Package: adjustedCurves 0.12.0

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]

adjustedCurves_0.12.0.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
adjustedCurves/json (API)

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

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

Pkgdown/docs site:https://robindenz1.github.io

On CRAN:

Conda:

adjustedconfidence-intervalscumulative-incidencesurvival-curves

8.57 score 47 stars 136 scripts 1.2k downloads 17 exports 28 dependencies

Last updated from:5e6392e8b7. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develOK300
source / vignettesOK252
linux-releaseOK293
macos-releaseOK248
macos-oldrelOK185
windows-develOK278
windows-releaseOK223
windows-oldrelOK268
wasm-releaseOK114

Exports:adjusted_curve_diffadjusted_curve_ratioadjusted_curve_testadjusted_rmstadjusted_rmtladjusted_surv_quantileadjustedcifadjustedsurvas_ggsurvplot_dfCSC_MIFGR_MIplot_curve_diffplot_curve_ratioplot_rmst_curveplot_rmtl_curvesim_confounded_crisksim_confounded_surv

Dependencies:clicodetoolsdigestdoParalleldoRNGdplyrforeachgenericsglueiteratorslatticelifecyclemagrittrMatrixpillarpkgconfigR.methodsS3R.ooR.utilsR6rlangrngtoolssurvivaltibbletidyselectutf8vctrswithr

Overview of methods in adjustedCurves
Methods in adjustedsurv() | Methods in adjustedcif() | References
Rendered frommethod_overview.rmdusingknitr::rmarkdown

Last update: 2026-10-06
Started: 2024-02-04

Frequently Asked Questions about the adjustedCurves Package
How do I add a table with the number at risk below the plot? | How do I get a p-value? | Does this package support time-varying covariates? | Which method should I use? | How can I interpret the results? | Is it possible to obtain adjusted survival curves for data with competing events? | Can I use this package if the variable I am interested in is continuous? | Does this package offer an adjusted log-rank test? | How do I deal with missing values? | I have fit a coxph model with start/stop type data. Can I use this model to obtain adjusted survival curves? | Can interactions be included when estimating adjusted survival curves or CIFs? | Why do adjusted survival curves produced with method="direct" have a different shape than Kaplan-Meier curves? | Should I include a strata() term for the variable of interest when using a Cox model with method="direct"? | How do I cite this package? | References
Rendered fromfaq.rmdusingknitr::rmarkdown

Last update: 2025-08-26
Started: 2024-03-29

An Introduction to the 'adjustedCurves' Package
Installation | Adjusted Survival Curves | Direct Standardization | Inverse Probability of Treatment Weighting | Augmented Inverse Probability of Treatment Weighting | Adjusted Cumulative Incidence Functions | Adjusted Curves with More than Two Groups | Further Topics | Implemented Methods | Plot Customization | Comparing Groups | FAQ | Literature
Rendered fromadjustedCurves.Rmdusingknitr::rmarkdown

Last update: 2025-06-04
Started: 2025-06-04

Comparing Adjusted Survival Curves or Cumulative Incidence Curves
Introduction | Adjusted Survival Curves | Illustrative Example Data | Contrasting Survival Probabilities at $t$ | Adjusted Survival Time Quantiles | Restricted Mean Survival Times | Bootstrap Hypothesis Testing | Adjusted Cumulative Incidence Curves | Discussion | References
Rendered fromcomparing_groups.rmdusingknitr::rmarkdown

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

Customizing Adjusted Survival Curve Plots
Introduction | Example Data | General Plot Aesthetics | Confidence Intervals | Median Survival Time Indicators | Censoring Indicators | Risk Tables | Changing the content of risk tables | Changing aesthetic parameters | Additional customization options | Putting it all together
Rendered fromplot_customization.rmdusingknitr::rmarkdown

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

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 Weighting Combined with Inverse Probability of Censoring Weightingsurv_iptw_cens
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