This package is considered a duplicate. The official version of this package is found at:https://tlverse.r-universe.dev/tmle3

Package: tmle3 0.2.0

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]

tmle3_0.2.0.tar.gz
tmle3_0.2.0.zip(r-4.7)tmle3_0.2.0.zip(r-4.6)tmle3_0.2.0.zip(r-4.5)
tmle3_0.2.0.tgz(r-4.6-any)tmle3_0.2.0.tgz(r-4.5-any)
tmle3_0.2.0.tar.gz(r-4.7-any)tmle3_0.2.0.tar.gz(r-4.6-any)
tmle3_0.2.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
tmle3/json (API)

# Install 'tmle3' in R:

install.packages('tmle3', repos = c('https://ictml-project.r-universe.dev', 'https://cloud.r-project.org'))

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

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

On CRAN:

causal-inference machine-learning targeted-learning variable-importance

7.60 score 43 stars 4 packages 310 scripts 80 exports 121 dependencies

Last updated from:ed72f8a20e. Checks:7 ERROR, 2 OK. Indexed: no.

Target	Result	Time
linux-devel-x86_64	ERROR	354
source / vignettes	OK	241
linux-release-x86_64	ERROR	357
macos-release-arm64	ERROR	228
macos-oldrel-arm64	ERROR	214
windows-devel	ERROR	355
windows-release	ERROR	307
windows-oldrel	ERROR	303
wasm-release	OK	154

Exports:all_ancestors bound CF_Likelihood define_lf define_node define_param delta_param_ATE delta_param_OR delta_param_PAF delta_param_PAR delta_param_RR density_formula discretize_variable fit_tmle3 get_propensity_scores LF_base LF_derived LF_emp LF_fit LF_known LF_static LF_targeted Likelihood Likelihood_cache make_CF_Likelihood make_Likelihood make_tmle3_Task Param_ATC Param_ATE Param_ATT Param_base Param_delta Param_mean Param_MSM Param_stratified Param_survival Param_TSM plot_vim point_tx_likelihood point_tx_npsem point_tx_task process_missing propensity_score_plot propensity_score_table submodel_logit summary_from_estimates survival_tx_likelihood survival_tx_npsem survival_tx_task Targeted_Likelihood time_ordering tmle_ATC tmle_ATE tmle_ATT tmle_MSM tmle_OR tmle_PAR tmle_RR tmle_stratified tmle_survival tmle_TSM_all tmle3 tmle3_Fit tmle3_Node tmle3_Spec tmle3_Spec_ATC tmle3_Spec_ATE tmle3_Spec_ATT tmle3_Spec_MSM tmle3_Spec_OR tmle3_Spec_PAR tmle3_Spec_RR tmle3_Spec_stratified tmle3_Spec_survival tmle3_Spec_TSM_all tmle3_Task tmle3_Update tmle3_Update_survival tmle3_vim train_lf

Dependencies:abind assertthat backports base64enc BBmisc bitops bslib cachem caret caTools checkmate class cli clock codetools cpp11 crayon data.table delayed diagram digest dplyr e1071 evaluate farver fastmap fontawesome foreach fs future future.apply generics ggplot2 globals glue gower gplots gtable gtools hardhat highr hms htmltools htmlwidgets igraph ipred isoband iterators jquerylib jsonlite KernSmooth knitr labeling lattice lava lifecycle listenv lubridate magrittr MASS Matrix memoise mime ModelMetrics mvtnorm nlme nnet numDeriv origami parallelly pillar pkgconfig plyr prettyunits pROC prodlim progress progressr proxy purrr R.methodsS3 R.oo R.utils R6 rappdirs rbibutils RColorBrewer Rcpp Rdpack recipes reshape2 rlang rmarkdown ROCR rpart rstackdeque S7 sass scales shape sl3 sparsevctrs SQUAREM stringi stringr survival tibble tidyr tidyselect timechange timeDate tinytex tzdb utf8 uuid vctrs viridisLite visNetwork withr xfun yaml

tmle3 Framework Overview

Rendered fromframework.Rmdusingknitr::rmarkdown

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Helper functions for the NPSEM	all_ancestors time_ordering
Bound (Truncate) Likelihoods	bound
Counterfactual Likelihood	CF_Likelihood make_CF_Likelihood
Define a Likelihood Factor	define_lf
Define a Parameter	define_param
PAR = Linear Contrast EY1-EY0	delta_param_ATE
Odds Ratio odds(Y1)/odds(Y0)	delta_param_OR
PAF = 1 - (1/RR(EY/E0))	delta_param_PAF
PAR = Linear Contrast EY-EY0	delta_param_PAR
Risk Ratio EY1/EY0	delta_param_RR
Get and Plot Propensity Scores	density_formula get_propensity_scores propensity_score_plot propensity_score_table
Discretize Continuous Variable	discretize_variable
Get Empirical Mean of EIFs from Estimates	ED_from_estimates
Base Class for Defining Likelihood Factors	LF_base
Derived Likelihood Factor Estimated from Data + Other Likelihood values, using sl3.	LF_derived
Likelihood Factor Estimated using Empirical Distribution	LF_emp
Likelihood Factor Estimated from Data using sl3.	LF_fit
Known True Likelihood Factor	LF_known
Static Likelihood Factor	LF_static
Use a likelihood factor from an existing targeted likelihood	LF_targeted
Class for Likelihood	Likelihood make_Likelihood
Cache Likelihood values, update those values	Likelihood_cache
Additive Effect of Treatment Among the Treated	Param_ATC
Average Treatment Effect	Param_ATE
Additive Effect of Treatment Among the Treated	Param_ATT
Base Class for Defining Parameters	Param_base
Delta Method Parameters	Param_delta
Mean of Outcome Node	Param_mean
Stratified Parameter Estimates via MSM	Param_MSM
Stratified Parameter Estimates	Param_stratified
Survival Curve	Param_survival
Treatment Specific Mean	Param_TSM
Plot results of variable importance analysis	plot_vim
Helper Functions for Point Treatment	point_tx_likelihood point_tx_npsem point_tx_task
Preprocess Data to Handle Missing Variables	process_missing
Logistic Submodel Fluctuation	submodel_logit
Summarize Estimates	summary_from_estimates
Helper Functions for Survival Analysis	survival_tx_likelihood survival_tx_npsem survival_tx_task
Targeted Likelihood	Targeted_Likelihood
All Treatment Specific Means	tmle_ATC
All Treatment Specific Means	tmle_ATE
All Treatment Specific Means	tmle_ATT
Make MSM version of Stratified TML estimator class	tmle_MSM
Odds Ratio	tmle_OR
PAR and PAF	tmle_PAR
Risk Ratio	tmle_RR
Stratified version of TML estimator from other Spec classes	tmle_stratified
Treatment Specific Survival	tmle_survival
All Treatment Specific Means	tmle_TSM_all
TMLE from a tmle3_Spec object	tmle3
TMLE fit object	fit_tmle3 tmle3_Fit
A Node (set of variables) in an NPSEM	define_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 Ratio	tmle3_Spec_OR
Defines a tmle (minus the data)	tmle3_Spec_PAR
Defines a TML Estimator for the Risk Ratio	tmle3_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 TMLE	make_tmle3_Task tmle3_Task
Defines an update procedure (submodel+loss function)	tmle3_Update
Defines an update procedure (submodel+loss function) for survival data	tmle3_Update_survival
Compute Variable Importance Measures (VIM) with any given parameter	tmle3_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 object	train_lf