R/CreateProject.R
In kwathen/OCTOPUS: OCTOPUS
Defines functions
MethodExists
ReplaceSimPatientOutcomeInfo
ReplaceAnalysisInfo
ReplaceBuildMeInfo
CreateProject
Documented in
CreateProject
##### COPYRIGHT #############################################################################################################
#
# Copyright (C) 2018 JANSSEN RESEARCH & DEVELOPMENT, LLC
# This package is governed by the JRD OCTOPUS License, which is the
# GNU General Public License V3 with additional terms. The precise license terms are located in the files
# LICENSE and GPL.
#
#############################################################################################################################.
#' @name CreateProject
#' @title CreateProject
#' @description Created an R Studio project with example files to simulate a platform trial utilizing the OCTOPUS package.
#' @param strProjectDirectory The complete path to where the project is created. If a complete path
#' is not provided then the directory is relative to the working directory. If this is left blank, the current working directory is used.
#' @param strProjectName The name of the project. A directory with the name strProjectName is created in strProjectDirectory if bCreateProjectSubdirectory = TRUE
#' @param strAnalysisName The name of the analysis that should be done. If the analysis is part of OCTOPUS, then no new
#' files are created. If the analysis is new, a file named RunAnalysis.strAnalysisName.R is created.
#' @param strSimPatientOutcomeName The name of the patient simulator that should be utilized. If the patient simulator
#' is part of OCTOPUS, then no new
#' files are created. If the patient simulator is new, a file named SimPatientOutocmes.strSimPatientOutcomeName.R is created.
#' @param strBorrowing Specify the option for sharing control patients across ISAs. If strBorrowing = "NoBorrowing"
#' then patients are not shared between ISAs. If strBorrowing = "AllControls" then all control patients are included in
#' the data set that is sent to the RunAnalysis funciton.
#' @param nQtyReps The number of replications to simulate for each scenario.
#' @param mQtyPatientsPerArm Matrix with 2 or more columns to define the number of patients per arm on each ISA. Each row represents an ISA and
#' column 1 the number of patients on control/placebo and column 2,... the number of patients on the treatment arms in the ISA. Each ISA must have
#' the same number of arms (a control or placbo and treatment arms(s) ). This option can be chnaged once the project is created by modifing the
#' SetupTrialDesign file. If this parameter is NULL you will need to change the options in the BuildMe.R file that is created as part of the project.
#' @param dQtyMonthsFU The number of months of follow-up the last patient before running the final analysis (FA). By default, the design created
#' only includes a final analysis with NO interim analysis. To use another option please see the TrialDesign.R file in the projected that is created.
#' @param bCreateProjectSubdirectory If TRUE the a subdirectory with the project name will be created, if FALSE then the project is created in strProjectDirectory.
#' @seealso { \href{https://github.com/kwathen/OCTOPUS/blob/master/R/CreateProject.R}{View Code on GitHub} }
#' @export
CreateProject <- function( strProjectDirectory = "",
strProjectName = "NewProject",
strAnalysisName = "NewAnalysisName",
strSimPatientOutcomeName = "NewSimOutcomeName",
strBorrowing = "NoBorrowing",
nQtyReps = 10,
mQtyPatientsPerArm = NULL,
dQtyMonthsFU = 1.0,
vISAStartTimes = NULL,
bCreateProjectSubdirectory = TRUE,
