[R] permutation test for Cox proportional hazards regression model

I would like to perform a permutation test for Cox proportional hazards regression model. I only find it for t-test and other tests (e.g. comparing two medians). Is there a way that I can perform a Cox PH model in R or SAS for the LR-test? I am doing the following B <- 1000; LRtestx <- rep(NA,B)

Re: [R] Permutation test with raster data

See in-line below. cheers, Rolf Turner On 04/01/14 12:48, Stefan Mühlbauer wrote: Hello! Â I am having two variables x and y (whereas y is a set of raster images) and want to quantify the correlation between x and y by calculating the Pearson Correlation Coefficient. In order

[R] Permutation test with raster data

Hello!   I am having two variables x and y (whereas y is a set of raster images) and want to quantify the correlation between x and y by calculating the Pearson Correlation Coefficient. In order to ensure how signficant the correlation results are, I am interested in getting the p-value (<0.1) fo

Re: [R] Permutation Test on Interactions {coin}

Axel, you need a model for such type of analyses and coin is completely model-free. Torsten On Mon, 23 Sep 2013, Axel Urbiz wrote: Dear List, I'm interested in performing a permutation test on the interaction between a binary treatment indicator and a covariate (either continuous or categ

[R] Permutation Test on Interactions {coin}

Dear List, I'm interested in performing a permutation test on the interaction between a binary treatment indicator and a covariate (either continuous or categorical). I'm interested in the p-value of the interaction effect from a permutation test, and I'm using the coin package for that purpose.

[R] Permutation test for GLM with proportional data

Dear all, I am trying to run permutation tests for GLM using the glmperm package. When I created my model, I followed The R book and Mixed effects models and extensions in ecology with R. In both books, response variables were specified by using cbind(). That is, response variable is in a matri

[R] permutation test for PLS/PLSDA

Hi, Is there any R package doing permutation/randomization test for PLS/PLSDA? I found some codes for MatLab, but I want to use R program. Thank you very much in advance. Kohkichi Hosoda __ R-help@r-project.org mailing list https://stat.ethz.ch/mailma

Re: [R] permutation test on paired samples

Henric, thanks a lot for the clarification. I guess your response also implies that there is no 'simple' equivalent or replacement for the (exactRankTests) function perm.test(y,x,paired = TRUE,...) in the package coin. Perhaps it will be added in the future. Meanwhile I can use your 'recipe

Re: [R] permutation test on paired samples

Holger, Thanks for providing a reproducible example. However, since your space key only works sporadically, the below is a little hard to read... ;) On 2012-07-12 20:26, Holger Taschenberger wrote: > Hi, > > I'm trying to run a permutation test on paired samples. > > First I tried the

[R] permutation test on paired samples

Hi, I'm trying to run a permutation test on paired samples. First I tried the package "exactRankTests": require("exactRankTests") x <- c(1.83,0.50,1.62,2.48,1.68,1.88,1.55,3.06,1.30) y <- c(0.878,0.647,0.598,2.05,1.06,1.29,1.06,3.14,1.29) wilcox.test(x,y,paired = TRUE,alternative = "gre

Re: [R] Permutation test

hi, Library DAAG has onet.permutation function for one-sample permutation test and twot.permutation function for two-sample permutation test. Anyway, p-value is a result of a test, what's your test? - A R learner. -- View this message in context: http://r.789695.n4.nabble.com/Permutation

[R] Permutation test

I have a sample in size of 2 rows, for instanse: idweightp value 100 125 101160 102 150 , how can I calculate the p value after the permutation and how the permutation test cab be done? Thanks, -- View this message in context: http://r.789695.n4.nabble.com/Permut

Re: [R] permutation test - query

You may find the multtest package helpful. It implements methods from Westfall and Young (Resampling based multiple testing). On Mon, Aug 31, 2009 at 5:37 AM, Yonatan Nissenbaum wrote: > Hi, > > My query is regarding permutation test and reshuffling of genotype/phenotype > data > I have been usi

[R] permutation test - query

Hi, My query is regarding permutation test and reshuffling of genotype/phenotype data I have been using the haplo.stats package of R. for haplotype analysis and I would like to perform an analysis which I'm requesting your advice. I have a data set of individuals genotyped for 12 SNP and a dichoto

Re: [R] Permutation test and R2 problem

> -Original Message- > From: r-help-boun...@r-project.org > [mailto:r-help-boun...@r-project.org] On Behalf Of Alex Roy > Sent: Freitag, 14. August 2009 12:05 > To: r-help@r-project.org > Subject: [R] Permutation test and R2 problem > > Hi, > > &g

[R] Permutation test and R2 problem

Hi, I have optimized the shrinkage parameter (GCV)for ridge and got my r2 value is 70% . to check the sensitivity of the result, I did permutation test. I permuted the response vector and run for 1000 times and draw a distribution. But now, I get r2 values highest 98% and some of them more than

Re: [R] permutation test assumption?

