Package: adjustedCurves 0.11.2.9000

Robin Denz

adjustedCurves: Confounder-Adjusted Survival Curves and Cumulative Incidence Functions

Estimate and plot confounder-adjusted survival curves using either 'Direct Adjustment', 'Direct Adjustment with Pseudo-Values', various forms of 'Inverse Probability of Treatment Weighting', two forms of 'Augmented Inverse Probability of Treatment Weighting', 'Empirical Likelihood Estimation' or 'Targeted Maximum Likelihood Estimation'. Also includes a significance test for the difference between two adjusted survival curves and the calculation of adjusted restricted mean survival times. Additionally enables the user to estimate and plot cause-specific confounder-adjusted cumulative incidence functions in the competing risks setting using the same methods (with some exceptions). For details, see Denz et. al (2023) <doi:10.1002/sim.9681>.

Authors:Robin Denz [aut, cre]

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

# Install 'adjustedCurves' in R:
install.packages('adjustedCurves', repos = c('https://robindenz1.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/robindenz1/adjustedcurves/issues

On CRAN:

adjustedconfidence-intervalscumulative-incidencesurvival-curves

8.11 score 37 stars 77 scripts 837 downloads 41 exports 29 dependencies

Last updated 2 months agofrom:27a185eaba. Checks:OK: 5 ERROR: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 22 2024
R-4.5-winOKNov 22 2024
R-4.5-linuxOKNov 22 2024
R-4.4-winOKNov 22 2024
R-4.4-macOKNov 22 2024
R-4.3-winERRORNov 22 2024
R-4.3-macERRORNov 22 2024

Exports:adjusted_curve_diffadjusted_curve_ratioadjusted_curve_testadjusted_rmstadjusted_rmtladjusted_surv_quantileadjustedcifadjustedsurvas_ggsurvplot_dfcif_aalen_johansencif_aiptwcif_aiptw_pseudocif_directcif_direct_pseudocif_iptwcif_iptw_pseudocif_matchingCSC_MIFGR_MIplot_curve_diffplot_curve_ratioplot_rmst_curveplot_rmtl_curvesim_confounded_crisksim_confounded_survsurv_aiptwsurv_aiptw_pseudosurv_directsurv_direct_pseudosurv_emp_liksurv_iptw_coxsurv_iptw_kmsurv_iptw_pseudosurv_iv_2SRIFsurv_kmsurv_matchingsurv_prox_aiptwsurv_prox_iptwsurv_strat_amatosurv_strat_cupplessurv_strat_nieto

Dependencies:clicodetoolsdigestdoParalleldoRNGdplyrfansiforeachgenericsglueiteratorslatticelifecyclemagrittrMatrixpillarpkgconfigR.methodsS3R.ooR.utilsR6rlangrngtoolssurvivaltibbletidyselectutf8vctrswithr

An Introduction to the 'adjustedCurves' Package

Robin Denz

Rendered fromintroduction.Rmdusingknitr::rmarkdownon Nov 22 2024.

Last update: 2024-03-29
Started: 2021-03-22

Comparing Adjusted Survival Curves or Cumulative Incidence Curves

Robin Denz

Rendered fromcomparing_groups.rmdusingknitr::rmarkdownon Nov 22 2024.

Last update: 2024-04-10
Started: 2024-03-29

Customizing Adjusted Survival Curve Plots

Robin Denz

Rendered fromplot_customization.rmdusingknitr::rmarkdownon Nov 22 2024.

Last update: 2024-04-10
Started: 2024-03-10

Frequently Asked Questions about the adjustedCurves Package

Robin Denz

Rendered fromfaq.rmdusingknitr::rmarkdownon Nov 22 2024.

Last update: 2024-03-29
Started: 2024-03-29

Overview of methods in adjustedCurves

Robin Denz

Rendered frommethod_overview.rmdusingknitr::rmarkdownon Nov 22 2024.

