tests/testthat/test_RandomizeWithinISA.R
In kwathen/OCTOPUS: OCTOPUS
##### 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.
#
#############################################################################################################################.
context("Test RandomizeWithinISA.R")
source("TestHelperFunctions.R")
###### RandomizeWithinISA.POCRandomizer######################################################################################
#
# Test - ISA 1 Randomizer - Should be a POCRandomizer
# When the call InitializeTrialRandomizer occurs the ISA randomizes are setup.
# The test could be run after the call to InitializeTrialRandomizer
# however, calling Randomize actually tests the the InitializeISARandomizer.XXX and Randomize.XXX
# both did the correct thing.
#
#############################################################################################################################.
#
strPrefixTest <- "ISA 2 Randomizer - POCRandomizer"
test_that(strPrefixTest,
{
gnPrintDetail <<- 0
#Set everything
vISAStartTime <- c(0, 0)
cTrialDesign <- SetupTrialDesign2ISA( )
cTrialRand <- InitializeTrialRandomizer( cTrialDesign, vISAStartTime )
strPrefixTest <- "ISA 1 Randomizer RandomizeWithinISA.POCRandomizer "
strExp <- "POCRandomizer"
strRet <- class( cTrialDesign$cISADesigns[[ "cISA1" ]] )
expect_equal( strRet, strExp )
#Check the ISARand in cTrialRand
strRet <- class( cTrialRand[[1]] )
#Set the status of ISA2 to 0 so it is not open yet and should not have patients randomized to it
vISAStatus <- c( 1, 0 )
bPassTest <- TRUE
vQtyISA <- c( 0, 0 ) #Keep count of the number of patients assigned to each ISA, this example should have ISA2 = 0
#ISA 1 utilizes a POCRandomzier so the initial patients should all be on two of the treatments
vQtyPatsInit <- cTrialDesign$cISADesigns[[1]]$vQtyPatsInit
vQtyPats <- cTrialDesign$cISADesigns[[1]]$vQtyPats
nQtyTrt <- length( vQtyPatsInit )
vTrt <- 1:nQtyTrt
nQtyPatsInit <- sum( vQtyPatsInit )
nQtyPats <- sum( vQtyPats )
nQtyPats2 <- nQtyPats - nQtyPatsInit
vProbTrtPt2 <- (vQtyPats - vQtyPatsInit)/nQtyPats2 # This is used in the last test to make sure we are getting about the right number of patients
bISATest <- TRUE # Used to make sure patients are only assigned to ISA2
bInitPatTest <- TRUE # Test to make sure the patients are only assigned to the open treatments in the POC part
bInitPatTest2 <- TRUE # Used to track if the patients are close to equally randomized in the POC
bPatTest2 <- TRUE
vTrtCount <- rep( 0, nQtyTrt )
vQtyISA <- c( 0, 0 ) #Keep count of the number of patients assigned to each ISA, this example should have ISA2 = 0
bExp <- TRUE
#The initial patient randomization will be done 10 times just to make sure it is not an accident that no patients are assigned to the
#incorrect treatments
# Randomize the patients for 10 trials and make sure no tests fail.
nQtyTest <- 20
for( iTest in 1:nQtyTest )
{
cTrialRand <- InitializeTrialRandomizer( cTrialDesign, vISAStartTime )
vTrtCount <- rep( 0, nQtyTrt )
for( i in 1:nQtyPatsInit )
{
lRandRet <- Randomize( cTrialRand, vISAStatus, 0.0 )
cTrialRand <- lRandRet$cRandomizer
vQtyISA[ lRandRet$nISA ] <- vQtyISA[ lRandRet$nISA ] + 1
vTrtCount[ lRandRet$nTrt ] <- vTrtCount[ lRandRet$nTrt ] + 1
}
# Test to make sure no patients were assigned to ISA2
nExp <- 0
nRet <- vQtyISA[ 2 ]
expect_equal( nRet, nExp )
#AddTest( cTestRandomizer, paste( strPrefixTest, " Number of patients assigned to ISA2 when it is closed was incorrect. "), nExp, nRet )
# Test to make sure the number of patients assigned to the treatments not open during the POC = 0
bInitPatTest <- ( sum( vTrtCount[ vQtyPatsInit== 0 ] ) == 0 )
expect_true( bInitPatTest )
# Test to make sure each of the open arms is near equal in terms of the number of patients
nCutoff <- qbinom( 0.99, nQtyPatsInit,0.5)
bInitPatTest2 <- all( vTrtCount < nCutoff )
expect_true( bInitPatTest2 )
vQtyISA2 <- rep( 0, nQtyTrt )
vTrtCount <- rep( 0, nQtyTrt )
# Randomize after the POC and keep track of the number of patients randomized to each treatment
nRand <- floor( nQtyPats2 - nQtyPats2/2 )
for( i in 1:nRand )
{
lRandRet <- Randomize( cTrialRand, vISAStatus, 0.0 )
cTrialRand <- lRandRet$cRandomizer
vTrtCount[ lRandRet$nTrt ] <- vTrtCount[ lRandRet$nTrt ] + 1
vQtyISA2[ lRandRet$nISA ] <- vQtyISA2[ lRandRet$nISA ] + 1
}
# Test to make sure no patients were assigned to ISA2 Number of patients assigned to ISA2 during non POC portion, when it is closed, was incorrect. "
nRet <- vQtyISA[ 2 ]
expect_equal( nRet, 0 )
# If the value from a chisq.test is small there is a possibility of a bug
# Note: this test is run ", nQtyTest, " times, if only 1-2 errors are reported it may not be a problem as this could happen by chance.")
