Re: [R] lines - defining the range that is plotted

2015-09-24 Thread Duncan Murdoch
On 24/09/2015 6:26 PM, Hermann Norpois wrote: > Hello, > > I am looking for a possibility to define something like ylim for lines. I > thought, there might be a possibility to define the range of lines by means > of par ("usr") but I did not find the correct syntax. In my toy example I > would lik

[R] Quantmod several indicators

2015-09-24 Thread bgnumis bgnum
Hi all, I´m trying to use quantmod and to display plot of Bollinger bands is working properly. ¿How should I add for instance addWPR(n =300 ) below the main plot? Could it would be plotted independently? chartSeries( IB,theme="white",TA = c(addBBands(200,2) ) Thanks in advance. [[alte

[R] lines - defining the range that is plotted

2015-09-24 Thread Hermann Norpois
Hello, I am looking for a possibility to define something like ylim for lines. I thought, there might be a possibility to define the range of lines by means of par ("usr") but I did not find the correct syntax. In my toy example I would like to stop the red line at y=0.3. Thanks Hermann toy examp

Re: [R] Welcome to the "R-help" mailing list (Digest mode)

2015-09-24 Thread John Kane
You seem to have sent the message in HTML and most of it did not arrive. R-help is a plain text mailing list and strips out any HTML as a security precaution. Please have a look at http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-ex ample and/or http://adv-r.had.c

Re: [R] 'R' Software Output Plagiarism

2015-09-24 Thread Vik Rubenfeld
Your professor should immediately recognize that the quoted code is standard regression input/output and that the Urkund results in this case are without merit. > On Sep 22, 2015, at 7:27 AM, BARRETT, Oliver wrote: > > > Dear 'R' community support, > > > I am a student at Skema business sc

Re: [R] Sampling the Distance Matrix

2015-09-24 Thread David Winsemius
On Sep 24, 2015, at 1:54 PM, Lorenzo Isella wrote: > On Thu, Sep 24, 2015 at 01:30:02PM -0700, David Winsemius wrote: >> >> On Sep 24, 2015, at 12:36 PM, Lorenzo Isella wrote: >> >>> Hi, >>> And thanks for your reply. >>> Essentially, your script gets the job done. >>> For instance, if I run >>

Re: [R] 'R' Software Output Plagiarism

2015-09-24 Thread John Kane
> -Original Message- > From: pda...@gmail.com > Sent: Thu, 24 Sep 2015 11:41:19 +0200 > To: murdoch.dun...@gmail.com > Subject: Re: [R] 'R' Software Output Plagiarism > > > On 23 Sep 2015, at 02:33 , Duncan Murdoch > wrote: > >> I don't see why this puzzles you. A simple explanation i

Re: [R] comparing 2 long lists in R

2015-09-24 Thread Shi, Tao via R-help
Bogdan, I would look into bioconductor for packages handling this type choromosomal range data. cntools is one poped into my mind. Tao On Thursday, September 24, 2015 12:59 PM, Sarah Goslee wrote: merge() most likely, but: are these really lists in the R sense? The correct answer depe

Re: [R] comparing 2 long lists in R

2015-09-24 Thread Bogdan Tanasa
Dear Bert and Sarah, thank you for your suggestions. Yes, I came across "dplyr" that has a few functions already implemented, thanks again ! On Thu, Sep 24, 2015 at 1:17 PM, Bert Gunter wrote: > Also, in addition to what Sarah told you, have you checked on the > Bioconductor site, as this sounds

Re: [R] Sampling the Distance Matrix

2015-09-24 Thread Lorenzo Isella
On Thu, Sep 24, 2015 at 01:30:02PM -0700, David Winsemius wrote: On Sep 24, 2015, at 12:36 PM, Lorenzo Isella wrote: Hi, And thanks for your reply. Essentially, your script gets the job done. For instance, if I run mm <- cbind(5/(1:5), -2*sqrt(1:5)) dst <- dist(mm) dst2 <- as.matrix(dst) diag

Re: [R] Sampling the Distance Matrix

2015-09-24 Thread David Winsemius
On Sep 24, 2015, at 12:36 PM, Lorenzo Isella wrote: > Hi, > And thanks for your reply. > Essentially, your script gets the job done. > For instance, if I run > > mm <- cbind(5/(1:5), -2*sqrt(1:5)) > dst <- dist(mm) > dst2 <- as.matrix(dst) > diag(dst2) <- NA > idx <- which(apply(dst2, 1, functio

