Description Usage Arguments Details Value Author(s) See Also Examples
View source: R/DAFOT_function.R
SCalculation
is used to calculate the effctive number of tree.
1 | SCalculation(sP, sQ, Tree, t)
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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. |
This function is used to calculate the effctive number of tree.
SCalculation
returns a value for effctive number of tree.
Shulei Wang
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 | 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))
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