Simulating Oncology Trials using an Illness-Death Model

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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