MaxBacteria: Putting the reference bacteria at the last row
In CoDaLoMic: Compositional Models to Longitudinal Microbiome Data

MaxBacteria

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

especie - Matrix that contains at row i the bacterial taxa of bacteria i at all time points but the bacteria with maximum (or minimum) mean abundance (or the bacteria indicated by the user) is placed at the last row.
especiemodi - Matrix that contains at row i the bacterial taxa of bacteria i at time points t=2,...,Tt but the bacteria with maximum (or minimum) mean abundance (or the bacteria indicated by the user) is placed at the last row.
nombres - Vector with the bacteria's names placed in the order in which appear in the rows of the matrices especie and especiemodi
EE - Row in which the bacterial with maximum (or minimum) mean abundance was (or the value of "which" if which is numerical).
EspecieMaxima - Row in which the bacterial with maximum (or minimum) mean abundance (or the bacteria indicated by the user) is in especie.) #'

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")

CoDaLoMic documentation built on April 12, 2025, 2:18 a.m.