Package: tmle3 0.2.1

Jeremy Coyle

tmle3: The Extensible TMLE Framework

A general framework supporting the implementation of targeted maximum likelihood estimators (TMLEs) of a diverse range of statistical target parameters through a unified interface. The goal is that the exposed framework be as general as the mathematical framework upon which it draws.

Authors:Jeremy Coyle [aut, cre, cph], Nima Hejazi [ctb]

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tmle3.pdf |tmle3.html✨
tmle3/json (API)
NEWS

# Install 'tmle3' in R:
install.packages('tmle3', repos = c('https://tlverse.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/tlverse/tmle3/issues

On CRAN:

causal-inferencemachine-learningtargeted-learningvariable-importance

6.42 score 35 stars 304 scripts 80 exports 123 dependencies

Last updated 15 hours agofrom:fa2bd55249 (on devel). Checks:OK: 1 ERROR: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 30 2024
R-4.5-winERROROct 30 2024
R-4.5-linuxERROROct 30 2024
R-4.4-winERROROct 30 2024
R-4.4-macERROROct 30 2024
R-4.3-winERROROct 30 2024
R-4.3-macERROROct 30 2024

Exports:all_ancestorsboundCF_Likelihooddefine_lfdefine_nodedefine_paramdelta_param_ATEdelta_param_ORdelta_param_PAFdelta_param_PARdelta_param_RRdensity_formuladiscretize_variablefit_tmle3get_propensity_scoresLF_baseLF_derivedLF_empLF_fitLF_knownLF_staticLF_targetedLikelihoodLikelihood_cachemake_CF_Likelihoodmake_Likelihoodmake_tmle3_TaskParam_ATCParam_ATEParam_ATTParam_baseParam_deltaParam_meanParam_MSMParam_stratifiedParam_survivalParam_TSMplot_vimpoint_tx_likelihoodpoint_tx_npsempoint_tx_taskprocess_missingpropensity_score_plotpropensity_score_tablesubmodel_logitsummary_from_estimatessurvival_tx_likelihoodsurvival_tx_npsemsurvival_tx_taskTargeted_Likelihoodtime_orderingtmle_ATCtmle_ATEtmle_ATTtmle_MSMtmle_ORtmle_PARtmle_RRtmle_stratifiedtmle_survivaltmle_TSM_alltmle3tmle3_Fittmle3_Nodetmle3_Spectmle3_Spec_ATCtmle3_Spec_ATEtmle3_Spec_ATTtmle3_Spec_MSMtmle3_Spec_ORtmle3_Spec_PARtmle3_Spec_RRtmle3_Spec_stratifiedtmle3_Spec_survivaltmle3_Spec_TSM_alltmle3_Tasktmle3_Updatetmle3_Update_survivaltmle3_vimtrain_lf

Dependencies:abindassertthatbackportsbase64encBBmiscbitopsbslibcachemcaretcaToolscheckmateclasscliclockcodetoolscolorspacecpp11crayondata.tabledelayeddiagramdigestdplyre1071evaluatefansifarverfastmapfontawesomeforeachfsfuturefuture.applygenericsggplot2globalsgluegowergplotsgtablegtoolshardhathighrhmshtmltoolshtmlwidgetsigraphipredisobanditeratorsjquerylibjsonliteKernSmoothknitrlabelinglatticelavalifecyclelistenvlubridatemagrittrMASSMatrixmemoisemgcvmimeModelMetricsmunsellmvtnormnlmennetnumDerivorigamiparallellypillarpkgconfigplyrprettyunitspROCprodlimprogressprogressrproxypurrrR.methodsS3R.ooR.utilsR6rappdirsrbibutilsRColorBrewerRcppRdpackrecipesreshape2rlangrmarkdownROCRrpartrstackdequesassscalesshapesl3SQUAREMstringistringrsurvivaltibbletidyrtidyselecttimechangetimeDatetinytextzdbutf8uuidvctrsviridisLitevisNetworkwithrxfunyaml

tmle3 Framework Overview

Jeremy Coyle

Rendered fromframework.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2021-03-12
Started: 2018-03-06

