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RISCA (version 1.0.4)

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

1.0.4

License

GPL (>= 2)

Maintainer

Yohann Foucher

Last Published

March 22nd, 2023

Functions in RISCA (1.0.4)

aft.llogis

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

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

Library of the Super Learner for Cox Regression
auc

Area Under ROC Curve From Sensitivities And Specificities.
cox.ridge

Library of the Super Learner for Ridge Cox Regression
cox.lasso

Library of the Super Learner for Lasso Cox Regression
cox.aic

Library of the Super Learner for Cox univariate significant model
cox.en

Library of the Super Learner for Elastic Net Cox Regression
aft.weibull

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

Data for First Kidney Transplant Recipients.
dataCSL

CSL Liver Chirrosis Data.
dataHepatology

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

A Sixth Sample Of The DIVAT Cohort.
dataDIVAT5

The Aggregated Kidney Graft Survival Stratified By The 1-year Serum Creatinine.
dataDIVAT3

A Third Sample From the DIVAT Data Bank.
dataDIVAT2

A Second Sample From the DIVAT Data Bank.
dataDIVAT1

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

Library of the Super Learner for an accelerated failure time (AFT) parametric model with a gamma distribution
dataDIVAT4

A Fourth Sample From the DIVAT Data Bank.
dataKi67

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

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

Numerical Differentiation with Finite Differences.
expect.utility2

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

Marginal Effect for Binary Outcome by G-computation.
fr.ratetable

Expected Mortality Rates of the General French Population
dataOFSEP

A Simulated Sample From the OFSEP Cohort.
dataSTR

Data for Second Kidney Transplant Recipients.
mixture.2states

Horizontal Mixture Model for Two Competing Events
metric

Metrics to Evaluate the Prognostic Capacities
ipw.survival

Adjusted Survival Curves by Using IPW.
lines.rocrisca

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

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

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

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

4-State Time-Inhomogeneous Markov Model
lrs.multistate

Likelihood Ratio Statistic to Compare Embedded Multistate Models
nn.time

Library of the Super Learner for Survival Neural Network
predict.nn.time

Prediction from a Survival Neural Network
predict.flexsurv

Prediction from an Flexible Parametric Model
predict.cox

Prediction from a Penalized Cox Regression
ph.exponential

Library of the Super Learner for an proportional hazards (PH) parametric model with an Exponential distribution
plot.survrisca

Plot Method for 'survrisca' Objects
ph.gompertz

Library of the Super Learner for an proportional hazards (PH) parametric model with a Gompertz distribution
plot.sl.time

Caliration Plot for Super Learner
plot.rocrisca

Plot Method for 'rocrisca' Objects
pred.mixture.2states

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

POsitivity-Regression Tree (PoRT) Algorithm to Identify Positivity Violations.
predict.rf.time

Prediction from a Suvival Random Forest Tree
roc.net

Net Time-Dependent ROC Curves With Right Censored Data.
rmst

Restricted Mean Survival Times.
roc.prognostic.aggregate

Prognostic ROC Curve Based on Survival Probabilities
roc.summary

Summary ROC Curve For Aggregated Data.
roc.binary

ROC Curves For Binary Outcomes.
roc.prognostic.individual

Prognostic ROC Curve based on Individual Data
predict.sl.time

Prediction from an Super Learner (SL) for Censored Outcomes
rf.time

Library of the Super Learner for Survival Random Forest Tree
print.sl.time

S3 method for Printing an 'sl.time' object
sl.time

Super Learner for Censored Outcomes
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.4states

4-State Semi-Markov Model
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
summary.sl.time

Summaries of a Super Learner
semi.markov.4states.rsadd

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

Summary Survival Curve And Comparison Between Strata.
tune.cox.aic

Tune cox step AIC with forward selection
tune.rf.time

Tune Survival Random Forest Tree
tune.cox.ridge

Tune Ridge Cox Regression
tune.nn.time

Tune a 1-Layer Survival Neural Network
tune.cox.lasso

Tune Lasso Cox Regression
semi.markov.3states

3-State Semi-Markov Model
tune.cox.en

Tune Elastic Net Cox Regression
roc.time

Time-Dependent ROC Curves With Right Censored Data.