Learn R Programming

⚠️There's a newer version (1.0.7) of this package.Take me there.

RISCA (version 1.0.3)

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.

Copy Link

Version

Install

install.packages('RISCA')

Monthly Downloads

430

Version

1.0.3

License

GPL (>= 2)

Maintainer

Yohann Foucher

Last Published

November 21st, 2022

Functions in RISCA (1.0.3)

auc

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

Library of the Super Learner for Lasso Cox Regression
aft.gamma

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

Library of the Super Learner for Ridge Cox Regression
aft.llogis

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

Library of the Super Learner for Cox univariate significant model
dataDIVAT3

A Third Sample From the DIVAT Data Bank.
dataCSL

CSL Liver Chirrosis Data.
dataHepatology

The Data Extracted From The Meta-Analysis By Cabibbo et al. (2010).
dataDIVAT1

A First Sample From The DIVAT Data Bank.
dataDIVAT4

A Fourth Sample From the DIVAT Data Bank.
dataDIVAT2

A Second Sample From the DIVAT Data Bank.
dataFTR

Data for First Kidney Transplant Recipients.
dataKi67

The Aggregated Data Published By de Azambuja et al. (2007).
dataDIVAT5

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

A Sixth Sample Of The DIVAT Cohort.
dataOFSEP

A Simulated Sample From the OFSEP Cohort.
expect.utility2

Cut-Off Estimation Of A Prognostic Marker (Two Groups Are observed).
expect.utility1

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

Numerical Differentiation with Finite Differences.
gc.logistic

Marginal Effect for Binary Outcome by G-computation.
gc.sl.binary

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

Expected Mortality Rates of the General French Population
dataSTR

Data for Second Kidney Transplant Recipients.
gc.sl.time

Marginal Effect for Censored Outcome by G-computation with a Super Learner for the Outcome Model.
gc.survival

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

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

3-State Time-Inhomogeneous Markov Model
lines.rocrisca

Add Lines to a ROC Plot
ipw.log.rank

Log-Rank Test for Adjusted Survival Curves.
markov.3states.rsadd

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

4-state Relative Survival Markov Model with Additive Risks
hr.sl.time

Conditionnal Effect for Censored Outcome with a Super Learner for the Outcome Model.
ipw.survival

Adjusted Survival Curves by Using IPW.
metric

Metrics to Evaluate the Prognostic Capacities
markov.4states

4-State Time-Inhomogeneous Markov Model
predict.cox

Prediction from a Penalized Cox Regression
plot.sl.time

Caliration Plot for Super Learner
plot.rocrisca

Plot Method for 'rocrisca' Objects
plot.survrisca

Plot Method for 'survrisca' Objects
port

POsitivity-Regression Tree (PoRT) Algorithm to Identify Positivity Violations.
ph.exponential

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

Prediction from an Flexible Parametric Model
nnet.time

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

Horizontal Mixture Model for Two Competing Events
ph.gompertz

Library of the Super Learner for an proportional hazards (PH) parametric model with a Gompertz distribution
rmst

Restricted Mean Survival Times.
rf.time

Library of the Super Learner for Survival Random Forest Tree
roc.binary

ROC Curves For Binary Outcomes.
roc.net

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

Prognostic ROC Curve Based on Survival Probabilities
roc.prognostic.individual

Prognostic ROC Curve based on Individual Data
pred.mixture.2states

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

Prediction from a Suvival Random Forest Tree
predict.nnet.time

Prediction from a Survival Neural Network
predict.sl.time

Prediction from an Super Learner (SL) for Censored Outcomes
survival.mr

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

Summary ROC Curve For Aggregated Data.
semi.markov.4states

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

Summaries of a Super Learner
semi.markov.3states.rsadd

3-State Relative Survival Semi-Markov Model With Additive Risks
sl.time

Super Learner for Censored Outcomes
semi.markov.3states.ic

3-State Semi-Markov Model With Interval-Censored Data
tune.cox.en

Tune Elastic Net Cox Regression
semi.markov.3states

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

Tune a 1-Layer Survival Neural Network
roc.time

Time-Dependent ROC Curves With Right Censored Data.
tune.rf.time

Tune Survival Random Forest Tree
tune.cox.aic

Tune cox step AIC with forward selection
survival.summary

Summary Survival Curve From Aggregated Data
tune.cox.ridge

Tune Ridge Cox Regression
survival.summary.strata

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

Tune Lasso Cox Regression
semi.markov.4states.rsadd

4-State Relative Survival Semi-Markov Model With Additive Risks