R/Fmntd.R

In NGSwenson/lefse_0.5: Phylogenetic and Functional Analyses for Ecology

Fmntd <-
function(dist.mat, my.sample){


Fmntd.sub = function(x){ 
		
## Get the names of the species present in a 
## community.
	com.names = names(x[x > 0])
		
## Make the community phylogenetic distance 
## matrix by extracting those rows and columns 
## that have species present in our community.
	my.com.dist = dist.mat[com.names, com.names]
		
## Set all diagonal values to NA so that the 
## zeros for conspecific comparisons do not 
## interfere with our calculation of nearest 
## neighbors.
	diag(my.com.dist) = NA
		
## Use apply() to calculate the minimum value in 
## each row of the community phylogenetic 
## distance matrix and take a mean of those 
## values.
	mean(apply(my.com.dist, MARGIN = 1, min, na.rm=T), na.rm=T)
	
}

apply(my.sample, MARGIN = 1, Fmntd.sub)

}