dPVal <- chisq.test( vTrtCount, p=vProbTrtPt2 )$p.value
bRet <- dPVal >= 0.05
expect_true( bRet )
nRand <- nQtyPats2 - nRand
for( i in 1:nRand )
{
lRandRet <- Randomize( cTrialRand, vISAStatus, 0.0 )
cTrialRand <- lRandRet$cRandomizer
vTrtCount[ lRandRet$nTrt ] <- vTrtCount[ lRandRet$nTrt ] + 1
}
vExp <- vQtyPats - vQtyPatsInit
# At the end of the trial in the non-POC the number of patients assigned to the treatments was incorrect."
expect_equal( vTrtCount, vExp )
}
})
###### Test ISA 2 Randomzier #############################################################################################
#
# Test - ISA 2 Randomizer - Should be an EqualRandomizer
# This test tests InitializeTrialRandomizer and subsequent calls to Randomizer
##########################################################################################################################.
strPrefixTest <- "ISA 2 Randomizer - Equal Randomizer"
test_that(strPrefixTest,
{
#Reset everything
gnPrintDetail <<- 0
vISAStartTime <- c(0, 0)
cTrialDesign <- SetupTrialDesign2ISA( )
cTrialRand <- InitializeTrialRandomizer( cTrialDesign, vISAStartTime )
nISA <- 2
strExp <- "EqualRandomizer"
strRet <- class( cTrialDesign$cISADesigns[[ "cISA2" ]] )
expect_equal( strRet, strExp )
#Check the ISARand in cTrialRand
strRet <- class( cTrialRand[[ nISA ]])
expect_equal( strRet, strExp )
#Set the status of ISA1 to 0 so it is not open yet and should not have patients randomized to it
vISAStatus <- c( 0, 1 )
bPassTest <- TRUE
vQtyISA <- c( 0, 0 ) #Keep count of the number of patients assigned to each ISA, this example should have ISA2 = 0
#ISA 1 utilizes a POCRandomzier so the initial patients should all be on two of the treatments
vQtyPats <- cTrialDesign$cISADesigns[[ nISA ]]$vQtyPats
nQtyTrt <- length( vQtyPats )
vTrt <- 1:nQtyTrt
nQtyPats <- sum( vQtyPats )
nQtyPats2 <- floor( nQtyPats/2 ) #Will split the patients in half to make sure each have is randomized in about the right proportions
vProbTrtPt <- (vQtyPats)/nQtyPats # This is used in the last test to make sure we are getting about the right number of patients
bISATest <- TRUE # Used to make sure patients are only assigned to ISA2
bInitPatTest <- TRUE # Test to make sure the patients are only assigned to the open treatments in the POC part
bInitPatTest2 <- TRUE # Used to track if the patients are close to equally randomized in the POC
bPatTest2 <- TRUE
vTrtCount <- rep( 0, length( cTrialDesign$vTrtLab ) )
vQtyISA <- c( 0, 0 ) #Keep count of the number of patients assigned to each ISA, this example should have ISA2 = 0
bExp <- TRUE
#The initial patient randomization will be done 10 times just to make sure it is not an accident that no patients are assigned to the
