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  "Package": "simIDM",
  "Title": "Simulating Oncology Trials using an Illness-Death Model",
  "Version": "0.1.0",
  "Authors@R": "c(\nperson(\"Alexandra\", \"Erdmann\", , \"alexandra.erdmann@uni-ulm.de\", role = c(\"aut\", \"cre\")),\nperson(\"Kaspar\", \"Rufibach\", , \"kaspar.rufibach@roche.com\", role = \"aut\"),\nperson(\"Holger\", \"Löwe\", , \"hbj.loewe@gmail.com\", role = \"aut\"),\nperson(\"Daniel\", \"Sabanés Bové\", , \"daniel.sabanes_bove@roche.com\", role = \"aut\"),\nperson(\"F. Hoffmann-La Roche AG\", role = c(\"cph\", \"fnd\")),\nperson(\"University of Ulm\", role = c(\"cph\", \"fnd\"))\n)",
  "Description": "Based on the illness-death model a large number of\nclinical trials with oncology endpoints progression-free\nsurvival (PFS) and overall survival (OS) can be simulated, see\nMeller, Beyersmann and Rufibach (2019) <doi:10.1002/sim.8295>.\nThe simulation set-up allows for random and event-driven\ncensoring, an arbitrary number of treatment arms, staggered\nstudy entry and drop-out.  Exponentially, Weibull and piecewise\nexponentially distributed survival times can be generated. The\ncorrelation between PFS and OS can be calculated.",
  "License": "Apache License 2.0",
  "URL": "https://github.com/insightsengineering/simIDM/",
  "BugReports": "https://github.com/insightsengineering/simIDM/issues",
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  "Repository": "https://insightsengineering.r-universe.dev",
  "Date/Publication": "2023-12-11 09:17:38 UTC",
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    "User": "root"
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  "Author": "Alexandra Erdmann [aut, cre],\nKaspar Rufibach [aut],\nHolger Löwe [aut],\nDaniel Sabanés Bové [aut],\nF. Hoffmann-La Roche AG [cph, fnd],\nUniversity of Ulm [cph, fnd]",
  "Maintainer": "Alexandra Erdmann <alexandra.erdmann@uni-ulm.de>",
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  "_created": "2026-05-27T08:38:47.000Z",
  "_published": "2026-05-27T08:44:40.177Z",
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  "_exports": [
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    "assert_intervals",
    "assert_positive_number",
    "avgHRExpOS",
    "avgHRIntegExpOS",
    "censoringByNumberEvents",
    "corPFSOS",
    "corTrans",
    "empSignificant",
    "estimateParams",
    "ExpHazOS",
    "exponential_transition",
    "ExpQuantOS",
    "ExpSurvOS",
    "ExpSurvPFS",
    "expvalOSInteg",
    "expvalPFSInteg",
    "getCensoredData",
    "getClinicalTrials",
    "getDatasetWideFormat",
    "getEventsAll",
    "getInit",
    "getNumberEvents",
    "getOneClinicalTrial",
    "getOneToTwoRows",
    "getPCWDistr",
    "getPWCHazard",
    "getResults",
    "getSimulatedData",
    "getSumPCW",
    "getTarget",
    "getTimePoint",
    "getWaitTimeSum",
    "haz",
    "log_p11",
    "logRankTest",
    "negLogLik",
    "passedLogRank",
    "PCWInversionMethod",
    "piecewise_exponential",
    "prepareData",
    "pwA",
    "PWCsurvOS",
    "PWCsurvPFS",
    "survOS",
    "survPFS",
    "survPFSOS",
    "survTrans",
    "trackEventsPerTrial",
    "WeibSurvOS",
    "WeibSurvPFS",
    "weibull_transition"
  ],
  "_help": [
    {
      "page": "simIDM-package",
      "title": "'simIDM' Package",
      "topics": [
        "simIDM-package",
        "simIDM"
      ]
    },
    {
      "page": "addStaggeredEntry",
      "title": "Staggered Study Entry",
      "topics": [
        "addStaggeredEntry"
      ]
    },
    {
      "page": "assert_intervals",
      "title": "Assertion for vector describing intervals",
      "topics": [
        "assert_intervals"
      ]
    },
    {
      "page": "assert_positive_number",
      "title": "Assertion for Positive Number",
      "topics": [
        "assert_positive_number"
      ]
    },
    {
      "page": "avgHRExpOS",
      "title": "Average OS Hazard Ratio from Constant Transition Hazards",
      "topics": [
        "avgHRExpOS"
      ]
    },
    {
      "page": "avgHRIntegExpOS",
      "title": "Helper Function for 'avgHRExpOS()'",
      "topics": [
        "avgHRIntegExpOS"
      ]
    },
    {
      "page": "censoringByNumberEvents",
      "title": "Event-driven censoring.",
      "topics": [
        "censoringByNumberEvents"
      ]
    },
    {
      "page": "corPFSOS",
      "title": "Correlation of PFS and OS event times for data from the IDM",
      "topics": [
        "corPFSOS"
      ]
    },
    {
      "page": "corTrans",
      "title": "Correlation of PFS and OS event times for Different Transition Models",
      "topics": [
        "corTrans"
      ]
    },
    {
      "page": "empSignificant",
      "title": "Empirical Significance for a List of Simulated Trials",
      "topics": [
