tests/testthat/test.data.parameter.R
In MikeKSmith/MSToolkit: The MSToolkit Library For Clinical Trial Design
# test_that("test.data.param.ext", {
# testParamFile <- "testParam.csv"
# otherFiles <- paste("testParam", c("nonmem", "spaceDelim",
# "tabDelim"), sep = ".")
# wrongTestParamFile <- "wrongTestParam.csv"
# expect_error(createExternalParameters(-20), info = "`subjects` must be positive")
# expect_error(createExternalParameters(20, names = ".54325,5432"),
# info = "invalid `names`")
# expect_error(createExternalParameters(20, names = "X,X"),
# info = "duplicated `names`")
# expect_error(createExternalParameters(20, names = "X,Y",
# idCol = "X"), info = "duplicated names between `SUBJ` and `names`")
# expect_error(createExternalParameters(20, names = "X", dataId = ".54325"),
# info = "invalid `dataId`")
# expect_error(createExternalParameters(20, names = "X", dataId = "ID,SUB"),
# info = "`dataId` should be of length one")
# expect_error(createExternalParameters(20, names = "X", idCol = ".54325"),
# info = "invalid `idCol`")
# expect_error(createExternalParameters(20, names = "X", idCol = "ID,SUB"),
# info = "`idCol` should be of length one")
# expect_error(createExternalParameters(20, names = "E0,ED50",
# file = testParamFile, workingPath = parameters.datapath,
# betNames = "B1,B1"), info = "Duplicated values in betNames")
# expect_error(createExternalParameters(20, names = "E0,ED50,EMAX",
# file = "doesNotExists.csv", workingPath = parameters.datapath),
# info = "File does not exist")
# expect_error(createExternalParameters(20, names = "E0,ED50,EMAX",
# file = wrongTestParamFile, workingPath = parameters.datapath),
# info = "wrong formatted file")
# expect_error(createExternalParameters(20, names = "X,Y,ED50",
# dataId = "ID", file = testParamFile, workingPath = parameters.datapath),
# info = "missing variables in file")
# expect_error(createExternalParameters(20, names = "E0,ED50",
# file = testParamFile, workingPath = parameters.datapath,
# idCol = "SUB"), info = "missing ID variables in file")
# expect_error(createExternalParameters(20, names = "E0,ED50",
# dataId = "ID", file = testParamFile, workingPath = parameters.datapath,
# errStruc = "w"), info = "wrong errStruc")
# 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)
# expect_true(all(dim(dataNone) == dim(newData)), info = paste("Check correct dimensions when importing",
# i))
# expect_true(all(names(dataNone) == names(newData)), info = paste("Check correct column names when importing",
# i))
# expect_true(all(round(dataNone$ED50, 3) == newData$ED50),
# info = paste("Check correct ED50 column when importing",
# i))
# expect_true(all(round(dataNone$B1, 3) == newData$B1),
# info = paste("Check correct B1 column when importing",
# i))
# }
# 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)
# expect_true(identical(dataNone$E0 + dataNone$B1, dataAdd$E0),
# info = "Testing the Additive errStruc")
# expect_true(identical(dataNone$ED50 + dataNone$B2, dataAdd$ED50),
# info = "Testing the Additive errStruc")
# expect_true(identical(dataNone$E0 * exp(dataNone$B1), dataLogNorm$E0),
# info = "Testing the Log-Normal errStruc")
# expect_true(identical(dataNone$ED50 * exp(dataNone$B2), dataLogNorm$ED50),
# info = "Testing the Log-Normal errStruc")
# expect_true(identical(dataNone$E0 * (1 + dataNone$B1), dataProp$E0),
# info = "Testing the Proportional errStruc")
# expect_true(identical(dataNone$ED50 * (1 + dataNone$B2),
# dataProp$ED50), info = "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)
# expect_true(identical(dataNone$E0 + dataNone$B2, dataAdd$E0),
# info = "Testing the Additive errStruc and betNums")
# expect_true(identical(dataNone$ED50 + dataNone$B1, dataAdd$ED50),
# info = "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)
# expect_true(identical(dataNone$E0 + dataNone$B1, dataAdd$E0),
# info = "Testing the Additive errStruc and betNums")
# expect_true(identical(dataNone$ED50, dataAdd$ED50), info = "Testing the Additive errStruc and betNums")
# expect_true(identical(dataNone$EMAX + dataNone$B2, dataAdd$EMAX),
# info = "Testing the Additive errStruc and betNums")
# expect_true(identical(dataNone$E0 * exp(dataNone$B1), dataLogNorm$E0),
# info = "Testing the Log-Normal errStruc and betNums")
# expect_true(identical(dataNone$ED50, dataLogNorm$ED50), info = "Testing the Log-Normal errStruc and betNums, variable without between should not be exponentiated when errStruc is prop")
