R: Simulating Oncology Trials using an Illness-Death Model

# Simulating Oncology Trials using an Illness-Death Model

## Documentation for package ‘simIDM’ version 0.1.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS

## Help Pages

simIDM-package | 'simIDM' Package
addStaggeredEntry | Staggered Study Entry
assert_intervals | Assertion for vector describing intervals
assert_positive_number | Assertion for Positive Number
avgHRExpOS | Average OS Hazard Ratio from Constant Transition Hazards
avgHRIntegExpOS | Helper Function for 'avgHRExpOS()'
censoringByNumberEvents | Event-driven censoring.
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
empSignificant | Empirical Significance for a List of Simulated Trials
estimateParams | Estimate Parameters of the Multistate Model Using Clinical Trial Data
ExpHazOS | OS Hazard Function from Constant Transition Hazards
exponential_transition | Transition Hazards for Exponential Event Times
ExpQuantOS | Quantile function for OS survival function induced by an illness-death model
ExpSurvOS | OS Survival Function from Constant Transition Hazards
ExpSurvPFS | PFS Survival Function from Constant Transition Hazards
expvalOSInteg | Helper Function for Computing E(OS^2)
expvalPFSInteg | Helper Function for Computing E(PFS^2)
getCensoredData | Helper function for 'censoringByNumberEvents'
getClinicalTrials | Simulation of a Large Number of Oncology Clinical Trials
getDatasetWideFormat | Conversion of a Data Set from One Row per Transition to One Row per Patient
getEventsAll | Number of recruited/censored/ongoing Patients.
getInit | Retrieve Initial Parameter Vectors for Likelihood Maximization
getInit.ExponentialTransition | Retrieve Initial Parameter Vectors for Likelihood Maximization
getInit.WeibullTransition | Retrieve Initial Parameter Vectors for Likelihood Maximization
getNumberEvents | Helper Function for 'trackEventsPerTrial'
getOneClinicalTrial | Simulation of a Single Oncology Clinical Trial
getOneToTwoRows | Transitions from the Intermediate State to the Absorbing State
getPCWDistr | Piecewise Exponentially Distributed Event Times
getPWCHazard | Piecewise Constant Hazard Values
getResults | Format Results of Parameter Estimation for Different Transition Models
getResults.ExponentialTransition | Format Results of Parameter Estimation for Different Transition Models
getResults.WeibullTransition | Format Results of Parameter Estimation for Different Transition Models
getSimulatedData | Simulate Data Set from an Illness-Death Model
getSumPCW | Sum of Two Piecewise Constant Hazards
getTarget | Generate the Target Function for Optimization
getTarget.ExponentialTransition | Generate the Target Function for Optimization
getTarget.WeibullTransition | Generate the Target Function for Optimization
getTimePoint | Time-point by which a specified number of events occurred.
getWaitTimeSum | Event Times Distributed as Sum of Weibull
haz | Hazard Function for Different Transition Models
haz.ExponentialTransition | Hazard Function for Different Transition Models
haz.PWCTransition | Hazard Function for Different Transition Models
haz.WeibullTransition | Hazard Function for Different Transition Models
logRankTest | Log-Rank Test for a Single Trial
log_p11 | Probability of Remaining in Progression Between Two Time Points for Different Transition Models
negLogLik | Compute the Negative Log-Likelihood for a Given Data Set and Transition Model
PCWInversionMethod | Single Piecewise Exponentially Distributed Event Time
piecewise_exponential | Transition Hazards for Piecewise Exponential Event Times
prepareData | Preparation of a Data Set to Compute Log-likelihood
pwA | Cumulative Hazard for Piecewise Constant Hazards
PWCsurvOS | OS Survival Function from Piecewise Constant Hazards
PWCsurvPFS | PFS Survival Function from Piecewise Constant Hazards
simIDM | 'simIDM' Package
survOS | OS Survival Function for Different Transition Models
survOS.ExponentialTransition | OS Survival Function for Different Transition Models
survOS.PWCTransition | OS Survival Function for Different Transition Models
survOS.WeibullTransition | OS Survival Function for Different Transition Models
survPFS | PFS Survival Function for Different Transition Models
survPFS.ExponentialTransition | PFS Survival Function for Different Transition Models
survPFS.PWCTransition | PFS Survival Function for Different Transition Models
survPFS.WeibullTransition | PFS Survival Function for Different Transition Models
survPFSOS | Survival Function of the Product PFS*OS for Different Transition Models
survTrans | Survival Function for Different Transition Models
survTrans.ExponentialTransition | Survival Function for Different Transition Models
survTrans.WeibullTransition | Survival Function for Different Transition Models
trackEventsPerTrial | Event tracking in an oncology trial.
WeibSurvOS | OS Survival Function from Weibull Transition Hazards
WeibSurvPFS | PFS Survival Function from Weibull Transition Hazards
weibull_transition | Transition Hazards for Weibull Distributed Event Times