> > > > > > -Original Message- > > From: [EMAIL PROTECTED] > > [mailto:[EMAIL PROTECTED] On Behalf Of João Fadista > > Sent: Tuesday, April 08, 2008 4:10 PM > > > > To: ONKELINX, Thierry; r-help@r-project.org > > Subject: Re: [R] permut

Re: [R] permutation test assumption?

nal Message- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of João Fadista > Sent: Tuesday, April 08, 2008 4:10 PM > To: ONKELINX, Thierry; r-help@r-project.org > Subject: Re: [R] permutation test assumption? > > Dear Thierry, > > Thanks for t

Re: [R] permutation test assumption?

_ > > De: Achim Zeileis [mailto:[EMAIL PROTECTED] > Enviada: qua 09-04-2008 0:26 > Para: João Fadista > Cc: ONKELINX, Thierry; r-help@r-project.org > Assunto: Re: [R] permutation test assumption? > > > > On Wed, 9 Apr 2008, João Fadista wrote: >

Re: [R] permutation test assumption?

> -Original Message- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of João Fadista > Sent: Tuesday, April 08, 2008 3:10 PM > To: ONKELINX, Thierry; r-help@r-project.org > Subject: Re: [R] permutation test assumption? > > Dear Thierry, > >

Re: [R] permutation test assumption?

regards, João De: Achim Zeileis [mailto:[EMAIL PROTECTED] Enviada: qua 09-04-2008 0:26 Para: João Fadista Cc: ONKELINX, Thierry; r-help@r-project.org Assunto: Re: [R] permutation test assumption? On Wed, 9 Apr 2008, João Fadista wrote: > Dear Thierry, > > Thanks for th

Re: [R] permutation test assumption?

mption is violated. Z > Best regards, > João Fadista > > > > > De: ONKELINX, Thierry [mailto:[EMAIL PROTECTED] > Enviada: ter 08-04-2008 15:27 > Para: João Fadista; r-help@r-project.org > Assunto: RE: [R] permutation test assumption? > &

Re: [R] permutation test assumption?

De: ONKELINX, Thierry [mailto:[EMAIL PROTECTED] Enviada: ter 08-04-2008 15:27 Para: João Fadista; r-help@r-project.org Assunto: RE: [R] permutation test assumption? Dear João, You can do permutation tests on an unbalanced design. HTH, Thierry

Re: [R] permutation test assumption?

-Oorspronkelijk bericht- Van: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Namens João Fadista Verzonden: dinsdag 8 april 2008 15:18 Aan: r-help@r-project.org Onderwerp: [R] permutation test assumption? Dear all, Can I do a permutation test if the number of individuals in one group is much bigger

[R] permutation test assumption?

Dear all, Can I do a permutation test if the number of individuals in one group is much bigger than in the other group? I searched the literature but I didin´t find any assumption that refers to this subject for permutation tests. Best regards João Fadista Ph.d. student

Re: [R] Permutation Test

> Am I right in thinking that the correct way of working out how many possible > permutations there can be in this instance is: N! / (n1!) (n2!) (n3!)... > (ni!). Where N is the number of taxa (14) and (for character 2) n1 could be > 'number of state zeros' (i.e., 2), n2 could be 'number of state

[R] Permutation Test

Dear R users, i am fairly new to R and am having trouble creating code to solve a problem. I've searched the list, combed Crawley's 'R book' and several others, but can't quite find what i want. I want to generate permutations of various 'blocks' of 14 numbers. Each number within a block is a ch

Re: [R] Permutation test, grouped data

Brian S Cade wrote: > Tom: Paul Mielke, emeritus professor at Colorado State University, > probably has some of the most efficient Fortran programs for enumerating > all possible permutations of small sample sizes for grouped comparisons > and Monte Carlo random sampling of the possible permuta

Re: [R] Permutation test, grouped data

s, CO 80526-8818 > > email: [EMAIL PROTECTED] > tel: 970 226-9326 > > > > Tom Backer Johnsen <[EMAIL PROTECTED]> > Sent by: [EMAIL PROTECTED] > 11/02/2007 08:16 AM > > To > [EMAIL PROTECTED] > cc > > Subject > [R] Permutation test, grouped d

Re: [R] Permutation test, grouped data

On Fri, 2 Nov 2007, Tom Backer Johnsen wrote: > I am perfectly aware that this question is not an R question, at least > not yet, but I have not succeeded in finding what I want in other > ways, so ... > > What I am looking for are two algorithms, preferabley in Pascal, but > other languages may d

[R] Permutation test, grouped data

I am perfectly aware that this question is not an R question, at least not yet, but I have not succeeded in finding what I want in other ways, so ... What I am looking for are two algorithms, preferabley in Pascal, but other languages may do. For (a) systematic (complete) permutations for gro