.09197* alternative hypothesis: true location shift is not equal to 0 As you can see the p Values are different (one with H0 rejection and the other one not). I tested whether it could be that the STATA one isn't paired but this doesn't seem to be the problem. I'm dumbfound what could lead to such a difference. I couldn't find any seetings I have missed but I somehow I guess I'm using the function in the wrong way... Any ideas? Thanks a lot in advance! [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Alain Guillet Statistician and Computer Scientist SMCS - IMMAQ - Université catholique de Louvain Bureau c.316 Voie du Roman Pays, 20 B-1348 Louvain-la-Neuve Belgium tel: +32 10 47 30 50 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] coef(summary) and plyr
On Aug 9, 2010, at 7:51 AM, moleps wrote: Dear all, I´m having trouble getting a list of regression variables back into a dataframe. mydf - data.frame(x1=rnorm(100), x2=rnorm(100), x3=rnorm(100)) mydf$fac-factor(sample((0:2),replace=T,100)) mydf$y- mydf$x1+0.01+mydf$x2*3-mydf$x3*19+rnorm(100) dlply(mydf,.(fac),function(df) lm(y~x1+x2+x3,data=df))-dl here I´d like to use ldply(dl,coef(summary)) or something similar but I cant figure it out... dfdl - ldply(dl, function(x) coef(summary(x)) ) Doesn't create a grouping variable, so: dfdl$group=rep(0:2, each=4) David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R Base Code
nancy_shackelford nancy.shackelford at gmail.com writes: Hello all, I need to imitate the 'q' function (qnorm, qweibull, etc) for Clark's 2Dt distribution model. I'm not skilled enough in R to code it myself, so I thought I could find the base code for one of the existing 'q' functions and just modify it. However, I'm having trouble navigating through the R Source Code on the CRAN website. I've searched some forum and help sites, but I can't find anything specific on locating function codes. I also read somewhere that Clark's 2Dt is available in the R distribution functions, but I haven't found anything that confirms that. You can find the C source code for qt in http://svn.r-project.org/R/trunk/src/nmath/qt.c and the R code is in http://svn.r-project.org/R/trunk/src/library/stats/R/distn.R but I don't think this is really what you want. As pointed out in Clark et al 1999 (Ecology), the Clark 2Dt function is just a bivariate version of the univariate t-distribution. I think that if you stare at the equations in Clark et al 1999 and (e.g.) in ?dt you can probably adapt the existing pt/qt functions to get where you need, adjusting normalizing constants as appropriate ... PS: when asking questions about field-specific topics on the general R list, it's a good idea to give a little more background -- even references, in case someone is interested. Few people outside of community ecology have heard of Clark's 2Dt ... good luck, Ben Bolker __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Difference Between R: wilcox.test and STATA: signrank
On Aug 9, 2010, at 3:03 PM, Alain Guillet wrote: Hi, Look at the output of the test made in R and you can see it is a Wilcoxon rank sum test and not a Wilcoxon signed rank test. It might be helpful to add that paired=TRUE is needed in the call to get the signed-rank test. If there are ties, I know I prefer wilcox.exact from the exactRankTests. (Not that much of an issue in larger sample sizes, I'd say. Even with binary data, the normal approximation works reasonably well under the usual assumptions of expected counts 5, since the tie-adjustment for the variance is exact for the distribution of the ranks. The continuity correction doesn't quite work though. Anyways, wilcox.exact is of course a nice thing to have.) Alain On 09-Aug-10 12:43, Capasia wrote: This is my first post to the mailing list and I guess it's a pretty stupid question but I can't figure it out. I hope this is the right forum for these kind of questions. Before I started using R I was using STATA to run a Wilcoxon signed-rank test on two variables. See data below: https://spreadsheets.google.com/pub?key=0ApodAA2GAEP_dDZkdzZHSFBqX1JHOWJBX1dMQUZCVkEhl=enoutput=html%20%20https://spreadsheets.google.com/pub?key=0ApodAA2GAEP_dDZkdzZHSFBqX1JHOWJBX1dMQUZCVkEhl=enoutput=html STATA Output: . signrank x=y Wilcoxon signed-rank test sign | obs sum ranksexpected -+- positive | 413101 2330.5 negative | 181560 2330.5 zero | 4912251225 -+- all | 10858865886 unadjusted variance 106438.50 adjustment for ties -282.38 adjustment for zeros -10106.25 -- adjusted variance 96049.88 Ho: transfer_2_a = transfer_2_b z = 2.486 Prob |z| = *0.0129* When running a Wilcoxon signed-rank test wilcox.test(datablatt$x, datablatt$y) Wilcoxon rank sum test with continuity correction data: datablatt$x and datablatt$y W = 7059.5, p-value = *0.09197* alternative hypothesis: true location shift is not equal to 0 As you can see the p Values are different (one with H0 rejection and the other one not). I tested whether it could be that the STATA one isn't paired but this doesn't seem to be the problem. I'm dumbfound what could lead to such a difference. I couldn't find any seetings I have missed but I somehow I guess I'm using the function in the wrong way... Any ideas? Thanks a lot in advance! [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Alain Guillet Statistician and Computer Scientist SMCS - IMMAQ - Université catholique de Louvain Bureau c.316 Voie du Roman Pays, 20 B-1348 Louvain-la-Neuve Belgium tel: +32 10 47 30 50 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Peter Dalgaard Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd@cbs.dk Priv: pda...@gmail.com __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] bind a data frame columns
Hello guys, I want to rbind the columns of a data frame but I don't know how to do it, let's say: A B C 1 2 3 1 2 3 I want to get 1 1 2 2 3 3 It seems very simple but I still didnt get a find of how to do it...Please help! -- View this message in context: http://r.789695.n4.nabble.com/bind-a-data-frame-columns-tp2318526p2318526.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] Two questions on R and cairo/Cairo
On a headless Linux server running R 2.9.2 I would like to enable support for cairo, but capabilities(cairo) keeps on giving me FALSE. Is it possible what I am trying to do or can this only be achieved at R build time? I do not have administrative rights on this server. After compiling cairo-1.8.10 and its dependencies from source in my home directory, I finally managed to install the Cairo package (capital C). Although capabilities(cairo) still gives me FALSE, I am now able to produce graphics. Apart from convenience, is there any difference between using built-in support for cairo or using the Cairo package? Carsten __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] ESS question. How to get rid of ess-smart-underscore?
