Package index • simIDM

Package

simIDM simIDM-package: simIDM Package

Assertions

assert_positive_number(): Assertion for Positive Number

assert_intervals(): Assertion for vector describing intervals

Transition parameters

exponential_transition(): Transition Hazards for Exponential Event Times

piecewise_exponential(): Transition Hazards for Piecewise Exponential Event Times

weibull_transition(): Transition Hazards for Weibull Distributed Event Times

Helper functions for piecewise or Weibull Hazards

getPWCHazard(): Piecewise Constant Hazard Values

getSumPCW(): Sum of Two Piecewise Constant Hazards

getPCWDistr(): Piecewise Exponentially Distributed Event Times

PCWInversionMethod(): Single Piecewise Exponentially Distributed Event Time

getWaitTimeSum(): Event Times Distributed as Sum of Weibull

Simulation of a single data set for a single treatment arm

getSimulatedData(): Simulate Data Set from an Illness-Death Model

getOneToTwoRows(): Transitions from the Intermediate State to the Absorbing State

addStaggeredEntry(): Staggered Study Entry

Simulation of a large number of clinical trials

getOneClinicalTrial(): Simulation of a Single Oncology Clinical Trial

getDatasetWideFormat(): Conversion of a Data Set from One Row per Transition to One Row per Patient

getClinicalTrials(): Simulation of a Large Number of Oncology Clinical Trials

Event tracking

getTimePoint(): Time-point by which a specified number of events occurred.

getCensoredData(): Helper function for censoringByNumberEvents

censoringByNumberEvents(): Event-driven censoring.

getEventsAll(): Number of recruited/censored/ongoing Patients.

getNumberEvents(): Helper Function for trackEventsPerTrial

trackEventsPerTrial(): Event tracking in an oncology trial.

Survival functions

ExpSurvPFS(): PFS Survival Function from Constant Transition Hazards

ExpSurvOS(): OS Survival Function from Constant Transition Hazards

ExpQuantOS(): Quantile function for OS survival function induced by an illness-death model

WeibSurvPFS(): PFS Survival Function from Weibull Transition Hazards

WeibSurvOS(): OS Survival Function from Weibull Transition Hazards

pwA(): Cumulative Hazard for Piecewise Constant Hazards

PWCsurvPFS(): PFS Survival Function from Piecewise Constant Hazards

PWCsurvOS(): OS Survival Function from Piecewise Constant Hazards

Hazard functions

ExpHazOS(): OS Hazard Function from Constant Transition Hazards

avgHRIntegExpOS(): Helper Function for avgHRExpOS()

avgHRExpOS(): Average OS Hazard Ratio from Constant Transition Hazards

Empirical significance

logRankTest(): Log-Rank Test for a Single Trial

empSignificant(): Empirical Significance for a List of Simulated Trials

Parameter Estimation

estimateParams(): Estimate Parameters of the Multistate Model Using Clinical Trial Data

getInit(): Retrieve Initial Parameter Vectors for Likelihood Maximization

getResults(): Format Results of Parameter Estimation for Different Transition Models

getTarget(): Generate the Target Function for Optimization

prepareData(): Preparation of a Data Set to Compute Log-likelihood

Likelihood

haz(): Hazard Function for Different Transition Models

survTrans(): Survival Function for Different Transition Models

negLogLik(): Compute the Negative Log-Likelihood for a Given Data Set and Transition Model

PFS-OS Correlation

corPFSOS(): Correlation of PFS and OS event times for data from the IDM

corTrans(): Correlation of PFS and OS event times for Different Transition Models

expvalPFSInteg(): Helper Function for Computing E(PFS^2)

expvalOSInteg(): Helper Function for Computing E(OS^2)

log_p11(): Probability of Remaining in Progression Between Two Time Points for Different Transition Models

survPFS(): PFS Survival Function for Different Transition Models

survPFSOS(): Survival Function of the Product PFS*OS for Different Transition Models

survOS(): OS Survival Function for Different Transition Models