# expect_true(identical(dataNone$EMAX * exp(dataNone$B2), dataLogNorm$EMAX),
# info = "Testing the Log-Normal errStruc and betNums")
# expect_true(identical(dataNone$E0 * (1 + dataNone$B1), dataProp$E0),
# info = "Testing the Proportional errStruc and betNums")
# expect_true(identical(dataNone$ED50, dataProp$ED50), info = "Testing the Proportional errStruc and betNums, variable without between should not be exponentiated when errStruc is prop")
# expect_true(identical(dataNone$EMAX * (1 + dataNone$B2),
# dataProp$EMAX), info = "Testing the Proportional errStruc and betNums")
# expect_error(createExternalParameters(20, names = "E0,ED50,EMAX",
# dataId = "ID", file = testParamFile, workingPath = parameters.datapath,
# refColName = "f09-124"), info = "wrong refColName")
# expect_error(createExternalParameters(20, names = "E0,ED50,EMAX",
# dataId = "ID", file = testParamFile, workingPath = parameters.datapath,
# refColName = "REF"), info = "refColName not in the data")
# expect_error(createExternalParameters(20, names = "E0,ED50,EMAX",
# dataId = "ID", file = testParamFile, workingPath = parameters.datapath,
# refColName = "ID", refCol = "1,2,3"), info = "refColName not in the data")
# testCovFile <- "testCovariates.csv"
# importCov <- createExternalCovariates(20, names = "X1", dataId = "ID",
# file = testCovFile, workingPath = covariates.datapath,
# refCol = "ID")
# refcolvalues <- importCov$ID.refCol
# importPar <- createExternalParameters(20, names = "B1,B2",
# dataId = "ID", file = testParamFile, workingPath = parameters.datapath,
# refColName = "ID", refCol = refcolvalues)
# iData <- read.csv(file.path(parameters.datapath, testParamFile))[,
# c("ID", "B1", "B2")]
# for (ref in refcolvalues) {
# expect_true(all(iData[iData$ID == ref, "B1"][1] == importPar[refcolvalues ==
# ref, "B1"]), info = "Testing the refCol system")
# }
# expect_error(createExternalParameters(20, names = "E0,ED50",
# dataId = "ID", file = testParamFile, workingPath = parameters.datapath,
# betNames = "B1,B2", betNums = "1"), info = "#betNames != #betNums")
# expect_error(createExternalParameters(20, names = "E0,ED50",
# dataId = "ID", file = testParamFile, workingPath = parameters.datapath,
# betNames = "B1,B2", betNums = "a,b"), info = "wrong betNums format")
# expect_error(createExternalParameters(20, names = "E0,ED50,EMAX",
# dataId = "ID", file = testParamFile, workingPath = parameters.datapath,
# betNames = "B1,B2"), info = "Need betNums if index mismatch")
# expect_error(createExternalParameters(20, names = "E0,ED50,EMAX",
# dataId = "ID", file = testParamFile, workingPath = parameters.datapath,
# subset = "@fewf-+fw"), info = "Non sense code")
# expect_error(createExternalParameters(20, names = "E0,ED50,EMAX",
# dataId = "ID", file = testParamFile, workingPath = parameters.datapath,
# subset = "E0 < 0 < EMAX < 1 "), info = "Too many comparators")
# expect_error(createExternalParameters(20, names = "E0,ED50,EMAX",
# dataId = "ID", file = testParamFile, workingPath = parameters.datapath,
# subset = "E0"), info = "Too few comparators")
# expect_true(all(createExternalParameters(20, names = "E0,ED50,EMAX",
# dataId = "ID", file = testParamFile, workingPath = parameters.datapath,
# subset = "E0 < 0")$E0 < 0), info = "test that the subset is applied correctly")
# subData <- createExternalParameters(20, names = "E0,ED50,EMAX",
# dataId = "ID", file = testParamFile, workingPath = parameters.datapath,
# subset = c("E0 < 0", "1 <= B1 <= 2"))
# expect_true(all(subData$E0 < 0), info = "test that the subset is applied correctly with multiple subsets")
# expect_true(all(subData$B1 >= 1 & subData$B1 <= 2), info = "test that the subset is applied correctly with two comparators")
# 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)
# expect_equal(data2, data1)
# })
test_that("test.data.param.norm", {
expect_error(createNormalParameters(-50),
info = "subjects must be positive")
expect_error(createNormalParameters(50,
names = "X, Y",
mean = "0,a"),
regexp = "Impossible to convert to numbers")
expect_error(createNormalParameters(50,
names = "X,X",
mean = "0,1"),
info = "Duplicated values in names")
expect_error(createNormalParameters(50,
names = "X,Y",
mean = "0,0,0"),
regexp = "wrong length")
expect_error(createNormalParameters(50,
names = "X,Y,Z",
mean = "0,0,0",
covariance = "1,1,1,1"),
regexp = "Dimension Problem")
expect_error(createNormalParameters(50,
names = "X,Y,Z",
mean = "0,0,0",
covariance = "1,-2,1,0,-2,1"),