#incorrect treatments
# Randomize the patients for 10 trials and make sure no tests fail.
nQtyTest <- 20
for( iTest in 1:nQtyTest )
{
cTrialRand <- InitializeTrialRandomizer( cTrialDesign, vISAStartTime )
vTrtCount <- rep( 0, length( cTrialDesign$vTrtLab ) )
for( i in 1:nQtyPats2 )
{
lRandRet <- Randomize( cTrialRand, vISAStatus, 0.0 )
cTrialRand <- lRandRet$cRandomizer
vQtyISA[ lRandRet$nISA ] <- vQtyISA[ lRandRet$nISA ] + 1
vIndex <- cTrialDesign$vTrtLab== lRandRet$nTrt & cTrialDesign$vISALab == nISA
vTrtCount[ vIndex ] <- vTrtCount[ vIndex ] + 1
}
vTrtCount <- vTrtCount[ cTrialDesign$vISALab == nISA ]
# Test to make sure no patients were assigned to ISA1
nExp <- 0
nRet <- vQtyISA[ 1 ]
expect_equal( nRet, nExp )
dPVal <- chisq.test( vTrtCount, p=vProbTrtPt )$p.value
strErr <- paste(" EqualRandomizer - Randomize first half of patients test for expected number of patients assigned to each treatment")
strErr <- paste( strErr, paste( vTrtCount, collapse = ", ") )
strErr <- paste( strErr, " Note: this test is run ", nQtyTest, " times, if only 1-2 errors are reported it may not be a problem as this could happen by chance.")
bRet <- dPVal >= 0.01
#if( !bRet )
# print(paste( "pval 1 ", dPVal))
expect_true( bRet, strErr)
vTrtCount2 <- rep( 0, length( cTrialDesign$vTrtLab ) )
for( i in (nQtyPats2+1):nQtyPats )
{
lRandRet <- Randomize( cTrialRand, vISAStatus, 0 )
cTrialRand <- lRandRet$cRandomizer
vQtyISA[ lRandRet$nISA ] <- vQtyISA[ lRandRet$nISA ] + 1
vIndex <- cTrialDesign$vTrtLab== lRandRet$nTrt & cTrialDesign$vISALab == nISA
vTrtCount2[ vIndex ] <- vTrtCount2[ vIndex ] + 1
}
# Test to make sure no patients were assigned to ISA1
nExp <- 0
nRet <- vQtyISA[ 1 ]
expect_equal( nRet, nExp )
vTrtCount2 <- vTrtCount2[ cTrialDesign$vISALab == nISA ]
dPVal <- chisq.test( vTrtCount2, p=vProbTrtPt )$p.value
#EqualRandomizer - Randomize second half of patients test for expected number of patients assigned to each treatment", paste( vTrtCount, collapse = ", "),
# Note: this test is run ", nQtyTest, " times, if only 1-2 errors are reported it may not be a problem as this could happen by chance.")
bRet <- dPVal >= 0.01
if( !bRet )
print(paste( "pval 2 ", dPVal))
expect_true( bRet )
vTrtCount <- vTrtCount + vTrtCount2
vExp <- vQtyPats
expect_equal( vTrtCount, vExp )
}
})
###### Test ISA 2 Randomzier - DelayedStartRandomizer ###################################################################
#
# Test - ISA 2 Randomizer - "DelayedStartRandomizer"
#
##########################################################################################################################.
strPrefixTest <- "ISA 2 Randomizer - DelayedStartRandomizer"
test_that(strPrefixTest,
{
#Reset everything
gnPrintDetail <<- 0
vISAStartTime <- c( 0, 6 )
cTrialDesign <- SetupTrialDesign2ISA(strISA2Randomizer = "DelayedStartRandomizer" )
cTrialRand <- InitializeTrialRandomizer( cTrialDesign, vISAStartTime )
nISA <- 2
strExp <- "DelayedStartRandomizer"
strRet <- class( cTrialDesign$cISADesigns[[ "cISA2" ]] )
expect_equal( strRet, strExp )
#Check the ISARand in cTrialRand
strRet <- class( cTrialRand[[ nISA ]])
expect_equal( strRet, strExp )
#Set the status of ISA1 to 0 so it is not open yet and should not have patients randomized to it
vISAStatus <- c( 0, 1 )
bPassTest <- TRUE
vQtyISA <- c( 0, 0 ) #Keep count of the number of patients assigned to each ISA, this example should have ISA2 = 0
#ISA 1 utilizes a POCRandomzier so the initial patients should all be on two of the treatments
vQtyPats <- cTrialDesign$cISADesigns[[ nISA ]]$vQtyPats
nQtyTrt <- length( vQtyPats )
vTrt <- 1:nQtyTrt
nQtyPats <- sum( vQtyPats )
#Splitting the patients into two parts, the first part should only receive dose 1,2,3 because 4 is not open.
