# Multivariate Methods with Unbiased Variable Selection

## Documentation for package ‘MUVR2’ version 0.1.0

- DESCRIPTION file.

## Help Pages

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
getVar | Get min, mid or max model from Elastic Net modelling
getVIRank | Get variable importance
get_rmsep | Get RMSEP
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
mergeModels | Merge two MUVR class objects
MUVR2 | MUVR2 with PLS and RF
MUVR2_EN | MUVR2 with EN
nearZeroVar | Identify variables with near zero variance
onehotencoding | One hot encoding
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
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.
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.
preProcess | Perform matrix pre-processing
Q2_calculation | Q2 calculation
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
Xotu | Microbiota composition in mosquitos for the classification tutorial
XRVIP | Metabolomics data for the rye metabolomics regression tutorial
XRVIP2 | Metabolomics data for the rye metabolomics regression tutorial, using unique individuals
Yotu | Village of capture of 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