SCalculation: The effctive number of tree calculation

In DAFOT: Detector of Active Flow on a Tree

Description

SCalculation is used to calculate the effctive number of tree.

Usage

SCalculation(sP, sQ, Tree, t)

Arguments

sP	a vector. The component-wise variance of 1st group
sQ	a vector. The component-wise variance of 2nd group
Tree	A phylo class. Phylogenetic tree
t	a numeric. The proportion of sample from 1st group.

Details

This function is used to calculate the effctive number of tree.

Value

SCalculation returns a value for effctive number of tree.

Author(s)

Shulei Wang

See Also

DAFOT

Examples

library(ape)
Tree=rtree(100)
alphaP=c(rep(1,length(Tree$tip.label)),rep(0,Tree$Nnode))
alphaQ=c(rep(1,length(Tree$tip.label)),rep(0,Tree$Nnode))
DataPQ<-DataGenerating(100,100,alphaP,alphaQ,1000)
sdP=apply(DataPQ$P,1,sd)
sdQ=apply(DataPQ$Q,1,sd)
SCalculation(sdP,sdQ,Tree,100/(100+100))

##must install metagenomeFeatures from Bioconductor before trying this example

library(metagenomeFeatures)
gg85 <- get_gg13.8_85MgDb()
gamma_16S <- mgDb_select(gg85, type = "all", keys = "Gammaproteobacteria", keytype = "Class")
Tree=gamma_16S$tree
Tree$tip.label<-1:length(Tree$tip.label)
alphaP=c(rep(1,length(Tree$tip.label)),rep(1,Tree$Nnode))
alphaQ=c(rep(1,length(Tree$tip.label)),rep(1,Tree$Nnode))
alphaQ[1]=alphaQ[1]+1
DataPQ<-DataGenerating(100,100,alphaP,alphaQ,1000)
sdP=apply(DataPQ$P,1,sd)
sdQ=apply(DataPQ$Q,1,sd)
SCalculation(sdP,sdQ,Tree,100/(100+100))

DAFOT documentation built on Oct. 9, 2019, 5:04 p.m.