H0_reference            Get reference distribution for resampling tests
H0_test                 Perform permutation or resampling tests
IDR                     Subject identifiers for the rye metabolomics
                        regression tutorial
IDR2                    Subject identifiers for the rye metabolomics
                        regression tutorial, using unique individuals
MUVR2                   MUVR2 with PLS and RF
MUVR2_EN                MUVR2 with EN
Q2_calculation          Q2 calculation
XRVIP                   Metabolomics data for the rye metabolomics
                        regression tutorial
XRVIP2                  Metabolomics data for the rye metabolomics
                        regression tutorial, using unique individuals
Xotu                    Microbiota composition in mosquitos for the
                        classification tutorial
YR                      Rye consumption for the rye metabolomics
                        regression tutorial
YR2                     Rye consumption for the rye metabolomics
                        regression tutorial, using unique individuals
Yotu                    Village of capture of mosquitos for the
                        classification tutorial
biplotPLS               PLS biplot
checkinput              Check input
confusionMatrix         Confusion matrix
crispEM                 Effect matrix for the crisp multilevel tutorial
customParams            Make custom parameters for internal modelling
getBER                  Get BER
getMISS                 Get number of misclassifications
getVIRank               Get variable importance
getVar                  Get min, mid or max model from Elastic Net
                        modelling
get_rmsep               Get RMSEP
mergeModels             Merge two MUVR class objects
nearZeroVar             Identify variables with near zero variance
onehotencoding          One hot encoding
pPerm                   Calculate permutation p-value Calculate
                        perutation p-value of actual model performance
                        vs null hypothesis distribution. 'pPerm' will
                        calculate the cumulative (1-tailed) probability
                        of 'actual' belonging to
                        'permutation_distribution'. 'side' is guessed
                        by actual value compared to
                        median(permutation_distribution). Test is
                        performed on original data OR ranked for
                        non-parametric statistics.
permutationPlot         Plot permutation analysis
plotMV                  Plot predictions
plotPCA                 PCA score plot
plotPerm                Plot for comparison of actual model fitness vs
                        permutation/resampling
plotPred                Plot predictions for PLS regression
plotStability           Plot stability
plotVAL                 Plot validation metric
plotVIRank              Plot variable importance ranking
preProcess              Perform matrix pre-processing
predMV                  Predict outcomes Predict MV object using a MUVR
                        class object and a X testing set. At present,
                        this function only supports predictions for PLS
                        regression type problems.
qMUVR2                  Wrapper for speedy access to MUVR2 (autosetup
                        of parallelization)
rdCV                    Wrapper for repeated double cross-validation
                        without variable selection
rdcvNetParams           Make custom parameters for rdcvNet internal
                        modelling
sampling_from_distribution
                        Sampling from the distribution of something
varClass                Report variables belonging to different classes
