MaxBacteriaPred {CoDaLoMic}R Documentation

Putting the reference bacteria at the last row

Description

This function calculates the mean abundance of each bacteria taking into account the time points used to estimate the model (t=1,2,...,Tt). 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) mean abundance (or the bacterial indicated by the user) is placed at the last row

Usage

MaxBacteriaPred(
  nombresOriginal,
  especieOriginal,
  E,
  Tt,
  Pred,
  K,
  especieOriginal.All,
  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 t=1,2,...,Tt, with Tt=Pred-1.

E

Number of bacteria available

Tt

Number of time points used to estimate the model (Tt=Pred-1)

Pred

Number. The data at t=1,...,Pred-1 will be used to estimate the model. The rest of the time points will be used to study the capacity of the model to predict. If Pred==0 all the datatset will be used to estimate the model.

K

Number of time points at the data

especieOriginal.All

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

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


names2=c("Bact1","Bact2","Bact3","Bact4","Bact5")
set.seed(314)
esp2=t(gtools::rdirichlet(n=6, c(1,1,5,1,1)))
e2=5

MaxBacteriaPred(names2,esp2[,-c(4,5,6)],e2,3,Pred=4, 6,esp2, "Max")


[Package CoDaLoMic version 0.1.1 Index]