nQtyPats2 <- floor( nQtyPats/2 )
strDelayedTrt <- cTrialDesign$cISADesigns[[2]]$vTrtLab[ 4 ]
bISATest <- TRUE # Used to make sure patients are only assigned to ISA2
bInitPatTest <- TRUE # Test to make sure the patients are only assigned to the open treatments in the POC part
bInitPatTest2 <- TRUE # Used to track if the patients are close to equally randomized in the POC
bPatTest2 <- TRUE
vTrtCount <- rep( 0, length( cTrialDesign$vTrtLab ) )
vQtyISA <- c( 0, 0 ) #Keep count of the number of patients assigned to each ISA, this example should have ISA2 = 0
bExp <- TRUE
#The initial patient randomization will be done 10 times just to make sure it is not an accident that no patients are assigned to the
#incorrect treatments
# Randomize the patients for nQtyTest trials and make sure no tests fail.
nQtyTest <- 20
for( iTest in 1:nQtyTest )
{
cTrialRand <- InitializeTrialRandomizer( cTrialDesign, vISAStartTime)
vTrtCount <- rep( 0, length( cTrialDesign$vTrtLab ) )
for( i in 1:nQtyPats2 )
{
#Testing a value greater than start time of ISA2 delayed doses.
lRandRet <- Randomize( cTrialRand, vISAStatus, 7.0 )
cTrialRand <- lRandRet$cRandomizer
lRandRet$nTrt
lRandRet$cRandomizer[[2]][[1]]
length(lRandRet$cRandomizer[[2]][[1]])
length( cTrialRand[[2]][[1]])
vQtyISA[ lRandRet$nISA ] <- vQtyISA[ lRandRet$nISA ] + 1
vIndex <- cTrialDesign$vTrtLab== lRandRet$nTrt & cTrialDesign$vISALab == nISA
vTrtCount[ vIndex ] <- vTrtCount[ vIndex ] + 1
}
vTrtCount <- vTrtCount[ cTrialDesign$vISALab == nISA ]
nQtyOfPatientsOnDelayedTrt <- vTrtCount[ cTrialDesign$cISADesigns[[2]]$vTrtLab == strDelayedTrt ]
expect_equal( nQtyOfPatientsOnDelayedTrt, 0, label= "Delayed treatment patient count greater than 0.")
#Since one treatment is delayes
# Test to make sure no patients were assigned to ISA1
nExp <- 0
nRet <- vQtyISA[ 1 ]
expect_equal( nRet, nExp )
# Need to drop the count on the teatment that is no open before testing.
dPVal <- chisq.test( vTrtCount[ -4 ], p=rep( 1/3,3) )$p.value
strErr <- paste(" EqualRandomizer - Randomize first half of patients test for expected number of patients assigned to each treatment")
strErr <- paste( strErr, paste( vTrtCount, collapse = ", ") )
strErr <- paste( strErr, " Note: this test is run ", nQtyTest, " times, if only 1-2 errors are reported it may not be a problem as this could happen by chance.")
bRet <- dPVal >= 0.01
#if( !bRet )
# print(paste( "pval 1 ", dPVal))
expect_true( bRet, strErr)
vTrtCount2 <- rep( 0, length( cTrialDesign$vTrtLab ) )
for( i in (nQtyPats2+1):nQtyPats )
{
lRandRet <- Randomize( cTrialRand, vISAStatus, 14.0 )
cTrialRand <- lRandRet$cRandomizer
vQtyISA[ lRandRet$nISA ] <- vQtyISA[ lRandRet$nISA ] + 1
vIndex <- cTrialDesign$vTrtLab== lRandRet$nTrt & cTrialDesign$vISALab == nISA
vTrtCount2[ vIndex ] <- vTrtCount2[ vIndex ] + 1
}
# Test to make sure no patients were assigned to ISA1
nExp <- 0
nRet <- vQtyISA[ 1 ]
expect_equal( nRet, nExp )
vTrtCount2 <- vTrtCount2[ cTrialDesign$vISALab == nISA ]
# dPVal <- chisq.test( vTrtCount2, p=rep( 0.25, 4 ) )$p.value
#
# #EqualRandomizer - Randomize second half of patients test for expected number of patients assigned to each treatment", paste( vTrtCount, collapse = ", "),
# # Note: this test is run ", nQtyTest, " times, if only 1-2 errors are reported it may not be a problem as this could happen by chance.")
#
#
# bRet <- dPVal >= 0.05
#
# if( !bRet )
# print(paste( "pval 2 ", dPVal))
# expect_true( bRet )
vTrtCount <- vTrtCount + vTrtCount2
vExp <- vQtyPats
expect_equal( vTrtCount, vExp )
}
})
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##### 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.