I bogged about 3 possible solutions recently (statbandit.wordpress.com). Possibly the 2nd most recent post. Abhijit On Aug 9, 2010 8:28 AM, W Eryk Wolski wewol...@gmail.com wrote: Hi, ESS replaces _ by -. How can I switch off this feature? I need to be able to type the underscore Thanks Eryk -- Witold Eryk Wolski Heidmark str 5 D-28329 Bremen tel.: 04215261837 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] bind a data frame columns
Hi! Would unlist() work for you? HTH, Ivan Le 8/9/2010 16:00, Anna Lippel a écrit : Hello guys, I want to rbind the columns of a data frame but I don't know how to do it, let's say: A B C 1 2 3 1 2 3 I want to get 1 1 2 2 3 3 It seems very simple but I still didnt get a find of how to do it...Please help! -- Ivan CALANDRA PhD Student University of Hamburg Biozentrum Grindel und Zoologisches Museum Abt. Säugetiere Martin-Luther-King-Platz 3 D-20146 Hamburg, GERMANY +49(0)40 42838 6231 ivan.calan...@uni-hamburg.de ** http://www.for771.uni-bonn.de http://webapp5.rrz.uni-hamburg.de/mammals/eng/mitarbeiter.php [[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] coef(summary) and plyr
If you look at the output (as I did) you should see that despite whatever expectations you have developed regarding plyr, that it did not produce a grouping variable: ldply(dl, function(x) coef(summary(x)) ) facEstimate Std. Error t value Pr(|t|) 10 -0.3563418 0.1438322 -2.477483 1.820555e-02 21 0.9197772 0.15259006.027768 7.097623e-07 32 3.0481679 0.1331307 22.896050 1.197920e-22 40 -18.7726473 0.1281064 -146.539553 2.125848e-50 51 -0.2961841 0.1885210 -1.571093 1.273942e-01 62 1.2846496 0.18333947.006946 1.277086e-07 70 2.9664816 0.1737222 17.076010 2.448612e-16 81 -18.7265068 0.2044723 -91.584567 3.048491e-36 92 0.3993073 0.19797132.016996 5.455569e-02 10 0 0.7657945 0.24774593.091048 4.846678e-03 11 1 3.0365005 0.1731814 17.533641 1.470033e-15 12 2 -19.2140081 0.1882448 -102.069256 2.741417e-34 Warning message: In data.frame(..., check.names = FALSE) : row names were found from a short variable and have been discarded -- David On Aug 9, 2010, at 10:11 AM, moleps wrote: ldply doesnt need a grouping variable as far as I understand the command.. Description For each element of a list, apply function then combine results into a data frame Usage ldply(.data, .fun = NULL, ..., .progress = none) regards, M On 9. aug. 2010, at 15.33, David Winsemius wrote: On Aug 9, 2010, at 7:51 AM, moleps wrote: Dear all, I´m having trouble getting a list of regression variables back into a dataframe. mydf - data.frame(x1=rnorm(100), x2=rnorm(100), x3=rnorm(100)) mydf$fac-factor(sample((0:2),replace=T,100)) mydf$y- mydf$x1+0.01+mydf$x2*3-mydf$x3*19+rnorm(100) dlply(mydf,.(fac),function(df) lm(y~x1+x2+x3,data=df))-dl here I´d like to use ldply(dl,coef(summary)) or something similar but I cant figure it out... dfdl - ldply(dl, function(x) coef(summary(x)) ) Doesn't create a grouping variable, so: dfdl$group=rep(0:2, each=4) David Winsemius, MD West Hartford, CT David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] package names in Latex
Dear R People: When putting R package names in Latex, do we use \it or \em, please? Thanks, Erin -- Erin Hodgess Associate Professor Department of Computer and Mathematical Sciences University of Houston - Downtown mailto: erinm.hodg...@gmail.com __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] m-estimators
check the robustbase package and rlm or hubers in MASS
You'll need to know which m-estimator you want, but both those packages
include at least some m-estimators.
Strictly, so does the base package; the mean is an m-estimator. Just
not a very robust one!
S Ellison
Iasonas Lamprianou lampria...@yahoo.com 06/08/2010 08:10:44
Dear colleagues
can somebody help me by showing how we can compute m-estimators in R?
thanks
Dr. Iasonas Lamprianou
Assistant Professor (Educational Research and Evaluation)
Department of Education Sciences
European University-Cyprus
P.O. Box 22006
1516 Nicosia
Cyprus
Tel.: +357-22-713178
Fax: +357-22-590539
Honorary Research Fellow
Department of Education
The University of Manchester
Oxford Road, Manchester M13 9PL, UK
Tel. 0044 161 275 3485
iasonas.lampria...@manchester.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.
***
This email and any attachments are confidential. Any use...{{dropped:8}}
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/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] Logistic Regression in R (SAS -like output)
On Mon, Aug 9, 2010 at 6:43 AM, Harsh singhal...@gmail.com wrote: Hello useRs, I have a problem at hand which I'd think is fairly common amongst groups were R is being adopted for Analytics in place of SAS. Users would like to obtain results for logistic regression in R that they have become accustomed to in SAS. Towards this end, I was able to propose the Design package in R which contains many functions to extract the various metrics that SAS reports. If you have suggestions pertaining to other packages, or sample code that replicates some of the SAS outputs for logistic regression, I would be glad to hear of them. Some of the requirements are: - Stepwise variable selection for logistic regression - Choose base level for factor variables - The Hosmer-Lemeshow statistic - concordant and discordant - Tau C statistic For stepwise logistic regression using AIC see: library(MASS) ?stepAIC For specifying reference level: ?relevel __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] package names in Latex
On 09.08.2010 16:30, Erin Hodgess wrote:
Dear R People:
When putting R package names in Latex, do we use \it or \em, please?
Thanks,
Erin
Depends.
For example, the style guide of the Journal of Statistical Software asks
you to use \pkg{} which is defined as
\newcommand{\pkg}[1]{{\fontseries{b}\selectfont #1}}
which is somehow similar to The R Journal's style.
Best,
Uwe Ligges
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/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] package names in Latex
On Aug 9, 2010, at 9:30 AM, Erin Hodgess wrote:
Dear R People:
When putting R package names in Latex, do we use \it or \em, please?
Thanks,
Erin
Erin,
I may be missing something specific to your application, but for the R Journal,
JSS and .Rd help files, package names would typically be bolded using a \pkg
directive (eg. \pkg{YourPackageName}), which would bold the package name within
the braces.
If you are doing this outside of those environments, you can duplicate the
effect by using \textbf{YourPackageName}, which would bold the text within the
braces only.
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.
[R] nested 'by'
Assuming a data frame or matrix with two columns representing variable that you want to aggregate over. you want to calculate column means, by year, for each Id example-data.frame(id=c(rep(12345,5),rep(54321,6),rep(45678,7)),Year=rep(seq(1900,1902,by=1),6), x=seq(1,18,by=1),y=seq(18,1,by=-1)) example id Year x y 1 12345 1900 1 18 2 12345 1901 2 17 3 12345 1902 3 16 4 12345 1900 4 15 5 12345 1901 5 14 6 54321 1902 6 13 7 54321 1900 7 12 8 54321 1901 8 11 9 54321 1902 9 10 10 54321 1900 10 9 11 54321 1901 11 8 12 45678 1902 12 7 13 45678 1900 13 6 14 45678 1901 14 5 15 45678 1902 15 4 16 45678 1900 16 3 17 45678 1901 17 2 18 45678 1902 18 1 result-by(example[,3:4], example$id, by(example[,3:4], example$Year,colMeans, na.rm=T)) Error in FUN(X[[1L]], ...) : could not find function FUN desired result should look like: id Year meanx mean y 1 12345 1900 ...... 2 12345 1901 ... 3 12345 1902 ... 4 54321 1900 5 54321 1901 6 54321 1902 7 45678 1900 8 45678 1901 9 45678 1902 [[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] image plot but data not on grid.
