Package: rtemis 0.98.1

E.D. Gennatas

rtemis: Machine Learning and Visualization

Advanced Machine Learning and Visualization. Unsupervised Learning (Clustering, Decomposition), Supervised Learning (Classification, Regression), Cross-Decomposition, Bagging, Boosting, Meta-models. Static and interactive graphics.

Authors:E.D. Gennatas [aut, cre]

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rtemis.pdf |rtemis.html
rtemis/json (API)
NEWS

# Install 'rtemis' in R:
install.packages('rtemis', repos = c('https://ictml-project.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/egenn/rtemis/issues

Datasets:

On CRAN:

data-sciencedata-visualizationmachine-learningmachine-learning-libraryvisualization

7.09 score 141 stars 2 packages 45 scripts 388 exports 12 dependencies

Last updated 3 days agofrom:5fa23f04f9. Checks:OK: 1 WARNING: 6. Indexed: no.

TargetResultDate
Doc / VignettesOKNov 19 2024
R-4.5-winWARNINGNov 19 2024
R-4.5-linuxWARNINGNov 19 2024
R-4.4-winWARNINGNov 19 2024
R-4.4-macWARNINGNov 19 2024
R-4.3-winWARNINGNov 19 2024
R-4.3-macWARNINGNov 19 2024

Exports:%BC%any_constantas.data.tree.rpartaucauc_pairsbaccbetas.lihadbias_variancebinmat2vecboostbootstrapbrier_scorec_CMeansc_DBSCANc_EMCc_H2OKMeansc_HARDCLc_HOPACHc_KMeansc_MeanShiftc_NGASc_PAMc_PAMKc_SPECcalibratecalibrate_cvcartLiteBoostTVcatrangecatsizecheck_datacheck_filescheckpoint_earlystopchillclass_errorclass_imbalanceclean_colnamesclean_namesclustcol2grayscalecol2hexcolMaxcolor_fadecolor_invertRGBcolor_meancolor_ordercolor_separatecolor_sqdistcolorAdjustcolorGradcolorGrad.xcolorgradient.xcolorMixcolorOpcols2listcrulesd_H2OAEd_H2OGLRMd_ICAd_Isomapd_KPCAd_LLEd_MDSd_NMFd_PCAd_SPCAd_SVDd_TSNEd_UMAPdat2bsplinematdat2polydate2factordate2ymdate2yqddb_collectddb_dataddScidecomdependency_checkdesaturatedescribedf_movecolumndistillTreeRulesdplot3_addtreedplot3_bardplot3_boxdplot3_calibrationdplot3_cartdplot3_confdplot3_fitdplot3_graphd3dplot3_graphjsdplot3_heatmapdplot3_leafletdplot3_linaddplot3_piedplot3_proteindplot3_pvalsdplot3_spectrogramdplot3_tabledplot3_tsdplot3_varimpdplot3_volcanodplot3_xdplot3_xtdplot3_xydplot3_xyzdrangedt_check_uniquedt_describedt_get_column_attrdt_get_duplicatesdt_get_factor_levelsdt_index_attrdt_inspect_typedt_keybin_reshapedt_mergedt_names_by_attrdt_names_by_classdt_pctmatchdt_pctmissingdt_set_autotypesdt_set_clean_alldt_set_cleanfactorlevelsdt_set_logical2factordt_set_oneHotearlystopexpand.boostexplainf1factor_harmonizefactor_NA2missingfactoryzefct_describeformatLightRulesformatRulesfwhm2sigmaget_loaded_pkg_versionget_modeget_rulesget_vars_from_rulesgetcharacternamesgetdatenamesgetfactornamesgetlogicalnamesgetnamesgetnamesandtypesgetnumericnamesggtheme_darkggtheme_lightglmLitegmeangpgraph_node_metricsgtTablehtestinspect_typeinvlogitis_constantis_discretekfoldlabelifylincoeflist2csvlogisticlogitloglossloocvlotri2edgeListlsapplymaemake_keymassGAMmassGLAMmassGLMmassUnimatchcasesmeta_modmgetnamesmhistmlegendmod_errormplot_AGGTEobjmplot_hsvmplot_rastermplot3_adsrmplot3_barmplot3_boxmplot3_confmplot3_confbinmplot3_decisionmplot3_fitmplot3_fretmplot3_graphmplot3_harmonographmplot3_heatmapmplot3_imgmplot3_lateralitymplot3_lollimplot3_missingmplot3_mosaicmplot3_prmplot3_prpmplot3_resmplot3_rocmplot3_survmplot3_survfitmplot3_varimpmplot3_xmplot3_xymplot3_xymmsemsewmultigplotnCrnlaregnunique_perfeatoddsratiooddsratiotableoneHotonehot2factorpalettizepermutepfreadplotly.heatprecisionpreprocesspreprocess_presentpresent_gridsearchpreviewcolorprune.addtreepsdqstatreadread_configrecyclereluresamplereverseLevelsrevfactorlevelsrfVarSelectrmsernormmatrowMaxrsdrsqrstudio_theme_rtemisrt_reactablert_savertemis_palettertInitProjectDirrtlayoutrtModLogrtModLoggerrtpalettertROCrtversionrtXDecomruleDistrules2medmodrunifmats_AdaBoosts_AddTrees_BARTs_BayesGLMs_BRUTOs_C50s_CARTs_CTrees_EVTrees_GAMs_GBMs_GLMs_GLMNETs_GLMTrees_GLSs_H2ODLs_H2OGBMs_H2ORFs_HALs_KNNs_LDAs_LightCARTs_LightGBMs_LightRFs_LightRuleFits_LIHADs_LIHADBoosts_LINADs_LINOAs_LMs_LMTrees_LOESSs_LOGISTICs_MARSs_MLRFs_MULTINOMs_NBayess_NLAs_NLSs_NWs_POLYs_PolyMARSs_PPRs_PSurvs_QDAs_QRNNs_Rangers_RFs_RFSRCs_RLMs_RuleFits_SDAs_SGDs_SPLSs_SVMs_TFNs_TLSs_XGBoosts_XRFsavePMMLseselect_clustselect_decomselect_learnselectitersensitivityseqlsetdiffsymsetup.bag.resamplesetup.colorsetup.cv.resamplesetup.decomposesetup.earlystopsetup.GBMsetup.grid.resamplesetup.LightRuleFitsetup.LIHADsetup.lincoefsetup.MARSsetup.meta.resamplesetup.preprocesssetup.Rangersetup.resamplesge_submitsigmoidsizesoftmaxsoftplussortedlinessparsernormspecificitystderrorstrat.bootstrat.substrata2factorstrictsummarizesurv_errorsvd1synth_multimodalsynth_reg_datatable1theme_blacktheme_blackgridtheme_blackigridtheme_darkgraytheme_darkgraygridtheme_darkgrayigridtheme_lightgraygridtheme_mediumgraygridtheme_whitetheme_whitegridtheme_whiteigridthemestimeProctohtmltrain_cvtunabletypesetuniprot_getuniquevalsperfeatwinsorizex_CCAxlsx2listxselect_decomxtdescribezipdist

Dependencies:base64enccodetoolsdata.tabledigestfastmapfutureglobalshtmltoolslistenvparallellyR6rlang

Readme and manuals

Help Manual

Help pageTopics
'rtemis': Machine Learning and Visualizationrtemis-package rtemis
Binary matrix times character vector%BC%
Check for constant columnsany_constant
Convert 'linadleaves' to 'data.tree' objectas.data.tree.linadleaves
Convert 'rpart' rules to 'data.tree' objectas.data.tree.rpart
Convert 'shyoptleaves' to 'data.tree' objectas.data.tree.shyoptleaves
Area under the ROC Curveauc
Area under the Curve by pairwise concordanceauc_pairs
Balanced Accuracybacc
Extract coefficients from Additive Tree leavesbetas.lihad
Bias-Variance Decompositionbias_variance
Binary matrix times character vectorbinmat2vec
String formatting utilitiesbold cyan gray green hilite hilitebig italic magenta orange red reset underline
Boost an 'rtemis' learner for regressionboost
Bootstrap Resamplingbootstrap
Brier Scorebrier_score
Fuzzy C-means Clusteringc_CMeans
Density-based spatial clustering of applications with noisec_DBSCAN
Expectation Maximization Clusteringc_EMC
K-Means Clustering with H2Oc_H2OKMeans
Clustering by Hard Competitive Learningc_HARDCL
Hierarchical Ordered Partitioning and Collapsing Hybridc_HOPACH
K-means Clusteringc_KMeans
Mean Shift Clusteringc_MeanShift
Neural Gas Clusteringc_NGAS
Partitioning Around Medoidsc_PAM
Partitioning Around Medoids with k Estimationc_PAMK
Spectral Clusteringc_SPEC
Calibrate predicted probabilities using GAMcalibrate
Calibrate cross-validated modelcalibrate_cv
Print range of continuous variablecatrange
Print Sizecatsize
Check Datacheck_data
Check file(s) existcheck_files
Early stopping checkcheckpoint_earlystop
Chillchill
Classification Errorclass_error
Class Imbalanceclass_imbalance
Clean column namesclean_colnames
Clean namesclean_names
Clustering with 'rtemis'clust
Extract coefficients from Hybrid Additive Tree leavescoef.lihad
Color to Grayscalecol2grayscale
Convert R color to hexadecimal codecol2hex
Collapse data.frame to vector by getting column maxcolMax
Fade color towards targetcolor_fade
Invert Color in RGB spacecolor_invertRGB
Average colorscolor_mean
Order colorscolor_order
Separate colorscolor_separate
Squared Color Distancecolor_sqdist
Adjust HSV ColorcolorAdjust
Color GradientcolorGrad
Color gradient for continuous variablecolorGrad.x
Color gradient for continuous variablecolorgradient.x
Create an alternating sequence of graded colorscolorMix
Simple Color OperationscolorOp
Convert data frame columns to list elementscols2list
Create rtemis configuration filecreate_config
Combine rulescrules
Autoencoder using H2Od_H2OAE
Generalized Low-Rank Models (GLRM) on H2Od_H2OGLRM
Independent Component Analysisd_ICA
Isomapd_Isomap
Kernel Principal Component Analysisd_KPCA
Locally Linear Embeddingd_LLE
Multidimensional Scalingd_MDS
Non-negative Matrix Factorization (NMF)d_NMF
Principal Component Analysisd_PCA
Sparse Principal Component Analysisd_SPCA
Singular Value Decompositiond_SVD
t-distributed Stochastic Neighbor Embeddingd_TSNE
Uniform Manifold Approximation and Projection (UMAP)d_UMAP
B-Spline matrix from datasetdat2bsplinemat
Create n-degree polynomial from data framedat2poly
Date to factor time bindate2factor
Date to year-month factordate2ym
Date to year-quarter factordate2yq
Collect a lazy-read duckdb tableddb_collect
Read CSV using DuckDBddb_data
Format Numbers for PrintingddSci
Matrix Decomposition with 'rtemis'decom
'rtemis' internal: Dependencies checkdependency_check
Pastelify a color (make a color more pastel)desaturate
Describe genericdescribe
Move data frame columndf_movecolumn
Distill rules from trained RF and GBM learnersdistillTreeRules
Plot AddTree treesdplot3_addtree
Interactive Barplotsdplot3_bar
Interactive Boxplots & Violin plotsdplot3_box
Draw calibration plotdplot3_calibration
Plot 'rpart' decision treesdplot3_cart
Plot confusion matrixdplot3_conf
True vs. Predicted Plotdplot3_fit
Plot graph using 'networkD3'dplot3_graphd3
Plot network using 'threejs::graphjs'dplot3_graphjs
Interactive Heatmapsdplot3_heatmap
Plot interactive choropleth map using 'leaflet'dplot3_leaflet
Plot a Linear Additive Tree trained by s_LINAD using _visNetwork_dplot3_linad
Interactive Pie Chartdplot3_pie
Plot the amino acid sequence with annotationsdplot3_protein
Barplot p-values using dplot3_bardplot3_pvals
Interactive Spectrogramdplot3_spectrogram
Simple HTML tabledplot3_table
Interactive Timeseries Plotsdplot3_ts
Interactive Variable Importance Plotdplot3_varimp
Volcano Plotdplot3_volcano
Interactive Univariate Plotsdplot3_x
Plot timeseries datadplot3_xt
Interactive Scatter Plotsdplot3_xy
Interactive 3D Plotsdplot3_xyz
Set Dynamic Rangedrange
Check if all levels in a column are uniquedt_check_unique
Describe data.tabledt_describe
Tabulate column attributesdt_get_column_attr
Get index of duplicate valuesdt_get_duplicates
Get factor levels from data.tabledt_get_factor_levels
Index columns by attribute name & valuedt_index_attr
Inspect column typesdt_inspect_type
Long to wide key-value reshapingdt_keybin_reshape
Merge data.tablesdt_merge
List column names by attributedt_names_by_attr
List column names by classdt_names_by_class
Get N and percent match of values between two columns of two data.tablesdt_pctmatch
Get percent of missing values from every columndt_pctmissing
Set column types automaticallydt_set_autotypes
Clean column names and factor levels in-placedt_set_clean_all
Clean factor levels of data.table in-placedt_set_cleanfactorlevels
Convert data.table logical columns to factor with custom labels in-placedt_set_logical2factor
Early stoppingearlystop
Expand boosting seriesexpand.boost
Explain individual-level model predictionsexplain
F1 scoref1
Factor harmonizefactor_harmonize
Factor NA to "missing" levelfactor_NA2missing
Factor Analysisfactoryze
Decribe factorfct_describe
Format method for 'call' objectsformat.call
Format LightRuleFit rulesformatLightRules
Format rulesformatRules
FWHM to Sigmafwhm2sigma
Get version of all loaded packages (namespaces)get_loaded_pkg_version
Get the mode of a factor or integerget_mode
Get RuleFit rulesget_rules
Extract variable names from rulesget_vars_from_rules
Get factor/numeric/logical/character names from data.frame/data.tableget-names getfactornames
Get names by string matchinggetcharacternames getdatenames getlogicalnames getnames getnumericnames
Get data.frame names and typesgetnamesandtypes
'rtemis' 'ggplot2' dark themeggtheme_dark
'rtemis' 'ggplot2' light themeggtheme_light
Bare bones decision tree derived from 'rpart'glmLite
Geometric meangmean
Bayesian Gaussian Processes [R]gp
Node-wise (i.e. vertex-wise) graph metricsgraph_node_metrics
'rtemis' internal: Grid checkgridCheck
Greater-than TablegtTable
Basic Bivariate Hypothesis Testing and Plottinghtest
Inspect character and factor vectorinspect_type
Inverse Logitinvlogit
Check if vector is constantis_constant
Check if variable is discrete (factor or integer)is_discrete
K-fold Resamplingkfold
Format text for label printinglabelify
Linear Model Coefficientslincoef
Write list elements to CSV fileslist2csv
Logistic functionlogistic
Logit transformlogit
Log Loss for a binary classifierlogloss
Leave-one-out Resamplingloocv
Connectivity Matrix to Edge Listlotri2edgeList
'lsapply'lsapply
Make key from data.table id - description columnsmake_key
Mass-univariate GAM AnalysismassGAM
Mass-univariate GLM AnalysismassGLAM
Mass-univariate GLM AnalysismassGLM
Mass-univariate AnalysismassUni
Match cases by covariatesmatchcases
Merge panel data treatment and outcome datamergelongtreatment
Meta Models for Regression (Model Stacking)meta_mod
Get names by string matching multiple patternsmgetnames
Histogramsmhist
Add legend to 'mplot3' plotmlegend
Error Metrics for Supervised Learningmod_error
Plot AGGTEobj objectmplot_AGGTEobj
Plot HSV color rangemplot_hsv
Plot Array as Raster Imagemplot_raster
'mplot3': ADSR Plotmplot3_adsr
'mplot3': Barplotmplot3_bar
'mplot3': Boxplotmplot3_box
Plot confusion matrixmplot3_conf
Plot extended confusion matrix for binary classificationmplot3_confbin
'mplot3': Decision boundariesmplot3_decision
True vs. Fitted plotmplot3_fit
'mplot3': Guitar Fretboardmplot3_fret
Plot 'igraph' networksmplot3_graph
Plot a harmonographmplot3_harmonograph
'mplot3' Heatmap ('image'; modified 'heatmap')mplot3_heatmap
Draw image (False color 2D)mplot3_img
Laterality scatter plotmplot3_laterality
'mplot3' Lollipop Plotmplot3_lolli
Plot missingnessmplot3_missing
Mosaic plotmplot3_mosaic
'mplot3' Precision Recall curvesmplot3_pr
Plot CART Decision Treemplot3_prp
'mplot3' Plot 'resample'mplot3_res
'mplot3' ROC curvesmplot3_roc
'mplot3': Survival Plotsmplot3_surv
'mplot3': Plot 'survfit' objectsmplot3_survfit
'mplot3': Variable Importancemplot3_varimp
'mplot3': Univariate plots: index, histogram, density, QQ-linemplot3_x
'mplot3': XY Scatter and line plotsmplot3_xy
Scatter plot with marginal density and/or histogrammplot3_xym
Error functionsmae mse msew rmse
Multipanel *ggplot2* plotsmultigplot
n Choose rnCr
Number of unique values per featurenunique_perfeat
Calculate odds ratio for a 2x2 contingency tableoddsratio
Odds ratio table from logistic regressionoddsratiotable
One hot encodingdt_set_oneHot oneHot oneHot.data.frame oneHot.data.table oneHot.default
Convert one-hot encoded matrix to factoronehot2factor
Palettize colorspalettize
Create permutationspermute
fread delimited file in partspfread
Plot 'massGAM' objectplot.massGAM
Plot 'massGLM' objectplot.massGLM
'plot' method for 'resample' objectplot.resample
Plot 'rtModCVCalibration' objectplot.rtModCVCalibration
Plot 'rtTest' objectplot.rtTest
Heatmap with 'plotly'plotly.heat
Precision (aka PPV)precision
Predict Method for MediBoost Modelpredict.addtree
Predict method for 'boost' objectpredict.boost
Predict method for 'cartLite' objectpredict.cartLite
Predict method for 'cartLiteBoostTV' objectpredict.cartLiteBoostTV
Predict method for 'glmLite' objectpredict.glmLite
Predict method for 'glmLiteBoostTV' objectpredict.glmLiteBoostTV
Predict method for 'hytboost' objectpredict.hytboost
Predict method for 'hytboostnow' objectpredict.hytboostnow
Predict method for 'hytreeLite' objectpredict.hytreenow
Predict method for 'hytreew' objectpredict.hytreew
'predict' method for 'LightRuleFit' objectpredict.LightRuleFit
Predict method for 'lihad' objectpredict.lihad
Predict method for 'linadleaves' objectpredict.linadleaves
Predict method for 'nlareg' objectpredict.nlareg
'rtemis' internal: predict for an object of class 'nullmod'predict.nullmod
Predict S3 method for 'rtBSplines'predict.rtBSplines
Predict using calibrated modelpredict.rtModCVCalibration
'predict.rtTLS': 'predict' method for 'rtTLS' objectpredict.rtTLS
'predict' method for 'rulefit' objectpredict.rulefit
Data preprocessingpreprocess
Data preprocessing (in-place)preprocess_
Present elevate modelspresent
Present gridsearch resultspresent_gridsearch
Preview color v2.0previewcolor
Print method for 'addtree' object created using s_AddTreeprint.addtree
Print method for boost objectprint.boost
Print method for cartLiteBoostTV objectprint.cartLiteBoostTV
Print 'CheckData' objectprint.CheckData
Print class_errorprint.class_error
Print method for 'glmLiteBoostTV' objectprint.glmLiteBoostTV
'print' method for 'gridSearch' objectprint.gridSearch
Print method for 'hytboost' objectprint.hytboost
Print method for 'boost' objectprint.hytboostnow
Print method for 'lihad' objectprint.lihad
Print method for 'linadleaves' objectprint.linadleaves
'print'massGAM objectprint.massGAM
'print'massGLM objectprint.massGLM
Print 'regError' objectprint.regError
'print' method for resample objectprint.resample
Print method for bias_varianceprint.rtBiasVariance
'print.rtDecom': 'print' method for 'rtDecom' objectprint.rtDecom
'print.rtTLS': 'print' method for 'rtTLS' objectprint.rtTLS
Print surv_errorprint.surv_error
Prune AddTree treeprune.addtree
Population Standard Deviationpsd
SGE qstatqstat
Read tabular data from a variety of formatsread
Read rtemis configuration fileread_config
Recycle values of vector to match length of targetrecycle
Regression Error Metricsreg_error
ReLU - Rectified Linear Unitrelu
Resampling methodsresample
Reverse factor levelsreverseLevels
Reverse factor level orderrevfactorlevels
Variable Selection by Random ForestrfVarSelect
Random Normal Matrixrnormmat
Collapse data.frame to vector by getting row maxrowMax
Coefficient of Variation (Relative standard deviation)rsd
R-squaredrsq
Apply rtemis theme for RStudiorstudio_theme_rtemis
View table using reactablert_reactable
Write 'rtemis' model to RDS filert_save
rtClust S3 methodsprint.rtClust rtClust-methods
Access rtemis palette colorsrtemis_palette
Initialize Project DirectoryrtInitProjectDir
Create multipanel plots with the 'mplot3' familyrtlayout
rtMeta S3 methodspredict.rtMeta rtMeta-methods
'rtMod' S3 methodscoef.rtMod fitted.rtMod plot.rtMod predict.rtMod predict.rtModLite print.rtMod residuals.rtMod rtMod-methods summary.rtMod
rtModBag S3 methodspredict.rtModBag rtModBag-methods
'rtemis' Classification Model ClassrtModClass rtModClass-class
S3 methods for 'rtModCV' class that differ from those of the 'rtMod' superclassdescribe.rtModCV plot.rtModCV predict.rtModCV rtModCV-methods summary.rtModCV
rtModLite S3 methodsprint.rtModLite rtModLite-methods
'rtemis' Supervised Model Log ClassrtModLog rtModLog-class
'rtemis' model loggerrtModLogger rtModLogger-class
'rtemis' Color Palettesrtpalette
UCSF ColorsamazonCol appleCol berkeleyCol brownCol californiaCol calpolyCol caltechCol chicagoCol cmuCol columbiaCol cornellCol csuCol dartmouthCol emoryCol ethCol firefoxCol googleCol hawaiiCol hmsCol illinoisCol imperialCol iowaCol jeffersonCol jhuCol mcgillCol michiganCol microsoftCol mitCol mozillaCol msuCol nhsCol nihCol nyuCol oxfordCol pennCol pennLightPalette pennPalette pennstateCol princetonCol rtPalettes rwthCol scrippsCol sfsuCol stanfordCol techCol texasCol torontoCol ubcCol ucdCol uciCol uclaCol uclCol ucmercedCol ucrColor ucsbCol ucscCol ucsdCol ucsfLegacyCol ucsfPalette umdCol usfCol uwCol vanderbiltCol washuCol yaleCol
Build an ROC curvertROC
'rtemis' default-setting functionsrtset
Get rtemis and OS version infortversion
R6 class for 'rtemis' cross-decompositionsrtXDecom rtXDecom-class
Rule distanceruleDist
Convert rules from cutoffs to median/mode and rangerules2medmod
Random Uniform Matrixrunifmat
Adaboost Binary Classifier Cs_AdaBoost
Additive Tree: Tree-Structured Boosting Cs_AddTree
Bayesian Additive Regression Trees (C, R)s_BART
Bayesian GLMs_BayesGLM
Projection Pursuit Regression (BRUTO) [R]s_BRUTO
C5.0 Decision Trees and Rule-Based Models Cs_C50
Classification and Regression Trees [C, R, S]s_CART
Conditional Inference Trees [C, R, S]s_CTree
Evolutionary Learning of Globally Optimal Trees (C, R)s_EVTree
Generalized Additive Model (GAM) (C, R)s_GAM
Gradient Boosting Machine [C, R, S]s_GBM
Generalized Linear Model (C, R)s_GLM
GLM with Elastic Net Regularization [C, R, S]s_GLMNET
Generalized Linear Model Tree [R]s_GLMTree
Generalized Least Squares [R]s_GLS
Deep Learning on H2O (C, R)s_H2ODL
Gradient Boosting Machine on H2O (C, R)s_H2OGBM
Random Forest on H2O (C, R)s_H2ORF
Highly Adaptive LASSO [C, R, S]s_HAL
k-Nearest Neighbors Classification and Regression (C, R)s_KNN
Linear Discriminant Analysiss_LDA
LightCART Classification and Regression (C, R)s_LightCART
LightGBM Classification and Regression (C, R)s_LightGBM
Random Forest using LightGBMs_LightRF
RuleFit with LightGBM (C, R)s_LightRuleFit
The Linear Hard Hybrid Tree: Hard Additive Tree (no gamma) with Linear Nodes [R]s_LIHAD
Boosting of Linear Hard Additive Trees [R]s_LIHADBoost
Linear Additive Tree (C, R)s_LINAD
Linear Optimized Additive Tree (C, R)s_LINOA
Linear models_LM
Linear Model Tree [R]s_LMTree
Local Polynomial Regression (LOESS) [R]s_LOESS
Logistic Regressions_LOGISTIC
Multivariate adaptive regression splines (MARS) (C, R)s_MARS
Spark MLlib Random Forest (C, R)s_MLRF
Multinomial Logistic Regressions_MULTINOM
Naive Bayes Classifier Cs_NBayes
NonLinear Activation unit Regression (NLA) [R]s_NLA
Nonlinear Least Squares (NLS) [R]s_NLS
Nadaraya-Watson kernel regression [R]s_NW
Polynomial Regressions_POLY
Multivariate adaptive polynomial spline regression (POLYMARS) (C, R)s_PolyMARS
Projection Pursuit Regression (PPR) [R]s_PPR
Parametric Survival Regression [S]s_PSurv
Quadratic Discriminant Analysis Cs_QDA
Quantile Regression Neural Network [R]s_QRNN
Random Forest Classification and Regression (C, R)s_Ranger
Random Forest Classification and Regression (C, R)s_RF
Random Forest for Classification, Regression, and Survival [C, R, S]s_RFSRC
Robust linear models_RLM
Rulefit [C, R]s_RuleFit
Sparse Linear Discriminant Analysiss_SDA
Stochastic Gradient Descent (SGD) (C, R)s_SGD
Sparse Partial Least Squares Regression (C, R)s_SPLS
Support Vector Machines (C, R)s_SVM
Feedforward Neural Network with 'tensorflow' (C, R)s_TFN
Total Least Squares Regression [R]s_TLS
XGBoost Classification and Regression (C, R)s_XGBoost
XGBoost Random Forest Classification and Regression (C, R)s_XRF
Save rtemis model to PMML filesavePMML
Extract standard error of fit from rtemis modelse
Select 'rtemis' Clustererselect_clust
Select 'rtemis' Decomposerselect_decom
Select 'rtemis' Learnerselect_learn
Select N of learning iterations based on lossselectiter
Sensitivitysensitivity
Sequence generation with automatic cyclingseql
Symmetric Set Differencesetdiffsym
Set resample parameters for 'rtMod' baggingsetup.bag.resample
Set colorGrad parameterssetup.color
'setup.cv.resample': resample defaults for cross-validationsetup.cv.resample
Set decomposition parameters for train_cv '.decompose' argumentsetup.decompose
Set earlystop parameterssetup.earlystop
Set s_GBM parameterssetup.GBM
Set resample parameters for 'gridSearchLearn'setup.grid.resample
Set s_LightRuleFit parameterssetup.LightRuleFit
Set s_LIHAD parameterssetup.LIHAD
Set lincoef parameterssetup.lincoef
Set s_MARS parameterssetup.MARS
Set resample parameters for meta model trainingsetup.meta.resample
Set preprocess parameters for train_cv '.preprocess' argumentsetup.preprocess
Set s_Ranger parameterssetup.Ranger
Set resample settingssetup.resample
Submit expression to SGE gridsge_submit
Sigmoid functionsigmoid
Size of matrix or vectorsize
Softmax functionsoftmax
Softplus functionsoftplus
lines, but sortedsortedlines
Sparse rnormsparsernorm
Sparseness and pairwise correlation of vectorssparseVectorSummary
Sparsify a vectorsparsify
Specificityspecificity
Standard Error of the Meanstderror
Stratified Bootstrap Resamplingstrat.boot
Resample using Stratified Subsamplesstrat.sub
Convert 'survfit' object's strata to a factorstrata2factor
Summarize numeric variablessummarize
'massGAM' object summarysummary.massGAM
'massGLM' object summarysummary.massGLM
Survival Analysis Metricssurv_error
'rtemis-internals' Project Variables to First Eigenvectorsvd1
Create "Multimodal" Synthetic Datasynth_multimodal
Synthesize Simple Regression Datasynth_reg_data
Table 1table1
Themes for 'mplot3' and 'dplot3' functionstheme_black theme_blackgrid theme_blackigrid theme_darkgray theme_darkgraygrid theme_darkgrayigrid theme_lightgraygrid theme_mediumgraygrid theme_white theme_whitegrid theme_whiteigrid
Print available rtemis themesthemes
Time a processtimeProc
Generate 'CheckData' object description in HTMLtohtml
Tune, Train, and Test an 'rtemis' Learner by Nested Resamplingtrain_cv
Print tunable hyperparameters for a supervised learning algorithmtunable
Set type of columnstypeset
UCI Heart Failure Datauci_heart_failure
Get protein sequence from UniProtuniprot_get
Unique values per featureuniquevalsperfeat
Winsorize vectorwinsorize
Sparse Canonical Correlation Analysis (CCA)x_CCA
Read all sheets of an XLSX file into a listxlsx2list
Select 'rtemis' cross-decomposerxselect_decom
Describe longitudinal datasetxtdescribe
Get Longitude and Lattitude for zip code(s)zip2longlat
Get distance between pairs of zip codeszipdist