        "empSignificant"
      ]
    },
    {
      "page": "estimateParams",
      "title": "Estimate Parameters of the Multistate Model Using Clinical Trial Data",
      "topics": [
        "estimateParams"
      ]
    },
    {
      "page": "ExpHazOS",
      "title": "OS Hazard Function from Constant Transition Hazards",
      "topics": [
        "ExpHazOS"
      ]
    },
    {
      "page": "exponential_transition",
      "title": "Transition Hazards for Exponential Event Times",
      "topics": [
        "exponential_transition"
      ]
    },
    {
      "page": "ExpQuantOS",
      "title": "Quantile function for OS survival function induced by an illness-death model",
      "topics": [
        "ExpQuantOS"
      ]
    },
    {
      "page": "ExpSurvOS",
      "title": "OS Survival Function from Constant Transition Hazards",
      "topics": [
        "ExpSurvOS"
      ]
    },
    {
      "page": "ExpSurvPFS",
      "title": "PFS Survival Function from Constant Transition Hazards",
      "topics": [
        "ExpSurvPFS"
      ]
    },
    {
      "page": "expvalOSInteg",
      "title": "Helper Function for Computing E(OS^2)",
      "topics": [
        "expvalOSInteg"
      ]
    },
    {
      "page": "expvalPFSInteg",
      "title": "Helper Function for Computing E(PFS^2)",
      "topics": [
        "expvalPFSInteg"
      ]
    },
    {
      "page": "getCensoredData",
      "title": "Helper function for 'censoringByNumberEvents'",
      "topics": [
        "getCensoredData"
      ]
    },
    {
      "page": "getClinicalTrials",
      "title": "Simulation of a Large Number of Oncology Clinical Trials",
      "topics": [
        "getClinicalTrials"
      ]
    },
    {
      "page": "getDatasetWideFormat",
      "title": "Conversion of a Data Set from One Row per Transition to One Row per Patient",
      "topics": [
        "getDatasetWideFormat"
      ]
    },
    {
      "page": "getEventsAll",
      "title": "Number of recruited/censored/ongoing Patients.",
      "topics": [
        "getEventsAll"
      ]
    },
    {
      "page": "getInit",
      "title": "Retrieve Initial Parameter Vectors for Likelihood Maximization",
      "topics": [
        "getInit",
        "getInit.ExponentialTransition",
        "getInit.WeibullTransition"
      ]
    },
    {
      "page": "getNumberEvents",
      "title": "Helper Function for 'trackEventsPerTrial'",
      "topics": [
        "getNumberEvents"
      ]
    },
    {
      "page": "getOneClinicalTrial",
      "title": "Simulation of a Single Oncology Clinical Trial",
      "topics": [
        "getOneClinicalTrial"
      ]
    },
    {
      "page": "getOneToTwoRows",
      "title": "Transitions from the Intermediate State to the Absorbing State",
      "topics": [
        "getOneToTwoRows"
      ]
    },
    {
      "page": "getPCWDistr",
      "title": "Piecewise Exponentially Distributed Event Times",
      "topics": [
        "getPCWDistr"
      ]
    },
    {
      "page": "getPWCHazard",
      "title": "Piecewise Constant Hazard Values",
      "topics": [
        "getPWCHazard"
      ]
    },
    {
      "page": "getResults",
      "title": "Format Results of Parameter Estimation for Different Transition Models",
      "topics": [
        "getResults",
        "getResults.ExponentialTransition",
        "getResults.WeibullTransition"
      ]
    },
    {
      "page": "getSimulatedData",
      "title": "Simulate Data Set from an Illness-Death Model",
      "topics": [
        "getSimulatedData"
      ]
    },
    {
      "page": "getSumPCW",
      "title": "Sum of Two Piecewise Constant Hazards",
      "topics": [
        "getSumPCW"
      ]
    },
    {
      "page": "getTarget",
      "title": "Generate the Target Function for Optimization",
      "topics": [
        "getTarget",
        "getTarget.ExponentialTransition",
        "getTarget.WeibullTransition"
      ]
    },
    {
      "page": "getTimePoint",
      "title": "Time-point by which a specified number of events occurred.",
      "topics": [
        "getTimePoint"
      ]
    },
    {
      "page": "getWaitTimeSum",
      "title": "Event Times Distributed as Sum of Weibull",
      "topics": [
        "getWaitTimeSum"
      ]
    },
    {
      "page": "haz",
      "title": "Hazard Function for Different Transition Models",
      "topics": [
        "haz",
        "haz.ExponentialTransition",
        "haz.PWCTransition",
        "haz.WeibullTransition"
      ]
    },
    {
      "page": "log_p11",
      "title": "Probability of Remaining in Progression Between Two Time Points for Different Transition Models",
      "topics": [
        "log_p11"
      ]
    },
    {
      "page": "logRankTest",
      "title": "Log-Rank Test for a Single Trial",
      "topics": [
        "logRankTest"
      ]
    },
    {
      "page": "negLogLik",
      "title": "Compute the Negative Log-Likelihood for a Given Data Set and Transition Model",
      "topics": [
        "negLogLik"
      ]
    },
    {
      "page": "PCWInversionMethod",
      "title": "Single Piecewise Exponentially Distributed Event Time",
      "topics": [
        "PCWInversionMethod"
      ]
    },
    {
      "page": "piecewise_exponential",
      "title": "Transition Hazards for Piecewise Exponential Event Times",
      "topics": [
        "piecewise_exponential"
      ]
    },
    {
      "page": "prepareData",
      "title": "Preparation of a Data Set to Compute Log-likelihood",
      "topics": [
        "prepareData"
      ]
    },
    {
      "page": "pwA",
      "title": "Cumulative Hazard for Piecewise Constant Hazards",
      "topics": [
        "pwA"
      ]
    },
    {
      "page": "PWCsurvOS",
      "title": "OS Survival Function from Piecewise Constant Hazards",
      "topics": [
        "PWCsurvOS"
      ]
    },
    {
      "page": "PWCsurvPFS",
      "title": "PFS Survival Function from Piecewise Constant Hazards",
      "topics": [
        "PWCsurvPFS"
      ]
    },
    {
      "page": "survOS",
      "title": "OS Survival Function for Different Transition Models",
      "topics": [
        "survOS",
        "survOS.ExponentialTransition",
        "survOS.PWCTransition",
        "survOS.WeibullTransition"
      ]
    },
    {
      "page": "survPFS",
      "title": "PFS Survival Function for Different Transition Models",
      "topics": [
        "survPFS",
        "survPFS.ExponentialTransition",
        "survPFS.PWCTransition",
        "survPFS.WeibullTransition"
      ]
    },
    {
      "page": "survPFSOS",
      "title": "Survival Function of the Product PFS*OS for Different Transition Models",
      "topics": [
        "survPFSOS"
      ]
    },
    {
      "page": "survTrans",
      "title": "Survival Function for Different Transition Models",
      "topics": [
        "survTrans",
        "survTrans.ExponentialTransition",
        "survTrans.WeibullTransition"
      ]
    },
    {
      "page": "trackEventsPerTrial",
      "title": "Event tracking in an oncology trial.",
      "topics": [
        "trackEventsPerTrial"
      ]
    },
    {
      "page": "WeibSurvOS",
      "title": "OS Survival Function from Weibull Transition Hazards",
      "topics": [
        "WeibSurvOS"
      ]
    },
    {
      "page": "WeibSurvPFS",
      "title": "PFS Survival Function from Weibull Transition Hazards",
      "topics": [
        "WeibSurvPFS"
      ]
    },
    {
      "page": "weibull_transition",
      "title": "Transition Hazards for Weibull Distributed Event Times",
      "topics": [
        "weibull_transition"
      ]
    }
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      "filename": "correlation.html",
      "title": "Correlation between PFS and OS",
      "author": "Holger Löwe",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Cor(PFS, OS): Statistical Background",
        "Example: Computing Cor(PFS, OS) directly",
        "Estimating Cor(PFS, OS) from data",
        "Example: Estimating Cor(PFS, OS) from data",
        "References"
      ],
      "created": "2023-12-07 15:17:44",
      "modified": "2023-12-11 09:17:38",
      "commits": 3
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    {
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      "filename": "quickstart.html",
      "title": "Getting Started",
      "author": "Alexandra Erdmann",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Simulation Specifications",
        "Application",
        "Output Data",
        "References"
      ],
      "created": "2022-07-18 08:55:06",
      "modified": "2023-12-11 09:17:38",
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      "title": "Piecewise Constant Hazards Calculations",
      "author": "Daniel Sabanés Bové",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Overall survival calculation",
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      "created": "2023-12-07 16:01:10",
      "modified": "2023-12-11 09:17:38",
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    {
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      "filename": "trialplanning.html",
      "title": "Power and Type I Error Calculations",
      "author": "Alexandra Erdmann, Holger Löwe",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Scenario -  PFS and OS as Co-primary Endpoints",
        "Type I Error - Simulation Under $H_0$",
        "Sample size and power calculation - simulation under $H_1$",
        "References"
      ],
      "created": "2023-01-18 12:43:34",
      "modified": "2023-12-11 09:17:38",
      "commits": 11
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