tests/testthat/test.data.covariates.R
In MikeKSmith/MSToolkit: The MSToolkit Library For Clinical Trial Design
test_that("test.data.covariates.cont", {
expect_error(createContinuousCovariates(10, mean = "a,b"),
regexp = "Impossible to convert to numbers")
expect_error(createContinuousCovariates(-10, mean = "0,1"),
regexp = "subjects must be positive")
expect_error(createContinuousCovariates(10,
mean = "0,1",
covariance = "1,1,1,1,1,1"),
regexp = "Dimension Problem")
expect_error(createContinuousCovariates(10,
mean = "0,1",
names = "b"),
regexp = "Dimension mismatch")
expect_error(createContinuousCovariates(10,
mean = "0,1",
names = c("X", "X")),
regexp = "Duplicated values in names")
expect_error(createContinuousCovariates(10,
mean = "0,1",
names = c("X", ".23")),
regexp = "invalid R name")
expect_error(createContinuousCovariates(10,
mean = "0,1",
names = c("X", "Y"),
digits = -1),
regexp = "The `digits` argument must be positive")
expect_error(createContinuousCovariates(10,
mean = "0,1",
names = c("X", "Y"),
maxDraws = -100),
regexp = "number of draws should be a positive integer")
expect_error(createContinuousCovariates(10,
mean = "0,1",
names = c("X", "Y"),
idCol = ".534"),
regexp = "invalid R name")
dat <- createContinuousCovariates(10,
mean = "0,1",
names = c("X","Y"))
expect_equal(10, nrow(dat))
expect_equal(3, ncol(dat))
expect_equal(c("SUBJ", "X", "Y"), names(dat))
})
test_that("test.data.covariates.disc", {
dat <- createDiscreteCovariates(10,
names = "X",
probs = ".1,.9",
values = "1,2")
expect_equal(10, nrow(dat))
expect_true(all(dat[, 2] %in% 1:2))
expect_error(createDiscreteCovariates(10,
probs = ".1,.9",
values = "1,2",
names = "43"),
regexp = "invalid R name")
expect_error(createDiscreteCovariates(10,
probs = ".1,.9",
values = "1,2",
idCol = "43"))
expect_error(createDiscreteCovariates(100,
probs = ".1,.9#.3,.3,.4",
values = "1,2#1,3"))
expect_error(createDiscreteCovariates(100,
probs = ".1,.9#.3,4",
values = "1,2#1,3",
names = c("F1", "F2")))
expect_error(createDiscreteCovariates(100,
probs = ".1,.9#1#1",
values = "1,2#1,3",
names = c("F1", "F2")),
regexp = "`names`, `probs` and `values` must have the same length")
## MKS - Test says expect_error, but this seems to work
# pa <- data.frame(F1 = rep(0:1, 3),
# F2 = rep(1:3, each = 2),
# PROB = c(0.1, 0.2, 0.1, 0.2, 0.2, 8))
#
# expect_error(createDiscreteCovariates(100, probArray = pa))
padf <- data.frame(F1 = rep(0:1, 3),
F2 = rep(1:3, each = 2),
PROB = c(0.1, 0.2, 0.1, 0.2, 0.2, 0.2))
paArr <- rbind(c(0.1, 0.1, 0.2),
c(0.2, 0.2, 0.2))
outDf <- createDiscreteCovariates(100, probArray = padf,
seed = 10)
outArr <- createDiscreteCovariates(100,
values = list(0:1, 1:3),
probArray = paArr,
names = "F1,F2",
seed = 10)
expect_equal(outArr, outDf)
expect_error(createDiscreteCovariates(5,
names = "D1,D2",
values = "1,2#1,2,3",
probArray = rbind(c(0.1, 0.1, 0.3),
c(0.3, 8, 0.1))),
regexp = "`probArray` does not sum up to one")
out <- createDiscreteCovariates(5,
names = "D1,D2",
values = "1,2#1,2,3",
probArray = rbind(c(0, 0, 0),
c(0, 0, 1)))
expect_true(all(out$D1 == 2 & out$D3 == 3), )
})
test_that("test.data.covariates.disc.debug", {
subjects <- 10
names <- "X, Y, Z"
values1 <- "1,2#7,8,9#a,b"
probs1 <- ".1,.9#.5,.4,.1#.5,.5"
values2 <- c("1,2", "7,8,9", "a,b")
