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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

545

Version

1.0.5

License

GPL (>= 2)

Maintainer

Yohann Foucher

Last Published

March 22nd, 2024

Functions in RISCA (1.0.5)

dataSTR

Data for Second Kidney Transplant Recipients.
dataKi67

The Aggregated Data Published By de Azambuja et al. (2007).
dataOFSEP

A Simulated Sample From the OFSEP Cohort.
gc.survival

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

Marginal Effect for Binary Outcome by G-computation.
ipw.log.rank

Log-Rank Test for Adjusted Survival Curves.
expect.utility1

Cut-Off Estimation Of A Prognostic Marker (Only One Observed Group).
gc.sl.binary

Marginal Effect for Binary Outcome by Super Learned G-computation.
expect.utility2

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

Expected Mortality Rates of the General French Population
markov.3states

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

Horizontal Mixture Model for Two Competing Events
ipw.survival

Adjusted Survival Curves by Using IPW.
plot.rocrisca

Plot Method for 'rocrisca' Objects
lines.rocrisca

Add Lines to a ROC Plot
markov.3states.rsadd

3-state Relative Survival Markov Model with Additive Risks
markov.4states.rsadd

4-state Relative Survival Markov Model with Additive Risks
rmst

Restricted Mean Survival Times.
lrs.multistate

Likelihood Ratio Statistic to Compare Embedded Multistate Models
roc.summary

Summary ROC Curve For Aggregated Data.
pred.mixture.2states

Cumulative Incidence Function Form Horizontal Mixture Model With Two Competing Events
port

POsitivity-Regression Tree (PoRT) Algorithm to Identify Positivity Violations.
roc.prognostic.aggregate

Prognostic ROC Curve Based on Survival Probabilities
plot.survrisca

Plot Method for 'survrisca' Objects
semi.markov.3states

3-State Semi-Markov Model
roc.time

Time-Dependent ROC Curves With Right Censored Data.
roc.net

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

ROC Curves For Binary Outcomes.
markov.4states

4-State Time-Inhomogeneous Markov Model
roc.prognostic.individual

Prognostic ROC Curve based on Individual Data
semi.markov.4states

4-State Semi-Markov Model
survival.mr

Multiplicative-Regression Model to Compare the Risk Factors Between Two Reference and Relative Populations
semi.markov.4states.rsadd

4-State Relative Survival Semi-Markov Model With Additive Risks
semi.markov.3states.ic

3-State Semi-Markov Model With Interval-Censored Data
semi.markov.3states.rsadd

3-State Relative Survival Semi-Markov Model With Additive Risks
survival.summary.strata

Summary Survival Curve And Comparison Between Strata.
survival.summary

Summary Survival Curve From Aggregated Data
dataFTR

Data for First Kidney Transplant Recipients.
dataDIVAT3

A Third Sample From the DIVAT Data Bank.
dataDIVAT4

A Fourth Sample From the DIVAT Data Bank.
dataDIVAT2

A Second Sample From the DIVAT Data Bank.
dataDIVAT1

A First Sample From The DIVAT Data Bank.
dataHepatology

The Data Extracted From The Meta-Analysis By Cabibbo et al. (2010).
dataDIVAT5

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

Area Under ROC Curve From Sensitivities And Specificities.
dataCSL

CSL Liver Chirrosis Data.
dataKTFS

A Sixth Sample Of The DIVAT Cohort.