amalgamate: Amalgamation contrast function

In reptalex/phylofactor: phylofactor

Amalgamation contrast function

Description

Amalgamation contrast function

Usage

amalgamate(Grps, TransformedData, pseudo.count = 0.65)

Arguments

Grps	Either a list of getPhyloGroups or a single getPhyloGroups element
TransformedData	Transformed Data. For amalgamation-phylofactorization, set transform.fcn=I and contrast.fcn=amalgamate.
pseudo.count	Numeric greater than 0. If aggregation of a group is zero, it will be replaced with pseudo.count

Examples

library(phylofactor)
set.seed(1)
m=50
n=20
tree <- rtree(m)
Grps <- getPhyloGroups(tree)
M <- matrix(rpois(m*n,1),nrow=m)
rownames(M) <- tree$tip.label
colnames(M) <- paste('Sample',1:n)

amalgamate(Grps,M)
amalgamate(Grps[[1]],M)

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