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Integration Point: Dropout - Continuous Outcome with Repeated Measures

Gabriel Potvin

January 16, 2025

IntegrationPointDropoutRepeatedMeasures.Rmd

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This integration point and outcome is currently available for the Two Arm Confirmatory Study Objective.

Input Variables

When creating a custom R script, you can optionally use specific variables provided by East Horizon’s engine itself. These variables are automatically available and do not need to be set by the user, except for the UserParam variable. Refer to the table below for the variables that are available for this integration point and outcome.

Variable Type Description
NumSub Integer Number of subjects in the trial.
NumArm Integer Number of arms in the trial ﴾including placebo/control, and experimental﴿.
TreatmentID Vector of Integer Vector of length NumSub, indicating the allocation of subjects to arms. Index 0 represents placebo/control. For example, [0, 0, 1] indicates three subjects: two in the control group and one experimental.
DropMethod Integer Selected input method for dropout parameters from the East Horizon dropdown list:
– 1: Cumulative probability of dropout by visit.
– 2: Cumulative probability of dropout by time.
NumVisit Integer Number of visits. Defaults to 1 if DropMethod = 2.
VisitTime Vector of Numeric Vector of length NumVisit, indicating the visit times.
ByTime – If DropMethod = 1: Vector of Numeric of length NumVisit
– If DropMethod = 2: Numeric		 By times for dropout. For DropMethod = 1, identical to VisitTime.
DropParamControl – If DropMethod = 1: Vector of Numeric of length NumVisit
– If DropMethod = 2: Numeric		 Parameter(s) used to generate dropout times for control arm.
DropParamTrt – If DropMethod = 1: Vector of Numeric of length NumVisit
– If DropMethod = 2: Numeric		 Parameter(s) used to generate dropout times for treatment arm.
UserParam List Contains all user-defined parameters specified in the East Horizon interface (refer to the Instructions section). To access these parameters in your R code, use the syntax: UserParam$NameOfTheVariable, replacing NameOfTheVariable with the appropriate parameter name.

Expected Output Variable

East Horizon expects an output of a specific type. Refer to the table below for the expected output for this integration point:

Type Description
List A named list containing ErrorCode and one of the following: DropOutTime, DropoutVisitID, or CensorInd1, CensorInd2, …, CensorIndNumVisit.

The output list can take one of these three forms.

Option 1: Expected Members of the Output List

Members Type Description
DropOutTime Vector of Numeric Vector of length NumSub, containing the generated dropout times for each subject. A value of Inf indicates that the subject does not drop out.
ErrorCode Integer Optional. Can be used to handle errors in your script:
– 0: No Error
– Positive Integer: Nonfatal Error, the current simulation will be aborted, but the next simulation will proceed.
– Negative Integer: Fatal Error, no further simulations will be attempted.

Option 2: Expected Members of the Output List

Members Type Description
DropoutVisitID Vector of Integer Vector of length NumSub, containing the visit ID after which each subject drops out.
ErrorCode Integer Optional. Can be used to handle errors in your script:
– 0: No Error
– Positive Integer: Nonfatal Error, the current simulation will be aborted, but the next simulation will proceed.
– Negative Integer: Fatal Error, no further simulations will be attempted.

Option 3: Expected Members of the Output List

Members Type Description
CensorInd1 Vector of Integer Vector of length NumSub, containing the generated censor indicator values for all subjects for the first visit:
– 0: Dropout
– 1: Completer
CensorInd2 Vector of Integer Vector of length NumSub, containing the generated censor indicator values for all subjects for the second visit:
– 0: Dropout
– 1: Completer
… Censor indicator values for additional visits follow the same format, incrementing the visit number (e.g., CensorInd3, CensorInd4, etc.).
CensorIndNumVisit Vector of Integer Final vector of length NumSub, containing the generated censor indicator values for all subjects for the last visit:
– 0: Dropout
– 1: Completer
NumVisit should be replaced by the number of visits.
ErrorCode Integer Optional. Can be used to handle errors in your script:
– 0: No error.
– Positive Integer: Nonfatal error, the current simulation will be aborted, but the next simulation will proceed.
– Negative Integer: Fatal error, no further simulations will be attempted.

Minimal Templates

Your R script could contain a function such as these ones, with a name of your choice. All input variables must be declared, even if they are not used in the script. We recommend always declaring UserParam as a default NULL value in the function arguments, as this will ensure that the same function will work regardless of whether the user has specified any custom parameters in East Horizon. A detailed template with step-by-step explanations is available here: SimulatePatientOutcome.Binary.R

Minimal Template for Option 1 

GenDropTimes <- function( NumSub, NumArm, NumVisit, VisitTime, TreatmentID,
                          DropMethod, ByTime, DropParamControl, DropParamTrt, UserParam = NULL )
{
  nError            <- 0 # Error handling (no error)
  vDropoutTime      <- rep( Inf, NumSub ) # Initializing dropout times vector to Inf (all patients are completers)  
  
  # Write the actual code here.
  # Store the generated dropout times in a vector called vDropoutTime.
  
  return( list( DropOutTime = as.double( vDropoutTime ), ErrorCode = as.integer( nError ) ) )
}

Minimal Template for Option 2 

GenDropVisitID <- function( NumSub, NumArm, NumVisit, VisitTime, TreatmentID,
                            DropMethod, ByTime, DropParamControl, DropParamTrt, UserParam = NULL )
{
  nError            <- 0 # Error handling (no error)
  vDropoutVisitID   <- rep( 1, NumSub ) # Initializing dropout visit IDs vector to 1 (all patients drop out after first visit)  
  
  # Write the actual code here.
  # Store the generated dropout visit IDs in a vector called vDropoutVisitID.
  
  return( list( DropoutVisitID = as.double( vDropoutVisitID ), ErrorCode = as.integer( nError ) ) )
}

Minimal Template for Option 3 

GenCensorInd <- function( NumSub, NumArm, NumVisit, VisitTime, TreatmentID,
                          DropMethod, ByTime, DropParamControl, DropParamTrt, UserParam = NULL )
{
  nError            <- 0 # Error handling (no error)
  vCensorInd        <- c()
  lReturn           <- list()
  
  # Add code to simulate the dropout data as desired. 
  # Example of how to create the return list with CensorInd1, CensorInd2, ..., CensorIndNumVisit.
  # Store the generated censor indicator values in a vector called vCensorInd for each subject.
  # Store the response vector in a list called lReturn for each visit.
  for(i in 1:NumVisit)
  {
    strCensorIndName              <- paste0( "CensorInd", i ) # CensorInd1, CensorInd2, ..., CensorIndNumVisit
    vCensorInd                    <- rep( 1, NumSub ) # Initializing censor array to 1 (all patients are completers)    
    lReturn[[ strCensorIndName ]] <- as.integer( vCensorInd )
  }
  
  lReturn$ErrorCode <- as.integer( nError )
  return( lReturn )
}

Examples

Explore the following examples for more context:

  1. 2-Arm, Single Endpoint - Simulate Patient Dropout