Nothing
inst/Runit/runit.data.parameter.R
In MSToolkit: The MSToolkit library for clinical trial design
if( !exists("unitTestPath")) unitTestPath <- system.file(package = "MSToolkit", "Runit")
parameters.datapath <- file.path( unitTestPath , "data", "createParameters" )
covariates.datapath <- file.path( unitTestPath , "data", "createCovariates" )
test.data.param.ext <- function(){
testParamFile <- "testParam.csv"
otherFiles <- paste("testParam", c("nonmem", "spaceDelim", "tabDelim"), sep=".")
wrongTestParamFile <- "wrongTestParam.csv"
# test the inputs
checkException( createExternalParameters( -20 ),
msg = "`subjects` must be positive" )
checkException( createExternalParameters( 20, names = ".54325,5432" ),
msg = "invalid `names`" )
checkException( createExternalParameters( 20, names = "X,X" ),
msg = "duplicated `names`" )
checkException( createExternalParameters( 20, names = "X,Y",idCol = "X" ),
msg = "duplicated names between `SUBJ` and `names`" )
checkException( createExternalParameters( 20, names = "X", dataId = ".54325" ),
msg = "invalid `dataId`" )
checkException( createExternalParameters( 20, names = "X", dataId = "ID,SUB" ),
msg = "`dataId` should be of length one" )
checkException( createExternalParameters( 20, names = "X", idCol = ".54325" ),
msg = "invalid `idCol`" )
checkException( createExternalParameters( 20, names = "X", idCol = "ID,SUB" ),
msg = "`idCol` should be of length one" )
checkException( createExternalParameters( 20, names = "E0,ED50",
file = testParamFile, workingPath = parameters.datapath,
betNames = "B1,B1" ),
msg = "Duplicated values in betNames" )
# tests about the file
checkException( createExternalParameters( 20, names = "E0,ED50,EMAX",
file = "doesNotExists.csv", workingPath = parameters.datapath ),
msg = "File does not exist" )
checkException( createExternalParameters( 20, names = "E0,ED50,EMAX",
file = wrongTestParamFile, workingPath = parameters.datapath ),
msg = "wrong formatted file" )
checkException( createExternalParameters( 20, names = "X,Y,ED50", dataId="ID",
file = testParamFile, workingPath = parameters.datapath ),
msg = "missing variables in file" )
checkException( createExternalParameters( 20, names = "E0,ED50",
file = testParamFile, workingPath = parameters.datapath, idCol = "SUB" ),
msg = "missing ID variables in file" )
# test about errStruc
checkException( createExternalParameters( 20, names = "E0,ED50", dataId="ID",
file = testParamFile, workingPath = parameters.datapath, errStruc = "w" ),
msg = "wrong errStruc" )
# Basic check: different delimiters
dataNone <- createExternalParameters( 20, names = "E0,ED50", dataId="ID",
file = testParamFile, workingPath = parameters.datapath,
errStruc = "None", betNames = "B1,B2", seed = 2 )
for (i in otherFiles) {
newData <- createExternalParameters( 20, names = "E0,ED50", dataId="ID",
file = i, workingPath = parameters.datapath,
errStruc = "None", betNames = "B1,B2", seed = 2 )
checkTrue(all(dim(dataNone) == dim(newData)), msg = paste("Check correct dimensions when importing", i))
checkTrue(all(names(dataNone) == names(newData)), msg = paste("Check correct column names when importing", i))
checkTrue(all(round(dataNone$ED50, 3) == newData$ED50), msg = paste("Check correct ED50 column when importing", i))
checkTrue(all(round(dataNone$B1, 3) == newData$B1), msg = paste("Check correct B1 column when importing", i))
}
# Basic working
dataAdd <- createExternalParameters( 20, names = "E0,ED50", dataId="ID",
file = testParamFile, workingPath = parameters.datapath,
errStruc = "Add", betNames = "B1,B2", seed = 2 )
dataLogNorm <- createExternalParameters( 20, names = "E0,ED50", dataId="ID",
file = testParamFile, workingPath = parameters.datapath,
errStruc = "Log", betNames = "B1,B2", seed = 2 )
dataProp <- createExternalParameters( 20, names = "E0,ED50", dataId="ID",
file = testParamFile, workingPath = parameters.datapath,
errStruc = "Pro", betNames = "B1,B2", seed = 2 )
checkTrue( identical( dataNone$E0 + dataNone$B1, dataAdd$E0 ), msg = "Testing the Additive errStruc" )
checkTrue( identical( dataNone$ED50 + dataNone$B2, dataAdd$ED50), msg = "Testing the Additive errStruc")
checkTrue( identical( dataNone$E0 * exp(dataNone$B1), dataLogNorm$E0 ), msg = "Testing the Log-Normal errStruc" )
checkTrue( identical( dataNone$ED50 * exp(dataNone$B2), dataLogNorm$ED50), msg = "Testing the Log-Normal errStruc")
checkTrue( identical( dataNone$E0 * (1 + dataNone$B1), dataProp$E0 ), msg = "Testing the Proportional errStruc" )
checkTrue( identical( dataNone$ED50 * (1 + dataNone$B2), dataProp$ED50), msg = "Testing the Proportional errStruc")
dataNone <- createExternalParameters( 20, names = "E0,ED50", dataId="ID",
file = testParamFile, workingPath = parameters.datapath,
errStruc = "N", betNames = "B1,B2", seed = 2 )
dataAdd <- createExternalParameters( 20, names = "E0,ED50", dataId="ID",
file = testParamFile, workingPath = parameters.datapath,
errStruc = "A", betNames = "B1,B2", betNums = "2,1", seed = 2 )
checkTrue( identical( dataNone$E0 + dataNone$B2, dataAdd$E0 ), msg = "Testing the Additive errStruc and betNums" )
checkTrue( identical( dataNone$ED50 + dataNone$B1, dataAdd$ED50), msg = "Testing the Additive errStruc and betNums")
dataNone <- createExternalParameters( 20, names = "E0,ED50,EMAX", dataId="ID",
file = testParamFile, workingPath = parameters.datapath,
errStruc = "N", betNames = "B1,B2", betNums = "1,3", seed = 2 )
dataAdd <- createExternalParameters( 20, names = "E0,ED50,EMAX", dataId="ID",
file = testParamFile, workingPath = parameters.datapath,
errStruc = "A", betNames = "B1,B2", betNums = "1,3", seed = 2 )
dataLogNorm <- createExternalParameters( 20, names = "E0,ED50,EMAX", dataId="ID",
file = testParamFile, workingPath = parameters.datapath,
errStruc = "L", betNames = "B1,B2", betNums = "1,3", seed = 2 )
dataProp <- createExternalParameters( 20, names = "E0,ED50,EMAX", dataId="ID",
file = testParamFile, workingPath = parameters.datapath,
errStruc = "P", betNames = "B1,B2", betNums = "1,3", seed = 2 )
checkTrue( identical( dataNone$E0 + dataNone$B1, dataAdd$E0 ), msg = "Testing the Additive errStruc and betNums" )
checkTrue( identical( dataNone$ED50, dataAdd$ED50), msg = "Testing the Additive errStruc and betNums")
checkTrue( identical( dataNone$EMAX + dataNone$B2, dataAdd$EMAX), msg = "Testing the Additive errStruc and betNums")
