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Package

jmpost jmpost-package
jmpost: Joint Models for Predicting Overall Survival Trajectories
set_options()
jmpost settings

Data Specification

DataJoint()
Joint Data Object and Constructor Function
DataSubject()
Subject Data Object and Constructor Function
DataLongitudinal()
Longitudinal Data Object and Constructor Function
DataSurvival()
Survival Data Object and Constructor Function

Data Simulation

SimJointData()
Simulating Joint Longitudinal and Time-to-Event Data
SimLongitudinal()
Abstract Simulation Class for Longitudinal Data
SimLongitudinalGSF()
Simulate Longitudinal Data from a GSF Model
SimLongitudinalSteinFojo()
Simulate Longitudinal Data from a Stein-Fojo Model
SimLongitudinalClaretBruno()
Simulate Longitudinal Data from a Claret-Bruno Model
SimLongitudinalRandomSlope()
Simulate Longitudinal Data from a Random Slope Model
SimSurvival()
Abstract Simulation Class for Survival Data
SimSurvivalLogLogistic()
Simulate Survival Data from a Log-Logistic Proportional Hazard Model
SimSurvivalExponential()
Simulate Survival Data from a Exponential Proportional Hazard Model
SimSurvivalWeibullPH()
Simulate Survival Data from a Weibull Proportional Hazard Model
SimGroup()
Define Simulation Group

Prior Distributions

Prior()
Prior Object and Constructor Function
prior_beta()
Beta Prior Distribution
prior_cauchy()
Cauchy Prior Distribution
prior_gamma()
Gamma Prior Distribution
prior_invgamma()
Inverse-Gamma Prior Distribution
prior_logistic()
Logistic Prior Distribution
prior_loglogistic()
Log-Logistic Prior Distribution
prior_lognormal()
Log-Normal Prior Distribution
prior_normal()
Normal Prior Distribution
prior_uniform()
Uniform Prior Distribution
prior_std_normal()
Standard Normal Prior Distribution
prior_student_t()
Student-t Prior Distribution
prior_init_only()
Initial Values Specification

Longitudinal Model Specification

LongitudinalRandomSlope()
LongitudinalRandomSlope
LongitudinalGSF()
LongitudinalGSF
LongitudinalSteinFojo()
LongitudinalSteinFojo
LongitudinalClaretBruno()
LongitudinalClaretBruno
LongitudinalModel()
LongitudinalModel

Survival Model Specification

SurvivalExponential()
SurvivalExponential
SurvivalLogLogistic()
SurvivalLogLogistic
SurvivalModel()
SurvivalModel
SurvivalWeibullPH()
SurvivalWeibullPH

Joint Model Specification

JointModel()
Joint Model Object and Constructor Function

Joint Model Fitting

compileStanModel()
compileStanModel
sampleStanModel()
sampleStanModel

Postprocessing

JointModelSamples-class .JointModelSamples JointModelSamples
JointModelSamples
LongitudinalQuantities()
LongitudinalQuantities Object & Constructor Function
SurvivalQuantities()
SurvivalQuantities Object & Constructor Function
generateQuantities()
generateQuantities
GridEven() GridEvent() GridFixed() GridGrouped() GridManual() GridObserved() GridPopulation() GridPrediction()
Quantity Grid Specification
summary(<LongitudinalQuantities>)
summary
summary(<SurvivalQuantities>)
summary
autoplot
Create a complete ggplot appropriate to a particular data type
autoplot(<LongitudinalQuantities>)
Automatic Plotting for LongitudinalQuantities
autoplot(<SurvivalQuantities>)
Automatic Plotting for `SurvivalQuantities``
brierScore()
brierScore
brierScore(<SurvivalQuantities>)
brierScore