#
#############################################################################################################################.
context("Test RandomizeWithinISA.R")
source("TestHelperFunctions.R")
###### RandomizeWithinISA.POCRandomizer######################################################################################
#
# Test - ISA 1 Randomizer - Should be a POCRandomizer
# When the call InitializeTrialRandomizer occurs the ISA randomizes are setup.
# The test could be run after the call to InitializeTrialRandomizer
# however, calling Randomize actually tests the the InitializeISARandomizer.XXX and Randomize.XXX
# both did the correct thing.
#
#############################################################################################################################.
#
strPrefixTest <- "ISA 2 Randomizer - POCRandomizer"
test_that(strPrefixTest,
{
gnPrintDetail <<- 0
#Set everything
vISAStartTime <- c(0, 0)
cTrialDesign <- SetupTrialDesign2ISA( )
cTrialRand <- InitializeTrialRandomizer( cTrialDesign, vISAStartTime )
strPrefixTest <- "ISA 1 Randomizer RandomizeWithinISA.POCRandomizer "
strExp <- "POCRandomizer"
strRet <- class( cTrialDesign$cISADesigns[[ "cISA1" ]] )
expect_equal( strRet, strExp )
#Check the ISARand in cTrialRand
strRet <- class( cTrialRand[[1]] )
#Set the status of ISA2 to 0 so it is not open yet and should not have patients randomized to it
vISAStatus <- c( 1, 0 )
bPassTest <- TRUE
vQtyISA <- c( 0, 0 ) #Keep count of the number of patients assigned to each ISA, this example should have ISA2 = 0
#ISA 1 utilizes a POCRandomzier so the initial patients should all be on two of the treatments
vQtyPatsInit <- cTrialDesign$cISADesigns[[1]]$vQtyPatsInit
vQtyPats <- cTrialDesign$cISADesigns[[1]]$vQtyPats
nQtyTrt <- length( vQtyPatsInit )
vTrt <- 1:nQtyTrt
nQtyPatsInit <- sum( vQtyPatsInit )
nQtyPats <- sum( vQtyPats )
nQtyPats2 <- nQtyPats - nQtyPatsInit
vProbTrtPt2 <- (vQtyPats - vQtyPatsInit)/nQtyPats2 # This is used in the last test to make sure we are getting about the right number of patients
bISATest <- TRUE # Used to make sure patients are only assigned to ISA2
bInitPatTest <- TRUE # Test to make sure the patients are only assigned to the open treatments in the POC part
bInitPatTest2 <- TRUE # Used to track if the patients are close to equally randomized in the POC
bPatTest2 <- TRUE
vTrtCount <- rep( 0, nQtyTrt )
vQtyISA <- c( 0, 0 ) #Keep count of the number of patients assigned to each ISA, this example should have ISA2 = 0
bExp <- TRUE
#The initial patient randomization will be done 10 times just to make sure it is not an accident that no patients are assigned to the
#incorrect treatments
# Randomize the patients for 10 trials and make sure no tests fail.
nQtyTest <- 20
for( iTest in 1:nQtyTest )
{
cTrialRand <- InitializeTrialRandomizer( cTrialDesign, vISAStartTime )
vTrtCount <- rep( 0, nQtyTrt )
for( i in 1:nQtyPatsInit )
{
lRandRet <- Randomize( cTrialRand, vISAStatus, 0.0 )
cTrialRand <- lRandRet$cRandomizer
vQtyISA[ lRandRet$nISA ] <- vQtyISA[ lRandRet$nISA ] + 1
vTrtCount[ lRandRet$nTrt ] <- vTrtCount[ lRandRet$nTrt ] + 1
}
# Test to make sure no patients were assigned to ISA2
nExp <- 0
nRet <- vQtyISA[ 2 ]
expect_equal( nRet, nExp )
#AddTest( cTestRandomizer, paste( strPrefixTest, " Number of patients assigned to ISA2 when it is closed was incorrect. "), nExp, nRet )
# Test to make sure the number of patients assigned to the treatments not open during the POC = 0
bInitPatTest <- ( sum( vTrtCount[ vQtyPatsInit== 0 ] ) == 0 )
expect_true( bInitPatTest )
# Test to make sure each of the open arms is near equal in terms of the number of patients
nCutoff <- qbinom( 0.99, nQtyPatsInit,0.5)
bInitPatTest2 <- all( vTrtCount < nCutoff )
expect_true( bInitPatTest2 )
vQtyISA2 <- rep( 0, nQtyTrt )
vTrtCount <- rep( 0, nQtyTrt )
# Randomize after the POC and keep track of the number of patients randomized to each treatment
nRand <- floor( nQtyPats2 - nQtyPats2/2 )
for( i in 1:nRand )
{
lRandRet <- Randomize( cTrialRand, vISAStatus, 0.0 )
cTrialRand <- lRandRet$cRandomizer
vTrtCount[ lRandRet$nTrt ] <- vTrtCount[ lRandRet$nTrt ] + 1
vQtyISA2[ lRandRet$nISA ] <- vQtyISA2[ lRandRet$nISA ] + 1
}
# Test to make sure no patients were assigned to ISA2 Number of patients assigned to ISA2 during non POC portion, when it is closed, was incorrect. "
nRet <- vQtyISA[ 2 ]
expect_equal( nRet, 0 )
# If the value from a chisq.test is small there is a possibility of a bug
# Note: this test is run ", nQtyTest, " times, if only 1-2 errors are reported it may not be a problem as this could happen by chance.")