checkTrue( identical( dataNone$E0 * exp(dataNone$B1), dataLogNorm$E0 ), msg = "Testing the Log-Normal errStruc and betNums" )
checkTrue( identical( dataNone$ED50, dataLogNorm$ED50), msg = "Testing the Log-Normal errStruc and betNums, variable without between should not be exponentiated when errStruc is prop")
checkTrue( identical( dataNone$EMAX * exp(dataNone$B2), dataLogNorm$EMAX), msg = "Testing the Log-Normal errStruc and betNums")
checkTrue( identical( dataNone$E0 * (1 + dataNone$B1), dataProp$E0 ), msg = "Testing the Proportional errStruc and betNums" )
checkTrue( identical( dataNone$ED50, dataProp$ED50), msg = "Testing the Proportional errStruc and betNums, variable without between should not be exponentiated when errStruc is prop")
checkTrue( identical( dataNone$EMAX * (1 + dataNone$B2), dataProp$EMAX), msg = "Testing the Proportional errStruc and betNums")
# testing the refCol settings
checkException( createExternalParameters( 20, names = "E0,ED50,EMAX", dataId="ID",
file = testParamFile, workingPath = parameters.datapath,refColName = "f09-124" ) ,
msg = "wrong refColName")
checkException( createExternalParameters( 20, names = "E0,ED50,EMAX", dataId="ID",
file = testParamFile, workingPath = parameters.datapath,refColName = "REF" ) ,
msg = "refColName not in the data")
checkException( createExternalParameters( 20, names = "E0,ED50,EMAX", dataId="ID",
file = testParamFile, workingPath = parameters.datapath,refColName = "ID", refCol = "1,2,3" ) ,
msg = "refColName not in the data")
testCovFile <- "testCovariates.csv"
importCov <- createExternalCovariates( 20, names = "X1", dataId="ID",
file = testCovFile, workingPath = covariates.datapath, refCol = "ID" )
refcolvalues <- importCov$ID.refCol
importPar <- createExternalParameters( 20, names = "B1,B2", dataId="ID",
file = testParamFile, workingPath = parameters.datapath, refColName = "ID",
refCol = refcolvalues )
iData <- read.csv( file.path( parameters.datapath, testParamFile) )[, c("ID", "B1", "B2")]
for( ref in refcolvalues ){
checkTrue( all( iData[ iData$ID == ref, "B1" ][1] == importPar[ refcolvalues == ref, "B1"] ) ,
msg = "Testing the refCol system")
}
# tests about betNums
checkException( createExternalParameters( 20, names = "E0,ED50", dataId="ID",
file = testParamFile, workingPath = parameters.datapath,
betNames = "B1,B2", betNums = "1" ),
msg = "#betNames != #betNums" )
checkException( createExternalParameters( 20, names = "E0,ED50", dataId="ID",
file = testParamFile, workingPath = parameters.datapath,
betNames = "B1,B2", betNums = "a,b" ),
msg = "wrong betNums format" )
checkException( createExternalParameters( 20, names = "E0,ED50,EMAX", dataId="ID",
file = testParamFile, workingPath = parameters.datapath,
betNames = "B1,B2" ),
msg = "Need betNums if index mismatch" )
# tests about subset
checkException( createExternalParameters( 20, names = "E0,ED50,EMAX", dataId="ID",
file = testParamFile, workingPath = parameters.datapath,
subset = "@fewf-+fw" ),
msg = "Non sense code" )
checkException( createExternalParameters( 20, names = "E0,ED50,EMAX", dataId="ID",
file = testParamFile, workingPath = parameters.datapath,
subset = "E0 < 0 < EMAX < 1 " ),
msg = "Too many comparators" )
checkException( createExternalParameters( 20, names = "E0,ED50,EMAX", dataId="ID",
file = testParamFile, workingPath = parameters.datapath,
subset = "E0" ),
msg = "Too few comparators" )
checkTrue( all( createExternalParameters( 20, names = "E0,ED50,EMAX", dataId="ID",
file = testParamFile, workingPath = parameters.datapath,
subset = "E0 < 0" )$E0 < 0 ),
msg = "test that the subset is applied correctly")
subData <- createExternalParameters( 20, names = "E0,ED50,EMAX", dataId="ID",
file = testParamFile, workingPath = parameters.datapath,
subset = c("E0 < 0", "1 <= B1 <= 2") )
checkTrue( all( subData$E0 < 0 ),
msg = "test that the subset is applied correctly with multiple subsets")
checkTrue( all( subData$B1 >= 1 & subData$B1 <= 2 ),
msg = "test that the subset is applied correctly with two comparators")
# seed
data1 <- createExternalParameters( 20, names = "E0,ED50,EMAX", dataId="ID",
file = testParamFile, workingPath = parameters.datapath,
errStruc = "A", betNames = "B1,B2", betNums = "1,3", seed = 81 )
rnorm(2100 ) + runif(2)
data2 <- createExternalParameters( 20, names = "E0,ED50,EMAX", dataId="ID",
file = testParamFile, workingPath = parameters.datapath,
errStruc = "A", betNames = "B1,B2", betNums = "1,3", seed = 81 )
checkEquals( data1, data2 )
}
test.data.param.norm <- function(){
checkException( createNormalParameters( -50 ) ,
msg = "subjects should be positive")
checkException( createNormalParameters( 50, names = "X, Y" , mean = "0,a") ,
msg = "wrong mean")
checkException( createNormalParameters( 50, names = "X,X" , mean = "0,a") ,
msg = "duplicated names")
checkException( createNormalParameters( 50, names = "X,Y" , mean = "0,0,0") ,
msg = "dimension problem")
checkException( createNormalParameters( 50, names = "X,Y,Z" ,
mean = "0,0,0", covariance = "1,0,0,-1,0,-1" ) ,
msg = "wrong covariance matrix")
checkException( createNormalParameters( 50, names = "X,Y,Z" ,
mean = "0,0,0", covariance = "1,0,0,1,0,1,2,3,4" ) ,
msg = "wrong covariance matrix dims")
checkException( createNormalParameters( 50, names = "X,Y,Z" ,
mean = "0,0,0", covariance = "1", maxDraws = -1 ) ,
msg = "wrong maxDraws value")
checkException( createNormalParameters( 50, names = "X,Y,Z" ,
mean = "0,0,0", covariance = "1", maxDraws = 5:6 ) ,
msg = "wrong maxDraws value")
checkException( createNormalParameters( 50, names = "X,Y,Z" ,
mean = "0,0,0", covariance = "1", digits = -1 ) ,
msg = "wrong digits value")
checkException( createNormalParameters( 50, names = "X,Y,Z" ,
mean = "0,0,0", covariance = "1", digits = 1:2 ) ,
msg = "wrong digits value")
checkException( createNormalParameters( 50, names = "X,Y,Z" ,
mean = "0,0,0", covariance = "1", betMean = "0",
betNames = ".45", betCov = "1" ) ,
msg = "wrong betNames value")
checkException( createNormalParameters( 50, names = "X,Y,Z" ,
mean = "0,0,0", covariance = "1", betMean = "0",
betNames = "R", betCov = "1" ) ,
msg = "wrong betNames value, not a subset of names")
checkException( createNormalParameters( 50, names = "X,Y,Z" ,
mean = "0,0,0", covariance = "1", betMean = "0",
betNames = "X", betCov = "-1" ) ,
msg = "wrong betCov matrix")
checkException( createNormalParameters( 50, names = "X,Y,Z" ,
mean = "0,0,0", covariance = "1", betMean = "0",
betNames = "X", betCov = "1,2,3" ) ,
msg = "wrong betCov matrix")
checkException( createNormalParameters( 50, names = "X,Y,Z" ,
mean = "0,0,0", covariance = "1", betMean = "0",
betNames = "X", betCov = "1", range = "]t43t534w-02354" ) ,
msg = "non sense code")
checkException( createNormalParameters( 50, names = "X,Y,Z" ,
mean = "0,0,0", covariance = "1", betMean = "0",
betNames = "X", betCov = "1", range = "X" ) ,
msg = "wrong range code, not enough comparators")
dataNone <- createNormalParameters( 50, names = "X,Y,Z" ,
mean = "0,0,0", covariance = "1", betNames = "X,Y,Z",
betCov = "1", betMean = "0,0,0", errStruc = "N", seed = 99 )
dataAdd <- createNormalParameters( 50, names = "X,Y,Z" ,
mean = "0,0,0", covariance = "1", betNames = "X,Y,Z",
betCov = "1", betMean = "0,0,0", errStruc = "A", seed = 99 )
dataLogNorm <- createNormalParameters( 50, names = "X,Y,Z" ,
mean = "0,0,0", covariance = "1", betNames = "X,Y,Z",
betCov = "1", betMean = "0,0,0", errStruc = "L", seed = 99 )
errStrucDiff <- round(dataAdd [,c("X", "Y", "Z") ] - (dataNone[,c("X", "Y", "Z") ] + dataNone[, paste( c("X", "Y", "Z") , ".Between", sep = "") ]), 2)
checkTrue( all(unlist(errStrucDiff == 0)) , msg = "checking the errStruc" )
checkTrue( all( dataLogNorm[,c("X", "Y", "Z") ] -
dataNone[,c("X", "Y", "Z") ] * exp( dataNone[,paste( c("X", "Y", "Z") , ".Between", sep ="") ] == 0) ) ,
msg = "checking the errStruc with None and Log Normal")
dataNone <- createNormalParameters( 50, names = "X,Y,Z" ,
mean = "0,50,100", covariance = "1", betNames = "X,Y",
betCov = "1", betMean = "0,0", errStruc = "None", seed = 99, digits = 10 )
dataNone$Z.Between <- rep(0, nrow(dataNone))
dataAdd <- createNormalParameters( 50, names = "X,Y,Z" ,
mean = "0,50,100", covariance = "1", betNames = "X,Y",
betCov = "1", betMean = "0,0", errStruc = "Add", seed = 99, digits = 10 )
dataLogNorm <- createNormalParameters( 50, names = "X,Y,Z" ,
mean = "0,50,100", covariance = "1", betNames = "X,Y",
betCov = "1", betMean = "0,0", errStruc = "Log", seed = 99, digits = 10 )
.roundIt <- MSToolkit:::.roundIt
checkTrue( identical( .roundIt(dataAdd [,c("X", "Y") ], 5), .roundIt(dataNone[,c("X", "Y") ] + dataNone[, paste( c("X", "Y"), ".Between", sep = "") ], 5) ) ,
msg = "check the errStruc, not all between, None and Add" )
#checkTrue( all( .roundIt(dataLogNorm[,c("Z", "Y") ] - (dataNone[,c("Z", "Y") ] * exp( dataNone[,paste( c("Z", "Y"), ".Between",sep ="") ])), 2) == 0 ) ,
# msg = "check the errStruc, not all between, None and Prop, different order")
v1 <- dataLogNorm[,c("Z", "Y") ]
v2 <- dataNone[,c("Z", "Y") ] * exp( dataNone[,paste( c("Z", "Y"), ".Between",sep ="") ])
checkEqualsNumeric(v1, v2, tolerance = 0.1, msg = "\ncheck the errStruc, not all between, None and Prop, different order(1)")
checkTrue( identical( dataAdd$Z , dataNone$Z ) , msg = "check the errStruc, not between, None and Add" )
checkTrue( identical( dataLogNorm$Z, dataNone$Z ) , msg = "check the errStruc, not between, None and Prop")
dataNone <- createNormalParameters( 50, names = "X,Y,Z" ,
mean = "0,50,100", covariance = "1", betNames = "Z,Y",
betCov = "1", betMean = "0,0", errStruc = "N", seed = 99, digits = 5 )
dataAdd <- createNormalParameters( 50, names = "X,Y,Z" ,
mean = "0,50,100", covariance = "1", betNames = "Z,Y",
betCov = "1", betMean = "0,0", errStruc = "A", seed = 99, digits = 5 )
dataLogNorm <- createNormalParameters( 50, names = "X,Y,Z" ,
mean = "0,50,100", covariance = "1", betNames = "Z,Y",
betCov = "1", betMean = "0,0", errStruc = "L", seed = 99, digits = 5 )
checkTrue( all( .roundIt(dataAdd [,c("Z", "Y") ]- (dataNone[,c("Z", "Y") ] + dataNone[,paste( c("Z", "Y"), ".Between",sep = "") ]), 3) ==0) ,
msg = "check the errStruc, not all between, None and Prop, different order")
#checkTrue( all( .roundIt(dataLogNorm[,c("Z", "Y") ] - (dataNone[,c("Z", "Y") ] * exp( dataNone[,paste( c("Z", "Y"), ".Between",sep ="") ])), 2) == 0 ) ,
# msg = "check the errStruc, not all between, None and Prop, different order")
v1 <- dataLogNorm[,c("Z", "Y") ]
v2 <- dataNone[,c("Z", "Y") ] * exp( dataNone[,paste( c("Z", "Y"), ".Between",sep ="") ])
checkEqualsNumeric(v1, v2, tolerance = 0.1, msg = "\ncheck the errStruc, not all between, None and Prop, different order(2)")
checkTrue( all( dataAdd$X - dataNone$X ==0) ,
msg = "check the errStruc, not between, None and Prop, different order")
checkTrue( all( dataLogNorm$X - dataNone$X ==0 ) ,
msg = "check the errStruc, not between, None and Prop, different order")
# check the outputs
dataFixed <- createNormalParameters( 50, names = "X,Y,Z" ,
mean = "0,50,100", covariance = "1" )
for( va in c("X", "Y", "Z")) {
checkTrue( all(diff( dataFixed[[va]] ) == 0), msg = "check the fixed parameters")
}
}
test.data.param.wrap <- function(){
testParamFile <- "testParam.csv"
wrongTestParamFile <- "wrongTestParam.csv"
checkException( createParameters( -10 ),
msg = "wrong subject (negative)" )
checkException( createParameters( 10, idCol = "ID, SUB" ),
msg = "wrong id (too long)" )
checkException( createParameters( 10, idCol = "08234ID" ),
msg = "wrong id" )
checkException( createParameters( 10, flagName = "PAROMIT, OMIT" ),
msg = "wrong flagName (too long)" )
checkException( createParameters( 10, idCol = "082PAROMIT" ),
msg = "wrong flagName" )
d1 <- createNormalParameters( 50, names = "X,Y,Z" ,
mean = "0,0,0", covariance = "1", betNames = "X,Y,Z",
betCov = "1", betMean = "0,0,0", errStruc = "A", seed = 99 )
d2 <- createParameters( 50, genNames = "X,Y,Z" ,
genFixedMean = "0,0,0", genFixedCov = "1", genBetweenNames = "X,Y,Z",
genBetweenCov = "1", genBetweenMean = "0,0,0", genErrStruc = "A", seed = 99 )
checkTrue( identical( d1, d2 ),
msg = "only normal" )
d1 <- createExternalParameters( 20, names = "E0,ED50,EMAX",
file = testParamFile, workingPath = parameters.datapath, dataId = "ID",
errStruc = "A", betNames = "B1,B2", betNums = "1,3", seed = 81 )
d2 <- createParameters( 20, extNames = "E0,ED50,EMAX", extDataId="ID",
extFile = testParamFile, workingPath = parameters.datapath,
extErrStruc = "A", extBetween = "B1,B2", extBetweenNums = "1,3",
seed = 81 )
checkTrue( identical( d1, d2 ),
msg = "only external" )
dNor <- createNormalParameters( 50, names = "X,Y,Z" ,
mean = "0,0,0", covariance = "1", betNames = "X,Y,Z",
betCov = "1", betMean = "0,0,0", errStruc = "A", seed = 81 )