With sweave, you need to explicitly print() the output of ggplot2 and lattice plots. Hadley On Mon, Aug 9, 2010 at 6:32 AM, W Eryk Wolski wewol...@gmail.com wrote: qplot does (?) what I was looking for! At least it plots what I want to plot in the interactive modus. However, it seems not to work with Sweave. Thanks On 7 August 2010 16:15, Michael Bedward michael.bedw...@gmail.com wrote: If it's regular, but incomplete, that method will work. If it's irregular, then no image method will work without first interpolating a regular grid. Thanks Hadley. As I suspected, but ggplot2 is so very clever that I thought it was worth asking :) Michael __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Witold Eryk Wolski Heidmark str 5 D-28329 Bremen tel.: 04215261837 -- Assistant Professor / Dobelman Family Junior Chair Department of Statistics / Rice University http://had.co.nz/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] 3d data plot
On 09.08.2010 13:17, szisziszilvi wrote: Hello! E.g. I have a file like sample.csv: condition1;condition2;myVar 0.902443929;0.879344831;0.963357725 0.91014254;0.717720763;0.953787867 0.899773581;0.871760835;1.031798755 0.892074969;0.863043345;1.080447426 0.847759139;0.894642857;1.080521187 0.847179086;0.89650009;1.111348011 0.849229318;0.912751303;1.154026236 See function plot3d() in package rgl, cloud() in lattice, scatterplot3d() in scatterplot3d, etc. Uwe Ligges (... some thousands of measurements, like (p,V,T) - just other types of physical quantities) (wherever a data misses, it's sign is -999) I can read it into a data frame like: mes- read.csv(sample.csv, sep=;, na.strings=-999) But what shall I do afterwards? I've tried to understand persp, but that doesn't really seem to be the solution. Maybe it would help if you could tell me just which example to check more carefully on the mentioned page. I've tried to search for one, but failed unfortunatelly. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] coef(summary) and plyr
On Mon, Aug 9, 2010 at 9:29 AM, David Winsemius dwinsem...@comcast.net wrote: If you look at the output (as I did) you should see that despite whatever expectations you have developed regarding plyr, that it did not produce a grouping variable: ldply(dl, function(x) coef(summary(x)) ) fac Estimate Std. Error t value Pr(|t|) 1 0 -0.3563418 0.1438322 -2.477483 1.820555e-02 2 1 0.9197772 0.1525900 6.027768 7.097623e-07 3 2 3.0481679 0.1331307 22.896050 1.197920e-22 4 0 -18.7726473 0.1281064 -146.539553 2.125848e-50 5 1 -0.2961841 0.1885210 -1.571093 1.273942e-01 6 2 1.2846496 0.1833394 7.006946 1.277086e-07 7 0 2.9664816 0.1737222 17.076010 2.448612e-16 8 1 -18.7265068 0.2044723 -91.584567 3.048491e-36 9 2 0.3993073 0.1979713 2.016996 5.455569e-02 10 0 0.7657945 0.2477459 3.091048 4.846678e-03 11 1 3.0365005 0.1731814 17.533641 1.470033e-15 12 2 -19.2140081 0.1882448 -102.069256 2.741417e-34 cf. ldply(dl, coef) fac (Intercept)x1 x2x3 1 0 -0.12051346 1.1391933 3.022287 -19.01828 2 1 -0.08890497 1.0741715 3.219577 -19.14279 3 2 -0.12728421 0.9284263 2.973905 -19.12774 which you can see maintains the original grouping variable fac. The problem is that summary stores the variable names as rownames, which does not make for easy rbinding. Hadley -- Assistant Professor / Dobelman Family Junior Chair Department of Statistics / Rice University http://had.co.nz/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] nested 'by'
Try this:
aggregate(example[c('x', 'y')], example[c('id', 'Year')], 'mean')
On Mon, Aug 9, 2010 at 11:46 AM, steven mosher mosherste...@gmail.comwrote:
Assuming a data frame or matrix with two columns representing variable that
you want to aggregate over.
you want to calculate column means, by year, for each Id
example-data.frame(id=c(rep(12345,5),rep(54321,6),rep(45678,7)),Year=rep(seq(1900,1902,by=1),6),
x=seq(1,18,by=1),y=seq(18,1,by=-1))
example
id Year x y
1 12345 1900 1 18
2 12345 1901 2 17
3 12345 1902 3 16
4 12345 1900 4 15
5 12345 1901 5 14
6 54321 1902 6 13
7 54321 1900 7 12
8 54321 1901 8 11
9 54321 1902 9 10
10 54321 1900 10 9
11 54321 1901 11 8
12 45678 1902 12 7
13 45678 1900 13 6
14 45678 1901 14 5
15 45678 1902 15 4
16 45678 1900 16 3
17 45678 1901 17 2
18 45678 1902 18 1
result-by(example[,3:4], example$id, by(example[,3:4],
example$Year,colMeans, na.rm=T))
Error in FUN(X[[1L]], ...) : could not find function FUN
desired result should look like:
id Year meanx mean y
1 12345 1900 ......
2 12345 1901 ...
3 12345 1902 ...
4 54321 1900
5 54321 1901
6 54321 1902
7 45678 1900
8 45678 1901
9 45678 1902
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Henrique Dallazuanna
Curitiba-Paraná-Brasil
25° 25' 40 S 49° 16' 22 O
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Invalid plot type '1'
The Introduction to R is rather terse, but a reasonable starting point. The other manuals listed on that page are special-purpose manuals for installation administration, development, etc.. You can try the manuals listed in the contributed documentation section too. Hi Ben, Thanks for your advice. I suppose you meant those documentation on following URL Contributed Documentation http://cran.r-project.org/other-docs.html The difficulty for a beginner learning R is to find the right document. There are many documents on Internet. It'll take lengthy time going through all of them to find a right document to follow. It is the same in learning other new subjects. Other advice noted and thanks B.R. Stephen L __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] RExcel: Sctools not available
Please post any qeustions regarding RExcel to the rcom-l mailing list. You can subscribe at rcom.univie.ac.at On Aug 9, 2010, at 1:42 PM, Andreas Scherer wrote: I have a problem with RExcel which I have now installed on top of R 2.11.0. The problem had been posted in 2009 on the forum by someone else, but no (useful) response had been uploaded. The issue is that whenever I am trying to start R from excel, or by clicking the[ RExcel2007 with RCommander] icon., I get the following messages boxes : SCTools not available then: there seems to be no R process connected to excel though both r and excel starts after I click the Icon!! Could you please help me with this issue? Thank you very much. [[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. -- Erich Neuwirth Didactic Center for Computer Science and Institute for Scientific Computing University of Vienna [[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] nested 'by'
That works.
Thanks
On Mon, Aug 9, 2010 at 7:55 AM, Henrique Dallazuanna www...@gmail.comwrote:
Try this:
aggregate(example[c('x', 'y')], example[c('id', 'Year')], 'mean')
On Mon, Aug 9, 2010 at 11:46 AM, steven mosher mosherste...@gmail.comwrote:
Assuming a data frame or matrix with two columns representing variable
that
you want to aggregate over.
you want to calculate column means, by year, for each Id
example-data.frame(id=c(rep(12345,5),rep(54321,6),rep(45678,7)),Year=rep(seq(1900,1902,by=1),6),
x=seq(1,18,by=1),y=seq(18,1,by=-1))
example
id Year x y
1 12345 1900 1 18
2 12345 1901 2 17
3 12345 1902 3 16
4 12345 1900 4 15
5 12345 1901 5 14
6 54321 1902 6 13
7 54321 1900 7 12
8 54321 1901 8 11
9 54321 1902 9 10
10 54321 1900 10 9
11 54321 1901 11 8
12 45678 1902 12 7
13 45678 1900 13 6
14 45678 1901 14 5
15 45678 1902 15 4
16 45678 1900 16 3
17 45678 1901 17 2
18 45678 1902 18 1
result-by(example[,3:4], example$id, by(example[,3:4],
example$Year,colMeans, na.rm=T))
Error in FUN(X[[1L]], ...) : could not find function FUN
desired result should look like:
id Year meanx mean y
1 12345 1900 ......
2 12345 1901 ...
3 12345 1902 ...