vPatientPerMonth = NULL)
{
strRet <- ""
if( strProjectDirectory == "" | is.na( strProjectDirectory ) | is.null( strProjectDirectory ))
{
# Use the current working directory and create a folder named strProjectName
strProjectDirectory <- getwd()
}
if( strProjectName == "" )
{
strProjectName <- "NewProject"
}
if( bCreateProjectSubdirectory )
strNewProjectDirectory <- paste( strProjectDirectory, "/", strProjectName, sep="" )
else
strNewProjectDirectory <- strProjectDirectory
dir.create( strNewProjectDirectory , recursive = TRUE )
#Copy the contents of the template project located in inst/ProjectTemplate director
strPackage <- "OCTOPUS"
#strTemplateDirectory <- paste( getwd(), "/inst/ProjectTemplate", sep="")
#Get the directory where OCTOPUS is installed
strTemplateDirectory <- system.file("ProjectTemplate", package = strPackage)
vFilesToCopy <- list.files( strTemplateDirectory, recursive = FALSE, include.dirs = TRUE)
vResults <- file.copy( file.path(strTemplateDirectory, vFilesToCopy ), strNewProjectDirectory, recursive = TRUE )
nCopySuccess <- sum( vResults )
nCopyFail <- length( vResults ) - nCopySuccess
strRProjName <- paste( strNewProjectDirectory, "/", "ProjectTemplate.Rproj", sep = "" )
if( file.exists( strRProjName ) )
{
strNewRProjName <- paste( strNewProjectDirectory, "/", strProjectName, ".Rproj", sep = "" )
file.rename( strRProjName, strNewRProjName )
strRProjName <- strNewRProjName
}
#Replace Analysis name everyone it needs to be changed
strAnalysisRet <- ReplaceAnalysisInfo( strNewProjectDirectory, strAnalysisName )
strSimOutRet <- ReplaceSimPatientOutcomeInfo( strNewProjectDirectory, strSimPatientOutcomeName )
#Replace options in the BuildMe.R file ####
ReplaceBuildMeInfo( strNewProjectDirectory, "BuildMe.R", mQtyPatientsPerArm, vISAStartTimes, strBorrowing, nQtyReps, dQtyMonthsFU, vPatientPerMonth )
ReplaceBuildMeInfo( strNewProjectDirectory, "BuildMeRunMultiCore.R", mQtyPatientsPerArm, vISAStartTimes, strBorrowing, nQtyReps, dQtyMonthsFU, vPatientPerMonth )
# strBuildMeFile <- paste( strNewProjectDirectory, "/BuildMe.R", sep="" )
# strTemplate <- readLines( strBuildMeFile )
# strTemplate <- gsub( "TEMP_BORROWING", strBorrowing, strTemplate)
# strTemplate <- gsub( "TEMP_QTY_REPS", nQtyReps, strTemplate )
# strTemplate <- gsub( "TMP_QTY_MONTHS_FU", dQtyMonthsFU, strTemplate )
#
# if( is.null( mQtyPatientsPerArm ) == FALSE )
# {
#
# strTemplate <- gsub( "TMP_MATRIX_DATA", paste( mQtyPatientsPerArm, collapse =","), strTemplate )
# strTemplate <- gsub( "TMP_NROW", nrow( mQtyPatientsPerArm ), strTemplate )
# strTemplate <- gsub( "TMP_NCOL", ncol( mQtyPatientsPerArm ), strTemplate )
# }
# if( is.null( vISAStartTimes ) == FALSE )
# {
# strTemplate <- gsub( "TEMP_ISA_START_TIME", paste( "c( ", paste( vISAStartTimes, collapse =","), ")" ), strTemplate )
# }
# else
# {
# strTemplate <- gsub( "TEMP_ISA_START_TIME", paste( "NULL" ), strTemplate )
# }
#
#
# #Save the updates to the file
# writeLines( strTemplate, con = strBuildMeFile )
strRet <- paste( nCopySuccess, "file(s) were successfully coppied and ", nCopyFail, " file(s) were not coppied correctly.")
strInstrucitons <- paste( "Use R Studio to open the", strRProjName, "project file and begin by reading the BuildMe.R file.")
strRet <- c( strRet, strAnalysisRet, strSimOutRet, strInstrucitons )
strRet <- paste( strRet, collapse = "\n")
return( strRet )
}
ReplaceBuildMeInfo <- function( strNewProjectDirectory, strFileName, mQtyPatientsPerArm, vISAStartTimes, strBorrowing, nQtyReps, dQtyMonthsFU, vPatientPerMonth )
{
#Replace options in the BuildMe.R file ####
