MaxBacteria {CoDaLoMic}R Documentation

Putting the reference bacteria at the last row

Description

This function calculates the mean abundance of each bacteria. Then, it creates a matrix where each row contains the abundance of one bacteria at all time points but the bacteria with maximum (or minimum or a bacteria indicated by the user) mean abundance is placed at the last row

Usage

MaxBacteria(nombresOriginal, especieOriginal, E, Tt, which.esp)

Arguments

nombresOriginal

Vector with the bacterial names at the same order than in DaTa. it must be fulfilled that lenght(nombresOriginal)==dim(DaTa)[2]-1

especieOriginal

Matrix that contains at row i the bacterial taxa of bacteria i at all time points

E

Number of bacteria available

Tt

Number of bacteria available

which.esp

If which=="Max" this function puts in the last position of the matrix the bacteria with maximum mean abundance. If which=="Min" this function puts in the last position of the matrix the bacteria with minimum mean abundance. If which is equal to a number this function puts in the last position of the matrix the bacteria that is in the "which" row of the especieOriginal matrix.

Value

Returns a list with

Examples


names1=c("Bact1","Bact2","Bact3")
set.seed(314)
esp1=t(gtools::rdirichlet(n=4, c(1,3,1)))
e1=3
t1=4

MaxBacteria(names1,esp1,e1,t1,"Max")


names3=c("Bact1","Bact2","Bact3","Bact4","Bact5")
set.seed(314)
esp3=t(gtools::rdirichlet(n=6, c(6,6,1,6,6)))
e3=5
t3=6
MaxBacteria(names3,esp3,e3,t3,"Min")



[Package CoDaLoMic version 0.1.1 Index]