4 54321 1900
5 54321 1901
6 54321 1902
7 45678 1900
8 45678 1901
9 45678 1902
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Henrique Dallazuanna
Curitiba-Paraná-Brasil
25° 25' 40 S 49° 16' 22 O
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Invalid plot type '1'
Stephen Liu wrote: The Introduction to R is rather terse, but a reasonable starting point. The other manuals listed on that page are special-purpose manuals for installation administration, development, etc.. You can try the manuals listed in the contributed documentation section too. Hi Ben, Thanks for your advice. I suppose you meant those documentation on following URL Contributed Documentation http://cran.r-project.org/other-docs.html The difficulty for a beginner learning R is to find the right document. There are many documents on Internet. It'll take lengthy time going through all of them to find a right document to follow. It is the same in learning other new subjects. Other advice noted and thanks I would consider a beginning R book if your budget allows it. The most useful book will depend on your background and interests, http://www.r-project.org/doc/bib/R-books.html __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Extract values from data frame in R
-Original Message-
From: r-help-boun...@r-project.org
[mailto:r-help-boun...@r-project.org] On Behalf Of Erik Iverson
Sent: Sunday, August 08, 2010 11:27 PM
To: Alexander Eggel
Cc: r-help@r-project.org
Subject: Re: [R] Extract values from data frame in R
On 08/09/2010 01:16 AM, Alexander Eggel wrote:
Using R, I would like to find out which Samples (S1, S2,
S3, S4, S5) fulfill
the following criteria:contain minimally one value (x, y or
z) bigger than
4. Any ideas? Thanks, Alex.
data
Sample xy z
1S1 -0.35.32.5
2S20.40.2 -1.2
3S31.2 -0.63.2
4S44.30.75.7
5S52.44.32.3
Untested:
Sample[apply(Sample[-1], 1, function(x) any(x) 4)), Sample]
The any(x)4 should be any(x4), as in:
f1 - function(data) data[apply(data[-1], 1, function(x) any(x
4)), Sample]
Note that operating a column at a time on a
data is often faster than operating a row at
a time. E.g.,
f2 - function(data) with(data, Sample[x4 | y4 | z4])
makeData - function (nrow, seed){
if (!missing(seed))
set.seed(seed)
data.frame(Sample = sample(paste(S, 1:5, sep = ), replace =
TRUE,
size = nrow), x = rgamma(nrow, 4), y = rgamma(nrow, 5),
z = rgamma(nrow, 3))
}
z - makeData(1, seed=73)
system.time(v1 - f1(z))
user system elapsed
0.270.000.25
system.time(v2 - f2(z))
user system elapsed
0.000.010.01
identical(v1, v2)
[1] TRUE
length(v1)
[1] 8390
(I prefer that non-apply approach because apply often
causes trouble when used with data.frames -- it is only
safe when all columns are numeric.)
Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.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] TRUE/FALSE
I can't understand why you doubled ( if((combos[e,f]==1) - A R learner. -- View this message in context: http://r.789695.n4.nabble.com/TRUE-FALSE-tp2318668p2318684.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] if several expressions (basic question)
Dear R users,
I have a basic question. In an if statement, when several expressions have
to be evaluated, they must be put inside curly braces, right ?
For example :
if (x2) {
y=3
z=2
}
Thank you very much,
Dwayne
[[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] TRUE/FALSE
On 09.08.2010 17:47, Wu Gong wrote: I can't understand why you doubled ( if((combos[e,f]==1) - A R learner. ? Can you please refer and quote the original messages you are replying to and can you please also include the one who asked the question? Not everybody is subscribed to this list. Thank you very much for your contributions. Best, Uwe Ligges __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] coef(summary) and plyr
On Aug 9, 2010, at 10:11 AM, moleps wrote: ldply doesnt need a grouping variable as far as I understand the command.. There is one further improvement to consider. When I tried using dlply to tackle a problem on which I had been bashing my head for the last three days and it gave just the results I had been looking for, I also noticed that the dlply function returns the grouping variable levels in an attribute, split_labels, which could be unlisted to use as an argument to the rep() call I suggested earlier: dfdl$group=rep(unlist(attr(dl, split_labels)), each=4) That might make the results more self-documenting in situations where the grouping levels were more involved than 0:2. (Now, if I can get rms::Predict to behave as nicely with the plyr functions as did rms::cph, I will be home free.) -- David. Description For each element of a list, apply function then combine results into a data frame Usage ldply(.data, .fun = NULL, ..., .progress = none) regards, M On 9. aug. 2010, at 15.33, David Winsemius wrote: On Aug 9, 2010, at 7:51 AM, moleps wrote: Dear all, I´m having trouble getting a list of regression variables back into a dataframe. mydf - data.frame(x1=rnorm(100), x2=rnorm(100), x3=rnorm(100)) mydf$fac-factor(sample((0:2),replace=T,100)) mydf$y- mydf$x1+0.01+mydf$x2*3-mydf$x3*19+rnorm(100) dlply(mydf,.(fac),function(df) lm(y~x1+x2+x3,data=df))-dl here I´d like to use ldply(dl,coef(summary)) or something similar but I cant figure it out... dfdl - ldply(dl, function(x) coef(summary(x)) ) Doesn't create a grouping variable, so: dfdl$group=rep(0:2, each=4) David Winsemius, MD West Hartford, CT David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] if several expressions (basic question)
On Mon, Aug 9, 2010 at 8:51 AM, Dwayne Blind dwaynebl...@gmail.com wrote:
Dear R users,
I have a basic question. In an if statement, when several expressions have
to be evaluated, they must be put inside curly braces, right ?
Yes.
if(1 2) {print(hello); print(world)}
if(4 2) {print(hello); print(world)}
For example :
if (x2) {
y=3
z=2
}
Thank you very much,
Dwayne
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Joshua Wiley
Ph.D. Student, Health Psychology
University of California, Los Angeles
http://www.joshuawiley.com/
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] if several expressions (basic question)
On Aug 9, 2010, at 12:14 PM, Joshua Wiley wrote:
On Mon, Aug 9, 2010 at 8:51 AM, Dwayne Blind dwaynebl...@gmail.com
wrote:
Dear R users,
I have a basic question. In an if statement, when several
expressions have
to be evaluated, they must be put inside curly braces, right ?
Yes.
if(1 2) {print(hello); print(world)}
if(4 2) {print(hello); print(world)}
Well, not actually. If they are all on the same line separated by
;'s the parser should accept.
if(TRUE) print(hello); print(world); y=3; z=2
y
z
--
David.
For example :
if (x2) {
y=3
z=2
}
Thank you very much,
Dwayne
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Joshua Wiley
Ph.D. Student, Health Psychology
University of California, Los Angeles
http://www.joshuawiley.com/
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
David Winsemius, MD
West Hartford, CT
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] if several expressions (basic question)
On Aug 9, 2010, at 12:29 PM, Joshua Wiley wrote:
On Mon, Aug 9, 2010 at 9:26 AM, David Winsemius dwinsem...@comcast.net
wrote:
On Aug 9, 2010, at 12:14 PM, Joshua Wiley wrote:
On Mon, Aug 9, 2010 at 8:51 AM, Dwayne Blind dwaynebl...@gmail.com
wrote:
Dear R users,
I have a basic question. In an if statement, when several
expressions
have
to be evaluated, they must be put inside curly braces, right ?
Yes.
if(1 2) {print(hello); print(world)}
if(4 2) {print(hello); print(world)}
Well, not actually. If they are all on the same line separated by
;'s the
parser should accept.
if(TRUE) print(hello); print(world); y=3; z=2
y
z
I thought that at first also but look at:
if(FALSE) print(hello); print(world)
At least on my version of R, hello is not printed but world is.