dPVal <- chisq.test( vTrtCount, p=vProbTrtPt2 )$p.value
bRet <- dPVal >= 0.05
expect_true( bRet )
nRand <- nQtyPats2 - nRand
for( i in 1:nRand )
{
lRandRet <- Randomize( cTrialRand, vISAStatus, 0.0 )
cTrialRand <- lRandRet$cRandomizer
vTrtCount[ lRandRet$nTrt ] <- vTrtCount[ lRandRet$nTrt ] + 1
}
vExp <- vQtyPats - vQtyPatsInit
# At the end of the trial in the non-POC the number of patients assigned to the treatments was incorrect."
expect_equal( vTrtCount, vExp )
}
})
###### Test ISA 2 Randomzier #############################################################################################
#
# Test - ISA 2 Randomizer - Should be an EqualRandomizer
# This test tests InitializeTrialRandomizer and subsequent calls to Randomizer
##########################################################################################################################.
strPrefixTest <- "ISA 2 Randomizer - Equal Randomizer"
test_that(strPrefixTest,
{
#Reset everything
gnPrintDetail <<- 0
vISAStartTime <- c(0, 0)
cTrialDesign <- SetupTrialDesign2ISA( )
cTrialRand <- InitializeTrialRandomizer( cTrialDesign, vISAStartTime )
nISA <- 2
strExp <- "EqualRandomizer"
strRet <- class( cTrialDesign$cISADesigns[[ "cISA2" ]] )
expect_equal( strRet, strExp )
#Check the ISARand in cTrialRand
strRet <- class( cTrialRand[[ nISA ]])
expect_equal( strRet, strExp )
#Set the status of ISA1 to 0 so it is not open yet and should not have patients randomized to it
vISAStatus <- c( 0, 1 )
bPassTest <- TRUE
vQtyISA <- c( 0, 0 ) #Keep count of the number of patients assigned to each ISA, this example should have ISA2 = 0
#ISA 1 utilizes a POCRandomzier so the initial patients should all be on two of the treatments
vQtyPats <- cTrialDesign$cISADesigns[[ nISA ]]$vQtyPats
nQtyTrt <- length( vQtyPats )
vTrt <- 1:nQtyTrt
nQtyPats <- sum( vQtyPats )
nQtyPats2 <- floor( nQtyPats/2 ) #Will split the patients in half to make sure each have is randomized in about the right proportions
vProbTrtPt <- (vQtyPats)/nQtyPats # This is used in the last test to make sure we are getting about the right number of patients
bISATest <- TRUE # Used to make sure patients are only assigned to ISA2
bInitPatTest <- TRUE # Test to make sure the patients are only assigned to the open treatments in the POC part
bInitPatTest2 <- TRUE # Used to track if the patients are close to equally randomized in the POC
bPatTest2 <- TRUE
vTrtCount <- rep( 0, length( cTrialDesign$vTrtLab ) )
vQtyISA <- c( 0, 0 ) #Keep count of the number of patients assigned to each ISA, this example should have ISA2 = 0
bExp <- TRUE
#The initial patient randomization will be done 10 times just to make sure it is not an accident that no patients are assigned to the
