ShanKothari
commented
6 years ago Hello Nikhail,
Imagine that you are storing the output of the function in some object FTD.dat:
FTD.dat<-FTD.comm(tdmat,spmat)
What do you get when you then run:
FTD.dat
Do you get NULL? Or something else?
I understand the trait distance matrices have to have all species present, but does this mean that all species must be present as columns in the same order as the site by species matrix? I ask this as this would make the last column redundant, as well as the first row ie. if a sample has 25 species then the trait distance matrix should have 25 rows and 25 columns? My tdmat has 25 species, but 24 columns and 24 rows.
That's right, they should be in the same order. How do you have 25 species in only 24 columns and 24 rows? I could imagine having a 25 x 24 matrix, if you removed the diagonal (which should be all 0s).
The important thing is that the columns of spmat should have the same species, in the same order, as both the rows and columns of tdmat. If the issue is that your tdmat has the wrong number of rows and columns to match the community abundance matrix (spmat), you should get a non-conformable arrays error. If you don't get that, there must be another issue (perhaps in addition to this one).
--Shan
nikhailarum
agusnov
Hello Mr. Kothari
I have recently tried using the code you developed for calculating functional diversity across multiple communities. In using the
FTD.commfunction on my datasets I get no outputs. I have specified my trait distance matrix astdmatand my site by species matrix asspmatwith species names as rows. Mytdmatobject is a distance matrix andspmatis a data matrix. They read correctly into R, however when I run theFTD.commfunction I get no outputs or error message, and FTD.comm is just listed as a function.I am using the unedited code from your github page, which reads as:
`function(tdmat,spmat,q=1,abund=F,match.names=T){
if(abund==F){ spmat[spmat>0]<- 1 spmat<-spmat/rowSums(spmat) }
n.comm<-nrow(spmat) if(match.names==T){ sp.arr<-match(rownames(as.matrix(tdmat)),colnames(spmat)) spmat<-spmat[,sp.arr] }
apply FTD to each community in turn
out<-apply(spmat,1,function(x) unlist(FTD(tdmat=tdmat,weights=x,q=q))) df.out<-data.frame(t(out)) rownames(df.out)<-rownames(spmat)
warning for zero-species communities
if(sum(df.out$nsp==0)>0){ warning("at least one community has no species") }
nsp<-sum(colSums(spmat>0))
calculate mean richness, dispersion, evenness, FTD
u.M<-sum(df.out$nsp*df.out$M)/sum(df.out$nsp) u.nsp<-mean(df.out$nsp)
to do: check if u.nsp is always calculated as arithmetic mean
if(q==1){
geometric mean -- limit of generalized mean as q->1
} else {
generalized mean with m=1-q
} u.M.prime<-u.M*u.nsp/(u.nsp-1)
calculate mean FTD and evenness
u.qDTM<-1+u.qDT*u.M u.Et<-u.qDT/u.nsp
list more things
list(com.FTD=df.out,nsp=nsp,u.nsp=u.nsp,u.M=u.M,u.M.prime=u.M.prime,u.Et=u.Et,u.qDT=u.qDT,u.qDTM=u.qDTM) }`
My trait distance matrices and site by species matrices are stored as .txt files, however they read into R without any issues. I understand the trait distance matrices have to have all species present, but does this mean that all species must be present as columns in the same order as the site by species matrix? I ask this as this would make the last column redundant, as well as the first row ie. if a sample has 25 species then the trait distance matrix should have 25 rows and 25 columns? My
tdmathas 25 species, but 24 columns and 24 rows. Is this the reason I am getting no outputs? I am struggling to understand why I get no outputs, yet no error messages either. Any help with this issue would be greatly appreciated. If needed I can upload examples of my trait distance matrix and my site by species matrix for you to view if needed.Regards Nikhail