strBuildMeFile <- paste( strNewProjectDirectory, "/", strFileName, sep="" )
strTemplate <- readLines( strBuildMeFile )
strTemplate <- gsub( "TEMP_BORROWING", strBorrowing, strTemplate)
strTemplate <- gsub( "TEMP_QTY_REPS", nQtyReps, strTemplate )
strTemplate <- gsub( "TMP_QTY_MONTHS_FU", dQtyMonthsFU, strTemplate )
if( !is.null(vPatientPerMonth ))
strTemplate <- gsub( "TEMP_PATIENTS_PER_MONTH", paste0( "c( ", paste( vPatientPerMonth, collapse = ", "), " )" ), strTemplate )
else
strTemplate <- gsub( "TEMP_PATIENTS_PER_MONTH", "NULL", strTemplate )
if( is.null( mQtyPatientsPerArm ) == FALSE )
{
strTemplate <- gsub( "TMP_MATRIX_DATA", paste( t(mQtyPatientsPerArm), collapse =","), strTemplate )
strTemplate <- gsub( "TMP_NROW", nrow( mQtyPatientsPerArm ), strTemplate )
strTemplate <- gsub( "TMP_NCOL", ncol( mQtyPatientsPerArm ), strTemplate )
}
if( is.null( vISAStartTimes ) == FALSE )
{
strTemplate <- gsub( "TEMP_ISA_START_TIME", paste( "c( ", paste( vISAStartTimes, collapse =","), ")" ), strTemplate )
}
else
{
strTemplate <- gsub( "TEMP_ISA_START_TIME", paste( "NULL" ), strTemplate )
}
#Save the updates to the file
writeLines( strTemplate, con = strBuildMeFile )
}
ReplaceAnalysisInfo <- function( strProjectDirectory, strAnalysisName )
{
strRet <- ""
if( strAnalysisName != "" )
{
strBuildMeFile <- paste( strProjectDirectory, "/BuildMe.R", sep="" )
strTemplate <- readLines( strBuildMeFile )
strTemplate <- gsub( "TEMP_ANALYSIS_MODEL", paste( strAnalysisName, sep=""), strTemplate)
writeLines( strTemplate, con = strBuildMeFile )
strBuildMeFile <- paste( strProjectDirectory, "/BuildMeRunMultiCore.R", sep="" )
strTemplate <- readLines( strBuildMeFile )
strTemplate <- gsub( "TEMP_ANALYSIS_MODEL", paste( strAnalysisName, sep=""), strTemplate)
writeLines( strTemplate, con = strBuildMeFile )
strBuildMeFile <- paste( strProjectDirectory, "/R/RunParallelSimulations.R", sep="" )
strTemplate <- readLines( strBuildMeFile )
strTemplate <- gsub( "TEMP_ANALYSIS_MODEL", paste( strAnalysisName, sep=""), strTemplate)
writeLines( strTemplate, con = strBuildMeFile )
if( !MethodExists( "RunAnalysis", strAnalysisName ) )
{
#This analysis is not part of OCTOPUS, need to create the new file and change the template to match
strRet <- paste( "The analysis you requested", strAnalysisName, "is not part of the OCTOPUS package. A file named" )
strRet <- paste( "RunAnalysis.", strAnalysisName, ".R was created and the BuildMe.R set to source the new file.", sep="" )
strAnalysisFileName <- paste( strProjectDirectory, "/R/RunAnalysis.", strAnalysisName, ".R", sep="")
file.rename( paste( strProjectDirectory, "/R/RunAnalysis.TEMP_ANALYSIS_MODEL.R", sep=""), strAnalysisFileName )
strTemplate <- readLines( strAnalysisFileName )
strTemplate <- gsub( "TEMP_ANALYSIS_MODEL", paste( strAnalysisName, sep=""), strTemplate)
writeLines( strTemplate, con = strAnalysisFileName )
strParallelSimulationsFileName <- paste( strProjectDirectory, "/R/RunParallelSimulations.R", sep="")
strTemplate <- readLines( strParallelSimulationsFileName )
strTemplate <- gsub( "TEMP_ANALYSIS_MODEL", paste( strAnalysisName, sep=""), strTemplate)
writeLines( strTemplate, con = strParallelSimulationsFileName )
}
else
{
#The analysis method exists, need to delete the file name and remove the source command for it from the BuildMe
strRet <- paste( "The analysis you requested, RunAnalysis.", strAnalysisName, " is part of the OCTOPUS package OR", sep="" )
strRet <- paste( strRet, " a function called RunAnalysis.", strAnalysisName, " exists in the current environement. ", sep="" )
strRet <- paste( strRet, " A new RunAnalysis function was NOT created.")
