doubt in generating loops with For
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.thiagoaugusto at gmail.com>:
Hi V?t,
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 - Laborat?rio de Ecologia e Sistem?tica - UNIFESP Email: pires.thiagoaugusto at 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 V?t Syrov?tka <syrovat at 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 - Laborat?rio de Ecologia e Sistem?tica - UNIFESP Email: pires.thiagoaugusto at 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 at r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology [[alternative HTML version deleted]] _______________________________________________ R-sig-ecology mailing list R-sig-ecology at r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology