Package: rtemis 1.4.2

rtemis: Schema-Driven Machine Learning and Visualization

Machine learning and visualization package with an 'S7' backend featuring comprehensive type checking and validation, observable runs, and auditable outputs. The functional API provides one-call access to supervised and unsupervised learning through train(), cluster(), and decomp(). All configuration steps are performed using setup functions and validated. A single call to train() can handle preprocessing, decomposition, hyperparameter tuning, model stacking, and testing with nested resampling. Supports 'data.frame', 'data.table', and 'tibble' inputs and parallel execution. Plot methods for trained and resampled supervised models draw interactive figures through 'rtemis.draw'. Includes native implementations of SuperLearner, RuleFit, and Linear Additive Trees, and supports conformal prediction. The package first appeared in E.D. Gennatas (2017) <https://repository.upenn.edu/entities/publication/d81892ea-3087-4b71-a6f5-739c58626d64>.

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

rtemis_1.4.2.tar.gz
rtemis_1.4.2.zip(r-4.7-any)rtemis_1.4.2.zip(r-4.6-any)rtemis_1.4.2.zip(r-4.5-any)
rtemis_1.4.2.tgz(r-4.6-any)rtemis_1.4.2.tgz(r-4.5-any)
rtemis_1.4.2.tar.gz(r-4.7-any)rtemis_1.4.2.tar.gz(r-4.6-any)
rtemis_1.4.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
rtemis/json (API)

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

Bug tracker:https://github.com/rtemis-org/rtemis/issues

Pkgdown/docs site:https://docs.rtemis.org

On CRAN:

Conda:

data-sciencedata-visualizationmachine-learningmachine-learning-libraryvisualization

8.37 score 150 stars 2 packages 53 scripts 434 downloads 233 exports 42 dependencies

Last updated from:dc9d6f83d1. Checks:9 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-develOK536
source / vignettesOK527
linux-releaseOK480
macos-releaseOK442
macos-oldrelOK429
windows-develOK392
windows-releaseOK467
windows-oldrelOK537
wasm-releaseOK269

Exports:.drop_meta_keys.get_alg_name.get_clust_name.get_decom_name.list_to_ClusteringConfig.list_to_DecompositionConfig.list_to_Hyperparameters.list_to_PreprocessorConfig.list_to_ResamplerConfig.list_to_SuperConfig.list_to_SupervisedPreprocessorConfig.list_to_TunerConfig.supervised_algorithms%BC%ai_reviewapplicable_metricsapply_decompapply_preprocessoravailable_calibrationavailable_clusteringavailable_decompositionavailable_supervisedbias_variancecalibratecheck_dataclass_imbalanceclassification_metricsclean_colnamesclean_namesclusterconformalconformal_metricsdata_fingerprintdata_profileddb_collectddb_dataddScidecompdecomp_metricsdecomposition_traitsdescribedf_movecolumndf_nunique_perfeatdraw_linaddt_describedt_inspect_typesdt_keybin_reshapedt_mergedt_names_by_attrdt_nunique_perfeatdt_pctmatchdt_pctmissingdt_set_autotypesdt_set_clean_alldt_set_cleanfactorlevelsdt_set_logical2factordt_set_one_hotexcexplainexplanation_methodsfeature_matrixfeature_namesfeaturesfit_predictfitted_configget_factor_namesget_learning_curveget_metricsget_modeget_varimpgetcharacternamesgetdatenamesgetfactornamesgetlogicalnamesgetnamesgetnamesandtypesgetnumericnamesHyperparameterCandidatesincindex_col_by_attringestinit_project_dirinspectinspect_typeis_constantis_wire_hyperparameters_setJSONSchema_to_S7labelifymassGLMmatchcasesmgetnamesnames_by_classnumeric_featuresone_hot2factoroutcomeoutcome_namepartitionplot_learningplot_manhattanplot_manhattan.MassGLMplot_metricplot_rocplot_sessionplot_true_predplot_varimppreprocesspreprocessedpresentreadread_configread_resultreconstructrecordregression_metricsresamplereviewrnormmatroc_curvertversionrunifmatS7_dispatcher_JSONSchemaS7_to_JSONSchemasame_datasesession_kind_colorssession_timelineset_outcomeset_positive_classsetdiffsymsetup_ARFFIngestsetup_ASWCriterionsetup_Autoencodersetup_BARTsetup_Bootstrapsetup_CARTsetup_CHCriterionsetup_ClusterConfigsetup_CMeanssetup_ConditionalSuperLearnersetup_CQRsetup_CUDAsetup_Customsetup_CVPlussetup_DBSCANsetup_DecomposeConfigsetup_DelimitedIngestsetup_DTAIngestsetup_FutureExecutionsetup_GAMsetup_GLMsetup_GLMNETsetup_GLMTreesetup_GMMsetup_GridSearchsetup_GroupPartitionsetup_HALsetup_HardCLsetup_HOPACHsetup_ICAsetup_Isomapsetup_Isotonicsetup_KFoldsetup_KMeanssetup_KNNsetup_LightCARTsetup_LightGBMsetup_LightRFsetup_LightRuleFitsetup_LINADsetup_LINADForestsetup_LinearSVMsetup_LOOCVsetup_MARSsetup_MDSsetup_MiraiExecutionsetup_MLPsetup_ModalityStackingsetup_MonotonicHALsetup_MultiASWCriterionsetup_NeuralGassetup_NMFsetup_NNLSsetup_Nystromsetup_PAMsetup_PAMKsetup_ParquetIngestsetup_PCAsetup_PCoAsetup_PredefinedPartitionsetup_Preprocessorsetup_RadialSVMsetup_RandomPartitionsetup_Rangersetup_RDSIngestsetup_Resamplersetup_SerialExecutionsetup_SHAPsetup_SpectralLaplacesetup_SpectralLocalsetup_SpectralRBFsetup_SplitConformalsetup_SPLSsetup_StratBootsetup_StratSubsetup_SuperConfigsetup_SuperConfigLivesetup_SuperLearnersetup_SupervisedPreprocessorsetup_TabNetsetup_TimePartitionsetup_tSNEsetup_UMAPsetup_VariationalAutoencodersetup_XLSXIngestshap_by_levelshap_caseshap_longshow_color_keysizetable_column_attrto_jsonto_markdowntraintune_overtuning_gridvalidate_configvarimp_tablewrite_configwrite_JSONSchemawrite_recordwrite_resultwrite_textwriteup

Dependencies:askpassbase64encbslibcachemclicodetoolsdata.tabledigestevaluatefastmapfontawesomefsfutureglobalshighrhtmltoolshtmlwidgetsjquerylibjsonliteknitrlifecyclelistenvMASSmemoisemimenanoparquetopensslparallellyR6rappdirsrlangrmarkdownrtemis.corertemis.drawS7sasssignalsystinytexviridisLitexfunyaml

Readme and manuals

Help Manual

Help pageTopics
'rtemis': Advanced Machine Learning and Visualizationrtemis-package rtemis
Binary matrix times character vector%BC%
Write an assessment of a model review with a language modelai_review
Which Decomposition Metrics Apply to Which Algorithmapplicable_metrics
Apply Decomposition to New Dataapply_decomp
Apply trained Preprocessor to new dataapply_preprocessor
Available Algorithmsavailable_algorithms available_calibration available_clustering available_decomposition available_supervised
Estimate Bias and Variancebias_variance
Calibrate 'Classification' & 'ClassificationRes' Modelscalibrate
Check Datacheck_data
Class Imbalanceclass_imbalance
Classification Metricsclassification_metrics
Perform Clusteringcluster
Conformal prediction regionsconformal
Score a Conformal Prediction Regionconformal_metrics
Fingerprint a datasetdata_fingerprint
Profile a datasetdata_profile
Collect a lazy-read duckdb tableddb_collect
Read CSV using DuckDBddb_data
Perform Data Decompositiondecomp
Decomposition Metricsdecomp_metrics
Decomposition Algorithm Traitsdecomposition_traits
Describe objectdescribe
Move data frame columndf_movecolumn
Unique values per featuredf_nunique_perfeat
Plot a Linear Additive Treedraw_linad
Describe data.tabledt_describe
Inspect column typesdt_inspect_types
Long to wide key-value reshapingdt_keybin_reshape
Merge data.tablesdt_merge
List column names by attributedt_names_by_attr
Number of unique values per featuredt_nunique_perfeat
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-place*_dt_set_clean_all
Clean factor levels of data.table _*in-place*_dt_set_cleanfactorlevels
Convert data.table logical columns to factorsdt_set_logical2factor
Convert data.table's factor to one-hot encoding _*in-place*_dt_set_one_hot
Exclude columns by character or numeric vector.exc
Explain a predictionexplain
Explanation Methods per Algorithmexplanation_methods
Convert tabular data to feature matrixfeature_matrix
Get feature namesfeature_names
Get features from tabular datafeatures
Fit a Learner and Predict New Datafit_predict
A 'Preprocessor''s config with its learned values filled infitted_config
Get factor namesget_factor_names
Learning curve of a fitted modelget_learning_curve
Get metricsget_metrics
Get the mode of a factor or integerget_mode
Get variable importanceget_varimp
Get names by string matching or classgetcharacternames getdatenames getfactornames getlogicalnames getnames getnumericnames
Get data.frame names and typesgetnamesandtypes
The values a tuner may choose among for one hyperparameterHyperparameterCandidates
Select (include) columns by character or numeric vector.inc
Index columns by attribute name & valueindex_col_by_attr
Read a data file and normalize it to Parquetingest
Initialize Project Directoryinit_project_dir
Inspect rtemis objectinspect
Inspect character and factor vectorinspect_type
Check if vector is constantis_constant
Build an S7 class from a JSON SchemaJSONSchema_to_S7
Mass-univariate GLM AnalysismassGLM
Match cases by covariatesmatchcases
Get names by string matching multiple patternsmgetnames
List column names by classnames_by_class
Get numeric features from tabular datanumeric_features
Convert one-hot encoded matrix to factorone_hot2factor
Get the outcome as a vectoroutcome
Get the name of the last columnoutcome_name
Split a dataset into training and held-out test partitionspartition
Plot a Model's Learning Curveplot_learning
Plot a MassGLM Resultplot.MassGLM plot_manhattan plot_manhattan.MassGLM
Plot Stored Metrics Across Model Resamplesplot_metric
Plot Classification ROC Curvesplot_roc
Plot a Supervised object's session timelineplot_session
Plot a Model's True Versus Predicted Valuesplot_true_pred
Plot a Model's Variable Importanceplot_varimp
Preprocess Datapreprocess
Get preprocessed data from 'Preprocessor'.preprocessed
Describe and Plot Fitted Modelspresent
Read tabular data from a variety of formatsread
Read an rtemis config from fileread_config
Read a portable result from a local schema registryread_result
Reconstruct Data from a Decompositionreconstruct
Derive a run record from a fitted modelrecord
Regression Metricsregression_metrics
Resample dataresample
Review a trained supervised modelreview
Random Normal Matrixrnormmat
ROC curve coordinatesroc_curve
rtemis error conditionsrtemis_conditions rtemis_data_error rtemis_dim_error rtemis_error rtemis_file_exists rtemis_file_not_found rtemis_input_error rtemis_io_error rtemis_length_error rtemis_level_mismatch rtemis_missing_data rtemis_null_input rtemis_outcome_error rtemis_range_error rtemis_runtime_error rtemis_type_error rtemis_unsupported_error rtemis_value_error
Get rtemis version and system infortversion
Random Uniform Matrixrunifmat
Generate a config family's dispatcher JSON SchemaS7_dispatcher_JSONSchema
Convert an S7 class built with prop_* factories to a JSON SchemaS7_to_JSONSchema
Do two fingerprints identify the same dataset?same_data
Standard error of the fitse
Session Execution Timeline Tablesession_timeline
Move outcome to last columnset_outcome
Set positive classset_positive_class
Symmetric Set Differencesetdiffsym
Set up an 'ARFFIngestConfig'setup_ARFFIngest
Setup ASWCriterionConfigsetup_ASWCriterion
Setup Autoencoder config.setup_Autoencoder
Setup BART Hyperparameterssetup_BART
Setup Bootstrap Resamplersetup_Bootstrap
Setup CART Hyperparameterssetup_CART
Setup CHCriterionConfigsetup_CHCriterion
Setup ClusterConfigsetup_ClusterConfig
Setup CMeansConfigsetup_CMeans
Setup ConditionalSuperLearner Hyperparameterssetup_ConditionalSuperLearner
Setup Conformalized Quantile Regressionsetup_CQR
Setup an NVIDIA GPU as the compute devicesetup_CUDA
Setup Custom Resamplersetup_Custom
Setup CV+ Conformal Predictionsetup_CVPlus
Setup DBSCANConfigsetup_DBSCAN
Setup DecomposeConfigsetup_DecomposeConfig
Set up a 'DelimitedIngestConfig'setup_DelimitedIngest
Set up a 'DTAIngestConfig'setup_DTAIngest
Set up a 'FutureExecutionConfig'setup_FutureExecution
Setup GAM Hyperparameterssetup_GAM
Setup GLM Hyperparameterssetup_GLM
Setup GLMNET Hyperparameterssetup_GLMNET
Setup GLMTree Hyperparameterssetup_GLMTree
Setup GMMConfigsetup_GMM
Setup Grid Search Configsetup_GridSearch
Set up a 'GroupPartitionConfig'setup_GroupPartition