#incorrect treatments
# Randomize the patients for 10 trials and make sure no tests fail.
nQtyTest <- 20
for( iTest in 1:nQtyTest )
{
cTrialRand <- InitializeTrialRandomizer( cTrialDesign, vISAStartTime )
vTrtCount <- rep( 0, length( cTrialDesign$vTrtLab ) )
for( i in 1:nQtyPats2 )
{
lRandRet <- Randomize( cTrialRand, vISAStatus, 0.0 )
cTrialRand <- lRandRet$cRandomizer
vQtyISA[ lRandRet$nISA ] <- vQtyISA[ lRandRet$nISA ] + 1
vIndex <- cTrialDesign$vTrtLab== lRandRet$nTrt & cTrialDesign$vISALab == nISA
vTrtCount[ vIndex ] <- vTrtCount[ vIndex ] + 1
}
vTrtCount <- vTrtCount[ cTrialDesign$vISALab == nISA ]
# Test to make sure no patients were assigned to ISA1
nExp <- 0
nRet <- vQtyISA[ 1 ]
expect_equal( nRet, nExp )
dPVal <- chisq.test( vTrtCount, p=vProbTrtPt )$p.value
strErr <- paste(" EqualRandomizer - Randomize first half of patients test for expected number of patients assigned to each treatment")
strErr <- paste( strErr, paste( vTrtCount, collapse = ", ") )
strErr <- paste( strErr, " Note: this test is run ", nQtyTest, " times, if only 1-2 errors are reported it may not be a problem as this could happen by chance.")
bRet <- dPVal >= 0.01
#if( !bRet )
# print(paste( "pval 1 ", dPVal))
expect_true( bRet, strErr)
vTrtCount2 <- rep( 0, length( cTrialDesign$vTrtLab ) )
for( i in (nQtyPats2+1):nQtyPats )
{
lRandRet <- Randomize( cTrialRand, vISAStatus, 0 )
cTrialRand <- lRandRet$cRandomizer
vQtyISA[ lRandRet$nISA ] <- vQtyISA[ lRandRet$nISA ] + 1
vIndex <- cTrialDesign$vTrtLab== lRandRet$nTrt & cTrialDesign$vISALab == nISA
vTrtCount2[ vIndex ] <- vTrtCount2[ vIndex ] + 1
}
# Test to make sure no patients were assigned to ISA1
nExp <- 0
nRet <- vQtyISA[ 1 ]
expect_equal( nRet, nExp )
vTrtCount2 <- vTrtCount2[ cTrialDesign$vISALab == nISA ]
dPVal <- chisq.test( vTrtCount2, p=vProbTrtPt )$p.value
#EqualRandomizer - Randomize second half of patients test for expected number of patients assigned to each treatment", paste( vTrtCount, collapse = ", "),
# Note: this test is run ", nQtyTest, " times, if only 1-2 errors are reported it may not be a problem as this could happen by chance.")
bRet <- dPVal >= 0.01
if( !bRet )
print(paste( "pval 2 ", dPVal))
expect_true( bRet )
vTrtCount <- vTrtCount + vTrtCount2
vExp <- vQtyPats
expect_equal( vTrtCount, vExp )
}
})
###### Test ISA 2 Randomzier - DelayedStartRandomizer ###################################################################
#
# Test - ISA 2 Randomizer - "DelayedStartRandomizer"
#
##########################################################################################################################.
strPrefixTest <- "ISA 2 Randomizer - DelayedStartRandomizer"
test_that(strPrefixTest,
{
#Reset everything
gnPrintDetail <<- 0
vISAStartTime <- c( 0, 6 )
cTrialDesign <- SetupTrialDesign2ISA(strISA2Randomizer = "DelayedStartRandomizer" )
cTrialRand <- InitializeTrialRandomizer( cTrialDesign, vISAStartTime )
nISA <- 2
strExp <- "DelayedStartRandomizer"
strRet <- class( cTrialDesign$cISADesigns[[ "cISA2" ]] )
expect_equal( strRet, strExp )
#Check the ISARand in cTrialRand
strRet <- class( cTrialRand[[ nISA ]])
expect_equal( strRet, strExp )
#Set the status of ISA1 to 0 so it is not open yet and should not have patients randomized to it
vISAStatus <- c( 0, 1 )
bPassTest <- TRUE
vQtyISA <- c( 0, 0 ) #Keep count of the number of patients assigned to each ISA, this example should have ISA2 = 0
#ISA 1 utilizes a POCRandomzier so the initial patients should all be on two of the treatments
vQtyPats <- cTrialDesign$cISADesigns[[ nISA ]]$vQtyPats
nQtyTrt <- length( vQtyPats )
vTrt <- 1:nQtyTrt
nQtyPats <- sum( vQtyPats )
#Splitting the patients into two parts, the first part should only receive dose 1,2,3 because 4 is not open.
