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RISCA (version 1.0.1)

Causal Inference and Prediction in Cohort-Based Analyses

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.

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Version

Install

install.packages('RISCA')

Monthly Downloads

430

Version

1.0.1

License

GPL (>= 2)

Maintainer

Y. Foucher

Last Published

May 2nd, 2022

Functions in RISCA (1.0.1)

cox.en

Library of the Super Learner for Elastic Net Cox Regression
cox.all

Library of the Super Learner for Cox Regression
aft.gamma

Library of the Super Learner for an accelerated failure time (AFT) parametric model with a gamma distribution
aft.ggamma

Library of the Super Learner for an accelerated failure time (AFT) parametric model with a generalized gamma distribution
auc

Area Under ROC Curve From Sensitivities And Specificities.
dataCSL

CSL Liver Chirrosis Data.
dataDIVAT4

A Fourth Sample From the DIVAT Data Bank.
dataDIVAT1

A First Sample From The DIVAT Data Bank.
aft.llogis

Library of the Super Learner for an accelerated failure time (AFT) parametric model with a log logistic distribution
dataDIVAT5

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

Library of the Super Learner for an accelerated failure time (AFT) parametric model with a Weibull distribution
dataKTFS

A Sixth Sample Of The DIVAT Cohort.
dataOFSEP

A Simulated Sample From the OFSEP Cohort.
dataFTR

Data for First Kidney Transplant Recipients.
dataKi67

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

Library of the Super Learner for Cox univariate significant model
dataSTR

Data for Second Kidney Transplant Recipients.
dataHepatology

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

Library of the Super Learner for Lasso Cox Regression
differentiation

Numerical Differentiation with Finite Differences.
lrs.multistate

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

3-State Time-Inhomogeneous Markov Model
fr.ratetable

Expected Mortality Rates of the General French Population
dataDIVAT3

A Third Sample From the DIVAT Data Bank.
expect.utility2

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

Metrics to Evaluate the Prognostic Capacities
markov.4states.rsadd

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

Plot Method for 'rocrisca' Objects
dataDIVAT2

A Second Sample From the DIVAT Data Bank.
gc.survival

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

Library of the Super Learner for Ridge Cox Regression
gc.sl.time

Marginal Effect for Censored Outcome by G-computation with a Super Learner for the Outcome Model.
ipw.log.rank

Log-Rank Test for Adjusted Survival Curves.
gc.logistic

Marginal Effect for Binary Outcome by G-computation.
plot.sl.time

Caliration Plot for Super Learner
hr.sl.time

Conditionnal Effect for Censored Outcome with a Super Learner for the Outcome Model.
nnet.time

Library of the Super Learner for Survival Neural Network
mixture.2states

Horizontal Mixture Model for Two Competing Events
predict.cox

Prediction from a Penalized Cox Regression
gc.sl.binary

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

Prediction from an Flexible Parametric Model
roc.binary

ROC Curves For Binary Outcomes.
expect.utility1

Cut-Off Estimation Of A Prognostic Marker (Only One Observed Group).
predict.rf.time

Prediction from a Suvival Random Forest Tree
ph.exponential

Library of the Super Learner for an proportional hazards (PH) parametric model with an Exponential distribution
markov.3states.rsadd

3-state Relative Survival Markov Model with Additive Risks
rf.time

Library of the Super Learner for Survival Random Forest Tree
markov.4states

4-State Time-Inhomogeneous Markov Model
predict.sl.time

Prediction from an Super Learner (SL) for Censored Outcomes
rmst

Restricted Mean Survival Times.
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
tune.nnet.time

Tune a 1-Layer Survival Neural Network
summary.sl.time

Summaries of a Super Learner
sl.time

Super Learner for Censored Outcomes
tune.cox.aic

Tune cox step AIC with forward selection
semi.markov.4states

4-State Semi-Markov Model
semi.markov.3states.rsadd

3-State Relative Survival Semi-Markov Model With Additive Risks
roc.prognostic.aggregate

Prognostic ROC Curve Based on Survival Probabilities
ph.gompertz

Library of the Super Learner for an proportional hazards (PH) parametric model with a Gompertz distribution
tune.cox.en

Tune Elastic Net Cox Regression
semi.markov.3states

3-State Semi-Markov Model
tune.rf.time

Tune Survival Random Forest Tree
roc.net

Net Time-Dependent ROC Curves With Right Censored Data.
plot.survrisca

Plot Method for 'survrisca' Objects
ipw.survival

Adjusted Survival Curves by Using IPW.
semi.markov.3states.ic

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

Summary Survival Curve And Comparison Between Strata.
survival.summary

Summary Survival Curve From Aggregated Data
roc.prognostic.individual

Prognostic ROC Curve based on Individual Data
port

POsitivity-Regression Tree (PoRT) Algorithm to Identify Positivity Violations.
lines.rocrisca

Add Lines to a ROC Plot
pred.mixture.2states

Cumulative Incidence Function Form Horizontal Mixture Model With Two Competing Events
predict.nnet.time

Prediction from a Survival Neural Network
roc.summary

Summary ROC Curve For Aggregated Data.
tune.cox.lasso

Tune Lasso Cox Regression
tune.cox.ridge

Tune Ridge Cox Regression
roc.time

Time-Dependent ROC Curves With Right Censored Data.