Re: [R] comparing 2 long lists in R

2015-09-24 Thread Bert Gunter
Also, in addition to what Sarah told you, have you checked on the Bioconductor site, as this sounds like the sort of thing that they may well have something for already. ... and you've posted here often enough that you shouldn't still be posting HTML and you should know about toy examples! Cheers

Re: [R] comparing 2 long lists in R

2015-09-24 Thread Sarah Goslee
merge() most likely, but: are these really lists in the R sense? The correct answer depends on what the format actually is; you need to use dput() or some other unambiguous way of providing sample data. Without a reproducible example that includes some sample data provided using dput() (fake is f

[R] comparing 2 long lists in R

2015-09-24 Thread Bogdan Tanasa
Dear all, please could you advise on a computationally quick way to compare and merge 2 long lists in R; the lists are of the following type, for example : <> in list 1 : chromosome, coordinateA, coordinateB, value1 chromosome, coordinateC, coordinateC, value2, etc <> in list 2 : chromosome, c

Re: [R] Sampling the Distance Matrix

2015-09-24 Thread Lorenzo Isella
Hi, And thanks for your reply. Essentially, your script gets the job done. For instance, if I run mm <- cbind(5/(1:5), -2*sqrt(1:5)) dst <- dist(mm) dst2 <- as.matrix(dst) diag(dst2) <- NA idx <- which(apply(dst2, 1, function(x) all(na.omit(x)>.9))) then it correctly detects the first two rows,

Re: [R] Comparing two populations based on the percentile values calculated from two independent samples

2015-09-24 Thread Cade, Brian
You can use quantile regression (in quantreg package) to compare percentiles between two groups in a linear model formulation. If you are really interested in "equivalence" testing and not just using the term informally, you might check out Cade (2011. Estimating equivalence with quantile regress

Re: [R] Comparing two populations based on the percentile values calculated from two independent samples

2015-09-24 Thread John Sorkin
Mohamed, You probably should seek the help of a local statistician, and should read about Pearson's chi square test and Fisher's exact test. John John David Sorkin M.D., Ph.D. Professor of Medicine Chief, Biostatistics and Informatics University of Maryland School of Medicine Division of Geronto

[R] Comparing two populations based on the percentile values calculated from two independent samples

2015-09-24 Thread Mohamed A.Abdel-Fattah Mansour via R-help
Dear AllI Have the data for two samples drawn from two different populations |   |   |   |   |   | Percentiles | |   | Mean | STD | Min | Max | 5th | 25th | 50th | 75th | 95th | | Sample 1 | 25 | 2 | 16 | 30 | 18

Re: [R] Welcome to the "R-help" mailing list (Digest mode)

2015-09-24 Thread Boris Steipe
You're posting in HTML and your link didn't make it :-( B. On Sep 24, 2015, at 1:34 PM, amir via R-help wrote: > I would greatly appreciate if anybody could help with the stack-overflow > question : Updating and Forecasting times series with new data > | | > | | | | | | | |

Re: [R] Welcome to the "R-help" mailing list (Digest mode)

2015-09-24 Thread amir via R-help
I would greatly appreciate if anybody could help with the stack-overflow question : Updating and Forecasting times series with new data |   | |   | |   |   |   |   |   | | Updating and Forecasting times series with new dataWe can fit a time series and use the model to make forecasts, for example

[R] backsolve, chol, Matrix, and SparseM

2015-09-24 Thread Benjamin Tyner
Hi I have some code which does (on a symmetric matrix 'x') backsolve(chol(x), diag(nrow(x))) and I am wondering what is the recommended way to accomplish this when x is also sparse (from package:Matrix). I know that package:Matrix provides a chol method for such matrices, but not a backsolve

Re: [R] boxplot overlap beeswarm

2015-09-24 Thread MacQueen, Don
I see that you have used add = TRUE in the boxplot call. Add only makes sense if there is already a plot to which to add the boxplot. But your boxplot is first, so there isn't anything to add it to. Try doing the beeswarm plot first? Will the two plots will have the same y axis ranges? Minor

Re: [R] Appropriate specification of random effects structure for EEG/ERP data: including Channels or not?

