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 |