Readme and manuals

Help Manual

Help pageTopics
Helper functions for the NPSEMall_ancestors time_ordering
Bound (Truncate) Likelihoodsbound
Counterfactual LikelihoodCF_Likelihood make_CF_Likelihood
Define a Likelihood Factordefine_lf
Define a Parameterdefine_param
PAR = Linear Contrast EY1-EY0delta_param_ATE
Odds Ratio odds(Y1)/odds(Y0)delta_param_OR
PAF = 1 - (1/RR(EY/E0))delta_param_PAF
PAR = Linear Contrast EY-EY0delta_param_PAR
Risk Ratio EY1/EY0delta_param_RR
Get and Plot Propensity Scoresdensity_formula get_propensity_scores propensity_score_plot propensity_score_table
Discretize Continuous Variablediscretize_variable
Get Empirical Mean of EIFs from EstimatesED_from_estimates
Base Class for Defining Likelihood FactorsLF_base
Derived Likelihood Factor Estimated from Data + Other Likelihood values, using sl3.LF_derived
Likelihood Factor Estimated using Empirical DistributionLF_emp
Likelihood Factor Estimated from Data using sl3.LF_fit
Known True Likelihood FactorLF_known
Static Likelihood FactorLF_static
Use a likelihood factor from an existing targeted likelihoodLF_targeted
Class for LikelihoodLikelihood make_Likelihood
Cache Likelihood values, update those valuesLikelihood_cache
Additive Effect of Treatment Among the TreatedParam_ATC
Average Treatment EffectParam_ATE
Additive Effect of Treatment Among the TreatedParam_ATT
Base Class for Defining ParametersParam_base
Delta Method ParametersParam_delta
Mean of Outcome NodeParam_mean
Stratified Parameter Estimates via MSMParam_MSM
Stratified Parameter EstimatesParam_stratified
Survival CurveParam_survival
Treatment Specific MeanParam_TSM
Plot results of variable importance analysisplot_vim
Helper Functions for Point Treatmentpoint_tx_likelihood point_tx_npsem point_tx_task
Preprocess Data to Handle Missing Variablesprocess_missing
Logistic Submodel Fluctuationsubmodel_logit
Summarize Estimatessummary_from_estimates
Helper Functions for Survival Analysissurvival_tx_likelihood survival_tx_npsem survival_tx_task
Targeted LikelihoodTargeted_Likelihood
All Treatment Specific Meanstmle_ATC
All Treatment Specific Meanstmle_ATE
All Treatment Specific Meanstmle_ATT
Make MSM version of Stratified TML estimator classtmle_MSM
Odds Ratiotmle_OR
PAR and PAFtmle_PAR
Risk Ratiotmle_RR
Stratified version of TML estimator from other Spec classestmle_stratified
Treatment Specific Survivaltmle_survival
All Treatment Specific Meanstmle_TSM_all
TMLE from a tmle3_Spec objecttmle3
TMLE fit objectfit_tmle3 tmle3_Fit
A Node (set of variables) in an NPSEMdefine_node tmle3_Node
Defines a TML Estimator (except for the data)tmle3_Spec
Defines a TML Estimator (except for the data)tmle3_Spec_ATC
Defines a TML Estimator (except for the data)tmle3_Spec_ATE
Defines a TML Estimator (except for the data)tmle3_Spec_ATT
Defines a Stratified TML Estimator with MSM (except for the data)tmle3_Spec_MSM
Defines a TML Estimator for the Odds Ratiotmle3_Spec_OR
Defines a tmle (minus the data)tmle3_Spec_PAR
Defines a TML Estimator for the Risk Ratiotmle3_Spec_RR
Defines a Stratified TML Estimator (except for the data)tmle3_Spec_stratified
Defines a TML Estimator (except for the data)tmle3_Spec_survival
Defines a TML Estimator (except for the data)tmle3_Spec_TSM_all
Class for Storing Data and NPSEM for TMLEmake_tmle3_Task tmle3_Task
Defines an update procedure (submodel+loss function)tmle3_Update
Defines an update procedure (submodel+loss function) for survival datatmle3_Update_survival
Compute Variable Importance Measures (VIM) with any given parametertmle3_vim
Manually Train Likelihood Factor The internal training process for likelihood factors is somewhat obtuse, so this function does the steps to manually train one, which is helpful if you want to use a likelihood factor independently of a likelihood objecttrain_lf