pf.crossValidateMap: Function for mapping phylogenetic factors in a phylofactor...

In reptalex/phylofactor: phylofactor

Function for mapping phylogenetic factors in a phylofactor object to a new community through universal tree

Description

Function for mapping phylogenetic factors in a phylofactor object to a new community through universal tree

Usage

pf.crossValidateMap(pf, universal.tree, new.community,
  factors = 1:pf$nfactors, fill.empty = FALSE)

Arguments

pf	phylofactor class object whose tree tip-labels are all in the universal.tree
universal.tree	Universal phylogeny containing all the tip-labels of pf and all elements of new.community
new.community	New community
factors	which factors to cross-map
fill.empty	Logical. Whether or not to fill any empty groups with the species from the original community. If true, the last element of the output will be a data frame indicating the species added to the factor-groups.

Examples

library(phylofactor)
set.seed(1)
m=10
n=20
tree <- rtree(m)
plot(tree,show.tip.label = F)
tiplabels()
tree$tip.label <- paste('t',1:10,sep='')
c1 <- tree$tip.label[setdiff(1:m,c(5,7))]
c2 <- tree$tip.label                       #t5 added to group1, t7 ignored
c3 <- tree$tip.label[setdiff(1:m,c(4,6))]  #t5 is the only member of our group 1
c4 <- tree$tip.label[setdiff(1:m,4:6)]     #our factor will be empty for this community 
clade1 <- c(4,6)
D <- matrix(0,nrow=m,ncol=n)
D[clade1,] <- rep(1:n,each=2)
rownames(D) <- tree$tip.label
D <- D[c1,]
metadata <- data.frame('a'=1:n,'b'=rnorm(n),'c'=rpois(n,2))
metadata <- data.frame('a'=1:n,'b'=factor(rep(0,1,each=n/2)))
pf <- PhyloFactor(D,tree,metadata,frmla = Data~a,nfactors=1,transform.fcn = I)
pf.groupsTospecies(pf)
pf.crossValidateMap(pf,tree,c1)  ## same as above
pf.crossValidateMap(pf,tree,c2)  ## add t5 to group1
pf.crossValidateMap(pf,tree,c3)  ## Group1 contains only 5
pf.crossValidateMap(pf,tree,c4)  ## group1 empty

cv <- pf.crossValidateMap(pf,tree,c4,fill.empty = T) 
## group1 same as in our original community - empty groups filled.
cv$groups
cv$filler.species                                    
## factor1, group1 received species t4, t6 as fillers for an empty group.

reptalex/phylofactor documentation built on Feb. 28, 2024, 3:19 p.m.