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gestate (version 1.6.0)

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 stochastic estimation of these same properties. Thirdly, it provides parametric event prediction using blinded trial data, including creation of prediction intervals. Methods are based upon numerical integration and a flexible object-orientated structure for defining event, censoring and recruitment distributions (Curves).

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Version

Install

install.packages('gestate')

Monthly Downloads

274

Version

1.6.0

License

GPL-3

Maintainer

James Bell

Last Published

April 26th, 2023

Functions in gestate (1.6.0)

createRFfunction,Curve-method

Method for creating a random draw function from a Curve object
MixWei

Mixture Weibull Curve constructor function
createRFfunction

Method for creating a random draw function from a Curve object
Weibull

Weibull Curve constructor function
ZV2power

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

Analyse simulations of time-to-event data using arbitrary event, censoring and recruitment distributions.
RCurve-class

RCurve Class for defining recruitment distributions
PieceR

PieceR RCurve constructor function
PieceRMaxF

PieceR RCurve constructor function
PieceExponential

Piecewise Exponential Curve constructor function
event_prediction_prior

Event prediction using patient-level survival data, prior data and a recruitment RCurve
event_prediction_KM

Event prediction using a lifetable and a recruitment RCurve
evaluatePDFfunction

Method for evaluating the PDF function for a Curve object at x
event_prediction

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

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

Method for evaluating the inverse-CDF function for a Curve object at p
evaluateInvfunction

Method for evaluating the inverse-CDF function for a Curve object at p
getCDFfunction,Curve-method

Method for returning the CDF function for a Curve object
freedmanpower

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

Method for evaluating the PDF function for a Curve object at x
getAssessCDFfunction,RCurve-method

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

Method for evaluating the CDF function for a Curve object at q
events2power

Calculate Schoenfeld or Event Proportion power from number of events
create_tte_prior

Create an arbitrary prior data set from a specified Curve object
getAssessCDFfunction

Method for returning the CDF function for a RCurve object
getCDFfunction

Method for returning the CDF function for a Curve object
getN

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

Method for returning the total patient number from a RCurve
fit_KM

Fit Weibull, Log-Normal or Exponential survival curves to Kaplan Meier estimates
getNames

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

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

Method for returning the recruitment length from a RCurve
getLength

Method for returning the recruitment length from a RCurve
fit_tte_data_prior

Fit Weibull survival curves to patient-level time-to-event data by including patient-level weighted prior data
fit_tte_data

Fit Weibull, Log-Normal or Exponential survival curves to patient-level time-to-event data
getInvfunction,Curve-method

Method for returning the inverse-CDF function for a Curve object
getInvfunction

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

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

Method for returning a single parameter from a Curve object
getNactive

Method for returning the active arm patient number from a RCurve
getParam,Curve-method

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

Method for returning the RF function for a Curve object
getRFfunction

Method for returning the RF function for a Curve object
getMaxF

Method for returning maximum duration of patient follow-up from a RCurve
getNcontrol,RCurve-method

Method for returning the control arm patient number from a RCurve
getMaxF,RCurve-method

Method for returning maximum duration of patient follow-up from a RCurve
getPDFfunction

Method for returning the PDF function for a Curve object
getParamsV

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

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

Kaplan Meier Plot of Curve-Fit
getParamsV,Curve-method

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

Plot output from nph_traj
getPatients

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

Method for returning the PDF function for a Curve object
getParams

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

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

Calculate Frontier power from number of events
getType

Method for returning the Curve type
run_gestate

Load Shiny for Gestate Loads the Shiny interactive GUI for gestate
getPatients,RCurve-method

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

Method for returning the Curve type
random_draw

Method for taking random draws from a Curve object distribution
plotSF

Method for plotting the Survival Function of a Curve object
plot_ep

Plot event prediction output
show,RCurve-method

Method for displaying RCurve objects neatly - replaces standard show method
show,Curve-method

Method for displaying Curve objects neatly - replaces standard show method
getRatio,RCurve-method

Method for returning the recruitment ratio from a RCurve
nph_traj

Calculate analytic time-to-event trial properties under non-proportional hazards and complex assumptions
getRatio

Method for returning the recruitment ratio from a RCurve
plotRecruitment

Method for plotting the Recruitment Function of a RCurve object
power2events

Calculate Schoenfeld or Event Proportion based event numbers from power
random_draw,Curve-method

Method for taking random draws from a Curve object distribution
setPatients

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

Method for plotting the Survival Function of a Curve object
simulate_trials

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

Method for setting N's in an RCurve
simulate_trials_strata

Perform multi-strata 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
set_assess_time

Adjusts assessment time for simulations
plotCDF

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

Method for plotting the Recruitment Function of a RCurve object
set_event_number

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

Create lifetable quickly
summarise_analysis

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

Mixture Exponential Curve constructor function
Gompertz

Gompertz Curve constructor function
Lognormal

Log-normal Curve constructor function
GGamma

Generalised Gamma Curve constructor function
InstantR

InstantR RCurve constructor function
Exponential

Exponential Curve constructor function
LogLogistic

Log-logistic Curve constructor function
Blank

Blank Curve constructor function
LinearR

LinearR RCurve constructor function
Curve-class

Curve Class for defining distributions