Sorry for the noise. I misinterpreted the results.
--
David.
--
David.
For example :
if (x2) {
y=3
z=2
}
Thank you very much,
Dwayne
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Joshua Wiley
Ph.D. Student, Health Psychology
University of California, Los Angeles
http://www.joshuawiley.com/
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
David Winsemius, MD
West Hartford, CT
--
Joshua Wiley
Ph.D. Student, Health Psychology
University of California, Los Angeles
http://www.joshuawiley.com/
David Winsemius, MD
West Hartford, CT
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] if several expressions (basic question)
Thanks to all of you.
Dwayne
2010/8/9 David Winsemius dwinsem...@comcast.net
On Aug 9, 2010, at 12:29 PM, Joshua Wiley wrote:
On Mon, Aug 9, 2010 at 9:26 AM, David Winsemius dwinsem...@comcast.net
wrote:
On Aug 9, 2010, at 12:14 PM, Joshua Wiley wrote:
On Mon, Aug 9, 2010 at 8:51 AM, Dwayne Blind dwaynebl...@gmail.com
wrote:
Dear R users,
I have a basic question. In an if statement, when several expressions
have
to be evaluated, they must be put inside curly braces, right ?
Yes.
if(1 2) {print(hello); print(world)}
if(4 2) {print(hello); print(world)}
Well, not actually. If they are all on the same line separated by ;'s
the
parser should accept.
if(TRUE) print(hello); print(world); y=3; z=2
y
z
I thought that at first also but look at:
if(FALSE) print(hello); print(world)
At least on my version of R, hello is not printed but world is.
Sorry for the noise. I misinterpreted the results.
--
David.
--
David.
For example :
if (x2) {
y=3
z=2
}
Thank you very much,
Dwayne
[[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.htmlhttp://www.r-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Joshua Wiley
Ph.D. Student, Health Psychology
University of California, Los Angeles
http://www.joshuawiley.com/
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.htmlhttp://www.r-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
David Winsemius, MD
West Hartford, CT
--
Joshua Wiley
Ph.D. Student, Health Psychology
University of California, Los Angeles
http://www.joshuawiley.com/
David Winsemius, MD
West Hartford, CT
[[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] regression line of 2 independent variables
Hi, I would like to a draw a scatterplot of x1 and x2 (plot (x1, x2)), and also want to draw a sort of regression line across the data points. But x1 and x2 are just 2 independent variables, so in this case a regression of x1 over x2, or vice versa, is not appropriate per se. What would be an appropriate way to do this? Thanks for any suggestions. John __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] TRUE/FALSE
Hi Uwe, I'm sorry for the inconvenience I caused. I read posts of R Help through nabble forum. When I reply a post through the forum, it is distinctly clear that my message is a reply to the original poster's post, just like a conversation. Those posts which quote the original message which itself might quote the original original message .., seem to be too much redundant to me. I have been trying to be a well-behaved member of the R community:) Best Regards, Wu Gong Uwe Ligges-3 wrote: Can you please refer and quote the original messages you are replying to and can you please also include the one who asked the question? Not everybody is subscribed to this list. Thank you very much for your contributions. - A R learner. -- View this message in context: http://r.789695.n4.nabble.com/TRUE-FALSE-tp2318668p2318778.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] if several expressions (basic question)
The safe bit is to always use the curly brackets on the 'if'
statements to avoid problems. I always do
if (..) {
statement
}
On Mon, Aug 9, 2010 at 12:29 PM, Joshua Wiley jwiley.ps...@gmail.com wrote:
On Mon, Aug 9, 2010 at 9:26 AM, David Winsemius dwinsem...@comcast.net
wrote:
On Aug 9, 2010, at 12:14 PM, Joshua Wiley wrote:
On Mon, Aug 9, 2010 at 8:51 AM, Dwayne Blind dwaynebl...@gmail.com
wrote:
Dear R users,
I have a basic question. In an if statement, when several expressions
have
to be evaluated, they must be put inside curly braces, right ?
Yes.
if(1 2) {print(hello); print(world)}
if(4 2) {print(hello); print(world)}
Well, not actually. If they are all on the same line separated by ;'s the
parser should accept.
if(TRUE) print(hello); print(world); y=3; z=2
y
z
I thought that at first also but look at:
if(FALSE) print(hello); print(world)
At least on my version of R, hello is not printed but world is.
--
David.
For example :
if (x2) {
y=3
z=2
}
Thank you very much,
Dwayne
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Joshua Wiley
Ph.D. Student, Health Psychology
University of California, Los Angeles
http://www.joshuawiley.com/
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
David Winsemius, MD
West Hartford, CT
--
Joshua Wiley
Ph.D. Student, Health Psychology
University of California, Los Angeles
http://www.joshuawiley.com/
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem that you are trying to solve?
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] coef(summary) and plyr
There is one further improvement to consider. When I tried using dlply to tackle a problem on which I had been bashing my head for the last three days and it gave just the results I had been looking for, I also noticed that the dlply function returns the grouping variable levels in an attribute, split_labels, which could be unlisted to use as an argument to the rep() call I suggested earlier: dfdl$group=rep(unlist(attr(dl, split_labels)), each=4) That might make the results more self-documenting in situations where the grouping levels were more involved than 0:2. That's exactly what dlply does - so you should never have to do that yourself. Hadley -- Assistant Professor / Dobelman Family Junior Chair Department of Statistics / Rice University http://had.co.nz/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] optimization subject to constraints
Dear R users, I'm looking for tools to perform optimization subject to constraints, both linear and non-linear. I don't mind which algorithm may be used, my primary aim is to get something general and easy-to-use to study simples examples. Thanks for helping, Gildas __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] optimization subject to constraints
Hi ! Why not constrOptim ? Dwayne 2010/8/9 Gildas Mazo gildas.m...@curie.fr Dear R users, I'm looking for tools to perform optimization subject to constraints, both linear and non-linear. I don't mind which algorithm may be used, my primary aim is to get something general and easy-to-use to study simples examples. Thanks for helping, Gildas __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.htmlhttp://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] List of lists ?
