Multivariate Methods with Unbiased Variable Selection

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Documentation for package ‘MUVR2’ version 0.1.0

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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