CVLasoelascox           Cross Validations for Lasso Elastic Net
                        Survival predictive models and Classification
CVMSpecificCoxPh        Cross validation for the Taxon specific
                        analysis
CVMajorityvotes         Cross validation for majority votes
CVPcaPls                Cross Validations for PCA and PLS based methods
CVSITaxa                Cross validation for sequentially increases
                        taxa
CoxPHUni                This function will fit the full and reduced
                        models and calculate LRT raw p-value and
                        adjusted p-value based on BH Method
DistHR                  Null Distribution of the Estimated HR
EstimateHR              Classification, Survival Estimation and
                        Visualization
FirstFilter             This function is used for the first step of
                        filtering which removes OTUs having all zeros
                        (inactive OTUs). The input is an OTU matrix
                        with rows are OTUs and columns are subjects.
GetRA                   This function convert OTU matrix to RA matrix.
Lasoelascox             Wapper function for glmnet
MSpecificCoxPh          Taxon by taxon Cox proportional analysis
Majorityvotes           Classifiction for Majority Votes
MiFreq                  Frequency of Selected Taxa from the LASSO,
                        Elastic-net Cross-Validation
QuantileAnalysis        Quantile sensitivity analysis
SITaxa                  Sequential Increase in Taxa for the PCA or PLS
                        classifier
SecondFilter            This function is used for the second step of
                        filtering which removes OTUs based on a
                        threshold.
SummaryData             This function gives indices such as Observed
                        richness, Shannon index, Inverse Simpson, ...
                        of higher level such as levelily, order,
                        phylum, ...
SurvPcaClass            Survival PCA and Classification for microbiome
                        data
SurvPlsClass            Survival PLS and Classification for microbiome
                        data
Top1Uni                 This function finds out the taxon has the
                        smallest p-value, then calculate risk score of
                        patients based on that taxon. Categorized
                        subjects into high or low risk groups based on
                        the mean of the risk score as a cutoff point
                        Checking whether the two groups are significant
                        difference in the probability to be survival.
Week3_otu               OTU table at week 3.
Week3_response          Response datase.
ZerosPerGroup           This function returns a matrix with rows are
                        Micros and 9 columns containing number and the
                        proportion of zeros per groups of treatments
                        and in total.
cvle-class              The cvle Class.
cvmm-class              The cvmm Class.
cvmv-class              The cvmv Class.
cvpp-class              The cvpp Class.
cvsit-class             The cvsit Class.
data_zero_per_group_otu_w3
                        Zero per treatment groups.
fam_info_w3             Information at family level.
fam_shan_trim_w3        Dataset at family level.
metadata_taxonomy       Metadata taxonomy.
ms-class                The ms Class.
perm-class              The perm Class.