Dear list, I have to use a list of lists containing vectors. For instance : [[1]] [[1]][[1]] [1] 1 2 3 [[1]][[2]] [1] 3 2 1 I want to attribute vectors to the main list without use of an intermediate list, but it does not work : x - list() x[[1]][[1]] - c(1, 2, 3) x[[1]][[2]] - c(3, 2, 1) Thanks in advance, Carlos __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] optimization subject to constraints
You may want to look at: http://cran.r-project.org/web/packages/alabama/index.html Ravi. -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Gildas Mazo Sent: Monday, August 09, 2010 12:49 PM To: r-help@r-project.org Subject: [R] optimization subject to constraints Dear R users, I'm looking for tools to perform optimization subject to constraints, both linear and non-linear. I don't mind which algorithm may be used, my primary aim is to get something general and easy-to-use to study simples examples. Thanks for helping, Gildas __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] optimization subject to constraints
try command solnp in package Rsolnp Am 09.08.2010 18:56, schrieb Dwayne Blind: Hi ! Why not constrOptim ? Dwayne 2010/8/9 Gildas Mazogildas.m...@curie.fr Dear R users, I'm looking for tools to perform optimization subject to constraints, both linear and non-linear. I don't mind which algorithm may be used, my primary aim is to get something general and easy-to-use to study simples examples. Thanks for helping, Gildas __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] optimization subject to constraints
constrOptim can only handle linear inequality constraints. It cannot handle equality (linear or nonlinear) as well as nonlinear inequality constraints. Ravi. -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Dwayne Blind Sent: Monday, August 09, 2010 12:56 PM To: Gildas Mazo Cc: r-help@r-project.org Subject: Re: [R] optimization subject to constraints Hi ! Why not constrOptim ? Dwayne 2010/8/9 Gildas Mazo gildas.m...@curie.fr Dear R users, I'm looking for tools to perform optimization subject to constraints, both linear and non-linear. I don't mind which algorithm may be used, my primary aim is to get something general and easy-to-use to study simples examples. Thanks for helping, Gildas __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.htmlhttp://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-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] TRUE/FALSE
Here is my code
# determine the DDOA measurements
for(e in 1:numSensors)
{
for(f in 1:numSensors)
{
if((combos[e,f]==1)
{
# true distance between each sensor and the target
truedistance[e]-sqrt((targetX-sensorX[e])^2+(targetY-sensorY[e])^2)
# add an error that has a N(0, sigma^2) distribution
truedistance[e]-(truedistance[e]+rnorm(1, 0, sigma))
}
#truedistance[1] - (truedistance[1]+50)
#determine DDOA measurements (reference sensor is
sensor #1 here)
index-1
for(e in 1:numSensors)
{
if(e!=r)
{
measurement[index]-(truedistance[f]-truedistance[e])
index - (index+1)
}
}
}
if(combos[e,f]!=1)
{
}
}
combos is just a matrix containing 1's and 0's
This error keeps appearing
Error in if (combos[e, f] == 1) { : missing value where TRUE/FALSE needed
Any ideas?
--
View this message in context:
http://r.789695.n4.nabble.com/TRUE-FALSE-tp2318668p2318668.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] coef(summary) and plyr
ldply doesnt need a grouping variable as far as I understand the command.. Description For each element of a list, apply function then combine results into a data frame Usage ldply(.data, .fun = NULL, ..., .progress = none) regards, M On 9. aug. 2010, at 15.33, David Winsemius wrote: On Aug 9, 2010, at 7:51 AM, moleps wrote: Dear all, I´m having trouble getting a list of regression variables back into a dataframe. mydf - data.frame(x1=rnorm(100), x2=rnorm(100), x3=rnorm(100)) mydf$fac-factor(sample((0:2),replace=T,100)) mydf$y- mydf$x1+0.01+mydf$x2*3-mydf$x3*19+rnorm(100) dlply(mydf,.(fac),function(df) lm(y~x1+x2+x3,data=df))-dl here I´d like to use ldply(dl,coef(summary)) or something similar but I cant figure it out... dfdl - ldply(dl, function(x) coef(summary(x)) ) Doesn't create a grouping variable, so: dfdl$group=rep(0:2, each=4) David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Changing downloaded source code into a package
I am wanting to change some lines of code in the R package named nlme http://cran.r-project.org/web/packages/nlme/index.html To do this I have downloaded the Package source named nlme_3.1-96.tar.gz, opened up the file and changed the text documents within the folder named R, specifically the cor.Struct.txt file. I now want to know how can I use this modified nlme_3.1-96.tar.gz file in R 2.10. How do I convert this source code into a package? I have looked on the internet and tried using cmd.exe then the code Rmcd.exe INSTALL -1 ~/nlme_3.1-96.tar.gz I end up getting the message The system can't find the specified path, when I have the file in the directory that Rmcd.exe is in. -- View this message in context: http://r.789695.n4.nabble.com/Changing-downloaded-source-code-into-a-package-tp2318559p2318559.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] Turning a source into a Package
I want to edit a function in the nlme package. I download the package source nlme_3.1-96.tar.gz from the link below then edit it one of the scripts inside of it. From this stage how can I turn it into a package that I can use in R? http://cran.r-project.org/web/packages/nlme/index.html -- View this message in context: http://r.789695.n4.nabble.com/Turning-a-source-into-a-Package-tp2318796p2318796.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] Difference Between R: wilcox.test and STATA: signrank
On Aug 9, 2010, at 9:52 AM, peter dalgaard wrote: On Aug 9, 2010, at 3:03 PM, Alain Guillet wrote: Hi, Look at the output of the test made in R and you can see it is a Wilcoxon rank sum test and not a Wilcoxon signed rank test. It might be helpful to add that paired=TRUE is needed in the call to get the signed-rank test. If there are ties, I know I prefer wilcox.exact from the exactRankTests. (Not that much of an issue in larger sample sizes, I'd say. Even with binary data, the normal approximation works reasonably well under the usual assumptions of expected counts 5, since the tie- adjustment for the variance is exact for the distribution of the ranks. The continuity correction doesn't quite work though. Anyways, wilcox.exact is of course a nice thing to have.) The OP's data: table(xvals=dat$x, yvals=dat$y) yvals xvals 0 0.25 0.5 1 1.1 1.5 2 3 3.5 5 5.5 6 8 0350 0 1 0 1 2 1 0 0 0 0 0 0.5 21 1 0 0 0 0 0 0 0 0 0 0 0.75 00 1 0 0 0 0 0 0 0 0 0 0 1 70 1 3 0 0 1 0 1 0 0 0 0 1.1 00 0 0 1 0 0 0 0 0 0 0 0 1.5 11 0 4 0 2 0 0 0 0 0 0 0 2 30 0 6 0 2 4 2 1 0 0 0 0 2.1 00 1 0 0 0 0 0 0 0 0 0 0 2.5 00 0 0 0 1 0 0 0 2 0 0 0 3 20 0 0 0 0 5 3 1 1 0 0 0 3.3 10 0 0 0 0 0 0 0 0 0 0 0 3.33 00 0 1 0 0 0 0 0 0 0 0 0 3.5 00 0 1 0 1 0 0 0 1 1 0 0 5 00 0 0 0 0 0 0 0 2 0 1 1 1000 0 0 0 0 0 0 0 1 0 0 0 Adding paired=TRUE to the wilcox.test call give the signed rank test although tht is not likely to satisfy the OP since she seems to be expecting a higher degree of congruence with Stata. The wilcox.test and wilcox.exact give results that only differ at the 4th decimal place. wilcox.test(dat$x, dat$y, paired=TRUE) Wilcoxon signed rank test with continuity correction data: dat$x and dat$y V = 1181, p-value = 0.08872 alternative hypothesis: true location shift is not equal to 0 wilcox.exact(dat$x, dat$y, paired=TRUE) Asymptotic Wilcoxon signed rank test data: dat$x and dat$y V = 1181, p-value = 0.08805 alternative hypothesis: true mu is not equal to 0 The Stata output indicates some sort of adjustment for zeros. The wilcox.test basically throws out the zeros (presumably the zero differences), so there may be a difference in the algorithm. Her data has 51 zero differences and 61 non-zero differences. sum(dat$x==dat$y) [1] 51 sum(dat$x!