info = "matrix not positive definite")
expect_error(createNormalParameters(50,
names = "X,Y,Z",
mean = "0,0,0",
covariance = "1",
maxDraws = -1),
regexp = "maximum number of draws should be a positive integer")
expect_error(createNormalParameters(50,
names = "X,Y,Z",
mean = "0,0,0",
covariance = "1",
maxDraws = 5:6),
regexp = "wrong length")
expect_error(createNormalParameters(50,
names = "X,Y,Z",
mean = "0,0,0",
covariance = "1",
digits = -1),
regexp = "`digits` argument must be positive")
expect_error(createNormalParameters(50,
names = "X,Y,Z",
mean = "0,0,0",
covariance = "1",
digits = 1:2),
regexp = "`digits should be of length one or 3, not 2`")
expect_error(createNormalParameters(50,
names = "X,Y,Z",
mean = "0,0,0",
covariance = "1",
betMean = "0",
betNames = ".45",
betCov = "1"),
regexp = "invalid R name")
expect_error(createNormalParameters(50,
names = "X,Y,Z",
mean = "0,0,0",
covariance = "1",
betMean = "0",
betNames = "R",
betCov = "1"),
regexp = "between subject effects don't have a corresponding fixed parameter")
expect_error(createNormalParameters(50,
names = "X,Y,Z",
mean = "0,0,0",
covariance = "1",
betMean = "0",
betNames = "X",
betCov = "-1"),
regexp = "matrix not positive definite")
expect_error(createNormalParameters(50,
names = "X,Y,Z",
mean = "0,0,0",
covariance = "1",
betMean = "0",
betNames = "X",
betCov = "1,2,3"),
regexp = "Dimension problem")
expect_error(createNormalParameters(50,
names = "X,Y,Z",
mean = "0,0,0",
covariance = "1",
betMean = "0",
betNames = "X",
betCov = "1",
range = "]t43t534w-02354"),
regexp = "No comparator in the code")
expect_error(createNormalParameters(50,
names = "X,Y,Z",
mean = "0,0,0",
covariance = "1",
betMean = "0",
betNames = "X",
betCov = "1",
range = "X"),
regexp = "No comparator in the code")
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)
expect_true(all(unlist(errStrucDiff == 0)))
logNorm <- dataLogNorm[1, c("X", "Y", "Z")]
logNorm2 <- dataNone[1, c("X", "Y", "Z")] *
exp(dataNone[1, paste(c("X", "Y", "Z"), ".Between", sep = "")])
logNorm3 <- round(logNorm2,3)
expect_true(all(logNorm - logNorm3 == 0))
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$Z.Between <- rep(0, nrow(dataNone))
dataAdd <- createNormalParameters(50,
names = "X,Y,Z",
mean = "0,50,100",
covariance = "1",
betNames = "X,Y",
betCov = "1",
betMean = "0,0",
errStruc = "Add",
seed = 99,
digits = 10)
dataLogNorm <- createNormalParameters(50,
names = "X,Y,Z",
mean = "0,50,100",
covariance = "1",
betNames = "X,Y",
betCov = "1",
betMean = "0,0",
errStruc = "Log",
seed = 99,
digits = 10)
.roundIt <- MSToolkit:::.roundIt
expect_true(identical(.roundIt(dataAdd[, c("X", "Y")], 5),
.roundIt(dataNone[, c("X", "Y")] +
dataNone[, paste(c("X", "Y"),
".Between",
sep = "")],
5)))
v1 <- dataLogNorm[, c("Z", "Y")]
v2 <- dataNone[, c("Z", "Y")] * exp(dataNone[, paste(c("Z","Y"),
".Between",
sep = "")])
expect_equal(v2, v1)
expect_equal(dataAdd$Z, dataNone$Z, tolerance = 0.00001)
expect_equal(dataLogNorm$Z, dataNone$Z, tolerance = 0.00001)
dataNone <- createNormalParameters(50,
names = "X,Y,Z",
mean = "0,50,100",
covariance = "1",
betNames = "Z,Y",
betCov = "1",
betMean = "0,0",
errStruc = "N",
seed = 99,
digits = 5)
dataAdd <- createNormalParameters(50,
names = "X,Y,Z",
mean = "0,50,100",
covariance = "1",
betNames = "Z,Y",
betCov = "1",
betMean = "0,0",
errStruc = "A",
seed = 99,
digits = 5)
dataLogNorm <- createNormalParameters(50,
names = "X,Y,Z",
mean = "0,50,100",
covariance = "1",
betNames = "Z,Y",
betCov = "1",
betMean = "0,0",
errStruc = "L",
seed = 99,
digits = 5)
expect_true(all(.roundIt(dataAdd[, c("Z", "Y")] -
(dataNone[,c("Z", "Y")] +
dataNone[, paste(c("Z", "Y"), ".Between",sep = "")]
), 3)
== 0))
v1 <- dataLogNorm[, c("Z", "Y")]
v2 <- dataNone[, c("Z", "Y")] *
exp(dataNone[, paste(c("Z", "Y"), ".Between", sep = "")])
expect_equal(v2, v1, tolerance=0.001)
expect_true(all(dataAdd$X - dataNone$X == 0))
expect_true(all(dataLogNorm$X - dataNone$X == 0))
dataFixed <- createNormalParameters(50,
names = "X,Y,Z",
mean = "0,50,100",
covariance = "1")
for (va in c("X", "Y", "Z")) {
expect_true(all(diff(dataFixed[[va]]) == 0))
}
})
