R: Compositional Models to Longitudinal Microbiome Data

# Compositional Models to Longitudinal Microbiome Data

## Documentation for package ‘CoDaLoMic’ version 0.1.1

- DESCRIPTION file

## Help Pages

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