=dat$y) [1] 61 Wait a minute; the Stata report said she had 49 zeros and only 108 records. Different data. Different results. I suppose it could be my editing errors. Taking out all the extraneous html junk and restoring missing delimiters was kind of a pain. Capasia; Don't use Google sheets to transmit data. Instead use dput on the datablatt object and just post the results of that output. -- David. Alain On 09-Aug-10 12:43, Capasia wrote: This is my first post to the mailing list and I guess it's a pretty stupid question but I can't figure it out. I hope this is the right forum for these kind of questions. Before I started using R I was using STATA to run a Wilcoxon signed-rank test on two variables. See data below: https://spreadsheets.google.com/pub?key=0ApodAA2GAEP_dDZkdzZHSFBqX1JHOWJBX1dMQUZCVkEhl=enoutput=html %20%20https://spreadsheets.google.com/pub?key=0ApodAA2GAEP_dDZkdzZHSFBqX1JHOWJBX1dMQUZCVkEhl=enoutput=html STATA Output: . signrank x=y Wilcoxon signed-rank test sign | obs sum ranksexpected -+- positive | 413101 2330.5 negative | 181560 2330.5 zero | 4912251225 -+- all | 10858865886 unadjusted variance 106438.50 adjustment for ties -282.38 adjustment for zeros -10106.25 -- adjusted variance 96049.88 Ho: transfer_2_a = transfer_2_b z = 2.486 Prob |z| = *0.0129* When running a Wilcoxon signed-rank test wilcox.test(datablatt$x, datablatt$y) Wilcoxon rank sum test with continuity correction data: datablatt$x and datablatt$y W = 7059.5, p-value = *0.09197* alternative hypothesis: true location shift is not equal to 0 As you can see the p Values are different (one with H0 rejection and the other one not). I tested whether it could be that the STATA one isn't paired but this doesn't seem to be the problem. I'm dumbfound what could lead to such a difference. I couldn't find any seetings I have missed but I somehow I guess I'm using the function in the wrong way... Any ideas? Thanks a lot in advance! [[alternative HTML
[R] Pie Chart in map
Hey R'rs, So im sick of dealing with ESRI products and am looking to stream line a process i now use GIS to do using R. I have made a lot of maps using R but have not yet seen a map that puts pie charts within the map to help represent data like the attachment. http://r.789695.n4.nabble.com/file/n2318816/template1.bmp I found Tanimura et al. work Proportional Symbol Mapping in R, but after a discussion with one of the authors i have learned that the function is out of date and would require a great deal of reworking. I also found hexbinpie on the R graphics gallery that i could incorporate. Before i go through the process of rewriting or out right creation of a process to replicate my GIS results i was hoping to make sure there wasnt something out there i could use to start or use altogether. Or perhaps a set of functions that already exists that i havent thought to use. Thanks for the insights everyone. JR -- View this message in context: http://r.789695.n4.nabble.com/Pie-Chart-in-map-tp2318816p2318816.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] TRUE/FALSE
most likely 'combos[e,f]' is NA; take a look at your data. Also put
options(error=utils::recover)
in your program so that when the error occurs you can learn to use the
debugging mode to trace down the problem.
On Mon, Aug 9, 2010 at 11:38 AM, Turn Fall turnandf...@live.co.uk wrote:
Here is my code
# determine the DDOA measurements
for(e in 1:numSensors)
{
for(f in 1:numSensors)
{
if((combos[e,f]==1)
{
# true distance between each sensor and the target
truedistance[e]-sqrt((targetX-sensorX[e])^2+(targetY-sensorY[e])^2)
# add an error that has a N(0, sigma^2) distribution
truedistance[e]-(truedistance[e]+rnorm(1, 0, sigma))
}
#truedistance[1] - (truedistance[1]+50)
#determine DDOA measurements (reference sensor is
sensor #1 here)
index-1
for(e in 1:numSensors)
{
if(e!=r)
{
measurement[index]-(truedistance[f]-truedistance[e])
index - (index+1)
}
}
}
if(combos[e,f]!=1)
{
}
}
combos is just a matrix containing 1's and 0's
This error keeps appearing
Error in if (combos[e, f] == 1) { : missing value where TRUE/FALSE needed
Any ideas?
--
View this message in context:
http://r.789695.n4.nabble.com/TRUE-FALSE-tp2318668p2318668.html
Sent from the R help mailing list archive at Nabble.com.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem that you are trying to solve?
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] List of lists ?
On Aug 9, 2010, at 12:57 PM, Carlos Petti wrote: Dear list, I have to use a list of lists containing vectors. For instance : [[1]] [[1]][[1]] [1] 1 2 3 [[1]][[2]] [1] 3 2 1 I want to attribute vectors to the main list without use of an intermediate list, but it does not work : More specifically it produces an error that has information in it. x[[1]][[1]] - c(1, 2, 3) Error in `*tmp*`[[1]] : subscript out of bounds x - list() x[[1]][[1]] - c(1, 2, 3) x[[1]][[2]] - c(3, 2, 1) So thinking perhaps we just needed another level of subscripting available I tried: x - list(list()) x[[1]][[1]] - c(1, 2, 3) x[[1]][[2]] - c(3, 2, 1) x [[1]] [[1]][[1]] [1] 1 2 3 [[1]][[2]] [1] 3 2 1 Success. Moral: Read the error messages for meaning or at least clues. (Further testing showed that almost anything inside the original list() call, even NULL, would have created enough structure for the interpreter to work with. David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] List of lists ?
Is this what you want: x - list() x[[1]] - list(1:3) x[[2]] - list(3:1) x [[1]] [[1]][[1]] [1] 1 2 3 [[2]] [[2]][[1]] [1] 3 2 1 On Mon, Aug 9, 2010 at 12:57 PM, Carlos Petti carlos.pe...@gmail.com wrote: Dear list, I have to use a list of lists containing vectors. For instance : [[1]] [[1]][[1]] [1] 1 2 3 [[1]][[2]] [1] 3 2 1 I want to attribute vectors to the main list without use of an intermediate list, but it does not work : x - list() x[[1]][[1]] - c(1, 2, 3) x[[1]][[2]] - c(3, 2, 1) Thanks in advance, Carlos __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem that you are trying to solve? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] package names in Latex
When putting R package names in Latex, do we use \it or \em, please? As far as I know, the only difference between \it and \em is that \em words are unitalicized in an italics portion of the text, which is desirable in most cases. However, I am not sure that italics is the most common solution, perhaps because it is really important for a package name to be very easy to read and spell even if the name is a meaningless sequence of letters, which is not always the case in italics. In some R manuals (such as the Short Introduction to R), package names are boldfaced. Personally, I tend to type them in TT font, as if they were function names. I guess all solutions are OK if they are used consistently throughout the document. Arnaud. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] optimization subject to constraints
To find every help page containing the term constrained
optimization, you can try the following:
library(sos)
co - findFn('constrained optimization')
Printing this co object opens a table in a web browser with
all matches sorted first by the package with the most matches and with
hot links to the documentation page.
writeFindFn2xls(co)
This writes an excel file, with the browser table as the second
tab and the first being a summary of the packages. This summary table
can be made more complete and useful using the installPackages
function, as noted in the sos vignette.
A shameless plug from the lead author of the sos package.
Spencer Graves
On 8/9/2010 10:01 AM, Ravi Varadhan wrote:
constrOptim can only handle linear inequality constraints. It cannot handle
equality (linear or nonlinear) as well as nonlinear inequality constraints.
Ravi.
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of Dwayne Blind
Sent: Monday, August 09, 2010 12:56 PM
To: Gildas Mazo
Cc: r-help@r-project.org
Subject: Re: [R] optimization subject to constraints
Hi !
Why not constrOptim ?
Dwayne
2010/8/9 Gildas Mazogildas.m...@curie.fr
Dear R users,
I'm looking for tools to perform optimization subject to constraints,
both linear and non-linear. I don't mind which algorithm may be used, my
primary aim is to get something general and easy-to-use to study simples
examples.
Thanks for helping,
Gildas
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.htmlhttp://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-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Spencer Graves, PE, PhD
President and Chief Operating Officer
Structure Inspection and Monitoring, Inc.