file.remove( paste( strProjectDirectory, "/R/RunAnalysis.TEMP_ANALYSIS_MODEL.R", sep="") )
strBuildMeFile <- paste( strProjectDirectory, "/BuildMe.R", sep="" )
strTemplate <- readLines( strBuildMeFile )
strSouceCmd <- paste( "source\\( 'R/RunAnalysis.", strAnalysisName, ".R' \\)", sep = "")
strTemplate <- gsub( strSouceCmd, "", strTemplate)
writeLines( strTemplate, con = strBuildMeFile )
strBuildMeFile <- paste( strProjectDirectory, "/BuildMeRunMultiCore.R", sep="" )
strTemplate <- readLines( strBuildMeFile )
strSouceCmd <- paste( "source\\( 'R/RunAnalysis.", strAnalysisName, ".R' \\)", sep = "")
strTemplate <- gsub( strSouceCmd, "", strTemplate)
writeLines( strTemplate, con = strBuildMeFile )
strParallelSimulationsFileName <- paste( strProjectDirectory, "/R/RunParallelSimulations.R", sep="")
strSouceCmd <- paste( "source\\( 'R/RunAnalysis.", strAnalysisName, ".R' \\)", sep = "")
strTemplate <- readLines( strParallelSimulationsFileName )
strTemplate <- gsub( strSouceCmd, "", strTemplate)
writeLines( strTemplate, con = strParallelSimulationsFileName )
}
}
return( strRet )
}
ReplaceSimPatientOutcomeInfo <- function( strProjectDirectory, strSimPatientOutcomeName )
{
strRet <- ""
if( strSimPatientOutcomeName != "" )
{
strBuildMeFile <- paste( strProjectDirectory, "/BuildMe.R", sep="" )
strTemplate <- readLines( strBuildMeFile )
strTemplate <- gsub( "TEMP_SIM_PATIENT_OUTCOME", paste( strSimPatientOutcomeName, sep=""), strTemplate)
writeLines( strTemplate, con = strBuildMeFile )
strBuildMeFile <- paste( strProjectDirectory, "/BuildMeRunMultiCore.R", sep="" )
strTemplate <- readLines( strBuildMeFile )
strTemplate <- gsub( "TEMP_SIM_PATIENT_OUTCOME", paste( strSimPatientOutcomeName, sep=""), strTemplate)
writeLines( strTemplate, con = strBuildMeFile )
strBuildMeFile <- paste( strProjectDirectory, "/R/RunParallelSimulations.R", sep="" )
strTemplate <- readLines( strBuildMeFile )
strTemplate <- gsub( "TEMP_SIM_PATIENT_OUTCOME", paste( strSimPatientOutcomeName, sep=""), strTemplate)
writeLines( strTemplate, con = strBuildMeFile )
if( !MethodExists( "SimPatientOutcomes", strSimPatientOutcomeName) )
{
#This SimPatient is not part of OCTOPUS, need to create the new file and change the template to match
strRet <- paste( "The patient simualator, SimPatientOutcomes", strSimPatientOutcomeName, "is not part of the OCTOPUS package. A file named" )
strRet <- paste( "SimPatientOutcomes.", strSimPatientOutcomeName, ".R was created and the BuildMe.R set to source the new file.", sep="" )
strFileName <- paste( strProjectDirectory, "/R/SimPatientOutcomes.", strSimPatientOutcomeName, ".R", sep="")
file.rename( paste( strProjectDirectory, "/R/SimPatientOutcomes.TEMP_SIM_PATIENT_OUTCOME.R", sep=""), strFileName )
strTemplate <- readLines( strFileName )
strTemplate <- gsub( "TEMP_SIM_PATIENT_OUTCOME", paste( strSimPatientOutcomeName, sep=""), strTemplate)
writeLines( strTemplate, con = strFileName )
}
else
{
strRet <- paste( "The patient simulator, SimPatientOutcomes.", strSimPatientOutcomeName, "is part of the OCTOPUS package OR" )
strRet <- paste( strRet, " a function called SimPatientOutcomes.", strSimPatientOutcomeName, " exists in the current environement. ", sep="" )
strRet <- paste( strRet, " A new SimPatientOutcomes function was NOT created.")
#The SimPatientOutcome method exists, need to delete the file name and remove the source command for it from the BuildMe
file.remove( paste( strProjectDirectory, "/R/SimPatientOutcomes.TEMP_SIM_PATIENT_OUTCOME.R", sep="") )
strBuildMeFile <- paste( strProjectDirectory, "/BuildMe.R", sep="" )
strTemplate <- readLines( strBuildMeFile )
strSouceCmd <- paste( "source\\( 'R/SimPatientOutcomes.", strSimPatientOutcomeName, ".R' \\)", sep = "")
strTemplate <- gsub( strSouceCmd, "", strTemplate)
writeLines( strTemplate, con = strBuildMeFile )
strBuildMeFile <- paste( strProjectDirectory, "/BuildMeRunMultiCore.R", sep="" )
strTemplate <- readLines( strBuildMeFile )
strSouceCmd <- paste( "source\\( 'R/SimPatientOutcomes.", strSimPatientOutcomeName, ".R' \\)", sep = "")
strTemplate <- gsub( strSouceCmd, "", strTemplate)
writeLines( strTemplate, con = strBuildMeFile )
strBuildMeFile <- paste( strProjectDirectory, "/R/RunParallelSimulations.R", sep="" )
strTemplate <- readLines( strBuildMeFile )
strSouceCmd <- paste( "source\\( 'R/SimPatientOutcomes.", strSimPatientOutcomeName, ".R' \\)", sep = "")
strTemplate <- gsub( strSouceCmd, "", strTemplate)
writeLines( strTemplate, con = strBuildMeFile )
}
}
return( strRet )
}
MethodExists <- function( strGenericFctnName, strClassName )
{
bFound <- !is.null( getS3method(strGenericFctnName, strClassName, optional=TRUE) )
return( bFound )
}
kwathen/OCTOPUS documentation built on Oct. 24, 2024, 12:36 p.m.
