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gestate (version 1.3.2)

Generalised Survival Trial Assessment Tool Environment

Description

Provides tools to assist planning and monitoring of time-to-event trials under complicated censoring assumptions and/or non-proportional hazards. There are three main components: The first is analytic calculation of predicted time-to-event trial properties, providing estimates of expected hazard ratio, event numbers and power under different analysis methods. The second is simulation, allowing calculation of these same properties. Finally, it also provides parametric event prediction using blinded trial data, including creation of confidence intervals. Methods are based upon numerical integration and a flexible object-orientated structure for defining event, censoring and recruitment curves.

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Version

Install

install.packages('gestate')

Monthly Downloads

274

Version

1.3.2

License

GPL-3

Maintainer

James Bell

Last Published

April 26th, 2019

Functions in gestate (1.3.2)

analyse_sim

Analyse simulations of time-to-event data using arbitrary event, censoring and recruitment distributions.
createRFfunction,Curve-method

Method for running the RF function for a Curve object
createRFfunction

Method for running the RF function for a Curve object
getNactive,RCurve-method

Method for returning the active arm patient number from a RCurve
getAssessCDFfunction

Method for returning the CDF function for a RCurve object
getAssessCDFfunction,RCurve-method

Method for returning the CDF function for a RCurve object
getPatients

Method for calculating expected number of recruited patients at a given time from an RCurve
evaluateCDFfunction,Curve-method

Method for evaluating the CDF function for a Curve object at q
getPatients,RCurve-method

Method for calculating expected number of recruited patients at a given time from an RCurve
getNactive

Method for returning the active arm patient number from a RCurve
evaluateCDFfunction

Method for evaluating the CDF function for a Curve object at q
run_gestate

Load Shiny for Gestate Loads the Shiny interactive GUI for gestate
Curve-class

Curve Class for defining distributions
Weibull

Weibull Curve constructor function
getLength,RCurve-method

Method for returning the recruitment length from a RCurve
getLength

Method for returning the recruitment length from a RCurve
ZV2power

Calculate Normal distribution test power based on Effect size and Variance
PieceR

PieceR RCurve constructor function
RCurve-class

RCurve Class for defining recruitment distributions
event_prediction_KM

Event prediction using a lifetable and a recruitment RCurve
event_prediction

Event prediction using patient-level survival data and a recruitment RCurve
freedmanpower

Calculate Freedman power from number of events
getParam,Curve-method

Method for returning a single parameter from a Curve object
getParams,Curve-method

Method for returning all parameters from a Curve object as a list
getParams

Method for returning all parameters from a Curve object as a list
getRatio,RCurve-method

Method for returning the recruitment ratio from a RCurve
getRatio

Method for returning the recruitment ratio from a RCurve
plotRecruitment

Method for plotting the Recruitment Function of a RCurve object
plotSF,Curve-method

Method for plotting the Survival Function of a Curve object
set_event_number

Adjusts simulations so that administrative censoring occurs at a fixed event number, rather than a fixed time
getParam

Method for returning a single parameter from a Curve object
setPatients,RCurve-method

Method for setting N's in an RCurve
getCDFfunction,Curve-method

Method for returning the CDF function for a Curve object
show,RCurve-method

Method for displaying RCurve objects neatly - replaces standard show method
events2power

Calculate Schoenfeld or Event Proportion power from number of events
frontierpower

Calculate Frontier power from number of events
show,Curve-method

Method for displaying Curve objects neatly - replaces standard show method
nph_traj

Calculate analytic time-to-event trial properties under non-proportional hazards or other complex assumptions
simulate_trials

Perform simulations of time-to-event data using arbitrary event, censoring and recruitment distributions.
plotCDF,Curve-method

Method for plotting the CDF of a Curve object
plot_npht

Plot output from nph_traj
getNames,Curve-method

Method for returning all parameter names from a Curve object
getNcontrol,RCurve-method

Method for returning the control arm patient number from a RCurve
getNames

Method for returning all parameter names from a Curve object
getNcontrol

Method for returning the control arm patient number from a RCurve
power2events

Calculate Schoenfeld or Event Proportion based event numbers from power
getCDFfunction

Method for returning the CDF function for a Curve object
getRFfunction,Curve-method

Method for returning the RF function for a Curve object
getPDFfunction,Curve-method

Method for returning the PDF function for a Curve object
getRFfunction

Method for returning the RF function for a Curve object
getPDFfunction

Method for returning the PDF function for a Curve object
simulate_trials_strata

Perform multi-strata simulations of time-to-event data using arbitrary event, censoring and recruitment distributions.
summarise_analysis

Summarise analyses of simulations of time-to-event data using arbitrary event, censoring and recruitment distributions.
MixWei

Mixture Weibull Curve constructor function
PieceExponential

Piecewise Exponential Curve constructor function
fit_KM

Fit Weibull and Log-Normal survival curves to Kaplan Meier estimates
plotSF

Method for plotting the Survival Function of a Curve object
fit_tte_data

Fit Weibull and Log-Normal survival curves to patient-level time-to-event data
getN,RCurve-method

Method for returning the total patient number from a RCurve
plot_ep

Plot event prediction output
getN

Method for returning the total patient number from a RCurve
getParamsV,Curve-method

Method for returning all parameters from a Curve object as a vector
getParamsV

Method for returning all parameters from a Curve object as a vector
getType,Curve-method

Method for returning the Curve type
getType

Method for returning the Curve type
plotCDF

Method for plotting the CDF of a Curve object
plotRecruitment,RCurve-method

Method for plotting the Recruitment Function of a RCurve object
setPatients

Method for setting N's in an RCurve
set_assess_time

Adjusts assessment time for simulations
Lognormal

Log-normal Curve constructor function
LinearR

LinearR RCurve constructor function
Gompertz

Gompertz Curve constructor function
Exponential

Exponential Curve constructor function
MixExp

Mixture Exponential Curve constructor function
Blank

Blank Curve constructor function
InstantR

InstantR RCurve constructor function
LogLogistic

Log-logistic Curve constructor function
GGamma

Generalised Gamma Curve constructor function