DESCRIPTION

Package: jmpost
Title: Joint Models for Predicting Overall Survival Trajectories
Version: 0.0.1
Authors@R: c(
    person("Craig", "Gower-Page", email = "craig.gower-page@roche.com", role = c("aut", "cre")),
    person("Francois", "Mercier", email = "francois.mercier@roche.com", role = "aut"),
    person("Daniel", "Sabanes Bove", email = "daniel.sabanes_bove@roche.com", role = "aut"),
    person("Georgios", "Kazantzidis", email = "georgios.kazantzidis@roche.com", role = c("aut")),
    person("Isaac", "Gravestock", email = "isaac.gravestock@roche.com", role = "aut"),
    person("Xiaoyan", "Fang", email = "xiaoyan.fang@roche.com", role = "aut"),
    person("F. Hoffmann-La Roche AG", role = c("cph", "fnd"))
    )
Description: Implements joint models combining a non-linear mixed effects model for
    longitudinal measurements with a time-to-event model for the survival 
    outcome. The acronym 'jmpost' stands for Joint Models for Predicting 
    Overall Survival Trajectories, which refers to the application.
    In phase 1 studies patients are followed until progression only. 
    Thus, reliable overall survival data and hence estimates are not available. 
    However, we can use additional information from previous clinical trials 
    or real-world data - we can correlate the tumour response data, that are 
    longitudinal measurements, with the overall survival of the patients or their 
    hazard ratios. Thereby we can predict the overall survival from our phase 1 study
    data and therefore make better decisions.
License: Apache License (>= 2)
Encoding: UTF-8
Language: en-GB
URL: https://genentech.github.io/jmpost/
BugReports: https://github.com/Genentech/jmpost/issues
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
Depends:
    R (>= 4.1.0)
Imports:
    assertthat,
    Rdpack,
    checkmate,
    dplyr,
    stringr,
    ggplot2,
    ggplot2.utils,
    statmod,
    jinjar,
    survival,
    glue,
    tibble,
    methods,
    digest,
    posterior,
    stats
Suggests:
    cmdstanr,
    bayesplot,
    knitr,
    rmarkdown,
    rstan,
    testthat (>= 3.0.0),
    scales,
    lme4,
    flexsurv,
    purrr,
    vdiffr,
    prodlim,
    brms,
    tidyr,
    loo
Additional_repositories: https://stan-dev.r-universe.dev
Config/testthat/edition: 3
Config/testthat/parallel: true
Collate:
    'DataSubject.R'
    'utilities.R'
    'generics.R'
    'DataLongitudinal.R'
    'DataSurvival.R'
    'DataJoint.R'
    'Grid.R'
    'GridEven.R'
    'GridEvent.R'
    'GridFixed.R'
    'GridGrouped.R'
    'GridManual.R'
    'GridObserved.R'
    'GridPopulation.R'
    'GridPrediction.R'
    'constants.R'
    'StanModule.R'
    'Prior.R'
    'Parameter.R'
    'ParameterList.R'
    'StanModel.R'
    'LongitudinalModel.R'
    'LinkComponent.R'
    'Link.R'
    'SurvivalModel.R'
    'JointModel.R'
    'Quantities.R'
    'SurvivalQuantities.R'
    'JointModelSamples.R'
    'LongitudinalClaretBruno.R'
    'LongitudinalGSF.R'
    'LongitudinalQuantities.R'
    'LongitudinalRandomSlope.R'
    'LongitudinalSteinFojo.R'
    'Promise.R'
    'QuantityGeneratorPopulation.R'
    'QuantityGeneratorPrediction.R'
    'QuantityGeneratorSubject.R'
    'SimGroup.R'
    'SimJointData.R'
    'SimLongitudinal.R'
    'SimLongitudinalClaretBruno.R'
    'SimLongitudinalGSF.R'
    'SimLongitudinalRandomSlope.R'
    'SimLongitudinalSteinFojo.R'
    'SimSurvival.R'
    'SurvivalExponential.R'
    'SurvivalGamma.R'
    'SurvivalLoglogistic.R'
    'SurvivalWeibullPH.R'
    'brier_score.R'
    'defaults.R'
    'external-exports.R'
    'jmpost-package.R'
    'link_generics.R'
    'settings.R'
    'standalone-s3-register.R'
    'zzz.R'
VignetteBuilder: knitr
RdMacros: Rdpack