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RISCA: an R Package for Causal Inference and Prediction in Cohort-Based Analyses

What is the ‘RISCA’ package?

Description: Numerous functions for cohort-based analyses, either for prediction or causal inference. For causal inference, it includes Inverse Probability Weighting and G-computation for marginal estimation of an exposure effect when confounders are expected. We deal with binary outcomes, times-to-events, competing events, and multi-state data. For multistate data, semi-Markov model with interval censoring may be considered, and we propose the possibility to consider the excess of mortality related to the disease compared to reference lifetime tables. For predictive studies, we propose a set of functions to estimate time-dependent receiver operating characteristic (ROC) curves with the possible consideration of right-censoring times-to-events or the presence of confounders. Finally, several functions are available to assess time-dependent ROC curves or survival curves from aggregated data.

Installation

Install the latest release from CRAN:

install.packages("RISCA")

Install the development version from GitHub:

remotes::install_github("foucher-y/RISCA")

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Version

Install

install.packages('RISCA')

Monthly Downloads

430

Version

1.0.6

License

GPL (>= 2)

Maintainer

Yohann Foucher

Last Published

January 20th, 2025

Functions in RISCA (1.0.6)

dataKi67

The Aggregated Data Published By de Azambuja et al. (2007).
ipw.log.rank

Log-Rank Test for Adjusted Survival Curves.
fr.ratetable

Expected Mortality Rates of the General French Population
gc.logistic

Marginal Effect for Binary Outcome by G-computation.
gc.survival

Marginal Effect for Censored Outcome by G-computation with a Cox Regression for the Outcome Model.
gc.sl.binary

Marginal Effect for Binary Outcome by Super Learned G-computation.
dataSTR

Data for Second Kidney Transplant Recipients.
expect.utility2

Cut-Off Estimation Of A Prognostic Marker (Two Groups Are observed).
dataOFSEP

A Simulated Sample From the OFSEP Cohort.
expect.utility1

Cut-Off Estimation Of A Prognostic Marker (Only One Observed Group).
lines.rocrisca

Add Lines to a ROC Plot
markov.4states.rsadd

4-state Relative Survival Markov Model with Additive Risks
plot.rocrisca

Plot Method for 'rocrisca' Objects
ipw.survival

Adjusted Survival Curves by Using IPW.
markov.3states.rsadd

3-state Relative Survival Markov Model with Additive Risks
plot.survrisca

Plot Method for 'survrisca' Objects
lrs.multistate

Likelihood Ratio Statistic to Compare Embedded Multistate Models
markov.3states

3-State Time-Inhomogeneous Markov Model
markov.4states

4-State Time-Inhomogeneous Markov Model
mixture.2states

Horizontal Mixture Model for Two Competing Events
roc.net

Net Time-Dependent ROC Curves With Right Censored Data.
roc.prognostic.individual

Prognostic ROC Curve based on Individual Data
roc.prognostic.aggregate

Prognostic ROC Curve Based on Survival Probabilities
roc.summary

Summary ROC Curve For Aggregated Data.
port

POsitivity-Regression Tree (PoRT) Algorithm to Identify Positivity Violations.
semi.markov.4states

4-State Semi-Markov Model
semi.markov.4states.rsadd

4-State Relative Survival Semi-Markov Model With Additive Risks
pred.mixture.2states

Cumulative Incidence Function Form Horizontal Mixture Model With Two Competing Events
survival.summary.strata

Summary Survival Curve And Comparison Between Strata.
rmst

Restricted Mean Survival Times.
roc.binary

ROC Curves For Binary Outcomes.
semi.markov.3states

3-State Semi-Markov Model
roc.time

Time-Dependent ROC Curves With Right Censored Data.
semi.markov.3states.ic

3-State Semi-Markov Model With Interval-Censored Data
survival.mr

Multiplicative-Regression Model to Compare the Risk Factors Between Two Reference and Relative Populations
survival.summary

Summary Survival Curve From Aggregated Data
semi.markov.3states.rsadd

3-State Relative Survival Semi-Markov Model With Additive Risks
dataDIVAT1

A First Sample From The DIVAT Data Bank.
dataDIVAT4

A Fourth Sample From the DIVAT Data Bank.
dataHepatology

The Data Extracted From The Meta-Analysis By Cabibbo et al. (2010).
auc

Area Under ROC Curve From Sensitivities And Specificities.
dataKTFS

A Sixth Sample Of The DIVAT Cohort.
dataDIVAT3

A Third Sample From the DIVAT Data Bank.
dataCSL

CSL Liver Chirrosis Data.
dataDIVAT2

A Second Sample From the DIVAT Data Bank.
dataDIVAT5

The Aggregated Kidney Graft Survival Stratified By The 1-year Serum Creatinine.
dataFTR

Data for First Kidney Transplant Recipients.