Stan Code

Parameter()
Parameter
names(<Parameter>) initialValues(<Parameter>) size(<Parameter>)
Parameter Getter Functions
ParameterList()
ParameterList
names(<ParameterList>) initialValues(<ParameterList>) size(<ParameterList>)
Parameter-List Getter Functions
initialValues(<Prior>)
Prior Getter Functions
read_stan()
Stan Code as Character
StanModel()
Stan Model Object and Constructor Function
StanModule()
StanModule Object and Constructor Function
write_stan()
write_stan
getParameters()
getParameters

Convenience Functions

initialValues()
initialValues
merge()
merge
show
Printing of Different Classes
as_stan_list()
as_stan_list
as.CmdStanMCMC()
Coerce to CmdStanMCMC
as.character(<JointModel>)
JointModel -> character
as.StanModule(<Parameter>)
Parameter -> StanModule
as.StanModule(<ParameterList>)
ParameterList -> StanModule
as.StanModule(<Prior>)
Prior -> StanModule
as.StanModule(<JointModel>)
JointModel -> StanModule
as.StanModule(<Link>)
Link -> StanModule
as.StanModule(<LinkComponent>)
LinkComponent -> StanModule
as.StanModule(<JointModelSamples>)
JointModelSamples -> StanModule
as.character(<Parameter>)
Parameter -> Character
as.character(<Prior>)
Prior -> Character
show(<DataSubject>) show(<DataLongitudinal>) show(<DataSurvival>) show(<DataJoint>) show(<StanModule>) show(<Prior>) show(<Parameter>) show(<ParameterList>) show(<StanModel>) show(<LinkComponent>) show(<Link>) show(<JointModel>) show(<Quantities>) show(<SurvivalQuantities>) show(<JointModelSamples>) show(<LongitudinalQuantities>) show(<SimJointData>) show(<SimLongitudinal>) show(<SimSurvival>)
Show an Object
as_stan_list(<Parameter>)
Parameter -> list
as_stan_list(<ParameterList>)
ParameterList -> list
as_stan_list(<Prior>)
Prior -> list
as.character(<StanModule>)
StanModule -> character
as.data.frame(<DataSubject>)
DataSubject -> data.frame
as.data.frame(<DataLongitudinal>)
DataLongitudinal -> data.frame
as.data.frame(<DataSurvival>)
DataSurvival -> data.frame
as.data.frame(<LongitudinalQuantities>)
as.data.frame
as.data.frame(<SurvivalQuantities>)
as.data.frame
as_stan_list(<DataSubject>) as.list(<DataSubject>) as_stan_list(<DataLongitudinal>) as.list(<DataLongitudinal>) as_stan_list(<DataSurvival>) as.list(<DataSurvival>) as_stan_list(<DataJoint>) as.list(<DataJoint>)
Data Object -> list
as.list(<ParameterList>)
ParameterList -> list
as.list(<StanModel>)
StanModel -> list
as.list(<StanModule>)
StanModule -> list
as.list(<Link>)
Link -> list
as.list(<LinkComponent>)
LinkComponent -> list
length(<Link>)
Link -> list
subset(<DataJoint>)
Subsetting DataJoint as a data.frame
extractVariableNames(<DataLongitudinal>)
Extract Mapping to Standardised Variable Names
hazardWindows()
Generate time windows for evaluating a hazard function
sampleObservations()
Generate Simulated Observations
sampleSubjects()
Generate Simulated Subjects
enableLink()
Enable Link Generic
enableGQ()
Enable Generated Quantities Generic
as_formula()
As Formula
getPredictionNames()
Get Prediction Names
set_limits()
Set Constraints

Promises

Promise-class .Promise Promise
Promise
PromiseLinkComponent()
Promise of a LinkComponent
PromiseLongitudinalModel()
Promise of a LongitudinalModel
resolvePromise()
Resolve a Promise
resolvePromise(<Link>)
Resolve any promises
resolvePromise(<PromiseLinkComponent>)
Resolve a PromiseLinkComponent

Miscellaneous

STAN_BLOCKS
List of Stan Blocks