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Defines functions MethodExists ReplaceSimPatientOutcomeInfo ReplaceAnalysisInfo ReplaceBuildMeInfo CreateProject
Documented in CreateProject
##### COPYRIGHT #############################################################################################################
#
# Copyright (C) 2018 JANSSEN RESEARCH & DEVELOPMENT, LLC
# This package is governed by the JRD OCTOPUS License, which is the
# GNU General Public License V3 with additional terms. The precise license terms are located in the files
# LICENSE and GPL.
#
#############################################################################################################################.
#' @name CreateProject
#' @title CreateProject
#' @description Created an R Studio project with example files to simulate a platform trial utilizing the OCTOPUS package.
#' @param strProjectDirectory The complete path to where the project is created. If a complete path
#' is not provided then the directory is relative to the working directory. If this is left blank, the current working directory is used.
#' @param strProjectName The name of the project. A directory with the name strProjectName is created in strProjectDirectory if bCreateProjectSubdirectory = TRUE
#' @param strAnalysisName The name of the analysis that should be done. If the analysis is part of OCTOPUS, then no new
#' files are created. If the analysis is new, a file named RunAnalysis.strAnalysisName.R is created.
#' @param strSimPatientOutcomeName The name of the patient simulator that should be utilized. If the patient simulator
#' is part of OCTOPUS, then no new
#' files are created. If the patient simulator is new, a file named SimPatientOutocmes.strSimPatientOutcomeName.R is created.
#' @param strBorrowing Specify the option for sharing control patients across ISAs. If strBorrowing = "NoBorrowing"
#' then patients are not shared between ISAs. If strBorrowing = "AllControls" then all control patients are included in
#' the data set that is sent to the RunAnalysis funciton.
#' @param nQtyReps The number of replications to simulate for each scenario.
#' @param mQtyPatientsPerArm Matrix with 2 or more columns to define the number of patients per arm on each ISA. Each row represents an ISA and
#' column 1 the number of patients on control/placebo and column 2,... the number of patients on the treatment arms in the ISA. Each ISA must have
#' the same number of arms (a control or placbo and treatment arms(s) ). This option can be chnaged once the project is created by modifing the
#' SetupTrialDesign file. If this parameter is NULL you will need to change the options in the BuildMe.R file that is created as part of the project.
#' @param dQtyMonthsFU The number of months of follow-up the last patient before running the final analysis (FA). By default, the design created
#' only includes a final analysis with NO interim analysis. To use another option please see the TrialDesign.R file in the projected that is created.
#' @param bCreateProjectSubdirectory If TRUE the a subdirectory with the project name will be created, if FALSE then the project is created in strProjectDirectory.
#' @seealso { \href{https://github.com/kwathen/OCTOPUS/blob/master/R/CreateProject.R}{View Code on GitHub} }
#' @export
CreateProject <- function( strProjectDirectory = "",
strProjectName = "NewProject",
strAnalysisName = "NewAnalysisName",
strSimPatientOutcomeName = "NewSimOutcomeName",
strBorrowing = "NoBorrowing",
nQtyReps = 10,
mQtyPatientsPerArm = NULL,
dQtyMonthsFU = 1.0,
vISAStartTimes = NULL,
bCreateProjectSubdirectory = TRUE,