# test_that("test.data.param.wrap", {
# testParamFile <- "testParam.csv"
# wrongTestParamFile <- "wrongTestParam.csv"
# expect_error(createParameters(-10), info = "wrong subject (negative)")
# expect_error(createParameters(10, idCol = "ID, SUB"), info = "wrong id (too long)")
# expect_error(createParameters(10, idCol = "08234ID"), info = "wrong id")
# expect_error(createParameters(10, flagName = "PAROMIT, OMIT"),
# info = "wrong flagName (too long)")
# expect_error(createParameters(10, idCol = "082PAROMIT"),
# info = "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)
# expect_true(identical(d1, d2), info = "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)
# expect_true(identical(d1, d2), info = "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")
# expect_true(identical(dNor[, c("SUBJ", "X", "Y", "Z")], dAll[,
# c("SUBJ", "X", "Y", "Z")]), info = "all + nor")
# expect_true(identical(dExt[, c("SUBJ", "E0", "ED50", "EMAX")],
# dAll[, c("SUBJ", "E0", "ED50", "EMAX")]), info = "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")
# expect_true(identical(dNor[, c("SUBJ", "X", "Y", "Z")], dAll[,
# c("SUBJ", "X", "Y", "Z")]), info = "all + nor")
# expect_true(identical(dExt[, c("SUBJ", "E0", "ED50", "EMAX")],
# dAll[, c("SUBJ", "E0", "ED50", "EMAX")]), info = "all + ext")
# expect_equal(dAll$PAROMIT, dNor$PAROMIT, info = "checking the PAROMIT")
# })
#
# test_that("test.parameter.rangeExclude", {
# expect_error(createNormalParameters(500, names = "X,Y,Z",
# mean = "0,50,100", covariance = "1", betNames = "X,Y",
# betCov = "1", errStruc = "A", seed = 99, range = "Y < 50",
# maxDraws = 1, parRangeTolerance = 0.9), info = "Bad range specified")
# expect_true(is.data.frame(createNormalParameters(500, names = "X,Y,Z",
# mean = "0,50,100", covariance = "1", betNames = "X,Y",
# betCov = "1", errStruc = "A", seed = 99, range = "Y < 100",
# maxDraws = 1, parRangeTolerance = 0.9)), info = "Good range specified")
# warnData <- suppressWarnings(createNormalParameters(500,
# names = "X,Y,Z", mean = "0,50,100", covariance = "1",
# betNames = "X,Y", betCov = "1", errStruc = "A", seed = 99,
# range = "Y < 50", parRangeTolerance = 0.1, maxDraws = 1))
# expect_true(is.data.frame(warnData) & any(warnData$PAROMIT ==
# 1), info = "Dataset returned with parameter omits")
# })
#
# test_that("test.parameter.sf3", {
# expect_error(createNormalParameters(50, names = "X,Y,Z",
# mean = "100,100,100", covariance = "1", betNames = "X,Y",
# betCov = "1", betMean = "0,0", errStruc = "N", digits = -1),
# info = "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")
# expect_equal(round(dataAdd[, c("X", "Y", "Z")], 2), dataAdd[,
# c("X", "Y", "Z")], info = "check the atomic digits (add)")
# expect_equal(round(dataLogNorm[, c("X", "Y", "Z")], 2), dataLogNorm[,
# c("X", "Y", "Z")], info = "check the atomic digits (prop)")
# expect_equal(round(dataNone[, c("X", "Y", "Z", "X.Between",
# "Y.Between")], 2), dataNone[, c("X", "Y", "Z", "X.Between",
# "Y.Between")], info = "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")
# expect_equal(round(dataAdd$X, 2), dataAdd$X, info = "check the vector digits (add,X)")
# expect_equal(round(dataAdd$Y, 3), dataAdd$Y, info = "check the vector digits (add,Y)")
# expect_equal(round(dataAdd$Z, 2), dataAdd$Z, info = "check the vector digits (add,Y)")
# expect_equal(round(dataLogNorm$X, 2), dataLogNorm$X, info = "check the vector digits (Prop,X)")
# expect_equal(round(dataLogNorm$Y, 3), dataLogNorm$Y, info = "check the vector digits (Prop,Y)")
# expect_equal(round(dataLogNorm$Z, 2), dataLogNorm$Z, info = "check the vector digits (Prop,Y)")
# expect_equal(round(dataNone$X, 2), dataNone$X, info = "check the vector digits (None,X)")
# expect_equal(round(dataNone$Y, 3), dataNone$Y, info = "check the vector digits (None,Y)")
# expect_equal(round(dataNone$Z, 2), dataNone$Z, info = "check the vector digits (None,Y)")
# expect_equal(round(dataNone$X.Between, 2), dataNone$X.Between,
# info = "check the vector digits (None,X.Between)")
# expect_equal(round(dataNone$Y.Between, 3), dataNone$Y.Between,
# info = "check the vector digits (None,Y.Between)")
# })
#
# test_that("test.parameter.sf8", {
# dataNone <- createNormalParameters(50, names = "X,Y,Z", mean = "0,50,100",
# betNames = "X,Y", covariance = "1", betMean = "0,0",
# errStruc = "N", seed = 99)
# expect_true(all(dataNone[, c("X.Between", "Y.Between")] ==
# 0), info = "checking 0 covariance by default for between effects")
# data.sf8 <- createNormalParameters(500, names = "X,Y,Z",
# mean = "0,50,100", seed = 99)
# expect_true(all(sweep(data.sf8[, c("X", "Y", "Z")], 2, c(0,
# 50, 100), "-") == 0), info = "checking the 0 covariance by default")
# })
#
MikeKSmith/MSToolkit documentation built on Feb. 15, 2024, 5:32 p.m.
