Package: RISCA 1.0.5

RISCA: Causal Inference and Prediction in Cohort-Based Analyses

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.

Authors:Yohann Foucher [aut, cre], Florent Le Borgne [aut], Arthur Chatton [aut]

RISCA_1.0.5.tar.gz
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RISCA.pdf |RISCA.html✨
RISCA/json (API)

# Install 'RISCA' in R:
install.packages('RISCA', repos = c('https://foucher-y.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/foucher-y/risca/issues

Datasets:
  • dataCSL - CSL Liver Chirrosis Data.
  • dataDIVAT1 - A First Sample From The DIVAT Data Bank.
  • dataDIVAT2 - A Second Sample From the DIVAT Data Bank.
  • dataDIVAT3 - A Third Sample From the DIVAT Data Bank.
  • dataDIVAT4 - A Fourth 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.
  • dataHepatology - The Data Extracted From The Meta-Analysis By Cabibbo et al. (2010).
  • dataKTFS - A Sixth Sample Of The DIVAT Cohort.
  • dataKi67 - The Aggregated Data Published By de Azambuja et al. (2007).
  • dataOFSEP - A Simulated Sample From the OFSEP Cohort.
  • dataSTR - Data for Second Kidney Transplant Recipients.
  • fr.ratetable - Expected Mortality Rates of the General French Population

On CRAN:

31 exports 1.54 score 181 dependencies 3 mentions 24 scripts 494 downloads

Last updated 5 months agofrom:b17b78ab87. Checks:OK: 1 WARNING: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 09 2024
R-4.5-winWARNINGSep 09 2024
R-4.5-linuxWARNINGSep 09 2024
R-4.4-winWARNINGSep 09 2024
R-4.4-macWARNINGSep 09 2024
R-4.3-winWARNINGSep 09 2024
R-4.3-macWARNINGSep 09 2024

Exports:aucexpect.utility1expect.utility2gc.logisticgc.sl.binarygc.survivalipw.log.rankipw.survivallrs.multistatemarkov.3statesmarkov.3states.rsaddmarkov.4statesmarkov.4states.rsaddmixture.2statesportpred.mixture.2statesrmstroc.binaryroc.netroc.prognostic.aggregateroc.prognostic.individualroc.summaryroc.timesemi.markov.3statessemi.markov.3states.icsemi.markov.3states.rsaddsemi.markov.4statessemi.markov.4states.rsaddsurvival.mrsurvival.summarysurvival.summary.strata

Dependencies:backportsbase64encbitbit64bitopsbslibcachemcaretcaToolscheckmateclassclicliprclockclustercmprskcodetoolscolorspacecpp11crayoncubaturecvAUCdata.tabledatediagramdialsDiceDesigndigestdoFuturedoParalleldplyre1071evaluatefansifarverfastmapfontawesomeforcatsforeachforeignFormulafsfurrrfuturefuture.applygamgenericsggformulaggplot2ggridgesglmnetglobalsgluegowerGPfitgplotsgridExtragtablegtoolshardhathavenherehighrHmischmshtmlTablehtmltoolshtmlwidgetsipredisobanditeratorsjquerylibjsonlitekernlabKernSmoothknitrlabelinglabelledlatticelavalazyevallhslifecyclelistenvlubridatemagrittrMASSMatrixMatrixModelsmemoisemetsmgcvmimemodelenvModelMetricsmosaicmosaicCoremosaicDatamultcompmunsellmvtnormnlmennetnnlsnumDerivpammtoolsparallellyparsnippecpillarpkgconfigplotrixplyrpngpolsplineprettyunitspROCprodlimprogressprogressrproxyPublishpurrrquantregR6rangerrappdirsRColorBrewerRcppRcppArmadilloRcppEigenRcppTOMLreadrrecipesrelsurvreshape2reticulateriskRegressionrlangrmarkdownrmsROCRrpartrprojrootrsamplerstudioapisandwichsassscalessfdshapesliderSparseMSQUAREMstatmodstringistringrSuperLearnersurvivalTH.datatibbletidyrtidyselecttimechangetimeDatetimeregtinytextunetzdbutf8vctrsviridisviridisLitevroomwarpwithrworkflowsxfunyamlyardstickzoo

Readme and manuals

Help Manual

Help pageTopics
Area Under ROC Curve From Sensitivities And Specificities.auc
CSL Liver Chirrosis Data.dataCSL
A First Sample From The DIVAT Data Bank.dataDIVAT1
A Second Sample From the DIVAT Data Bank.dataDIVAT2
A Third Sample From the DIVAT Data Bank.dataDIVAT3
A Fourth Sample From the DIVAT Data Bank.dataDIVAT4
The Aggregated Kidney Graft Survival Stratified By The 1-year Serum Creatinine.dataDIVAT5
Data for First Kidney Transplant Recipients.dataFTR
The Data Extracted From The Meta-Analysis By Cabibbo et al. (2010).dataHepatology
The Aggregated Data Published By de Azambuja et al. (2007).dataKi67
A Sixth Sample Of The DIVAT Cohort.dataKTFS
A Simulated Sample From the OFSEP Cohort.dataOFSEP
Data for Second Kidney Transplant Recipients.dataSTR
Cut-Off Estimation Of A Prognostic Marker (Only One Observed Group).expect.utility1
Cut-Off Estimation Of A Prognostic Marker (Two Groups Are observed).expect.utility2
Expected Mortality Rates of the General French Populationfr.ratetable
Marginal Effect for Binary Outcome by G-computation.gc.logistic
Marginal Effect for Binary Outcome by Super Learned G-computation.gc.sl.binary
Marginal Effect for Censored Outcome by G-computation with a Cox Regression for the Outcome Model.gc.survival
Log-Rank Test for Adjusted Survival Curves.ipw.log.rank
Adjusted Survival Curves by Using IPW.ipw.survival
Add Lines to a ROC Plotlines.rocrisca
Likelihood Ratio Statistic to Compare Embedded Multistate Modelslrs.multistate
3-State Time-Inhomogeneous Markov Modelmarkov.3states
3-state Relative Survival Markov Model with Additive Risksmarkov.3states.rsadd
4-State Time-Inhomogeneous Markov Modelmarkov.4states
4-state Relative Survival Markov Model with Additive Risksmarkov.4states.rsadd
Horizontal Mixture Model for Two Competing Eventsmixture.2states
Plot Method for 'rocrisca' Objectsplot.rocrisca
Plot Method for 'survrisca' Objectsplot.survrisca
POsitivity-Regression Tree (PoRT) Algorithm to Identify Positivity Violations.port
Cumulative Incidence Function Form Horizontal Mixture Model With Two Competing Eventspred.mixture.2states
Restricted Mean Survival Times.rmst
ROC Curves For Binary Outcomes.roc.binary
Net Time-Dependent ROC Curves With Right Censored Data.roc.net
Prognostic ROC Curve Based on Survival Probabilitiesroc.prognostic.aggregate
Prognostic ROC Curve based on Individual Dataroc.prognostic.individual
Summary ROC Curve For Aggregated Data.roc.summary
Time-Dependent ROC Curves With Right Censored Data.roc.time
3-State Semi-Markov Modelsemi.markov.3states
3-State Semi-Markov Model With Interval-Censored Datasemi.markov.3states.ic
3-State Relative Survival Semi-Markov Model With Additive Riskssemi.markov.3states.rsadd
4-State Semi-Markov Modelsemi.markov.4states
4-State Relative Survival Semi-Markov Model With Additive Riskssemi.markov.4states.rsadd
Multiplicative-Regression Model to Compare the Risk Factors Between Two Reference and Relative Populationssurvival.mr
Summary Survival Curve From Aggregated Datasurvival.summary
Summary Survival Curve And Comparison Between Strata.survival.summary.strata