Package: gfoRmula 1.1.0

Sean McGrath

gfoRmula: Parametric G-Formula

Implements the non-iterative conditional expectation (NICE) algorithm of the g-formula algorithm (Robins (1986) <doi:10.1016/0270-0255(86)90088-6>, Hernán and Robins (2024, ISBN:9781420076165)). The g-formula can estimate an outcome's counterfactual mean or risk under hypothetical treatment strategies (interventions) when there is sufficient information on time-varying treatments and confounders. This package can be used for discrete or continuous time-varying treatments and for failure time outcomes or continuous/binary end of follow-up outcomes. The package can handle a random measurement/visit process and a priori knowledge of the data structure, as well as censoring (e.g., by loss to follow-up) and two options for handling competing events for failure time outcomes. Interventions can be flexibly specified, both as interventions on a single treatment or as joint interventions on multiple treatments. See McGrath et al. (2020) <doi:10.1016/j.patter.2020.100008> for a guide on how to use the package.

Authors:Victoria Lin [aut], Sean McGrath [aut, cre], Zilu Zhang [aut], Roger W. Logan [aut], Lucia C. Petito [aut], Jing Li [aut], McGee Emma [aut], Cheng Carrie [aut], Jessica G. Young [aut], Miguel A. Hernán [aut], 2019 The President and Fellows of Harvard College [cph]

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

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

Peer review:

Bug tracker:https://github.com/causalinference/gformula/issues

Datasets:
  • basicdata - Example Dataset for a Survival Outcome with Censoring
  • basicdata_nocomp - Example Dataset for a Survival Outcome without Censoring
  • binary_eofdata - Example Dataset for a Binary Outcome at End of Follow-Up
  • censor_data - Example Dataset for a Survival Outcome with an Indicator of Censoring Variable
  • continuous_eofdata - Example Dataset for a Continuous Outcome at End of Follow-Up
  • continuous_eofdata_pb - Example Dataset for a Continuous Outcome at End of Follow-Up with Pre-Baseline Times

On CRAN:

11 exports 149 stars 4.98 score 79 dependencies 1 mentions 66 scripts 521 downloads

Last updated 2 days agofrom:d789dffd61. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 16 2024
R-4.5-winOKSep 16 2024
R-4.5-linuxOKSep 16 2024
R-4.4-winOKSep 16 2024
R-4.4-macOKSep 16 2024
R-4.3-winOKSep 16 2024
R-4.3-macOKSep 16 2024

Exports:carry_forwardcumavggformulagformula_binary_eofgformula_continuous_eofgformula_survivallagavglaggedsimple_restrictionstaticthreshold

Dependencies:abindbackportsbootbroomcarcarDataclicolorspacecorrplotcowplotcpp11crayondata.tableDerivdigestdoBydplyrfansifarvergenericsggplot2ggpubrggrepelggsciggsignifgluegridExtragtablehmsisobandlabelinglatticelifecyclelme4magrittrMASSMatrixMatrixModelsmaxLikmgcvmicrobenchmarkminqamiscToolsmodelrmunsellnlmenloptrnnetnumDerivpbkrtestpillarpkgconfigpolynomprettyunitsprogresspurrrquantregR6RColorBrewerRcppRcppEigenrlangrstatixsandwichscalesSparseMstringistringrsurvivaltibbletidyrtidyselecttruncnormtruncregutf8vctrsviridisLitewithrzoo

A Simplified Approach for Specifying Interventions in gfoRmula

Rendered fromIntervention-Specification.Rmdusingknitr::rmarkdownon Sep 16 2024.

Last update: 2024-07-20
Started: 2024-07-20

Using Custom Outcome Models in gfoRmula

Rendered fromCustom-Outcome-Models.Rmdusingknitr::rmarkdownon Sep 16 2024.

Last update: 2024-09-13
Started: 2024-09-13

Readme and manuals

Help Manual

Help pageTopics
Example Dataset for a Survival Outcome with Censoringbasicdata
Example Dataset for a Survival Outcome without Censoringbasicdata_nocomp
Example Dataset for a Binary Outcome at End of Follow-Upbinary_eofdata
Carry Forwardcarry_forward
Example Dataset for a Survival Outcome with an Indicator of Censoring Variablecensor_data
Coefficient method for objects of class "gformula"coef.gformula
Example Dataset for a Continuous Outcome at End of Follow-Upcontinuous_eofdata
Example Dataset for a Continuous Outcome at End of Follow-Up with Pre-Baseline Timescontinuous_eofdata_pb
Estimation of Survival Outcome, Continuous End-of-Follow-Up Outcome, or Binary End-of-Follow-Up Outcome Under the Parametric G-Formulagformula
Estimation of Binary End-of-Follow-Up Outcome Under the Parametric G-Formulagformula_binary_eof
Estimation of Continuous End-of-Follow-Up Outcome Under the Parametric G-Formulagformula_continuous_eof
Estimation of Survival Outcome Under the Parametric G-Formulagformula_survival
History functionscumavg lagavg lagged
Plot method for objects of class "gformula_binary_eof"plot.gformula_binary_eof
Plot method for objects of class "gformula_continuous_eof"plot.gformula_continuous_eof
Plot method for objects of class "gformula_survival"plot.gformula_survival
Print and summary methods for "gformula" objectsprint.gformula_binary_eof print.gformula_continuous_eof print.gformula_survival print.summary.gformula summary.gformula
Simple Restrictionsimple_restriction
Static Interventionstatic
Threshold Interventionthreshold
Variance-covariance method for objects of class "gformula"vcov.gformula