Package index • jmpost

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

SimSurvivalGamma(): Simulate Survival Data from a Gamma 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

SurvivalGamma(): SurvivalGamma

Link Specification

linkNone() linkTTG() linkDSLD() linkIdentity() linkGrowth() linkShrinkage(): Standard Links

Link(): Link

LinkComponent(): LinkComponent

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

LongitudinalRandomEffects(): Extract Random Effects Samples from a Longitudinal Model

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

populationHR(): Calculate Population Hazard Ratios

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

getRandomEffectsNames(): Get Random Effects Names

Convenience Functions

initialValues(): initialValues

merge(): merge

show: Printing of Different Classes

as_stan_list(): as_stan_list

as.CmdStanMCMC.JointModelSamples(): 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(<RandomEffectQuantities>) 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

summary(<RandomEffectQuantities>): summary

as.data.frame(<RandomEffectQuantities>): RandomEffectQuantities -> 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

saveObject(): Save Object to File

saveObject(<JointModelSamples>): Save a JointModelSamples object to a file.

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