dExt <- createExternalParameters( 50, names = "E0,ED50,EMAX", dataId="ID",
file = testParamFile, workingPath = parameters.datapath,
errStruc = "A", betNames = "B1,B2", betNums = "1,3", seed = 81 )
dAll <- createParameters( 50, extNames = "E0,ED50,EMAX",
extFile = testParamFile, workingPath = parameters.datapath,
extErrStruc = "A", extBetween = "B1,B2", extBetweenNums = "1,3", extDataId="ID",
seed = 81,
genNames = "X,Y,Z", genFixedMean = "0,0,0", genFixedCov = "1",
genBetweenNames = "X,Y,Z",
genBetweenCov = "1", genBetweenMean = "0,0,0", genErrStruc = "A" )
checkTrue( identical( dNor[, c("SUBJ", "X", "Y", "Z") ] , dAll[, c("SUBJ", "X", "Y", "Z")] ) ,
msg = "all + nor")
checkTrue( identical( dExt[,c("SUBJ", "E0", "ED50", "EMAX")], dAll[, c("SUBJ", "E0", "ED50", "EMAX")] ) ,
msg = "all + ext")
dNor <- createNormalParameters( 50, names = "X,Y,Z" ,
mean = "0,0,0", covariance = "1", betNames = "X,Y,Z",
betCov = "1", betMean = "0,0,0", errStruc = "A", seed = 81,
range = "Y < 3" )
dExt <- createExternalParameters( 50, names = "E0,ED50,EMAX",
file = testParamFile, workingPath = parameters.datapath, dataId="ID",
errStruc = "A", betNames = "B1,B2", betNums = "1,3", seed = 81,
)
dAll <- createParameters( 50, extNames = "E0,ED50,EMAX",
extFile = testParamFile, workingPath = parameters.datapath,
extErrStruc = "A", extBetween = "B1,B2", extBetweenNums = "1,3", extDataId="ID",
seed = 81,
genNames = "X,Y,Z", genFixedMean = "0,0,0", genFixedCov = "1",
genBetweenNames = "X,Y,Z",
genBetweenCov = "1", genBetweenMean = "0,0,0", genErrStruc = "A",
genRange = "Y < 3")
checkTrue( identical( dNor[, c("SUBJ", "X", "Y", "Z") ] , dAll[, c("SUBJ", "X", "Y", "Z")] ) ,
msg = "all + nor")
checkTrue( identical( dExt[,c("SUBJ", "E0", "ED50", "EMAX")], dAll[, c("SUBJ", "E0", "ED50", "EMAX")] ) ,
msg = "all + ext")
checkEquals( dNor$PAROMIT , dAll$PAROMIT,
msg = "checking the PAROMIT")
}
test.parameter.sf3 <- function() {
checkException( createNormalParameters( 50, names = "X,Y,Z" ,
mean = "100,100,100", covariance = "1", betNames = "X,Y",
betCov = "1", betMean = "0,0", errStruc = "N", digits = -1),
msg = "digits should be positive")
dataNone <- createNormalParameters( 50, names = "X,Y,Z" ,
mean = "100,100,100", covariance = "1", betNames = "X,Y",
betCov = "1", betMean = "0,0", errStruc = "N", digits = "2" )
dataAdd <- createNormalParameters( 50, names = "X,Y,Z" ,
mean = "100,100,100", covariance = "1", betNames = "X,Y",
betCov = "1", betMean = "0,0", errStruc = "A", digits = "2")
dataLogNorm <- createNormalParameters( 50, names = "X,Y,Z" ,
mean = "100,100,100", covariance = "1", betNames = "X,Y",
betCov = "1", betMean = "0,0", errStruc = "L", digits = "2")
checkEquals( dataAdd[, c("X", "Y", "Z")], round(dataAdd[, c("X", "Y", "Z")],2),
msg = "check the atomic digits (add)" )
checkEquals( dataLogNorm[, c("X", "Y", "Z")], round(dataLogNorm[, c("X", "Y", "Z")],2),
msg = "check the atomic digits (prop)" )
checkEquals( dataNone[, c("X", "Y", "Z", "X.Between", "Y.Between")],
round(dataNone[, c("X", "Y", "Z", "X.Between", "Y.Between")],2),
msg = "check the atomic digits (prop)" )
dataNone <- createNormalParameters( 50, names = "X,Y,Z" ,
mean = "100,100,100", covariance = "1", betNames = "X,Y",
betCov = "1", betMean = "0,0", errStruc = "N", digits = "2,3,2" )
dataAdd <- createNormalParameters( 50, names = "X,Y,Z" ,
mean = "100,100,100", covariance = "1", betNames = "X,Y",
betCov = "1", betMean = "0,0", errStruc = "A", digits = "2,3,2")
dataLogNorm <- createNormalParameters( 50, names = "X,Y,Z" ,
mean = "100,100,100", covariance = "1", betNames = "X,Y",
betCov = "1", betMean = "0,0", errStruc = "L", digits = "2,3,2")
checkEquals( dataAdd$X, round(dataAdd$X,2), msg = "check the vector digits (add,X)" )
checkEquals( dataAdd$Y, round(dataAdd$Y,3), msg = "check the vector digits (add,Y)" )
checkEquals( dataAdd$Z, round(dataAdd$Z,2), msg = "check the vector digits (add,Y)" )
checkEquals( dataLogNorm$X, round(dataLogNorm$X,2), msg = "check the vector digits (Prop,X)" )
checkEquals( dataLogNorm$Y, round(dataLogNorm$Y,3), msg = "check the vector digits (Prop,Y)" )
checkEquals( dataLogNorm$Z, round(dataLogNorm$Z,2), msg = "check the vector digits (Prop,Y)" )
checkEquals( dataNone$X, round(dataNone$X,2), msg = "check the vector digits (None,X)" )
checkEquals( dataNone$Y, round(dataNone$Y,3), msg = "check the vector digits (None,Y)" )
checkEquals( dataNone$Z, round(dataNone$Z,2), msg = "check the vector digits (None,Y)" )
checkEquals( dataNone$X.Between, round(dataNone$X.Between,2), msg = "check the vector digits (None,X.Between)" )
checkEquals( dataNone$Y.Between, round(dataNone$Y.Between,3), msg = "check the vector digits (None,Y.Between)" )
}
# SF issue 8
# Tue Jul 24 10:40:43 BST 2007 @444 /Internet Time/
test.parameter.sf8 <- function(){
# checking betCov = 0 by default
dataNone <- createNormalParameters( 50, names = "X,Y,Z" ,
mean = "0,50,100", betNames = "X,Y", covariance = "1",
betMean = "0,0", errStruc = "N", seed = 99 )
checkTrue( all( dataNone[,c("X.Between", "Y.Between")] == 0),
msg = "checking 0 covariance by default for between effects")
data.sf8 <- createNormalParameters( 500, names = "X,Y,Z" , mean = "0,50,100", seed = 99 )
checkTrue(all(sweep( data.sf8[, c("X", "Y", "Z")] ,2, c(0,50,100), "-")==0) ,
msg = "checking the 0 covariance by default")
}
test.parameter.rangeExclude <- function(){
# checking betCov = 0 by default
checkException(createNormalParameters( 500, names = "X,Y,Z" ,
mean = "0,50,100", covariance = "1",
betNames = "X,Y", betCov = "1",
errStruc = "A", seed = 99,
range = "Y < 50", maxDraws = 1, parRangeTolerance = .9 ), msg = "Bad range specified")
checkTrue(is.data.frame(createNormalParameters( 500, names = "X,Y,Z" ,
mean = "0,50,100", covariance = "1",
betNames = "X,Y", betCov = "1",
errStruc = "A", seed = 99,
range = "Y < 100", maxDraws = 1, parRangeTolerance = .9 )), msg = "Good range specified")
warnData <- suppressWarnings(createNormalParameters( 500, names = "X,Y,Z" ,
mean = "0,50,100", covariance = "1",
betNames = "X,Y", betCov = "1",
errStruc = "A", seed = 99,
range = "Y < 50", parRangeTolerance = .1, maxDraws = 1 ))
checkTrue(is.data.frame(warnData) & any(warnData$PAROMIT == 1), msg = "Dataset returned with parameter omits")
}
Try the MSToolkit package in your browser
Any scripts or data that you put into this service are public.