Last update: 2024-04-10
Started: 2024-02-04

Readme and manuals

Help Manual

Help pageTopics
Confounder-Adjusted Survival Curves and Cumulative Incidence FunctionsadjustedCurves-package
Estimate the difference between or the ratio of two Confounder-Adjusted Survival Curves or CIFsadjusted_curve_diff adjusted_curve_ratio
Test if there is a difference between two Confounder-Adjusted Survival Curves or CIFsadjusted_curve_test
Estimate Confounder-Adjusted Restricted Mean Survival Timesadjusted_rmst
Estimate Confounder-Adjusted Restricted Mean Time Lostadjusted_rmtl
Estimate Confounder-Adjusted Survival Time Quantilesadjusted_surv_quantile
Estimate Cause-Specific Confounder-Adjusted Cumulative Incidence Functionsadjustedcif
Estimate Confounder-Adjusted Survival Curvesadjustedsurv
Extract a 'data.frame' containing the estimated survival curves from a 'adjustedsurv' objectas_ggsurvplot_df
Group-Specific Aalen-Johansen CIFscif_aalen_johansen
Augmented Inverse Probability of Treatment Weighted CIFscif_aiptw
Augmented Inverse Probability of Treatment Weighted CIFs using Pseudo-Valuescif_aiptw_pseudo
Direct Adjusted Cumulative Incidence Functionscif_direct
Direct Adjusted CIFs using Pseudo-Valuescif_direct_pseudo
Inverse Probability of Treatment Weighted CIFscif_iptw
Inverse Probability of Treatment Weighted CIFs using Pseudo-Valuescif_iptw_pseudo
Using Propensity-Score Matching to Calculate Adjusted CIFscif_matching
Cause-Specific Cox Regression with Multiple ImputationCSC_MI
Fine & Gray Model with Multiple ImputationFGR_MI
List of supported models in 'cif_direct'models_cif_direct
List of supported models in 'surv_direct'models_surv_direct
Plot the Difference Between or the Ratio of Two Adjusted Survival Curves or CIFsplot_curve_diff plot_curve_ratio
Plot Adjusted Restricted Mean Survival Time Curvesplot_rmst_curve
Plot Adjusted Restricted Mean Time Lost Curvesplot_rmtl_curve
Plot Confounder-Adjusted Cumulative Incidence Functionsplot.adjustedcif
Plot Confounder-Adjusted Survival Curvesplot.adjustedsurv
Plot Method for 'curve_test' Objectsplot.curve_test
Print Method for 'curve_test' Objectsprint.curve_test
Simulate Competing Risks Data with Confounderssim_confounded_crisk
Simulate Survival Data with Confounderssim_confounded_surv
Augmented Inverse Probability of Treatment Weighted Survival Curvessurv_aiptw
Augmented Inverse Probability of Treatment Weighted Survival Curves using Pseudo-Valuessurv_aiptw_pseudo
Direct Adjusted Survival Curvessurv_direct
Direct Adjusted Survival Curves using Pseudo-Valuessurv_direct_pseudo
Empirical Likelihood Estimation Survival Curvessurv_emp_lik
Inverse Probability of Treatment Weighted Survival using Cox-Regressionsurv_iptw_cox
Inverse Probability of Treatment Weighted Kaplan-Meier estimatessurv_iptw_km
Inverse Probability of Treatment Weighted Survival Estimates using Pseudo-Valuessurv_iptw_pseudo
Instrumental Variable based Survival Curve Estimation using the Two Stage Residual Inclusion method with a Frailty Term (2SRI-F)surv_iv_2SRIF
Group-Specific Kaplan-Meier Survival Curvessurv_km
Using Propensity-Score Matching to Calculate Adjusted Survival Curvessurv_matching
Proximal Augmented Inverse Probability of Treatment Weighted Survival Curve Estimatessurv_prox_aiptw
Proximal Inverse Probability of Treatment Weighted Survival Curve Estimatessurv_prox_iptw
Adjusted Survival Curves for Categorical Confounders using the Method by Amato (1988)surv_strat_amato
Adjusted Survival Curves for Categorical Confounders using the Method by Cupples et al. (1995)surv_strat_cupples
Adjusted Survival Curves for Categorical Confounders using the Method by Gregory (1988) and Nieto & Coresh (1996)surv_strat_nieto