2015-09-24 Thread Phillip Alday
There is actually a fair amount of ERP literature using mixed-effects modelling, though you may have to branch out from the traditional psycholinguistics journals a bit (even just more "neurolinguistics" or language studies published in "psychology" would get you more!). But just in the traditional

Re: [R] Friedman test

2015-09-24 Thread peter dalgaard
On 24 Sep 2015, at 15:07 , Agustin Lobo wrote: > I would like to make sure that I'm using friedman.test() correctly, > because I have to reformat my data set to fulfil the requirement > "exactly one observation in y for each combination of levels of groups > and blocks" mentioned > in the help p

Re: [R] doubt with Odds ratio - URGENT HELP NEEDED

2015-09-24 Thread Eik Vettorazzi
Dear Rosa, coefficents of a probit-regression do not have a odds-ratio interpretation, you should use a logit link for that. cheers. Am 24.09.2015 um 09:51 schrieb Michael Dewey: > Dear Rosa > > Please keep the list on the recipients as others may be able to help. > > See inline > > On 23/09/2

[R] Friedman test

2015-09-24 Thread Agustin Lobo
I would like to make sure that I'm using friedman.test() correctly, because I have to reformat my data set to fulfil the requirement "exactly one observation in y for each combination of levels of groups and blocks" mentioned in the help page of function friedman.test(). Assuming data from http://

Re: [R] RWeka and multicore package

2015-09-24 Thread Luís Paulo F . Garcia
A better solution provide by Adriano Rivolli: library(parallel) models <- mclapply(1:10, function(i) { model <- RWeka::J48(Species ~., iris[sample(nrow(iris))[1:100],]) rJava::.jcache(model$classifier) model }); 2013-10-24 10:16 GMT-02:00 Luís Paulo F. Garcia : > Dear, Patrick. > > I

Re: [R] Special characters in regular expressions

2015-09-24 Thread Upton, Stephen (Steve) (CIV)
and a somewhat convoluted solution, if A or K are always in the second "position" x <- c("LBAM 5|A|15C|3h", "LBAM 5|K|15C|2h") unlist(lapply(strsplit(x,"\\|"),function(y) paste(y[c(1,3,4)],collapse="|"))) Stephen C. Upton SEED (Simulation Experiments & Efficient Designs) Center Operations Rese

Re: [R] doubt with Odds ratio - URGENT HELP NEEDED

2015-09-24 Thread Rosa Oliveira
Dear Michael (and all :)) Thank you very much. I fixed my problem, I think ;) Best, RO Atenciosamente, Rosa Oliveira -- Rosa Celeste dos Santos Oliveira, E-mail: rosit...@gmail.com Tlm: +351 939355143 Linkedin:

Re: [R] Special characters in regular expressions

2015-09-24 Thread peter dalgaard
On 24 Sep 2015, at 12:05 , Thierry Onkelinx wrote: > gsub("[A|K]\\|", "", x) That'll probably do it, but what was the point of the | in [A|K] ?? I don't think it does what I think you think it does... Somewhat safer, maybe: gsub("\\|[AK]\\|","\\|", x) (avoids surprises from, say, "LBAM 5|A|

Re: [R] Special characters in regular expressions

2015-09-24 Thread Thierry Onkelinx
gsub("[A|K]\\|", "", x) ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance Kliniekstraat 25 1070 Anderlecht Belgium To call in the statistician after the experiment is done ma

[R] Special characters in regular expressions

2015-09-24 Thread Patrick Connolly
I need to change a vector dd that looks like this: c("LBAM 5|A|15C|3h", "LBAM 5|K|15C|2h") into this: c("LBAM 5|15C|3h", "LBAM 5|15C|2h") It's not very imaginative, but I could use a complicated nesting of gsub() as so: gsub("-", "\\|", gsub("K-", "", gsub("A-", "", gsub("\\|", "-", dd Or

Re: [R] 'R' Software Output Plagiarism

2015-09-24 Thread peter dalgaard
On 23 Sep 2015, at 02:33 , Duncan Murdoch wrote: > I don't see why this puzzles you. A simple explanation is that Urkund > is incompetent. That much I figured. What I was puzzled about was _how_ it was being incompetent. Also how it could be so in a way that wouldn't be obvious to the profes

Re: [R] doubt with Odds ratio - URGENT HELP NEEDED

2015-09-24 Thread Michael Dewey
Dear Rosa Please keep the list on the recipients as others may be able to help. See inline On 23/09/2015 19:19, Rosa Oliveira wrote: Dear Michael, *New cleaned code :)(I think :))* casedata <-read.spss("tas_05112008.sav") tas.data<-data.frame(casedata) #Delete patients that were not dis

[R] boxplot overlap beeswarm

2015-09-24 Thread Julia89
Hi everybody, I'm new and i need help very fast. I will make a transparent boxplot overlap a beeswarm. I don't want to use ggplot2, i will use ggplot. Here is my own script but it doesn't worked. Maybe you can help me. Thanks in advance Julia require(beeswarm)#rohdaten boxplots rm(list=ls()) setw