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# test_that("test.data.param.ext", {
# testParamFile <- "testParam.csv"
# otherFiles <- paste("testParam", c("nonmem", "spaceDelim",
# "tabDelim"), sep = ".")
# wrongTestParamFile <- "wrongTestParam.csv"
# expect_error(createExternalParameters(-20), info = "`subjects` must be positive")
# expect_error(createExternalParameters(20, names = ".54325,5432"),
# info = "invalid `names`")
# expect_error(createExternalParameters(20, names = "X,X"),
# info = "duplicated `names`")
# expect_error(createExternalParameters(20, names = "X,Y",
# idCol = "X"), info = "duplicated names between `SUBJ` and `names`")
# expect_error(createExternalParameters(20, names = "X", dataId = ".54325"),
# info = "invalid `dataId`")
# expect_error(createExternalParameters(20, names = "X", dataId = "ID,SUB"),
# info = "`dataId` should be of length one")
# expect_error(createExternalParameters(20, names = "X", idCol = ".54325"),
# info = "invalid `idCol`")
# expect_error(createExternalParameters(20, names = "X", idCol = "ID,SUB"),
# info = "`idCol` should be of length one")
# expect_error(createExternalParameters(20, names = "E0,ED50",
# file = testParamFile, workingPath = parameters.datapath,
# betNames = "B1,B1"), info = "Duplicated values in betNames")
# expect_error(createExternalParameters(20, names = "E0,ED50,EMAX",
# file = "doesNotExists.csv", workingPath = parameters.datapath),
# info = "File does not exist")
# expect_error(createExternalParameters(20, names = "E0,ED50,EMAX",
# file = wrongTestParamFile, workingPath = parameters.datapath),
# info = "wrong formatted file")
# expect_error(createExternalParameters(20, names = "X,Y,ED50",
# dataId = "ID", file = testParamFile, workingPath = parameters.datapath),
# info = "missing variables in file")
# expect_error(createExternalParameters(20, names = "E0,ED50",
# file = testParamFile, workingPath = parameters.datapath,
# idCol = "SUB"), info = "missing ID variables in file")
# expect_error(createExternalParameters(20, names = "E0,ED50",
# dataId = "ID", file = testParamFile, workingPath = parameters.datapath,
# errStruc = "w"), info = "wrong errStruc")
# 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)
# expect_true(all(dim(dataNone) == dim(newData)), info = paste("Check correct dimensions when importing",
# i))
# expect_true(all(names(dataNone) == names(newData)), info = paste("Check correct column names when importing",
# i))
# expect_true(all(round(dataNone$ED50, 3) == newData$ED50),
# info = paste("Check correct ED50 column when importing",
# i))
# expect_true(all(round(dataNone$B1, 3) == newData$B1),
# info = paste("Check correct B1 column when importing",
# i))
# }
# 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)
# expect_true(identical(dataNone$E0 + dataNone$B1, dataAdd$E0),
# info = "Testing the Additive errStruc")
# expect_true(identical(dataNone$ED50 + dataNone$B2, dataAdd$ED50),
# info = "Testing the Additive errStruc")
# expect_true(identical(dataNone$E0 * exp(dataNone$B1), dataLogNorm$E0),
# info = "Testing the Log-Normal errStruc")
# expect_true(identical(dataNone$ED50 * exp(dataNone$B2), dataLogNorm$ED50),
# info = "Testing the Log-Normal errStruc")
# expect_true(identical(dataNone$E0 * (1 + dataNone$B1), dataProp$E0),
# info = "Testing the Proportional errStruc")
# expect_true(identical(dataNone$ED50 * (1 + dataNone$B2),
# dataProp$ED50), info = "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)
# expect_true(identical(dataNone$E0 + dataNone$B2, dataAdd$E0),
# info = "Testing the Additive errStruc and betNums")
# expect_true(identical(dataNone$ED50 + dataNone$B1, dataAdd$ED50),
# info = "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)
# expect_true(identical(dataNone$E0 + dataNone$B1, dataAdd$E0),
# info = "Testing the Additive errStruc and betNums")
# expect_true(identical(dataNone$ED50, dataAdd$ED50), info = "Testing the Additive errStruc and betNums")
# expect_true(identical(dataNone$EMAX + dataNone$B2, dataAdd$EMAX),
# info = "Testing the Additive errStruc and betNums")
# expect_true(identical(dataNone$E0 * exp(dataNone$B1), dataLogNorm$E0),
# info = "Testing the Log-Normal errStruc and betNums")
# expect_true(identical(dataNone$ED50, dataLogNorm$ED50), info = "Testing the Log-Normal errStruc and betNums, variable without between should not be exponentiated when errStruc is prop")
# expect_true(identical(dataNone$EMAX * exp(dataNone$B2), dataLogNorm$EMAX),
# info = "Testing the Log-Normal errStruc and betNums")
# expect_true(identical(dataNone$E0 * (1 + dataNone$B1), dataProp$E0),
# info = "Testing the Proportional errStruc and betNums")
# expect_true(identical(dataNone$ED50, dataProp$ED50), info = "Testing the Proportional errStruc and betNums, variable without between should not be exponentiated when errStruc is prop")
# expect_true(identical(dataNone$EMAX * (1 + dataNone$B2),
# dataProp$EMAX), info = "Testing the Proportional errStruc and betNums")
# expect_error(createExternalParameters(20, names = "E0,ED50,EMAX",
# dataId = "ID", file = testParamFile, workingPath = parameters.datapath,
# refColName = "f09-124"), info = "wrong refColName")
# expect_error(createExternalParameters(20, names = "E0,ED50,EMAX",
# dataId = "ID", file = testParamFile, workingPath = parameters.datapath,
# refColName = "REF"), info = "refColName not in the data")
# expect_error(createExternalParameters(20, names = "E0,ED50,EMAX",
# dataId = "ID", file = testParamFile, workingPath = parameters.datapath,
# refColName = "ID", refCol = "1,2,3"), info = "refColName not in the data")
# testCovFile <- "testCovariates.csv"
# importCov <- createExternalCovariates(20, names = "X1", dataId = "ID",
# file = testCovFile, workingPath = covariates.datapath,
# refCol = "ID")
# refcolvalues <- importCov$ID.refCol
# importPar <- createExternalParameters(20, names = "B1,B2",
# dataId = "ID", file = testParamFile, workingPath = parameters.datapath,
# refColName = "ID", refCol = refcolvalues)
# iData <- read.csv(file.path(parameters.datapath, testParamFile))[,
# c("ID", "B1", "B2")]
# for (ref in refcolvalues) {
# expect_true(all(iData[iData$ID == ref, "B1"][1] == importPar[refcolvalues ==
# ref, "B1"]), info = "Testing the refCol system")
# }
# expect_error(createExternalParameters(20, names = "E0,ED50",
# dataId = "ID", file = testParamFile, workingPath = parameters.datapath,
# betNames = "B1,B2", betNums = "1"), info = "#betNames != #betNums")
# expect_error(createExternalParameters(20, names = "E0,ED50",
# dataId = "ID", file = testParamFile, workingPath = parameters.datapath,
# betNames = "B1,B2", betNums = "a,b"), info = "wrong betNums format")
# expect_error(createExternalParameters(20, names = "E0,ED50,EMAX",
# dataId = "ID", file = testParamFile, workingPath = parameters.datapath,
# betNames = "B1,B2"), info = "Need betNums if index mismatch")
# expect_error(createExternalParameters(20, names = "E0,ED50,EMAX",
# dataId = "ID", file = testParamFile, workingPath = parameters.datapath,
# subset = "@fewf-+fw"), info = "Non sense code")
# expect_error(createExternalParameters(20, names = "E0,ED50,EMAX",
# dataId = "ID", file = testParamFile, workingPath = parameters.datapath,
# subset = "E0 < 0 < EMAX < 1 "), info = "Too many comparators")
# expect_error(createExternalParameters(20, names = "E0,ED50,EMAX",
# dataId = "ID", file = testParamFile, workingPath = parameters.datapath,
# subset = "E0"), info = "Too few comparators")
# expect_true(all(createExternalParameters(20, names = "E0,ED50,EMAX",
# dataId = "ID", file = testParamFile, workingPath = parameters.datapath,
# subset = "E0 < 0")$E0 < 0), info = "test that the subset is applied correctly")
# subData <- createExternalParameters(20, names = "E0,ED50,EMAX",
# dataId = "ID", file = testParamFile, workingPath = parameters.datapath,
# subset = c("E0 < 0", "1 <= B1 <= 2"))
# expect_true(all(subData$E0 < 0), info = "test that the subset is applied correctly with multiple subsets")
# expect_true(all(subData$B1 >= 1 & subData$B1 <= 2), info = "test that the subset is applied correctly with two comparators")
# 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)
# expect_equal(data2, data1)
# })
test_that("test.data.param.norm", {
expect_error(createNormalParameters(-50),
info = "subjects must be positive")
expect_error(createNormalParameters(50,
names = "X, Y",
mean = "0,a"),
regexp = "Impossible to convert to numbers")
expect_error(createNormalParameters(50,
names = "X,X",
mean = "0,1"),
info = "Duplicated values in names")
expect_error(createNormalParameters(50,
names = "X,Y",
mean = "0,0,0"),
regexp = "wrong length")
expect_error(createNormalParameters(50,
names = "X,Y,Z",
mean = "0,0,0",
covariance = "1,1,1,1"),
regexp = "Dimension Problem")
expect_error(createNormalParameters(50,
names = "X,Y,Z",
mean = "0,0,0",
covariance = "1,-2,1,0,-2,1"),