vPatientPerMonth = NULL)
{
strRet <- ""
if( strProjectDirectory == "" | is.na( strProjectDirectory ) | is.null( strProjectDirectory ))
{
# Use the current working directory and create a folder named strProjectName
strProjectDirectory <- getwd()
}
if( strProjectName == "" )
{
strProjectName <- "NewProject"
}
if( bCreateProjectSubdirectory )
strNewProjectDirectory <- paste( strProjectDirectory, "/", strProjectName, sep="" )
else
strNewProjectDirectory <- strProjectDirectory
dir.create( strNewProjectDirectory , recursive = TRUE )
#Copy the contents of the template project located in inst/ProjectTemplate director
strPackage <- "OCTOPUS"
#strTemplateDirectory <- paste( getwd(), "/inst/ProjectTemplate", sep="")
#Get the directory where OCTOPUS is installed
strTemplateDirectory <- system.file("ProjectTemplate", package = strPackage)
vFilesToCopy <- list.files( strTemplateDirectory, recursive = FALSE, include.dirs = TRUE)
vResults <- file.copy( file.path(strTemplateDirectory, vFilesToCopy ), strNewProjectDirectory, recursive = TRUE )
nCopySuccess <- sum( vResults )
nCopyFail <- length( vResults ) - nCopySuccess
strRProjName <- paste( strNewProjectDirectory, "/", "ProjectTemplate.Rproj", sep = "" )
if( file.exists( strRProjName ) )
{
strNewRProjName <- paste( strNewProjectDirectory, "/", strProjectName, ".Rproj", sep = "" )
file.rename( strRProjName, strNewRProjName )
strRProjName <- strNewRProjName
}
#Replace Analysis name everyone it needs to be changed
strAnalysisRet <- ReplaceAnalysisInfo( strNewProjectDirectory, strAnalysisName )
strSimOutRet <- ReplaceSimPatientOutcomeInfo( strNewProjectDirectory, strSimPatientOutcomeName )
#Replace options in the BuildMe.R file ####
ReplaceBuildMeInfo( strNewProjectDirectory, "BuildMe.R", mQtyPatientsPerArm, vISAStartTimes, strBorrowing, nQtyReps, dQtyMonthsFU, vPatientPerMonth )
ReplaceBuildMeInfo( strNewProjectDirectory, "BuildMeRunMultiCore.R", mQtyPatientsPerArm, vISAStartTimes, strBorrowing, nQtyReps, dQtyMonthsFU, vPatientPerMonth )
# strBuildMeFile <- paste( strNewProjectDirectory, "/BuildMe.R", sep="" )
# strTemplate <- readLines( strBuildMeFile )
# strTemplate <- gsub( "TEMP_BORROWING", strBorrowing, strTemplate)
# strTemplate <- gsub( "TEMP_QTY_REPS", nQtyReps, strTemplate )
# strTemplate <- gsub( "TMP_QTY_MONTHS_FU", dQtyMonthsFU, strTemplate )
#
# if( is.null( mQtyPatientsPerArm ) == FALSE )
# {
#
# strTemplate <- gsub( "TMP_MATRIX_DATA", paste( mQtyPatientsPerArm, collapse =","), strTemplate )
# strTemplate <- gsub( "TMP_NROW", nrow( mQtyPatientsPerArm ), strTemplate )
# strTemplate <- gsub( "TMP_NCOL", ncol( mQtyPatientsPerArm ), strTemplate )
# }
# if( is.null( vISAStartTimes ) == FALSE )
# {
# strTemplate <- gsub( "TEMP_ISA_START_TIME", paste( "c( ", paste( vISAStartTimes, collapse =","), ")" ), strTemplate )
# }
# else
# {
# strTemplate <- gsub( "TEMP_ISA_START_TIME", paste( "NULL" ), strTemplate )
# }
#
#
# #Save the updates to the file
# writeLines( strTemplate, con = strBuildMeFile )
strRet <- paste( nCopySuccess, "file(s) were successfully coppied and ", nCopyFail, " file(s) were not coppied correctly.")
strInstrucitons <- paste( "Use R Studio to open the", strRProjName, "project file and begin by reading the BuildMe.R file.")
strRet <- c( strRet, strAnalysisRet, strSimOutRet, strInstrucitons )
strRet <- paste( strRet, collapse = "\n")
return( strRet )
}
ReplaceBuildMeInfo <- function( strNewProjectDirectory, strFileName, mQtyPatientsPerArm, vISAStartTimes, strBorrowing, nQtyReps, dQtyMonthsFU, vPatientPerMonth )
{
#Replace options in the BuildMe.R file ####