751 Emerson Ct.
San José, CA 95126
ph: 408-655-4567
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Changing downloaded source code into a package
On Mon, Aug 9, 2010 at 10:22 AM, JH dealing_with_do...@hotmail.com wrote: I am wanting to change some lines of code in the R package named nlme http://cran.r-project.org/web/packages/nlme/index.html To do this I have downloaded the Package source named nlme_3.1-96.tar.gz, opened up the file and changed the text documents within the folder named R, specifically the cor.Struct.txt file. I now want to know how can I use this modified nlme_3.1-96.tar.gz file in R 2.10. How do I convert this source code into a package? I have looked on the internet and tried using cmd.exe then the code Rmcd.exe INSTALL -1 ~/nlme_3.1-96.tar.gz I end up getting the message The system can't find the specified path, when I have the file in the directory that Rmcd.exe is in. Assuming you have installed Rtools and have the R bin directory and the Rtools bin directory on your path cd to.wherever.your.tar.gz.file.is.located Rcmd INSTALL nlme_3.1-9.96.tar.gz Alternately, at http://batchfiles.googlecode.com is a file Rcmd.bat that you can call which will find Rtools and R in the registry and then run Rcmd.exe so you don't have to add anything to your path. In that case you just place Rcmd.bat somewhere on your existing path and don't have to change your path at all. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Pie Chart in map
Check out the gallery of R chart; here is one to look at: http://addictedtor.free.fr/graphiques/RGraphGallery.php?graph=143 On Mon, Aug 9, 2010 at 1:04 PM, LCOG1 jr...@lcog.org wrote: Hey R'rs, So im sick of dealing with ESRI products and am looking to stream line a process i now use GIS to do using R. I have made a lot of maps using R but have not yet seen a map that puts pie charts within the map to help represent data like the attachment. http://r.789695.n4.nabble.com/file/n2318816/template1.bmp I found Tanimura et al. work Proportional Symbol Mapping in R, but after a discussion with one of the authors i have learned that the function is out of date and would require a great deal of reworking. I also found hexbinpie on the R graphics gallery that i could incorporate. Before i go through the process of rewriting or out right creation of a process to replicate my GIS results i was hoping to make sure there wasnt something out there i could use to start or use altogether. Or perhaps a set of functions that already exists that i havent thought to use. Thanks for the insights everyone. JR -- View this message in context: http://r.789695.n4.nabble.com/Pie-Chart-in-map-tp2318816p2318816.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem that you are trying to solve? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] coef(summary) and plyr
On Aug 9, 2010, at 12:47 PM, Hadley Wickham wrote: There is one further improvement to consider. When I tried using dlply to tackle a problem on which I had been bashing my head for the last three days and it gave just the results I had been looking for, I also noticed that the dlply function returns the grouping variable levels in an attribute, split_labels, which could be unlisted to use as an argument to the rep() call I suggested earlier: dfdl$group=rep(unlist(attr(dl, split_labels)), each=4) That might make the results more self-documenting in situations where the grouping levels were more involved than 0:2. That's exactly what dlply does - so you should never have to do that yourself. I'm unclear what you are saying. Are you saying that the plyr function _should_ have examined the objects in that list and determined that there were 4 rows and properly labeled the rows to indicate which list they came from? Hadley -- Assistant Professor / Dobelman Family Junior Chair Department of Statistics / Rice University http://had.co.nz/ David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] coef(summary) and plyr
That's exactly what dlply does - so you should never have to do that yourself. I'm unclear what you are saying. Are you saying that the plyr function _should_ have examined the objects in that list and determined that there were 4 rows and properly labeled the rows to indicate which list they came from? Yes, exactly. It's the output from coef(summary(x)) that makes it look like this isn't happening. Hadley -- Assistant Professor / Dobelman Family Junior Chair Department of Statistics / Rice University http://had.co.nz/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Changing downloaded source code into a package
See comments below. On Mon, 2010-08-09 at 10:22 -0400, JH wrote: I am wanting to change some lines of code in the R package named nlme http://cran.r-project.org/web/packages/nlme/index.html To do this I have downloaded the Package source named nlme_3.1-96.tar.gz, opened up the file and changed the text documents within the folder named R, specifically the cor.Struct.txt file. I couldn't find this file. Do you mean corStruct.R, or maybe corStruct.c? I now want to know how can I use this modified nlme_3.1-96.tar.gz file in R 2.10. How do I convert this source code into a package? The source code, along with the documentation, data files, etc. _is_ the package. When the package contains source code from a compiled language (C or Fortran), as nlme does, this code must be compiled for your platform before the package is installed. The CRAN maintainers kindly pre-compile this code for Windows and Mac OS X users. If you make modifications to C or Fortran code in a package, you must re-compile the code yourself, or use a service such as R-Forge. The R manual `Writing R Extensions` is the standard reference for packages. See also the `R Administration and Installation' manual. See the information here http://www.murdoch-sutherland.com/Rtools/ for compiling package code in Windows. Lastly, before you follow the instructions at the URL above, I urge you to consider GNU Linux as a platform for programming. I've found the tools available in standard GNU Linux distributions (such as that available at http://www.debian.org) much simpler to install and work with. I have looked on the internet and tried using cmd.exe then the code Rmcd.exe INSTALL -1 ~/nlme_3.1-96.tar.gz I end up getting the message The system can't find the specified path, when I have the file in the directory that Rmcd.exe is in. -- Matthew S. Shotwell Graduate Student Division of Biostatistics and Epidemiology Medical University of South Carolina __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] plot the dependent variable against one of the predictors with other predictors as constant
Look at the TkPredict and Predict.Plot functions in the TeachingDemos package as a couple of options. -- 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 Yi Sent: Saturday, August 07, 2010 3:13 PM To: R (r-help@R-project.org) Subject: [R] plot the dependent variable against one of the predictors with other predictors as constant Hi, folks, Happy work in weekends _ My question is how to plot the dependent variable against one of the predictors with other predictors as constant. Not for the original data, but after prediction. It means y is the predicted value of the dependent variables. The constane value of the other predictors may be the average or some fixed value. ### y=1:10 x=10:1 z=2:11 lin_model=lm(z~x+y) x_new=11:2 ### How to plot predicted value of z from the regression model with x takes x_new and y as a constant (let's say y=1) I am thinking about using 'predict' command to generate the prediction of z with the new data.frame but there should be a better way. Thanks all. Yi [[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] Logistic Regression in R (SAS -like output)
Note that stepwise variale selection based on AIC has all the problems of stepwise variable selection based on P-values. AIC is just a restatement of the P-Value. Frank Frank E Harrell Jr Professor and ChairmanSchool of Medicine Department of Biostatistics Vanderbilt University On Mon, 9 Aug 2010, Gabor Grothendieck wrote: On Mon, Aug 9, 2010 at 6:43 AM, Harsh singhal...@gmail.com wrote: Hello useRs, I have a problem at hand which I'd think is fairly common amongst groups were R is being adopted for Analytics in place of SAS. Users would like to obtain results for logistic regression in R that they have become accustomed to in SAS. Towards this end, I was able to propose the Design package in R which contains many functions to extract the various metrics that SAS reports. If you have suggestions pertaining to other packages, or sample code that replicates some of the SAS outputs for logistic regression, I would be glad to hear of them. Some of the requirements are: - Stepwise variable selection for logistic regression - Choose base level for factor variables - The Hosmer-Lemeshow statistic - concordant and discordant - Tau C statistic For stepwise logistic regression using AIC see: library(MASS) ?stepAIC For specifying reference level: ?relevel __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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.
