TableBPBM: Obtaining a table with the SPBal information of the BPBM

In CoDaLoMic: Compositional Models to Longitudinal Microbiome Data

Obtaining a table with the SPBal information of the BPBM

Description

Returns a table with the percentage of variance that each SPBal has, the bacteria that goes in the numerator and denominator of the balance, the relationship between the group in the numerator and the denominator and the bacteria most influenced by this SPBal.

Usage

TableBPBM(
  NumSPBal,
  DemSPBal,
  PerVar,
  MatrizPBmodelo,
  Estimated.Param,
  BB = 0.55,
  names,
  E
)

Arguments

NumSPBal	List. Output of "ObtainigValueSPBal" function.List. The component i of the list has the number of the row of the matrix especie where the bacteria in the numerator of the selected principal balance i are placed.
DemSPBal	List. Output of "ObtainigValueSPBal" function.List. The component i of the list has the number of the row of the matrix especie where the bacteria in the denominator of the selected principal balance i are placed.
PerVar	Vector. Output of "ObtainigValueSPBal" function. The component of the vector i contains the percentage of variance of the SPBal with numerator NumSPBal[[i]] and denominator DemSPBal[[i]].
MatrizPBmodelo	Matrix. Output of "ObtainigValueSPBal" function. MatrixSPBal is the matrix that contains the covariates of the model. The first line es equal to 1 for all columns. The other rows contain the value of one SPBal at all time points. The selected principal balance of the row i+1 has at its numerator the bacteria placed in the rows NumSPBal[[i]] of the "especie". The selected principal balance of the row i+1 has at its denominator the bacteria placed in the rows DemSPBal[[i]] of the "especie".
Estimated.Param	Vector. Column "mean" of the output of StudyingParam function.
BB	The bacteria in the numerator and the denominator of the balance are considered similar if the mean of the SPBal is between (-BB,BB).Default: 0.55.
names	Vector with the bacteria's names placed in the order in which appear in the rows of the matrices especie and especiemodi.
E	number of bacteria in the dataset.

Value

Returns the table written in latex

Examples

NumSPBal=list(c(3,4),3,2)
DemSPBal=list(1,5,4)
PerVar=c(41.37487, 21.08270, 19.16870)
MatrizPBmodelo=rbind(c(1.00000000,  1.0000000,  1.0000000,  1.0000000 , 1.0000000),
                    c(1.84449081, -1.3569851, -0.1388348, -0.5269079, -1.3288684),
                    c(0.27531685,  0.4741394, -1.9045554, -0.3581268, -0.4768543),
                    c( 0.07782991,  0.3492473, -0.7138882,  1.4332828, -0.7203295))
namesOr=c("Bact1", "Bact2","Bact3","Bact4","Bact5")
Estimated.Param=c(0.5, 0.3, -0.2,0.1)
E=5

TableBPBM(NumSPBal,
         DemSPBal,
         PerVar,
         MatrizPBmodelo,
         Estimated.Param,
         BB=0.55,
         namesOr,
         E)

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