Compositional Models to Longitudinal Microbiome Data

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Documentation for package ‘CoDaLoMic’ version 0.1.1

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CoDaLoMic-package CoDaLoMic
B1MODImatrizP Ridge regression matrix
B1MODImodel Obtaining the regression value of the FBM
Balance Calculating the balance of the FBM model
BPBM_Matrix Obtains the matrix of covariates of the BPBM
cockroach cockroach dataset
CoDaLoMic CoDaLoMic
Estimate_Param_EstParmFunc Estimating Parameters of EstParmFunc
Estimate_Param_FBM Estimating Parameters of EstParmFunc_FBM
Estimating_BPBM Estimating BPBM
EstParmFunc Writting the loglikelihood of the dirichlet
EstParmFunc_FBM Writting the loglikelihood of the dirichlet
ExpectedValuess_BPBM Obtainig the value of the dirichlet parameters, the expected value and the variance.
ExpectedValues_EstParmFunc_FBM Obtainig the value of the dirichlet parameters, the expected value and the variance.
ExpectedValue_EstParmFunc Obtaining the value of the Dirichlet parameters, the expected value and the variance.
FromVectorToMatrix_BPBM Writting the parameters in the matrix form required in BPBM model
FVectorPBmodeloPredi Obtaining a vector with the covariates of the prediction
Graphics Plots the time series
GraphicsPrediction Plots the time series
GraphicsPredictionBPBM Plots the time series
GraphicsSPBal Obtaining the graphic of the SPBal at all time points
LogVeroFuncBUENA Writting the loglikelihood of the dirichlet
MaxBacteria Putting the reference bacteria at the last row
MaxBacteriaPred Putting the reference bacteria at the last row
ObtainigValuePB Obtaining the principal balances values
ObtainigValueSPBal Obtaining the selected principal balances values
ObtainingDIC Writting the loglikelihood of the dirichlet
PBalance Calculating balances
PBalancePredi Calculating balances for a composition
PBmodel Obtaining the regression value of the BPBM
PCAbiplot PCA of the estimated parameters
Percen_Variance Percentage of variance
PlotDendogram Plotting a dendogram
PredictionBPBM Predicting using BPBM
PredictionEstParmFunc Predicting using dirichl-gLV
PredictionFBM Predicting using FBM
PreparingTheData Preparing dataset
QualityControl Analysing the quality of the estimation
ridgeregression Ridge regression
rxnrate Solving the right side of the gLV equations
Simulated Gut microbiome simulated dataset
StudyingParam Controlling quality of the convergence in BPBM
TableBPBM Obtaining a table with the SPBal information
TableFBM Obtainig a table with the interpretable parameters
Table_alr_Dirich_glv Obtainig a table with the interpretable parameters
TauAndParameters_EstParmFunc_FBM Obtaining the value of tau and the estimate value of the rest of the parameters
vecttor Alr of a bacteria
ZeroData Zero replacement