strBuildMeFile <- paste( strNewProjectDirectory, "/", strFileName, sep="" )
strTemplate <- readLines( strBuildMeFile )
strTemplate <- gsub( "TEMP_BORROWING", strBorrowing, strTemplate)
strTemplate <- gsub( "TEMP_QTY_REPS", nQtyReps, strTemplate )
strTemplate <- gsub( "TMP_QTY_MONTHS_FU", dQtyMonthsFU, strTemplate )
if( !is.null(vPatientPerMonth ))
strTemplate <- gsub( "TEMP_PATIENTS_PER_MONTH", paste0( "c( ", paste( vPatientPerMonth, collapse = ", "), " )" ), strTemplate )
else
strTemplate <- gsub( "TEMP_PATIENTS_PER_MONTH", "NULL", strTemplate )
if( is.null( mQtyPatientsPerArm ) == FALSE )
{
strTemplate <- gsub( "TMP_MATRIX_DATA", paste( t(mQtyPatientsPerArm), collapse =","), strTemplate )
strTemplate <- gsub( "TMP_NROW", nrow( mQtyPatientsPerArm ), strTemplate )
strTemplate <- gsub( "TMP_NCOL", ncol( mQtyPatientsPerArm ), strTemplate )
}
if( is.null( vISAStartTimes ) == FALSE )
{
strTemplate <- gsub( "TEMP_ISA_START_TIME", paste( "c( ", paste( vISAStartTimes, collapse =","), ")" ), strTemplate )
}
else
{
strTemplate <- gsub( "TEMP_ISA_START_TIME", paste( "NULL" ), strTemplate )
}
#Save the updates to the file
writeLines( strTemplate, con = strBuildMeFile )
}
ReplaceAnalysisInfo <- function( strProjectDirectory, strAnalysisName )
{
strRet <- ""
if( strAnalysisName != "" )
{
strBuildMeFile <- paste( strProjectDirectory, "/BuildMe.R", sep="" )
strTemplate <- readLines( strBuildMeFile )
strTemplate <- gsub( "TEMP_ANALYSIS_MODEL", paste( strAnalysisName, sep=""), strTemplate)
writeLines( strTemplate, con = strBuildMeFile )
strBuildMeFile <- paste( strProjectDirectory, "/BuildMeRunMultiCore.R", sep="" )
strTemplate <- readLines( strBuildMeFile )
strTemplate <- gsub( "TEMP_ANALYSIS_MODEL", paste( strAnalysisName, sep=""), strTemplate)
writeLines( strTemplate, con = strBuildMeFile )
strBuildMeFile <- paste( strProjectDirectory, "/R/RunParallelSimulations.R", sep="" )
strTemplate <- readLines( strBuildMeFile )
strTemplate <- gsub( "TEMP_ANALYSIS_MODEL", paste( strAnalysisName, sep=""), strTemplate)
writeLines( strTemplate, con = strBuildMeFile )
if( !MethodExists( "RunAnalysis", strAnalysisName ) )
{
#This analysis is not part of OCTOPUS, need to create the new file and change the template to match
strRet <- paste( "The analysis you requested", strAnalysisName, "is not part of the OCTOPUS package. A file named" )
strRet <- paste( "RunAnalysis.", strAnalysisName, ".R was created and the BuildMe.R set to source the new file.", sep="" )
strAnalysisFileName <- paste( strProjectDirectory, "/R/RunAnalysis.", strAnalysisName, ".R", sep="")
file.rename( paste( strProjectDirectory, "/R/RunAnalysis.TEMP_ANALYSIS_MODEL.R", sep=""), strAnalysisFileName )
strTemplate <- readLines( strAnalysisFileName )
strTemplate <- gsub( "TEMP_ANALYSIS_MODEL", paste( strAnalysisName, sep=""), strTemplate)
writeLines( strTemplate, con = strAnalysisFileName )
strParallelSimulationsFileName <- paste( strProjectDirectory, "/R/RunParallelSimulations.R", sep="")
strTemplate <- readLines( strParallelSimulationsFileName )
strTemplate <- gsub( "TEMP_ANALYSIS_MODEL", paste( strAnalysisName, sep=""), strTemplate)
writeLines( strTemplate, con = strParallelSimulationsFileName )
}
else
{
#The analysis method exists, need to delete the file name and remove the source command for it from the BuildMe
strRet <- paste( "The analysis you requested, RunAnalysis.", strAnalysisName, " is part of the OCTOPUS package OR", sep="" )
strRet <- paste( strRet, " a function called RunAnalysis.", strAnalysisName, " exists in the current environement. ", sep="" )
strRet <- paste( strRet, " A new RunAnalysis function was NOT created.")
