Package: gestate 1.6.0

gestate: Generalised Survival Trial Assessment Tool Environment

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).

Authors:James Bell [aut, cre], Jasmin Ruehl [ctb]

gestate_1.6.0.tar.gz
gestate_1.6.0.zip(r-4.5)gestate_1.6.0.zip(r-4.4)gestate_1.6.0.zip(r-4.3)
gestate_1.6.0.tgz(r-4.4-any)gestate_1.6.0.tgz(r-4.3-any)
gestate_1.6.0.tar.gz(r-4.5-noble)gestate_1.6.0.tar.gz(r-4.4-noble)
gestate_1.6.0.tgz(r-4.4-emscripten)gestate_1.6.0.tgz(r-4.3-emscripten)
gestate.pdf |gestate.html
gestate/json (API)

# Install 'gestate' in R:
install.packages('gestate', repos = c('https://jamescbell.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

2.60 score 2 stars 8 scripts 281 downloads 61 exports 38 dependencies

Last updated 2 years agofrom:4eda0e9fcc. Checks:OK: 3 NOTE: 4. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 16 2024
R-4.5-winNOTENov 16 2024
R-4.5-linuxNOTENov 16 2024
R-4.4-winNOTENov 16 2024
R-4.4-macNOTENov 16 2024
R-4.3-winOKNov 16 2024
R-4.3-macOKNov 16 2024

Exports:analyse_simBlankcreate_tte_priorcreateRFfunctionevaluateCDFfunctionevaluateInvfunctionevaluatePDFfunctionevent_predictionevent_prediction_KMevent_prediction_priorExponentialfit_KMfit_tte_datafit_tte_data_priorfrontierpowergetAssessCDFfunctiongetCDFfunctiongetInvfunctiongetLengthgetMaxFgetNgetNactivegetNamesgetNcontrolgetParamgetParamsgetParamsVgetPatientsgetPDFfunctiongetRatiogetRFfunctiongetTypeGGammaGompertzInstantRLinearRLogLogisticLognormalMixExpMixWeinph_trajPieceExponentialPieceRPieceRMaxFplot_epplot_km_fitplot_nphtplotCDFplotRecruitmentplotSFrandom_drawrun_gestateset_assess_timeset_event_numbersetPatientsshowsimulate_trialssimulate_trials_stratasummarise_analysissurvfit_fastWeibull

Dependencies:base64encbslibcachemclicodetoolscommonmarkcrayondigestdoParallelfastmapfontawesomeforeachfsgluehtmltoolshttpuviteratorsjquerylibjsonlitelaterlatticelifecyclemagrittrMatrixmemoisemimepromisesR6rappdirsRcpprlangsassshinyshinythemessourcetoolssurvivalwithrxtable

Event Prediction with the gestate Package

Rendered fromevent_prediction.Rmdusingknitr::rmarkdownon Nov 16 2024.

Last update: 2023-04-26
Started: 2019-04-26

Planning Time-To-Event Trials with gestate

Rendered fromtrial_planning.Rmdusingknitr::rmarkdownon Nov 16 2024.