MSToolkit documentation built on May 2, 2019, 6:30 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
if( !exists("unitTestPath")) unitTestPath <- system.file(package = "MSToolkit", "Runit")
parameters.datapath <- file.path( unitTestPath , "data", "createParameters" )
covariates.datapath <- file.path( unitTestPath , "data", "createCovariates" )
test.data.param.ext <- function(){
testParamFile <- "testParam.csv"
otherFiles <- paste("testParam", c("nonmem", "spaceDelim", "tabDelim"), sep=".")
wrongTestParamFile <- "wrongTestParam.csv"
# test the inputs
checkException( createExternalParameters( -20 ),
msg = "`subjects` must be positive" )
checkException( createExternalParameters( 20, names = ".54325,5432" ),
msg = "invalid `names`" )
checkException( createExternalParameters( 20, names = "X,X" ),
msg = "duplicated `names`" )
checkException( createExternalParameters( 20, names = "X,Y",idCol = "X" ),
msg = "duplicated names between `SUBJ` and `names`" )
checkException( createExternalParameters( 20, names = "X", dataId = ".54325" ),
msg = "invalid `dataId`" )
checkException( createExternalParameters( 20, names = "X", dataId = "ID,SUB" ),
msg = "`dataId` should be of length one" )
checkException( createExternalParameters( 20, names = "X", idCol = ".54325" ),
msg = "invalid `idCol`" )
checkException( createExternalParameters( 20, names = "X", idCol = "ID,SUB" ),
msg = "`idCol` should be of length one" )
checkException( createExternalParameters( 20, names = "E0,ED50",
file = testParamFile, workingPath = parameters.datapath,
betNames = "B1,B1" ),
msg = "Duplicated values in betNames" )
# tests about the file
checkException( createExternalParameters( 20, names = "E0,ED50,EMAX",
file = "doesNotExists.csv", workingPath = parameters.datapath ),
msg = "File does not exist" )
checkException( createExternalParameters( 20, names = "E0,ED50,EMAX",
file = wrongTestParamFile, workingPath = parameters.datapath ),
msg = "wrong formatted file" )
checkException( createExternalParameters( 20, names = "X,Y,ED50", dataId="ID",
file = testParamFile, workingPath = parameters.datapath ),
msg = "missing variables in file" )
checkException( createExternalParameters( 20, names = "E0,ED50",
file = testParamFile, workingPath = parameters.datapath, idCol = "SUB" ),
msg = "missing ID variables in file" )
# test about errStruc
checkException( createExternalParameters( 20, names = "E0,ED50", dataId="ID",
file = testParamFile, workingPath = parameters.datapath, errStruc = "w" ),
msg = "wrong errStruc" )
# Basic check: different delimiters
dataNone <- createExternalParameters( 20, names = "E0,ED50", dataId="ID",
file = testParamFile, workingPath = parameters.datapath,
errStruc = "None", betNames = "B1,B2", seed = 2 )
for (i in otherFiles) {
newData <- createExternalParameters( 20, names = "E0,ED50", dataId="ID",
file = i, workingPath = parameters.datapath,
errStruc = "None", betNames = "B1,B2", seed = 2 )
checkTrue(all(dim(dataNone) == dim(newData)), msg = paste("Check correct dimensions when importing", i))
checkTrue(all(names(dataNone) == names(newData)), msg = paste("Check correct column names when importing", i))
checkTrue(all(round(dataNone$ED50, 3) == newData$ED50), msg = paste("Check correct ED50 column when importing", i))
checkTrue(all(round(dataNone$B1, 3) == newData$B1), msg = paste("Check correct B1 column when importing", i))
}
# Basic working
dataAdd <- createExternalParameters( 20, names = "E0,ED50", dataId="ID",
file = testParamFile, workingPath = parameters.datapath,
errStruc = "Add", betNames = "B1,B2", seed = 2 )
dataLogNorm <- createExternalParameters( 20, names = "E0,ED50", dataId="ID",
file = testParamFile, workingPath = parameters.datapath,
errStruc = "Log", betNames = "B1,B2", seed = 2 )
dataProp <- createExternalParameters( 20, names = "E0,ED50", dataId="ID",
file = testParamFile, workingPath = parameters.datapath,
errStruc = "Pro", betNames = "B1,B2", seed = 2 )
checkTrue( identical( dataNone$E0 + dataNone$B1, dataAdd$E0 ), msg = "Testing the Additive errStruc" )
checkTrue( identical( dataNone$ED50 + dataNone$B2, dataAdd$ED50), msg = "Testing the Additive errStruc")
checkTrue( identical( dataNone$E0 * exp(dataNone$B1), dataLogNorm$E0 ), msg = "Testing the Log-Normal errStruc" )
checkTrue( identical( dataNone$ED50 * exp(dataNone$B2), dataLogNorm$ED50), msg = "Testing the Log-Normal errStruc")
checkTrue( identical( dataNone$E0 * (1 + dataNone$B1), dataProp$E0 ), msg = "Testing the Proportional errStruc" )
checkTrue( identical( dataNone$ED50 * (1 + dataNone$B2), dataProp$ED50), msg = "Testing the Proportional errStruc")
dataNone <- createExternalParameters( 20, names = "E0,ED50", dataId="ID",
file = testParamFile, workingPath = parameters.datapath,
errStruc = "N", betNames = "B1,B2", seed = 2 )
dataAdd <- createExternalParameters( 20, names = "E0,ED50", dataId="ID",
file = testParamFile, workingPath = parameters.datapath,
errStruc = "A", betNames = "B1,B2", betNums = "2,1", seed = 2 )
checkTrue( identical( dataNone$E0 + dataNone$B2, dataAdd$E0 ), msg = "Testing the Additive errStruc and betNums" )
checkTrue( identical( dataNone$ED50 + dataNone$B1, dataAdd$ED50), msg = "Testing the Additive errStruc and betNums")
dataNone <- createExternalParameters( 20, names = "E0,ED50,EMAX", dataId="ID",
file = testParamFile, workingPath = parameters.datapath,
errStruc = "N", betNames = "B1,B2", betNums = "1,3", seed = 2 )
dataAdd <- createExternalParameters( 20, names = "E0,ED50,EMAX", dataId="ID",
file = testParamFile, workingPath = parameters.datapath,
errStruc = "A", betNames = "B1,B2", betNums = "1,3", seed = 2 )
dataLogNorm <- createExternalParameters( 20, names = "E0,ED50,EMAX", dataId="ID",
file = testParamFile, workingPath = parameters.datapath,
errStruc = "L", betNames = "B1,B2", betNums = "1,3", seed = 2 )
dataProp <- createExternalParameters( 20, names = "E0,ED50,EMAX", dataId="ID",
file = testParamFile, workingPath = parameters.datapath,
errStruc = "P", betNames = "B1,B2", betNums = "1,3", seed = 2 )
checkTrue( identical( dataNone$E0 + dataNone$B1, dataAdd$E0 ), msg = "Testing the Additive errStruc and betNums" )
checkTrue( identical( dataNone$ED50, dataAdd$ED50), msg = "Testing the Additive errStruc and betNums")
checkTrue( identical( dataNone$EMAX + dataNone$B2, dataAdd$EMAX), msg = "Testing the Additive errStruc and betNums")
checkTrue( identical( dataNone$E0 * exp(dataNone$B1), dataLogNorm$E0 ), msg = "Testing the Log-Normal errStruc and betNums" )
checkTrue( identical( dataNone$ED50, dataLogNorm$ED50), msg = "Testing the Log-Normal errStruc and betNums, variable without between should not be exponentiated when errStruc is prop")
checkTrue( identical( dataNone$EMAX * exp(dataNone$B2), dataLogNorm$EMAX), msg = "Testing the Log-Normal errStruc and betNums")
checkTrue( identical( dataNone$E0 * (1 + dataNone$B1), dataProp$E0 ), msg = "Testing the Proportional errStruc and betNums" )
checkTrue( identical( dataNone$ED50, dataProp$ED50), msg = "Testing the Proportional errStruc and betNums, variable without between should not be exponentiated when errStruc is prop")
checkTrue( identical( dataNone$EMAX * (1 + dataNone$B2), dataProp$EMAX), msg = "Testing the Proportional errStruc and betNums")
# testing the refCol settings
checkException( createExternalParameters( 20, names = "E0,ED50,EMAX", dataId="ID",
file = testParamFile, workingPath = parameters.datapath,refColName = "f09-124" ) ,
msg = "wrong refColName")
checkException( createExternalParameters( 20, names = "E0,ED50,EMAX", dataId="ID",
file = testParamFile, workingPath = parameters.datapath,refColName = "REF" ) ,
msg = "refColName not in the data")
checkException( createExternalParameters( 20, names = "E0,ED50,EMAX", dataId="ID",
file = testParamFile, workingPath = parameters.datapath,refColName = "ID", refCol = "1,2,3" ) ,
msg = "refColName not in the data")
testCovFile <- "testCovariates.csv"
importCov <- createExternalCovariates( 20, names = "X1", dataId="ID",
file = testCovFile, workingPath = covariates.datapath, refCol = "ID" )
refcolvalues <- importCov$ID.refCol
importPar <- createExternalParameters( 20, names = "B1,B2", dataId="ID",
file = testParamFile, workingPath = parameters.datapath, refColName = "ID",
refCol = refcolvalues )
iData <- read.csv( file.path( parameters.datapath, testParamFile) )[, c("ID", "B1", "B2")]
for( ref in refcolvalues ){
checkTrue( all( iData[ iData$ID == ref, "B1" ][1] == importPar[ refcolvalues == ref, "B1"] ) ,
msg = "Testing the refCol system")
}
# tests about betNums
checkException( createExternalParameters( 20, names = "E0,ED50", dataId="ID",
file = testParamFile, workingPath = parameters.datapath,
betNames = "B1,B2", betNums = "1" ),
msg = "#betNames != #betNums" )
checkException( createExternalParameters( 20, names = "E0,ED50", dataId="ID",
file = testParamFile, workingPath = parameters.datapath,
betNames = "B1,B2", betNums = "a,b" ),
msg = "wrong betNums format" )
checkException( createExternalParameters( 20, names = "E0,ED50,EMAX", dataId="ID",
file = testParamFile, workingPath = parameters.datapath,
betNames = "B1,B2" ),
msg = "Need betNums if index mismatch" )
# tests about subset
checkException( createExternalParameters( 20, names = "E0,ED50,EMAX", dataId="ID",
file = testParamFile, workingPath = parameters.datapath,
subset = "@fewf-+fw" ),
msg = "Non sense code" )
checkException( createExternalParameters( 20, names = "E0,ED50,EMAX", dataId="ID",
file = testParamFile, workingPath = parameters.datapath,
subset = "E0 < 0 < EMAX < 1 " ),
msg = "Too many comparators" )
checkException( createExternalParameters( 20, names = "E0,ED50,EMAX", dataId="ID",
file = testParamFile, workingPath = parameters.datapath,
subset = "E0" ),
msg = "Too few comparators" )
checkTrue( all( createExternalParameters( 20, names = "E0,ED50,EMAX", dataId="ID",
file = testParamFile, workingPath = parameters.datapath,
subset = "E0 < 0" )$E0 < 0 ),
msg = "test that the subset is applied correctly")
subData <- createExternalParameters( 20, names = "E0,ED50,EMAX", dataId="ID",
file = testParamFile, workingPath = parameters.datapath,
subset = c("E0 < 0", "1 <= B1 <= 2") )
checkTrue( all( subData$E0 < 0 ),
msg = "test that the subset is applied correctly with multiple subsets")
checkTrue( all( subData$B1 >= 1 & subData$B1 <= 2 ),
msg = "test that the subset is applied correctly with two comparators")
# seed
data1 <- createExternalParameters( 20, names = "E0,ED50,EMAX", dataId="ID",
file = testParamFile, workingPath = parameters.datapath,
errStruc = "A", betNames = "B1,B2", betNums = "1,3", seed = 81 )
rnorm(2100 ) + runif(2)
data2 <- createExternalParameters( 20, names = "E0,ED50,EMAX", dataId="ID",
file = testParamFile, workingPath = parameters.datapath,
errStruc = "A", betNames = "B1,B2", betNums = "1,3", seed = 81 )
checkEquals( data1, data2 )
}
test.data.param.norm <- function(){
checkException( createNormalParameters( -50 ) ,
msg = "subjects should be positive")
checkException( createNormalParameters( 50, names = "X, Y" , mean = "0,a") ,
msg = "wrong mean")
checkException( createNormalParameters( 50, names = "X,X" , mean = "0,a") ,
msg = "duplicated names")
checkException( createNormalParameters( 50, names = "X,Y" , mean = "0,0,0") ,
msg = "dimension problem")
checkException( createNormalParameters( 50, names = "X,Y,Z" ,
mean = "0,0,0", covariance = "1,0,0,-1,0,-1" ) ,
msg = "wrong covariance matrix")
checkException( createNormalParameters( 50, names = "X,Y,Z" ,
mean = "0,0,0", covariance = "1,0,0,1,0,1,2,3,4" ) ,
msg = "wrong covariance matrix dims")
checkException( createNormalParameters( 50, names = "X,Y,Z" ,
mean = "0,0,0", covariance = "1", maxDraws = -1 ) ,
msg = "wrong maxDraws value")
checkException( createNormalParameters( 50, names = "X,Y,Z" ,
mean = "0,0,0", covariance = "1", maxDraws = 5:6 ) ,
msg = "wrong maxDraws value")
checkException( createNormalParameters( 50, names = "X,Y,Z" ,
mean = "0,0,0", covariance = "1", digits = -1 ) ,
msg = "wrong digits value")
checkException( createNormalParameters( 50, names = "X,Y,Z" ,
mean = "0,0,0", covariance = "1", digits = 1:2 ) ,
msg = "wrong digits value")
checkException( createNormalParameters( 50, names = "X,Y,Z" ,
mean = "0,0,0", covariance = "1", betMean = "0",
betNames = ".45", betCov = "1" ) ,
msg = "wrong betNames value")
checkException( createNormalParameters( 50, names = "X,Y,Z" ,
mean = "0,0,0", covariance = "1", betMean = "0",
betNames = "R", betCov = "1" ) ,
msg = "wrong betNames value, not a subset of names")
checkException( createNormalParameters( 50, names = "X,Y,Z" ,
mean = "0,0,0", covariance = "1", betMean = "0",
betNames = "X", betCov = "-1" ) ,
msg = "wrong betCov matrix")
checkException( createNormalParameters( 50, names = "X,Y,Z" ,
mean = "0,0,0", covariance = "1", betMean = "0",
betNames = "X", betCov = "1,2,3" ) ,
msg = "wrong betCov matrix")
checkException( createNormalParameters( 50, names = "X,Y,Z" ,
mean = "0,0,0", covariance = "1", betMean = "0",
betNames = "X", betCov = "1", range = "]t43t534w-02354" ) ,
msg = "non sense code")
checkException( createNormalParameters( 50, names = "X,Y,Z" ,
mean = "0,0,0", covariance = "1", betMean = "0",
betNames = "X", betCov = "1", range = "X" ) ,
msg = "wrong range code, not enough comparators")
dataNone <- createNormalParameters( 50, names = "X,Y,Z" ,
mean = "0,0,0", covariance = "1", betNames = "X,Y,Z",
betCov = "1", betMean = "0,0,0", errStruc = "N", seed = 99 )
dataAdd <- createNormalParameters( 50, names = "X,Y,Z" ,
mean = "0,0,0", covariance = "1", betNames = "X,Y,Z",
betCov = "1", betMean = "0,0,0", errStruc = "A", seed = 99 )
dataLogNorm <- createNormalParameters( 50, names = "X,Y,Z" ,
mean = "0,0,0", covariance = "1", betNames = "X,Y,Z",
betCov = "1", betMean = "0,0,0", errStruc = "L", seed = 99 )
errStrucDiff <- round(dataAdd [,c("X", "Y", "Z") ] - (dataNone[,c("X", "Y", "Z") ] + dataNone[, paste( c("X", "Y", "Z") , ".Between", sep = "") ]), 2)
checkTrue( all(unlist(errStrucDiff == 0)) , msg = "checking the errStruc" )
checkTrue( all( dataLogNorm[,c("X", "Y", "Z") ] -
dataNone[,c("X", "Y", "Z") ] * exp( dataNone[,paste( c("X", "Y", "Z") , ".Between", sep ="") ] == 0) ) ,
msg = "checking the errStruc with None and Log Normal")
dataNone <- createNormalParameters( 50, names = "X,Y,Z" ,
mean = "0,50,100", covariance = "1", betNames = "X,Y",
betCov = "1", betMean = "0,0", errStruc = "None", seed = 99, digits = 10 )
dataNone$Z.Between <- rep(0, nrow(dataNone))
dataAdd <- createNormalParameters( 50, names = "X,Y,Z" ,
mean = "0,50,100", covariance = "1", betNames = "X,Y",
betCov = "1", betMean = "0,0", errStruc = "Add", seed = 99, digits = 10 )
dataLogNorm <- createNormalParameters( 50, names = "X,Y,Z" ,
mean = "0,50,100", covariance = "1", betNames = "X,Y",
betCov = "1", betMean = "0,0", errStruc = "Log", seed = 99, digits = 10 )
.roundIt <- MSToolkit:::.roundIt
checkTrue( identical( .roundIt(dataAdd [,c("X", "Y") ], 5), .roundIt(dataNone[,c("X", "Y") ] + dataNone[, paste( c("X", "Y"), ".Between", sep = "") ], 5) ) ,
msg = "check the errStruc, not all between, None and Add" )
#checkTrue( all( .roundIt(dataLogNorm[,c("Z", "Y") ] - (dataNone[,c("Z", "Y") ] * exp( dataNone[,paste( c("Z", "Y"), ".Between",sep ="") ])), 2) == 0 ) ,
# msg = "check the errStruc, not all between, None and Prop, different order")
v1 <- dataLogNorm[,c("Z", "Y") ]
v2 <- dataNone[,c("Z", "Y") ] * exp( dataNone[,paste( c("Z", "Y"), ".Between",sep ="") ])
checkEqualsNumeric(v1, v2, tolerance = 0.1, msg = "\ncheck the errStruc, not all between, None and Prop, different order(1)")
checkTrue( identical( dataAdd$Z , dataNone$Z ) , msg = "check the errStruc, not between, None and Add" )
checkTrue( identical( dataLogNorm$Z, dataNone$Z ) , msg = "check the errStruc, not between, None and Prop")
dataNone <- createNormalParameters( 50, names = "X,Y,Z" ,
mean = "0,50,100", covariance = "1", betNames = "Z,Y",
betCov = "1", betMean = "0,0", errStruc = "N", seed = 99, digits = 5 )
dataAdd <- createNormalParameters( 50, names = "X,Y,Z" ,
mean = "0,50,100", covariance = "1", betNames = "Z,Y",
betCov = "1", betMean = "0,0", errStruc = "A", seed = 99, digits = 5 )
dataLogNorm <- createNormalParameters( 50, names = "X,Y,Z" ,
mean = "0,50,100", covariance = "1", betNames = "Z,Y",
betCov = "1", betMean = "0,0", errStruc = "L", seed = 99, digits = 5 )
checkTrue( all( .roundIt(dataAdd [,c("Z", "Y") ]- (dataNone[,c("Z", "Y") ] + dataNone[,paste( c("Z", "Y"), ".Between",sep = "") ]), 3) ==0) ,
msg = "check the errStruc, not all between, None and Prop, different order")
#checkTrue( all( .roundIt(dataLogNorm[,c("Z", "Y") ] - (dataNone[,c("Z", "Y") ] * exp( dataNone[,paste( c("Z", "Y"), ".Between",sep ="") ])), 2) == 0 ) ,
# msg = "check the errStruc, not all between, None and Prop, different order")
v1 <- dataLogNorm[,c("Z", "Y") ]
v2 <- dataNone[,c("Z", "Y") ] * exp( dataNone[,paste( c("Z", "Y"), ".Between",sep ="") ])
checkEqualsNumeric(v1, v2, tolerance = 0.1, msg = "\ncheck the errStruc, not all between, None and Prop, different order(2)")
checkTrue( all( dataAdd$X - dataNone$X ==0) ,
msg = "check the errStruc, not between, None and Prop, different order")
checkTrue( all( dataLogNorm$X - dataNone$X ==0 ) ,
msg = "check the errStruc, not between, None and Prop, different order")
# check the outputs
dataFixed <- createNormalParameters( 50, names = "X,Y,Z" ,
mean = "0,50,100", covariance = "1" )
for( va in c("X", "Y", "Z")) {
checkTrue( all(diff( dataFixed[[va]] ) == 0), msg = "check the fixed parameters")
}
}
test.data.param.wrap <- function(){
testParamFile <- "testParam.csv"
wrongTestParamFile <- "wrongTestParam.csv"
checkException( createParameters( -10 ),
msg = "wrong subject (negative)" )
checkException( createParameters( 10, idCol = "ID, SUB" ),
msg = "wrong id (too long)" )
checkException( createParameters( 10, idCol = "08234ID" ),
msg = "wrong id" )
checkException( createParameters( 10, flagName = "PAROMIT, OMIT" ),
msg = "wrong flagName (too long)" )
checkException( createParameters( 10, idCol = "082PAROMIT" ),
msg = "wrong flagName" )
d1 <- createNormalParameters( 50, names = "X,Y,Z" ,
mean = "0,0,0", covariance = "1", betNames = "X,Y,Z",
betCov = "1", betMean = "0,0,0", errStruc = "A", seed = 99 )
d2 <- createParameters( 50, genNames = "X,Y,Z" ,
genFixedMean = "0,0,0", genFixedCov = "1", genBetweenNames = "X,Y,Z",
genBetweenCov = "1", genBetweenMean = "0,0,0", genErrStruc = "A", seed = 99 )
checkTrue( identical( d1, d2 ),
msg = "only normal" )
d1 <- createExternalParameters( 20, names = "E0,ED50,EMAX",
file = testParamFile, workingPath = parameters.datapath, dataId = "ID",
errStruc = "A", betNames = "B1,B2", betNums = "1,3", seed = 81 )
d2 <- createParameters( 20, extNames = "E0,ED50,EMAX", extDataId="ID",
extFile = testParamFile, workingPath = parameters.datapath,
extErrStruc = "A", extBetween = "B1,B2", extBetweenNums = "1,3",
seed = 81 )
checkTrue( identical( d1, d2 ),
msg = "only external" )
dNor <- createNormalParameters( 50, names = "X,Y,Z" ,
mean = "0,0,0", covariance = "1", betNames = "X,Y,Z",
betCov = "1", betMean = "0,0,0", errStruc = "A", seed = 81 )
dExt <- createExternalParameters( 50, names = "E0,ED50,EMAX", dataId="ID",
file = testParamFile, workingPath = parameters.datapath,
errStruc = "A", betNames = "B1,B2", betNums = "1,3", seed = 81 )
dAll <- createParameters( 50, extNames = "E0,ED50,EMAX",
extFile = testParamFile, workingPath = parameters.datapath,
extErrStruc = "A", extBetween = "B1,B2", extBetweenNums = "1,3", extDataId="ID",
seed = 81,
genNames = "X,Y,Z", genFixedMean = "0,0,0", genFixedCov = "1",
genBetweenNames = "X,Y,Z",
genBetweenCov = "1", genBetweenMean = "0,0,0", genErrStruc = "A" )
checkTrue( identical( dNor[, c("SUBJ", "X", "Y", "Z") ] , dAll[, c("SUBJ", "X", "Y", "Z")] ) ,
msg = "all + nor")
checkTrue( identical( dExt[,c("SUBJ", "E0", "ED50", "EMAX")], dAll[, c("SUBJ", "E0", "ED50", "EMAX")] ) ,
msg = "all + ext")
dNor <- createNormalParameters( 50, names = "X,Y,Z" ,
mean = "0,0,0", covariance = "1", betNames = "X,Y,Z",
betCov = "1", betMean = "0,0,0", errStruc = "A", seed = 81,
range = "Y < 3" )
dExt <- createExternalParameters( 50, names = "E0,ED50,EMAX",
file = testParamFile, workingPath = parameters.datapath, dataId="ID",
errStruc = "A", betNames = "B1,B2", betNums = "1,3", seed = 81,
)
dAll <- createParameters( 50, extNames = "E0,ED50,EMAX",
extFile = testParamFile, workingPath = parameters.datapath,
extErrStruc = "A", extBetween = "B1,B2", extBetweenNums = "1,3", extDataId="ID",
seed = 81,
genNames = "X,Y,Z", genFixedMean = "0,0,0", genFixedCov = "1",
genBetweenNames = "X,Y,Z",
genBetweenCov = "1", genBetweenMean = "0,0,0", genErrStruc = "A",
genRange = "Y < 3")
checkTrue( identical( dNor[, c("SUBJ", "X", "Y", "Z") ] , dAll[, c("SUBJ", "X", "Y", "Z")] ) ,
msg = "all + nor")
checkTrue( identical( dExt[,c("SUBJ", "E0", "ED50", "EMAX")], dAll[, c("SUBJ", "E0", "ED50", "EMAX")] ) ,
msg = "all + ext")
checkEquals( dNor$PAROMIT , dAll$PAROMIT,
msg = "checking the PAROMIT")
}
test.parameter.sf3 <- function() {
checkException( createNormalParameters( 50, names = "X,Y,Z" ,
mean = "100,100,100", covariance = "1", betNames = "X,Y",
betCov = "1", betMean = "0,0", errStruc = "N", digits = -1),
msg = "digits should be positive")
dataNone <- createNormalParameters( 50, names = "X,Y,Z" ,
mean = "100,100,100", covariance = "1", betNames = "X,Y",
betCov = "1", betMean = "0,0", errStruc = "N", digits = "2" )
dataAdd <- createNormalParameters( 50, names = "X,Y,Z" ,
mean = "100,100,100", covariance = "1", betNames = "X,Y",
betCov = "1", betMean = "0,0", errStruc = "A", digits = "2")
dataLogNorm <- createNormalParameters( 50, names = "X,Y,Z" ,
mean = "100,100,100", covariance = "1", betNames = "X,Y",
betCov = "1", betMean = "0,0", errStruc = "L", digits = "2")
checkEquals( dataAdd[, c("X", "Y", "Z")], round(dataAdd[, c("X", "Y", "Z")],2),
msg = "check the atomic digits (add)" )
checkEquals( dataLogNorm[, c("X", "Y", "Z")], round(dataLogNorm[, c("X", "Y", "Z")],2),
msg = "check the atomic digits (prop)" )
checkEquals( dataNone[, c("X", "Y", "Z", "X.Between", "Y.Between")],
round(dataNone[, c("X", "Y", "Z", "X.Between", "Y.Between")],2),
msg = "check the atomic digits (prop)" )
dataNone <- createNormalParameters( 50, names = "X,Y,Z" ,
mean = "100,100,100", covariance = "1", betNames = "X,Y",
betCov = "1", betMean = "0,0", errStruc = "N", digits = "2,3,2" )
dataAdd <- createNormalParameters( 50, names = "X,Y,Z" ,
mean = "100,100,100", covariance = "1", betNames = "X,Y",
betCov = "1", betMean = "0,0", errStruc = "A", digits = "2,3,2")
dataLogNorm <- createNormalParameters( 50, names = "X,Y,Z" ,
mean = "100,100,100", covariance = "1", betNames = "X,Y",
betCov = "1", betMean = "0,0", errStruc = "L", digits = "2,3,2")
checkEquals( dataAdd$X, round(dataAdd$X,2), msg = "check the vector digits (add,X)" )
checkEquals( dataAdd$Y, round(dataAdd$Y,3), msg = "check the vector digits (add,Y)" )
checkEquals( dataAdd$Z, round(dataAdd$Z,2), msg = "check the vector digits (add,Y)" )
checkEquals( dataLogNorm$X, round(dataLogNorm$X,2), msg = "check the vector digits (Prop,X)" )
checkEquals( dataLogNorm$Y, round(dataLogNorm$Y,3), msg = "check the vector digits (Prop,Y)" )
checkEquals( dataLogNorm$Z, round(dataLogNorm$Z,2), msg = "check the vector digits (Prop,Y)" )
checkEquals( dataNone$X, round(dataNone$X,2), msg = "check the vector digits (None,X)" )
checkEquals( dataNone$Y, round(dataNone$Y,3), msg = "check the vector digits (None,Y)" )
checkEquals( dataNone$Z, round(dataNone$Z,2), msg = "check the vector digits (None,Y)" )
checkEquals( dataNone$X.Between, round(dataNone$X.Between,2), msg = "check the vector digits (None,X.Between)" )
checkEquals( dataNone$Y.Between, round(dataNone$Y.Between,3), msg = "check the vector digits (None,Y.Between)" )
}
# SF issue 8
# Tue Jul 24 10:40:43 BST 2007 @444 /Internet Time/
test.parameter.sf8 <- function(){
# checking betCov = 0 by default
dataNone <- createNormalParameters( 50, names = "X,Y,Z" ,
mean = "0,50,100", betNames = "X,Y", covariance = "1",
betMean = "0,0", errStruc = "N", seed = 99 )
checkTrue( all( dataNone[,c("X.Between", "Y.Between")] == 0),
msg = "checking 0 covariance by default for between effects")
data.sf8 <- createNormalParameters( 500, names = "X,Y,Z" , mean = "0,50,100", seed = 99 )
checkTrue(all(sweep( data.sf8[, c("X", "Y", "Z")] ,2, c(0,50,100), "-")==0) ,
msg = "checking the 0 covariance by default")
}
test.parameter.rangeExclude <- function(){
# checking betCov = 0 by default
checkException(createNormalParameters( 500, names = "X,Y,Z" ,
mean = "0,50,100", covariance = "1",
betNames = "X,Y", betCov = "1",
errStruc = "A", seed = 99,
range = "Y < 50", maxDraws = 1, parRangeTolerance = .9 ), msg = "Bad range specified")
checkTrue(is.data.frame(createNormalParameters( 500, names = "X,Y,Z" ,
mean = "0,50,100", covariance = "1",
betNames = "X,Y", betCov = "1",
errStruc = "A", seed = 99,
range = "Y < 100", maxDraws = 1, parRangeTolerance = .9 )), msg = "Good range specified")
warnData <- suppressWarnings(createNormalParameters( 500, names = "X,Y,Z" ,
mean = "0,50,100", covariance = "1",
betNames = "X,Y", betCov = "1",
errStruc = "A", seed = 99,
range = "Y < 50", parRangeTolerance = .1, maxDraws = 1 ))
checkTrue(is.data.frame(warnData) & any(warnData$PAROMIT == 1), msg = "Dataset returned with parameter omits")
}
Try the MSToolkit package in your browser
Any scripts or data that you put into this service are public.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.