SimpleStudyProgressionGraph: Create a 'ProgressionGraph' describing a simple disease...

In scientific-computing-solutions/badminton: Simulation of Continuous-Time Discrete-Space Markov Chains

Description

This function creates the transition state graph for clinical trials with arbitrary number of arms, disease progression states and crossovers, returning an object of type ProgressionGraph. The disease progression and possible transitions must be the same for each arm and no drop out state is included.

Usage

SimpleStudyProgressionGraph(arms, armProgression, edges = "immediate",
  crossOvers = NULL, visitSchedule = NULL, isVisitNode = FALSE)

Arguments

arms	a vector of arm names
armProgression	a vector of states subjects experience for example "progressing", "progressed". This vector should not include the "death" state
edges	determines which edges are to be added for arm must be one of "none","immediate","death","all". none: no edges added immediate: must progress sequentially through all states death: must progress sequentially through all states or go straight to death all: can jump straight to any state (always progressing towards death)
crossOvers	a vector containing additional transitions of the form c("fromnode1","tonode1","fromnode2","tonode2")
visitSchedule	Either a VisitSchedule object which is the visit schedule to be used for the nodes of this Progression Graph or NULL if no visit schedule is being used (or visit Schedule is to be added later). Note the node 'death' will have the same visit schedule, which should not cause problems.
isVisitNode	A logical value. Are the nodes ‘visit’ nodes, i.e. node for which the transition into it is unknown until the next visit. If TRUE then all nodes in the graph are visit nodes, if false then none are. The function SetIsVisitNode.ProgressionGraph can be used to change the isVisitNode status of individual nodes

Details

If more complicated disease progression transitions are required then this function can be used in conjunction with AddArm.ProgressionGraph, AddEdge.ProgressionGraph, AddNode.ProgressionGraph

The Weibull shape parameter for the rates for each node will be 1, to change use SetShape.ProgressionGraph

The edges added by the crossOver argument default to having isResetEdge set to true (i.e. the patient switch times are reset when transitioning over this edge) This can be changed by calling SetIsResetEdge.ProgressionGraph

Value

An object of type ProgressionGraph which details the transition states of study

Examples

crossOver <- c("control.progressed","active.progressed")

SimpleStudyProgressionGraph(arms=c("control","active"),
                            armProgression=c("progressing","progressed"),
                            edge="immediate",
                            crossOver=crossOver)

scientific-computing-solutions/badminton documentation built on May 29, 2019, 3:43 p.m.