file.remove( paste( strProjectDirectory, "/R/RunAnalysis.TEMP_ANALYSIS_MODEL.R", sep="") )
strBuildMeFile <- paste( strProjectDirectory, "/BuildMe.R", sep="" )
strTemplate <- readLines( strBuildMeFile )
strSouceCmd <- paste( "source\\( 'R/RunAnalysis.", strAnalysisName, ".R' \\)", sep = "")
strTemplate <- gsub( strSouceCmd, "", strTemplate)
writeLines( strTemplate, con = strBuildMeFile )
strBuildMeFile <- paste( strProjectDirectory, "/BuildMeRunMultiCore.R", sep="" )
strTemplate <- readLines( strBuildMeFile )
strSouceCmd <- paste( "source\\( 'R/RunAnalysis.", strAnalysisName, ".R' \\)", sep = "")
strTemplate <- gsub( strSouceCmd, "", strTemplate)
writeLines( strTemplate, con = strBuildMeFile )
strParallelSimulationsFileName <- paste( strProjectDirectory, "/R/RunParallelSimulations.R", sep="")
strSouceCmd <- paste( "source\\( 'R/RunAnalysis.", strAnalysisName, ".R' \\)", sep = "")
strTemplate <- readLines( strParallelSimulationsFileName )
strTemplate <- gsub( strSouceCmd, "", strTemplate)
writeLines( strTemplate, con = strParallelSimulationsFileName )
}
}
return( strRet )
}
ReplaceSimPatientOutcomeInfo <- function( strProjectDirectory, strSimPatientOutcomeName )
{
strRet <- ""
if( strSimPatientOutcomeName != "" )
{
strBuildMeFile <- paste( strProjectDirectory, "/BuildMe.R", sep="" )
strTemplate <- readLines( strBuildMeFile )
strTemplate <- gsub( "TEMP_SIM_PATIENT_OUTCOME", paste( strSimPatientOutcomeName, sep=""), strTemplate)
writeLines( strTemplate, con = strBuildMeFile )
strBuildMeFile <- paste( strProjectDirectory, "/BuildMeRunMultiCore.R", sep="" )
strTemplate <- readLines( strBuildMeFile )
strTemplate <- gsub( "TEMP_SIM_PATIENT_OUTCOME", paste( strSimPatientOutcomeName, sep=""), strTemplate)
writeLines( strTemplate, con = strBuildMeFile )
strBuildMeFile <- paste( strProjectDirectory, "/R/RunParallelSimulations.R", sep="" )
strTemplate <- readLines( strBuildMeFile )
strTemplate <- gsub( "TEMP_SIM_PATIENT_OUTCOME", paste( strSimPatientOutcomeName, sep=""), strTemplate)
writeLines( strTemplate, con = strBuildMeFile )
if( !MethodExists( "SimPatientOutcomes", strSimPatientOutcomeName) )
{
#This SimPatient is not part of OCTOPUS, need to create the new file and change the template to match
strRet <- paste( "The patient simualator, SimPatientOutcomes", strSimPatientOutcomeName, "is not part of the OCTOPUS package. A file named" )
strRet <- paste( "SimPatientOutcomes.", strSimPatientOutcomeName, ".R was created and the BuildMe.R set to source the new file.", sep="" )
strFileName <- paste( strProjectDirectory, "/R/SimPatientOutcomes.", strSimPatientOutcomeName, ".R", sep="")
file.rename( paste( strProjectDirectory, "/R/SimPatientOutcomes.TEMP_SIM_PATIENT_OUTCOME.R", sep=""), strFileName )
strTemplate <- readLines( strFileName )
strTemplate <- gsub( "TEMP_SIM_PATIENT_OUTCOME", paste( strSimPatientOutcomeName, sep=""), strTemplate)
writeLines( strTemplate, con = strFileName )
}
else
{
strRet <- paste( "The patient simulator, SimPatientOutcomes.", strSimPatientOutcomeName, "is part of the OCTOPUS package OR" )
strRet <- paste( strRet, " a function called SimPatientOutcomes.", strSimPatientOutcomeName, " exists in the current environement. ", sep="" )
strRet <- paste( strRet, " A new SimPatientOutcomes function was NOT created.")
#The SimPatientOutcome method exists, need to delete the file name and remove the source command for it from the BuildMe
file.remove( paste( strProjectDirectory, "/R/SimPatientOutcomes.TEMP_SIM_PATIENT_OUTCOME.R", sep="") )
strBuildMeFile <- paste( strProjectDirectory, "/BuildMe.R", sep="" )
strTemplate <- readLines( strBuildMeFile )
strSouceCmd <- paste( "source\\( 'R/SimPatientOutcomes.", strSimPatientOutcomeName, ".R' \\)", sep = "")
strTemplate <- gsub( strSouceCmd, "", strTemplate)
writeLines( strTemplate, con = strBuildMeFile )
strBuildMeFile <- paste( strProjectDirectory, "/BuildMeRunMultiCore.R", sep="" )
strTemplate <- readLines( strBuildMeFile )
strSouceCmd <- paste( "source\\( 'R/SimPatientOutcomes.", strSimPatientOutcomeName, ".R' \\)", sep = "")
strTemplate <- gsub( strSouceCmd, "", strTemplate)
writeLines( strTemplate, con = strBuildMeFile )
strBuildMeFile <- paste( strProjectDirectory, "/R/RunParallelSimulations.R", sep="" )
strTemplate <- readLines( strBuildMeFile )
strSouceCmd <- paste( "source\\( 'R/SimPatientOutcomes.", strSimPatientOutcomeName, ".R' \\)", sep = "")
strTemplate <- gsub( strSouceCmd, "", strTemplate)
writeLines( strTemplate, con = strBuildMeFile )
}
}
return( strRet )
}
MethodExists <- function( strGenericFctnName, strClassName )
{
bFound <- !is.null( getS3method(strGenericFctnName, strClassName, optional=TRUE) )
return( bFound )
}
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