Dear Thiago, This will highlight the problem.
for (z in 1:1000) { comm1<-apply(comm,2,sample) cat("ncol: ", ncol(comm), " z: ", z, "\n") func.sim[z,]<- (t(comm[, z]) %*% (as.matrix(dist)^2) %*% comm[, z])/2/(sum(comm[, z])^2) } 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 may be no more than asking him to perform a post-mortem examination: he may be able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher The plural of anecdote is not data. ~ Roger Brinner The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. ~ John Tukey 2015-04-16 20:35 GMT+02:00 Thiago A. Pires <pires.thiagoaugu...@gmail.com>: > Hi Vít, > > Thank you for your quick response. Indeed, I did not put all the code, > because I thought it would mess up more than help. But I'll put here the > full code. I realized the issue of columns, I had come to this conclusion > also. However, I would like to generate a "random" matrix of community > based in a "real" community in every loop, and likewise, generating a > diversity measure of these communities, also in each loop. If you can help > me with this question , I'd appreciate. > > Code: > > require (vegan) > > comm<-t(data.frame(sp1=rpois(10, 1), sp2=rpois(10,1), sp3=rpois(10,1), > sp4=rpois(10,1), sp5=rpois(10,1))) > > traits<-t(data.frame(sp1=rnorm(5,1.2,.2),sp2=rnorm(5,2,.5), > sp3=rnorm(5,3,.3), sp4=rnorm(5,0.5,.2), > sp5=rnorm(5,.9,.6))) > > dist<-vegdist(traits,"gower") > comm<-as.matrix(comm) > func.sim<-data.frame(rep(NA, 1000)) > > for (z in 1:1000) > { > comm1<-apply(comm,2,sample) > func.sim[z,]<- (t(comm[, z]) %*% (as.matrix(dist)^2) %*% comm[, > z])/2/(sum(comm[, z])^2) > } > > Error in comm[ ,z] : subscript out of bounds > > > > > > Best regards, > > Thiago > > > > _____________________________________________________________ > > *Thiago A. Pires* > Ph.D. student in Ecology - Instituto de Biologia - UNICAMP > Collaborator Researcher - Laboratório de Ecologia e Sistemática - UNIFESP > > > Email: pires.thiagoaugu...@gmail.com / Skype: thiago.augusto.pires > Home Page: > http://thiagoaugustopires.wix.com/naturevisions > CV Lattes: > http://buscatextual.cnpq.br/buscatextual/visualizacv.do?id=K4298681Z0 > _____________________________________________________ > > > > > > 2015-04-16 4:40 GMT-03:00 Vít Syrovátka <syro...@sci.muni.cz>: > > > Hi Thiago, > > I am not familiar with the diversity measure you are trying to calculate > > and your example code is not complete - one can not simulate your comm > and > > dist objects. > > But at the first sight one can see that in your loop you are trying to > > select columns 1, 2, 3,... 1000 from the comm matrix, which probably has > > only 10 columns (if sites are in columns and species in rows, contrary to > > how such data are traditionally stored). > > > > for(z in 1:10) > > instead of > > for(z in 1:1000) > > should do the job. > > > > Vit > > > > Dne 2015-04-15 23:24, Thiago A. Pires napsal: > > > >> Hi guys, > >> > >> I have a question when trying to generate 1000 measures with "for" > >> function. For example, I have 10 locations with 5 species , and I want > to > >> apply a diversity measure on each site. But when I try to run one is > with > >> my function, I can not, I get an error message: "Error in com[, z] : > >> subscript out of bounds", and I think it should be a simple mistake, but > >> I'm not seeing. If you guys can help with it, I would appreciate. Right > >> below is an example for my code: > >> > >> comm= a community matrix with 10 sites and 5 species > >> dist= a pairwise distance-based matrix of species > >> > >> for (z in 1:1000) > >> { > >> > >> func.sim[z,]<- (t(comm[, z]) %*% (as.matrix(dist)^2) %*% > >> comm[, z])/2/(sum(comm[, z])^2) > >> > >> } > >> > >> > >> Error in comm[, z] : subscript out of bounds > >> > >> > >> > >> > >> > >> > >> Best regards, > >> > >> Thiago. > >> > >> > >> _____________________________________________________________ > >> > >> *Thiago A. Pires* > >> Ph.D. student in Ecology - Instituto de Biologia - UNICAMP > >> Collaborator Researcher - Laboratório de Ecologia e Sistemática - > UNIFESP > >> > >> > >> Email: pires.thiagoaugu...@gmail.com / Skype: thiago.augusto.pires > >> Home Page: > >> http://thiagoaugustopires.wix.com/naturevisions > >> CV Lattes: > >> http://buscatextual.cnpq.br/buscatextual/visualizacv.do?id=K4298681Z0 > >> _____________________________________________________ > >> > >> [[alternative HTML version deleted]] > >> > >> _______________________________________________ > >> R-sig-ecology mailing list > >> R-sig-ecology@r-project.org > >> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology > >> > > > > [[alternative HTML version deleted]] > > _______________________________________________ > R-sig-ecology mailing list > R-sig-ecology@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-ecology [[alternative HTML version deleted]] _______________________________________________ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology