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simIDM (version 0.1.0)

Simulating Oncology Trials using an Illness-Death Model

Description

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) . 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.

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install.packages('simIDM')

Monthly Downloads

202

Version

0.1.0

License

Apache License 2.0

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Repository

https://github.com/insightsengineering/simIDM/

Maintainer

Alexandra Erdmann

Last Published

December 11th, 2023

Functions in simIDM (0.1.0)

OS Survival Function from Constant Transition Hazards

PFS Survival Function from Piecewise Constant Hazards

Quantile function for OS survival function induced by an illness-death model

PCWInversionMethod

Single Piecewise Exponentially Distributed Event Time

OS Survival Function from Piecewise Constant Hazards

Helper Function for survPFSOS()

assert_positive_number

Assertion for Positive Number

addStaggeredEntry

Staggered Study Entry

getCensoredData

Helper function for censoringByNumberEvents

avgHRIntegExpOS

Helper Function for avgHRExpOS()

OS Survival Function from Weibull Transition Hazards

getClinicalTrials

Simulation of a Large Number of Oncology Clinical Trials

assert_intervals

Assertion for vector describing intervals

Average OS Hazard Ratio from Constant Transition Hazards

PFS Survival Function from Constant Transition Hazards

Helper Function for Computing E(PFS^2)

Helper Function for Computing E(OS^2)

PFS Survival Function from Weibull Transition Hazards

censoringByNumberEvents

Event-driven censoring.

getDatasetWideFormat

Conversion of a Data Set from One Row per Transition to One Row per Patient

Helper Function for WeibSurvOS()

exponential_transition

Transition Hazards for Exponential Event Times

Correlation of PFS and OS event times for data from the IDM

Generate the Target Function for Optimization

Hazard Function for Different Transition Models

Cumulative Hazard for Piecewise Constant Hazards

Time-point by which a specified number of events occurred.

Helper Function for Adding Progress Bar to Trial Simulation

Correlation of PFS and OS event times for Different Transition Models

Empirical Significance for a List of Simulated Trials

Event Times Distributed as Sum of Weibull

getNumberEvents

Helper Function for trackEventsPerTrial

Estimate Parameters of the Multistate Model Using Clinical Trial Data

Piecewise Constant Hazard Values

getSimulatedData

Simulate Data Set from an Illness-Death Model

simIDM Package

Helper Function for log_p11()

singleExpQuantOS

Helper Function for Single Quantile for OS Survival Function

getOneClinicalTrial

Simulation of a Single Oncology Clinical Trial

piecewise_exponential

Transition Hazards for Piecewise Exponential Event Times

Probability of Remaining in Progression Between Two Time Points for Different Transition Models

Sum of Two Piecewise Constant Hazards

Helper function to conduct log-rank tests for either PFS or OS

Format Results of Parameter Estimation for Different Transition Models

Compute the Negative Log-Likelihood for a Given Data Set and Transition Model

Retrieve Initial Parameter Vectors for Likelihood Maximization

Number of recruited/censored/ongoing Patients.

getOneToTwoRows

Transitions from the Intermediate State to the Absorbing State

integrateVector

Helper for Efficient Integration

Preparation of a Data Set to Compute Log-likelihood

trackEventsPerTrial

Event tracking in an oncology trial.

Piecewise Exponentially Distributed Event Times

OS Survival Function for Different Transition Models

Log-Rank Test for a Single Trial

Survival Function of the Product PFS*OS for Different Transition Models

PFS Survival Function for Different Transition Models

Survival Function for Different Transition Models

weibull_transition

Transition Hazards for Weibull Distributed Event Times

Helper Function of PWCsurvOS()

OS Hazard Function from Constant Transition Hazards