Setup HAL Hyperparameterssetup_HAL
Setup HardCLConfigsetup_HardCL
Setup HOPACHConfigsetup_HOPACH
setup_ICAsetup_ICA
Setup Isomap config.setup_Isomap
Setup Isotonic Hyperparameterssetup_Isotonic
Setup KFold Resamplersetup_KFold
Setup KMeansConfigsetup_KMeans
Setup KNN Hyperparameterssetup_KNN
Setup LightCART Hyperparameterssetup_LightCART
Setup LightGBM Hyperparameterssetup_LightGBM
Setup LightRF Hyperparameterssetup_LightRF
Setup LightRuleFit Hyperparameterssetup_LightRuleFit
Setup LINAD Hyperparameterssetup_LINAD
Setup LINADForest Hyperparameterssetup_LINADForest
Setup LinearSVM Hyperparameterssetup_LinearSVM
Setup LOOCV Resamplersetup_LOOCV
Setup MARS Hyperparameterssetup_MARS
Setup MDS config.setup_MDS
Set up a 'MiraiExecutionConfig'setup_MiraiExecution
Setup MLP Hyperparameterssetup_MLP
Setup ModalityStacking Hyperparameterssetup_ModalityStacking
Setup MonotonicHAL Hyperparameterssetup_MonotonicHAL
Setup MultiASWCriterionConfigsetup_MultiASWCriterion
Setup NeuralGasConfigsetup_NeuralGas
Setup NMF config.setup_NMF
Setup NNLS Hyperparameterssetup_NNLS
Setup NystromConfigsetup_Nystrom
Setup PAMConfigsetup_PAM
Setup PAMKConfigsetup_PAMK
Set up a 'ParquetIngestConfig'setup_ParquetIngest
Setup PCA config.setup_PCA
Setup PCoA config.setup_PCoA
Set up a 'PredefinedPartitionConfig'setup_PredefinedPartition
Setup Preprocessorsetup_Preprocessor
Setup RadialSVM Hyperparameterssetup_RadialSVM
Set up a 'RandomPartitionConfig'setup_RandomPartition
Setup Ranger Hyperparameterssetup_Ranger
Set up an 'RDSIngestConfig'setup_RDSIngest
Setup a Resampler (Deprecated)rtemis-deprecated setup_Resampler
Set up a 'SerialExecutionConfig'setup_SerialExecution
Setup SHAP Explanationsetup_SHAP
Setup SpectralLaplaceConfigsetup_SpectralLaplace
Setup SpectralLocalConfigsetup_SpectralLocal
Setup SpectralRBFConfigsetup_SpectralRBF
Setup Split Conformal Predictionsetup_SplitConformal
Setup SPLS Hyperparameterssetup_SPLS
Setup StratBoot Resamplersetup_StratBoot
Setup StratSub Resamplersetup_StratSub
Setup SuperConfigsetup_SuperConfig
Setup SuperConfigLivesetup_SuperConfigLive
Setup SuperLearner Hyperparameterssetup_SuperLearner
Setup Supervised Preprocessorsetup_SupervisedPreprocessor
Setup TabNet Hyperparameterssetup_TabNet
Set up a 'TimePartitionConfig'setup_TimePartition
Setup tSNE config.setup_tSNE
Setup UMAP config.setup_UMAP
Setup Variational Autoencoder config.setup_VariationalAutoencoder
Set up an 'XLSXIngestConfig'setup_XLSXIngest
Contributions of a categorical feature, by the level each case hasshap_by_level
One case's contributions, ordered by how much they moved the predictionshap_case
Every contribution, one row per case per featureshap_long
Show rtemis color keyshow_color_key
Size of objectsize
Tabulate column attributestable_column_attr
Train Supervised Learning Modelstrain
Mark the values to tune a hyperparameter overtune_over
Tuning grid of a Hyperparameters objecttuning_grid
Validate an rtemis config, against the schema and optionally against datavalidate_config
Variable importance as one tablevarimp_table
Write an rtemis config to a JSON filewrite_config
Write a run record to a JSON filewrite_record
Write a portable result with optional Parquet payloadswrite_result
Write a report as textwrite_text
Write the Methods and Results sections for a trained modelwriteup