info = "matrix not positive definite")
expect_error(createNormalParameters(50,
names = "X,Y,Z",
mean = "0,0,0",
covariance = "1",
maxDraws = -1),
regexp = "maximum number of draws should be a positive integer")
expect_error(createNormalParameters(50,
names = "X,Y,Z",
mean = "0,0,0",
covariance = "1",
maxDraws = 5:6),
regexp = "wrong length")
expect_error(createNormalParameters(50,
names = "X,Y,Z",
mean = "0,0,0",
covariance = "1",
digits = -1),
regexp = "`digits` argument must be positive")
expect_error(createNormalParameters(50,
names = "X,Y,Z",
mean = "0,0,0",
covariance = "1",
digits = 1:2),
regexp = "`digits should be of length one or 3, not 2`")
expect_error(createNormalParameters(50,
names = "X,Y,Z",
mean = "0,0,0",
covariance = "1",
betMean = "0",
betNames = ".45",
betCov = "1"),
regexp = "invalid R name")
expect_error(createNormalParameters(50,
names = "X,Y,Z",
mean = "0,0,0",
covariance = "1",
betMean = "0",
betNames = "R",
betCov = "1"),
regexp = "between subject effects don't have a corresponding fixed parameter")
expect_error(createNormalParameters(50,
names = "X,Y,Z",
mean = "0,0,0",
covariance = "1",
betMean = "0",
betNames = "X",
betCov = "-1"),
regexp = "matrix not positive definite")
expect_error(createNormalParameters(50,
names = "X,Y,Z",
mean = "0,0,0",
covariance = "1",
betMean = "0",
betNames = "X",
betCov = "1,2,3"),
regexp = "Dimension problem")
expect_error(createNormalParameters(50,
names = "X,Y,Z",
mean = "0,0,0",
covariance = "1",
betMean = "0",
betNames = "X",
betCov = "1",
range = "]t43t534w-02354"),
regexp = "No comparator in the code")
expect_error(createNormalParameters(50,
names = "X,Y,Z",
mean = "0,0,0",
covariance = "1",
betMean = "0",
betNames = "X",
betCov = "1",
range = "X"),
regexp = "No comparator in the code")
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)
expect_true(all(unlist(errStrucDiff == 0)))
logNorm <- dataLogNorm[1, c("X", "Y", "Z")]
logNorm2 <- dataNone[1, c("X", "Y", "Z")] *
exp(dataNone[1, paste(c("X", "Y", "Z"), ".Between", sep = "")])
logNorm3 <- round(logNorm2,3)
expect_true(all(logNorm - logNorm3 == 0))
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$Z.Between <- rep(0, nrow(dataNone))
dataAdd <- createNormalParameters(50,
names = "X,Y,Z",
mean = "0,50,100",
covariance = "1",
betNames = "X,Y",
betCov = "1",
betMean = "0,0",
errStruc = "Add",
seed = 99,
digits = 10)
dataLogNorm <- createNormalParameters(50,
names = "X,Y,Z",
mean = "0,50,100",
covariance = "1",
betNames = "X,Y",
betCov = "1",
betMean = "0,0",
errStruc = "Log",
seed = 99,
digits = 10)
.roundIt <- MSToolkit:::.roundIt
expect_true(identical(.roundIt(dataAdd[, c("X", "Y")], 5),
.roundIt(dataNone[, c("X", "Y")] +
dataNone[, paste(c("X", "Y"),
".Between",
sep = "")],
5)))
v1 <- dataLogNorm[, c("Z", "Y")]
v2 <- dataNone[, c("Z", "Y")] * exp(dataNone[, paste(c("Z","Y"),
".Between",
sep = "")])
expect_equal(v2, v1)
expect_equal(dataAdd$Z, dataNone$Z, tolerance = 0.00001)
expect_equal(dataLogNorm$Z, dataNone$Z, tolerance = 0.00001)
dataNone <- createNormalParameters(50,
names = "X,Y,Z",
mean = "0,50,100",
covariance = "1",
betNames = "Z,Y",
betCov = "1",
betMean = "0,0",
errStruc = "N",
seed = 99,
digits = 5)
dataAdd <- createNormalParameters(50,
names = "X,Y,Z",
mean = "0,50,100",
covariance = "1",
betNames = "Z,Y",
betCov = "1",
betMean = "0,0",
errStruc = "A",
seed = 99,
digits = 5)
dataLogNorm <- createNormalParameters(50,
names = "X,Y,Z",
mean = "0,50,100",
covariance = "1",
betNames = "Z,Y",
betCov = "1",
betMean = "0,0",
errStruc = "L",
seed = 99,
digits = 5)
expect_true(all(.roundIt(dataAdd[, c("Z", "Y")] -
(dataNone[,c("Z", "Y")] +
dataNone[, paste(c("Z", "Y"), ".Between",sep = "")]
), 3)
== 0))
v1 <- dataLogNorm[, c("Z", "Y")]
v2 <- dataNone[, c("Z", "Y")] *
exp(dataNone[, paste(c("Z", "Y"), ".Between", sep = "")])
expect_equal(v2, v1, tolerance=0.001)
expect_true(all(dataAdd$X - dataNone$X == 0))
expect_true(all(dataLogNorm$X - dataNone$X == 0))
dataFixed <- createNormalParameters(50,
names = "X,Y,Z",
mean = "0,50,100",
covariance = "1")
for (va in c("X", "Y", "Z")) {
expect_true(all(diff(dataFixed[[va]]) == 0))
}
})
# test_that("test.data.param.wrap", {
# testParamFile <- "testParam.csv"
# wrongTestParamFile <- "wrongTestParam.csv"
# expect_error(createParameters(-10), info = "wrong subject (negative)")
# expect_error(createParameters(10, idCol = "ID, SUB"), info = "wrong id (too long)")
# expect_error(createParameters(10, idCol = "08234ID"), info = "wrong id")
# expect_error(createParameters(10, flagName = "PAROMIT, OMIT"),
# info = "wrong flagName (too long)")
# expect_error(createParameters(10, idCol = "082PAROMIT"),
# info = "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)
# expect_true(identical(d1, d2), info = "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)
# expect_true(identical(d1, d2), info = "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")
# expect_true(identical(dNor[, c("SUBJ", "X", "Y", "Z")], dAll[,
# c("SUBJ", "X", "Y", "Z")]), info = "all + nor")
# expect_true(identical(dExt[, c("SUBJ", "E0", "ED50", "EMAX")],
# dAll[, c("SUBJ", "E0", "ED50", "EMAX")]), info = "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")
# expect_true(identical(dNor[, c("SUBJ", "X", "Y", "Z")], dAll[,
# c("SUBJ", "X", "Y", "Z")]), info = "all + nor")
# expect_true(identical(dExt[, c("SUBJ", "E0", "ED50", "EMAX")],
# dAll[, c("SUBJ", "E0", "ED50", "EMAX")]), info = "all + ext")
# expect_equal(dAll$PAROMIT, dNor$PAROMIT, info = "checking the PAROMIT")
# })
#
# test_that("test.parameter.rangeExclude", {
# expect_error(createNormalParameters(500, names = "X,Y,Z",
# mean = "0,50,100", covariance = "1", betNames = "X,Y",
# betCov = "1", errStruc = "A", seed = 99, range = "Y < 50",
# maxDraws = 1, parRangeTolerance = 0.9), info = "Bad range specified")
# expect_true(is.data.frame(createNormalParameters(500, names = "X,Y,Z",
# mean = "0,50,100", covariance = "1", betNames = "X,Y",
# betCov = "1", errStruc = "A", seed = 99, range = "Y < 100",
# maxDraws = 1, parRangeTolerance = 0.9)), info = "Good range specified")
# warnData <- suppressWarnings(createNormalParameters(500,
# names = "X,Y,Z", mean = "0,50,100", covariance = "1",
# betNames = "X,Y", betCov = "1", errStruc = "A", seed = 99,
# range = "Y < 50", parRangeTolerance = 0.1, maxDraws = 1))
# expect_true(is.data.frame(warnData) & any(warnData$PAROMIT ==
# 1), info = "Dataset returned with parameter omits")
# })
#
# test_that("test.parameter.sf3", {
# expect_error(createNormalParameters(50, names = "X,Y,Z",
# mean = "100,100,100", covariance = "1", betNames = "X,Y",
# betCov = "1", betMean = "0,0", errStruc = "N", digits = -1),
# info = "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")
# expect_equal(round(dataAdd[, c("X", "Y", "Z")], 2), dataAdd[,
# c("X", "Y", "Z")], info = "check the atomic digits (add)")
# expect_equal(round(dataLogNorm[, c("X", "Y", "Z")], 2), dataLogNorm[,
# c("X", "Y", "Z")], info = "check the atomic digits (prop)")
# expect_equal(round(dataNone[, c("X", "Y", "Z", "X.Between",
# "Y.Between")], 2), dataNone[, c("X", "Y", "Z", "X.Between",
# "Y.Between")], info = "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")
# expect_equal(round(dataAdd$X, 2), dataAdd$X, info = "check the vector digits (add,X)")
# expect_equal(round(dataAdd$Y, 3), dataAdd$Y, info = "check the vector digits (add,Y)")
# expect_equal(round(dataAdd$Z, 2), dataAdd$Z, info = "check the vector digits (add,Y)")
# expect_equal(round(dataLogNorm$X, 2), dataLogNorm$X, info = "check the vector digits (Prop,X)")
# expect_equal(round(dataLogNorm$Y, 3), dataLogNorm$Y, info = "check the vector digits (Prop,Y)")
# expect_equal(round(dataLogNorm$Z, 2), dataLogNorm$Z, info = "check the vector digits (Prop,Y)")
# expect_equal(round(dataNone$X, 2), dataNone$X, info = "check the vector digits (None,X)")
# expect_equal(round(dataNone$Y, 3), dataNone$Y, info = "check the vector digits (None,Y)")
# expect_equal(round(dataNone$Z, 2), dataNone$Z, info = "check the vector digits (None,Y)")
# expect_equal(round(dataNone$X.Between, 2), dataNone$X.Between,
# info = "check the vector digits (None,X.Between)")
# expect_equal(round(dataNone$Y.Between, 3), dataNone$Y.Between,
# info = "check the vector digits (None,Y.Between)")
# })
#
# test_that("test.parameter.sf8", {
# dataNone <- createNormalParameters(50, names = "X,Y,Z", mean = "0,50,100",
# betNames = "X,Y", covariance = "1", betMean = "0,0",
# errStruc = "N", seed = 99)
# expect_true(all(dataNone[, c("X.Between", "Y.Between")] ==
# 0), info = "checking 0 covariance by default for between effects")
# data.sf8 <- createNormalParameters(500, names = "X,Y,Z",
# mean = "0,50,100", seed = 99)
# expect_true(all(sweep(data.sf8[, c("X", "Y", "Z")], 2, c(0,
# 50, 100), "-") == 0), info = "checking the 0 covariance by default")
# })
#
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