Last update: 2023-04-26
Started: 2019-04-26

Readme and manuals

Help Manual

Help pageTopics
Analyse simulations of time-to-event data using arbitrary event, censoring and recruitment distributions.analyse_sim
Blank Curve constructor functionBlank
Create an arbitrary prior data set from a specified Curve objectcreate_tte_prior
Method for creating a random draw function from a Curve objectcreateRFfunction
Method for creating a random draw function from a Curve objectcreateRFfunction,Curve-method
Curve Class for defining distributionsCurve-class
Method for evaluating the CDF function for a Curve object at qevaluateCDFfunction
Method for evaluating the CDF function for a Curve object at qevaluateCDFfunction,Curve-method
Method for evaluating the inverse-CDF function for a Curve object at pevaluateInvfunction
Method for evaluating the inverse-CDF function for a Curve object at pevaluateInvfunction,Curve-method
Method for evaluating the PDF function for a Curve object at xevaluatePDFfunction
Method for evaluating the PDF function for a Curve object at xevaluatePDFfunction,Curve-method
Event prediction using patient-level survival data and a recruitment RCurveevent_prediction
Event prediction using a lifetable and a recruitment RCurveevent_prediction_KM
Event prediction using patient-level survival data, prior data and a recruitment RCurveevent_prediction_prior
Exponential Curve constructor functionExponential
Fit Weibull, Log-Normal or Exponential survival curves to Kaplan Meier estimatesfit_KM
Fit Weibull, Log-Normal or Exponential survival curves to patient-level time-to-event datafit_tte_data
Fit Weibull survival curves to patient-level time-to-event data by including patient-level weighted prior datafit_tte_data_prior
Calculate Frontier power from number of eventsfrontierpower
Method for returning the CDF function for a RCurve objectgetAssessCDFfunction
Method for returning the CDF function for a RCurve objectgetAssessCDFfunction,RCurve-method
Method for returning the CDF function for a Curve objectgetCDFfunction
Method for returning the CDF function for a Curve objectgetCDFfunction,Curve-method
Method for returning the inverse-CDF function for a Curve objectgetInvfunction
Method for returning the inverse-CDF function for a Curve objectgetInvfunction,Curve-method
Method for returning the recruitment length from a RCurvegetLength
Method for returning the recruitment length from a RCurvegetLength,RCurve-method
Method for returning maximum duration of patient follow-up from a RCurvegetMaxF
Method for returning maximum duration of patient follow-up from a RCurvegetMaxF,RCurve-method
Method for returning the total patient number from a RCurvegetN
Method for returning the total patient number from a RCurvegetN,RCurve-method
Method for returning the active arm patient number from a RCurvegetNactive
Method for returning the active arm patient number from a RCurvegetNactive,RCurve-method
Method for returning all parameter names from a Curve objectgetNames
Method for returning all parameter names from a Curve objectgetNames,Curve-method
Method for returning the control arm patient number from a RCurvegetNcontrol
Method for returning the control arm patient number from a RCurvegetNcontrol,RCurve-method
Method for returning a single parameter from a Curve objectgetParam
Method for returning a single parameter from a Curve objectgetParam,Curve-method
Method for returning all parameters from a Curve object as a listgetParams
Method for returning all parameters from a Curve object as a listgetParams,Curve-method
Method for returning all parameters from a Curve object as a vectorgetParamsV
Method for returning all parameters from a Curve object as a vectorgetParamsV,Curve-method
Method for calculating expected number of recruited patients at a given time from an RCurvegetPatients
Method for calculating expected number of recruited patients at a given time from an RCurvegetPatients,RCurve-method
Method for returning the PDF function for a Curve objectgetPDFfunction
Method for returning the PDF function for a Curve objectgetPDFfunction,Curve-method
Method for returning the recruitment ratio from a RCurvegetRatio
Method for returning the recruitment ratio from a RCurvegetRatio,RCurve-method
Method for returning the RF function for a Curve objectgetRFfunction
Method for returning the RF function for a Curve objectgetRFfunction,Curve-method
Method for returning the Curve typegetType
Method for returning the Curve typegetType,Curve-method
Generalised Gamma Curve constructor functionGGamma
Gompertz Curve constructor functionGompertz
InstantR RCurve constructor functionInstantR
LinearR RCurve constructor functionLinearR
Log-logistic Curve constructor functionLogLogistic
Log-normal Curve constructor functionLognormal
Mixture Exponential Curve constructor functionMixExp
Mixture Weibull Curve constructor functionMixWei
Calculate analytic time-to-event trial properties under non-proportional hazards and complex assumptionsnph_traj
Piecewise Exponential Curve constructor functionPieceExponential
PieceR RCurve constructor functionPieceR
PieceR RCurve constructor functionPieceRMaxF
Plot event prediction outputplot_ep
Kaplan Meier Plot of Curve-Fitplot_km_fit
Plot output from nph_trajplot_npht
Method for plotting the CDF of a Curve objectplotCDF
Method for plotting the CDF of a Curve objectplotCDF,Curve-method
Method for plotting the Recruitment Function of a RCurve objectplotRecruitment
Method for plotting the Recruitment Function of a RCurve objectplotRecruitment,RCurve-method
Method for plotting the Survival Function of a Curve objectplotSF
Method for plotting the Survival Function of a Curve objectplotSF,Curve-method
Method for taking random draws from a Curve object distributionrandom_draw
Method for taking random draws from a Curve object distributionrandom_draw,Curve-method
RCurve Class for defining recruitment distributionsRCurve-class
Load Shiny for Gestate Loads the Shiny interactive GUI for gestaterun_gestate
Adjusts assessment time for simulationsset_assess_time
Adjusts simulations so that administrative censoring occurs at a fixed event number, rather than a fixed timeset_event_number
Method for setting N's in an RCurvesetPatients
Method for setting N's in an RCurvesetPatients,RCurve-method
Method for displaying Curve objects neatly - replaces standard show methodshow,Curve-method
Method for displaying RCurve objects neatly - replaces standard show methodshow,RCurve-method
Perform simulations of time-to-event data using arbitrary event, censoring and recruitment distributions.simulate_trials
Perform multi-strata simulations of time-to-event data using arbitrary event, censoring and recruitment distributions.simulate_trials_strata
Summarise analyses of simulations of time-to-event data using arbitrary event, censoring and recruitment distributions.summarise_analysis
Create lifetable quicklysurvfit_fast
Weibull Curve constructor functionWeibull