Package: simIDM 0.1.0.9006

Alexandra Erdmann

simIDM: Simulating Oncology Trials using an Illness-Death Model

Based on the illness-death model a large number of clinical trials with oncology endpoints progression-free survival (PFS) and overall survival (OS) can be simulated, see Meller, Beyersmann and Rufibach (2019) <doi:10.1002/sim.8295>. The simulation set-up allows for random and event-driven censoring, an arbitrary number of treatment arms, staggered study entry and drop-out. Exponentially, Weibull and piecewise exponentially distributed survival times can be generated. The correlation between PFS and OS can be calculated.

Authors:Alexandra Erdmann [aut, cre], Kaspar Rufibach [aut], Holger Löwe [aut], Daniel Sabanés Bové [aut], F. Hoffmann-La Roche AG [cph, fnd], University of Ulm [cph, fnd]

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simIDM.pdf |simIDM.html✨
simIDM/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/insightsengineering/simidm/issues

On CRAN:

multistate-modelssimulation-engine

7.20 score 11 stars 9 scripts 179 downloads 52 exports 23 dependencies

Last updated 2 months agofrom:fc64d5d5ba. Checks:OK: 7. Indexed: no.

TargetResultDate
Doc / VignettesOKOct 16 2024
R-4.5-winOKOct 16 2024
R-4.5-linuxOKOct 16 2024
R-4.4-winOKOct 16 2024
R-4.4-macOKOct 16 2024
R-4.3-winOKOct 16 2024
R-4.3-macOKOct 16 2024

Exports:addStaggeredEntryassert_intervalsassert_positive_numberavgHRExpOSavgHRIntegExpOScensoringByNumberEventscorPFSOScorTransempSignificantestimateParamsExpHazOSexponential_transitionExpQuantOSExpSurvOSExpSurvPFSexpvalOSIntegexpvalPFSInteggetCensoredDatagetClinicalTrialsgetDatasetWideFormatgetEventsAllgetInitgetNumberEventsgetOneClinicalTrialgetOneToTwoRowsgetPCWDistrgetPWCHazardgetResultsgetSimulatedDatagetSumPCWgetTargetgetTimePointgetWaitTimeSumhazlog_p11logRankTestnegLogLikpassedLogRankPCWInversionMethodpiecewise_exponentialprepareDatapwAPWCsurvOSPWCsurvPFSsurvOSsurvPFSsurvPFSOSsurvTranstrackEventsPerTrialWeibSurvOSWeibSurvPFSweibull_transition

Dependencies:backportscheckmateclicodetoolsdata.tabledigestfurrrfutureglobalsgluelatticelifecyclelistenvmagrittrMatrixmstateparallellypurrrRColorBrewerrlangsurvivalvctrsviridisLite

Correlation between PFS and OS

Holger Löwe

Rendered fromcorrelation.Rmdusingknitr::rmarkdownon Oct 16 2024.

Last update: 2023-12-11
Started: 2023-12-07

Getting Started

Alexandra Erdmann

Rendered fromquickstart.Rmdusingknitr::rmarkdownon Oct 16 2024.

Last update: 2023-12-11
Started: 2022-07-18

Piecewise Constant Hazards Calculations

Daniel Sabanés Bové

Rendered frompwc_survival.Rmdusingknitr::rmarkdownon Oct 16 2024.

Last update: 2023-12-11
Started: 2023-12-07

Power and Type I Error Calculations

Alexandra Erdmann, Holger Löwe

Rendered fromtrialplanning.Rmdusingknitr::rmarkdownon Oct 16 2024.

Last update: 2024-01-10
Started: 2023-01-18

Readme and manuals

Help Manual

Help pageTopics
'simIDM' PackagesimIDM-package simIDM
Staggered Study EntryaddStaggeredEntry
Assertion for vector describing intervalsassert_intervals
Assertion for Positive Numberassert_positive_number
Average OS Hazard Ratio from Constant Transition HazardsavgHRExpOS
Helper Function for 'avgHRExpOS()'avgHRIntegExpOS
Event-driven censoring.censoringByNumberEvents
Correlation of PFS and OS event times for data from the IDMcorPFSOS
Correlation of PFS and OS event times for Different Transition ModelscorTrans
Empirical Significance for a List of Simulated TrialsempSignificant
Estimate Parameters of the Multistate Model Using Clinical Trial DataestimateParams
OS Hazard Function from Constant Transition HazardsExpHazOS
Transition Hazards for Exponential Event Timesexponential_transition
Quantile function for OS survival function induced by an illness-death modelExpQuantOS
OS Survival Function from Constant Transition HazardsExpSurvOS
PFS Survival Function from Constant Transition HazardsExpSurvPFS
Helper Function for Computing E(OS^2)expvalOSInteg
Helper Function for Computing E(PFS^2)expvalPFSInteg
Helper function for 'censoringByNumberEvents'getCensoredData
Simulation of a Large Number of Oncology Clinical TrialsgetClinicalTrials
Conversion of a Data Set from One Row per Transition to One Row per PatientgetDatasetWideFormat
Number of recruited/censored/ongoing Patients.getEventsAll
Retrieve Initial Parameter Vectors for Likelihood MaximizationgetInit getInit.ExponentialTransition getInit.WeibullTransition
Helper Function for 'trackEventsPerTrial'getNumberEvents
Simulation of a Single Oncology Clinical TrialgetOneClinicalTrial
Transitions from the Intermediate State to the Absorbing StategetOneToTwoRows
Piecewise Exponentially Distributed Event TimesgetPCWDistr
Piecewise Constant Hazard ValuesgetPWCHazard
Format Results of Parameter Estimation for Different Transition ModelsgetResults getResults.ExponentialTransition getResults.WeibullTransition
Simulate Data Set from an Illness-Death ModelgetSimulatedData
Sum of Two Piecewise Constant HazardsgetSumPCW
Generate the Target Function for OptimizationgetTarget getTarget.ExponentialTransition getTarget.WeibullTransition
Time-point by which a specified number of events occurred.getTimePoint
Event Times Distributed as Sum of WeibullgetWaitTimeSum
Hazard Function for Different Transition Modelshaz haz.ExponentialTransition haz.PWCTransition haz.WeibullTransition
Probability of Remaining in Progression Between Two Time Points for Different Transition Modelslog_p11
Log-Rank Test for a Single TriallogRankTest
Compute the Negative Log-Likelihood for a Given Data Set and Transition ModelnegLogLik
Single Piecewise Exponentially Distributed Event TimePCWInversionMethod
Transition Hazards for Piecewise Exponential Event Timespiecewise_exponential
Preparation of a Data Set to Compute Log-likelihoodprepareData
Cumulative Hazard for Piecewise Constant HazardspwA
OS Survival Function from Piecewise Constant HazardsPWCsurvOS
PFS Survival Function from Piecewise Constant HazardsPWCsurvPFS
OS Survival Function for Different Transition ModelssurvOS survOS.ExponentialTransition survOS.PWCTransition survOS.WeibullTransition
PFS Survival Function for Different Transition ModelssurvPFS survPFS.ExponentialTransition survPFS.PWCTransition survPFS.WeibullTransition
Survival Function of the Product PFS*OS for Different Transition ModelssurvPFSOS
Survival Function for Different Transition ModelssurvTrans survTrans.ExponentialTransition survTrans.WeibullTransition
Event tracking in an oncology trial.trackEventsPerTrial
OS Survival Function from Weibull Transition HazardsWeibSurvOS
PFS Survival Function from Weibull Transition HazardsWeibSurvPFS
Transition Hazards for Weibull Distributed Event Timesweibull_transition