# Tuned Data Mining in R

## Documentation for package ‘TDMR’ version 2.2

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Code demos. Use demo() to run them.

## Help Pages

TDMR-package | Tuned Data Mining in R
defaultOpts | Default settings for the data mining part of TDMR (list 'opts').
defaultSC | Default settings for the spotConfig part of TDMR.
dsetTest.TDMdata | Return test data of 'TDMdata' object
dsetTrnVa.TDMdata | Return train-validation data of 'TDMdata' object
Opts | Return the list 'opts'.
Opts.default | Return the list 'opts'.
Opts.tdmClass | Return the list 'opts'.
Opts.TDMclassifier | Return the list 'opts'.
Opts.TDMenvir | Return the list 'opts'.
Opts.tdmRegre | Return the list 'opts'.
Opts.TDMregressor | Return the list 'opts'.
predict.TDMclassifier | Make a prediction using the last model.
predict.TDMenvir | Make a prediction using the last model.
predict.TDMregressor | Make a prediction using the last model.
print.tdmClass | Print an overview for a 'TDMclassifier' object.
print.TDMclassifier | Print an overview for a 'TDMclassifier' object.
print.TDMdata | Print an overview for a 'TDMdata' object.
print.tdmRegre | Print an overview for a 'TDMregressor' object.
print.TDMregressor | Print an overview for a 'TDMregressor' object.
setParams | Merge the parameters from a partial list and the default list
tdmBigLoop | Tuning and unbiased evaluation in a big loop.
tdmBindResponse | Bind a column to a data frame.
TDMclassifier | Core classification double loop returning a 'TDMclassifier' object.
tdmClassify | Core classification function of TDMR.
tdmClassifyLoop | Core classification double loop returning a 'TDMclassifier' object.
tdmClassifySummary | Print summary output for 'result' from 'tdmClassifiyLoop' and add 'result$y'.
TDMdata | Read and split the task data.
tdmDefaultsFill | Default values for list 'tdm'.
TDMenvir | Construct a new environment envT of class 'TDMenvir'.
tdmEnvTAddBstRes | Add BST and RES data frames to an existing 'envT' environment.
tdmEnvTAddGetters | Add getter functions getBst and getRes to environment envT
tdmEnvTGetOpts | Return list opts from the 'k'-th element of 'envT$sCList'
tdmEnvTLoad | Load an 'envT'-type environment from file 'fileRData'.
tdmEnvTMakeNew | Construct a new environment envT of class 'TDMenvir'.
tdmEnvTReport | Make a report plot based on 'envT'
tdmEnvTReportSens | Function to generate a report with sensitivity plot.
tdmEnvTSetOpts | Set list opts for the 'k'-th element of 'envT$sCList'
tdmEnvTUpdate | Update 'envT$tdm'
tdmGraAndLogFinalize | Finalize graphics and log file
tdmGraAndLogInitialize | Initialize graphics and log file.
tdmGraphicCloseDev | Close all open graphic devices.
tdmGraphicCloseWin | Close active file ("png").
tdmGraphicInit | Initialize graphic device.
tdmGraphicNewWin | Initialize a new window.
tdmGraphicToTop | Bring the acitve window to the top
tdmMapDesApply | Apply the mapping from 'des' to 'opts'.
tdmMapDesLoad | Load the mapping files.
tdmModConfmat | Calculate confusion matrix, gain and RGain measure.
tdmModCreateCVindex | Create and return a training-validation-set index vector.
tdmModSortedRFimport | Sort the input variables decreasingly by their RF-importance.
tdmModVote2Target | Analyze how the vote fraction corresponds to reliability of prediction.
tdmOptsDefaultsSet | Default values for list 'opts'.
tdmParaBootstrap | Parametric bootstrap: add 'noisy copies' to a data frame (training data).
tdmPreAddMonomials | Add monomials of degree 2 to a data frame.
tdmPreFindConstVar | Find constant columns.
tdmPreGroupLevels | Group the levels of factor variable in 'dset[,colname]'.
tdmPreLevel2Target | Relate levels of a column with a target (column).
tdmPreNAroughfix | Replace <NA> values with suitable non <NA> values
tdmPrePCA.apply | Apply PCA (Principal Component Analysis) to new data.
tdmPrePCA.train | PCA (Principal Component Analysis) for numeric columns in a data frame.
tdmPreSFA.apply | Apply SFA (Slow Feature Analysis) to new data.
tdmPreSFA.train | SFA (Slow Feature Analysis) for numeric columns in a data frame.
TDMR | Tuned Data Mining in R
tdmRandomSeed | Generates pseudo-random random number seeds.
tdmReadAndSplit | Read and split the task data.
tdmReadDataset | Read data accoroding to 'opts' settings.
tdmReadTaskData | Read task data.
tdmRegress | Core regression function of TDMR.
tdmRegressLoop | Core regression double loop returning a 'TDMregressor' object.
TDMregressor | Core regression double loop returning a 'TDMregressor' object.
tdmRegressSummary | Print summary output for 'result' from 'tdmRegressLoop' and add 'result$y'.
tdmROCR.TDMclassifier | Interactive plot of ROC, lift or other charts for a 'TDMclassifier' object.
tdmROCRbase | Single plot of ROC, lift or other chart for a 'TDMclassifier' object.
tdmTuneIt | Tuning and unbiased evaluation (single tuning).
unbiasedRun | Perform unbiased runs with best-solution parameters.