nQtyPats2 <- floor( nQtyPats/2 )
strDelayedTrt <- cTrialDesign$cISADesigns[[2]]$vTrtLab[ 4 ]
bISATest <- TRUE # Used to make sure patients are only assigned to ISA2
bInitPatTest <- TRUE # Test to make sure the patients are only assigned to the open treatments in the POC part
bInitPatTest2 <- TRUE # Used to track if the patients are close to equally randomized in the POC
bPatTest2 <- TRUE
vTrtCount <- rep( 0, length( cTrialDesign$vTrtLab ) )
vQtyISA <- c( 0, 0 ) #Keep count of the number of patients assigned to each ISA, this example should have ISA2 = 0
bExp <- TRUE
#The initial patient randomization will be done 10 times just to make sure it is not an accident that no patients are assigned to the
#incorrect treatments
# Randomize the patients for nQtyTest trials and make sure no tests fail.
nQtyTest <- 20
for( iTest in 1:nQtyTest )
{
cTrialRand <- InitializeTrialRandomizer( cTrialDesign, vISAStartTime)
vTrtCount <- rep( 0, length( cTrialDesign$vTrtLab ) )
for( i in 1:nQtyPats2 )
{
#Testing a value greater than start time of ISA2 delayed doses.
lRandRet <- Randomize( cTrialRand, vISAStatus, 7.0 )
cTrialRand <- lRandRet$cRandomizer
lRandRet$nTrt
lRandRet$cRandomizer[[2]][[1]]
length(lRandRet$cRandomizer[[2]][[1]])
length( cTrialRand[[2]][[1]])
vQtyISA[ lRandRet$nISA ] <- vQtyISA[ lRandRet$nISA ] + 1
vIndex <- cTrialDesign$vTrtLab== lRandRet$nTrt & cTrialDesign$vISALab == nISA
vTrtCount[ vIndex ] <- vTrtCount[ vIndex ] + 1
}
vTrtCount <- vTrtCount[ cTrialDesign$vISALab == nISA ]
nQtyOfPatientsOnDelayedTrt <- vTrtCount[ cTrialDesign$cISADesigns[[2]]$vTrtLab == strDelayedTrt ]
expect_equal( nQtyOfPatientsOnDelayedTrt, 0, label= "Delayed treatment patient count greater than 0.")
#Since one treatment is delayes
# Test to make sure no patients were assigned to ISA1
nExp <- 0
nRet <- vQtyISA[ 1 ]
expect_equal( nRet, nExp )
# Need to drop the count on the teatment that is no open before testing.
dPVal <- chisq.test( vTrtCount[ -4 ], p=rep( 1/3,3) )$p.value
strErr <- paste(" EqualRandomizer - Randomize first half of patients test for expected number of patients assigned to each treatment")
strErr <- paste( strErr, paste( vTrtCount, collapse = ", ") )
strErr <- paste( strErr, " Note: this test is run ", nQtyTest, " times, if only 1-2 errors are reported it may not be a problem as this could happen by chance.")
bRet <- dPVal >= 0.01
#if( !bRet )
# print(paste( "pval 1 ", dPVal))
expect_true( bRet, strErr)
vTrtCount2 <- rep( 0, length( cTrialDesign$vTrtLab ) )
for( i in (nQtyPats2+1):nQtyPats )
{
lRandRet <- Randomize( cTrialRand, vISAStatus, 14.0 )
cTrialRand <- lRandRet$cRandomizer
vQtyISA[ lRandRet$nISA ] <- vQtyISA[ lRandRet$nISA ] + 1
vIndex <- cTrialDesign$vTrtLab== lRandRet$nTrt & cTrialDesign$vISALab == nISA
vTrtCount2[ vIndex ] <- vTrtCount2[ vIndex ] + 1
}
# Test to make sure no patients were assigned to ISA1
nExp <- 0
nRet <- vQtyISA[ 1 ]
expect_equal( nRet, nExp )
vTrtCount2 <- vTrtCount2[ cTrialDesign$vISALab == nISA ]
# dPVal <- chisq.test( vTrtCount2, p=rep( 0.25, 4 ) )$p.value
#
# #EqualRandomizer - Randomize second half of patients test for expected number of patients assigned to each treatment", paste( vTrtCount, collapse = ", "),
# # Note: this test is run ", nQtyTest, " times, if only 1-2 errors are reported it may not be a problem as this could happen by chance.")
#
#
# bRet <- dPVal >= 0.05
#
# if( !bRet )
# print(paste( "pval 2 ", dPVal))
# expect_true( bRet )
vTrtCount <- vTrtCount + vTrtCount2
vExp <- vQtyPats
expect_equal( vTrtCount, vExp )
}
})
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