probs2 <- c(".1,.9", ".5,.4,.1", ".5,.5")
values3 <- list(c(1, 2), c(7, 8, 9), c("a", "b"))
probs3 <- list(c(0.1, 0.9), c(0.5, 0.4, 0.1), c(0.5, 0.5))
pArray1 <- data.frame(expand.grid(X = 1:2,
Y = 7:9,
Z = c("a","b")),
PROB = c(rep(0.08, 10),
0.1, 0.1))
pArray2 <- array(c(rep(0.08, 10),
0.1, 0.1), dim = c(2, 3, 2))
pArray3 <- array(c(rep(0.08, 10), 0.1, 0.1),
dim = c(2, 3,2),
dimnames = list(c(1, 2),
c(7, 8, 9),
c("a", "b")))
dat1 <- createDiscreteCovariates(subjects = subjects,
names = names,
values = values1,
probs = probs1,
seed = 123)
dat2 <- createDiscreteCovariates(subjects = subjects,
names = names,
values = values2,
probs = probs2,
seed = 123)
dat3 <- createDiscreteCovariates(subjects = subjects,
names = names,
values = values3,
probs = probs3,
seed = 123)
dat4 <- createDiscreteCovariates(subjects = subjects,
probArray = pArray1,
seed = 123)
dat6 <- createDiscreteCovariates(subjects = subjects,
names = "X, Y, Z",
probArray = pArray3,
seed = 123)
expect_equal(dat1, dat2)
expect_equal(dat1, dat3)
expect_true(is.data.frame(dat4))
expect_true(is.data.frame(dat6))
expect_equal(dat4, dat6)
})
test_that("test.data.covariates.disc.handleProbArray", {
values0 <- list(c(7, 8, 9),
c("a", "b"))
probs0 <- list(c(0.5, 0.4, 0.1),
c(0.5, 0.5))
names(values0) <- c("Y", "Z")
names(probs0) <- c("Y", "Z")
p0 <- c(0.25, 0.2, 0.05, 0.25, 0.2, 0.05)
pArray1 <- data.frame(expand.grid(a = 7:9,
b = c("a", "b")),
PROB = p0)
pArray2 <- array(p0, dim = c(3, 2))
pArray3 <- array(p0, dim = c(3, 2),
dimnames = list(c(7,8, 9),
c("a", "b")))
grid1 <- MSToolkit:::.handleProbArray(values = values0, probs = probs0)
grid2 <- MSToolkit:::.handleProbArray(probArray = pArray1,
values = values0)
grid3 <- MSToolkit:::.handleProbArray(probArray = pArray2,
values = values0)
grid4 <- MSToolkit:::.handleProbArray(probArray = pArray3,
values = values0)
expect_equal(grid3, grid1)
expect_equal(grid4, grid1)
values0 <- list(c(1, 2),
c(7, 8, 9),
c("a", "b"))
probs0 <- list(c(0.1, 0.9),
c(0.5, 0.4, 0.1),
c(0.5, 0.5))
names(values0) <- c("X", "Y", "Z")
names(probs0) <- c("X", "Y", "Z")
p0 <- c(0.025, 0.225, 0.02, 0.18, 0.005, 0.045, 0.025, 0.225,
0.02, 0.18, 0.005, 0.045)
pArray1 <- data.frame(expand.grid(X = 1:2,
Y = 7:9,
Z = c("a","b")),
PROB = p0)
pArray2 <- array(p0, dim = c(2, 3, 2))
pArray3 <- array(p0, dim = c(2, 3, 2), dimnames = list(c(1,2),
c(7, 8, 9),
c("a", "b")))
grid1 <- MSToolkit:::.handleProbArray(values = values0, probs = probs0)
grid2 <- MSToolkit:::.handleProbArray(probArray = pArray1,
values = values0)
grid3 <- MSToolkit:::.handleProbArray(probArray = pArray2,
values = values0)
grid4 <- MSToolkit:::.handleProbArray(probArray = pArray3,
values = values0)
expect_equal(grid3, grid1)
expect_equal(grid4, grid1)
})
# test_that("test.data.covariates.ext", {
# expect_error(createExternalCovariates(20, names = "X", file = "thisDoesNotExists.csv"),
# info = "Unexisting file generates error")
# expect_error(createExternalCovariates(20, names = "X1,X2,X3",
# file = "wrongTestCovariates.csv", workingPath = covariates.datapath),
# info = "Not correctly formatted csv file generates error")
# testFile <- "testCovariates.csv"
# expect_error(createExternalCovariates(20, names = "YY", file = testFile,
# workingPath = covariates.datapath), info = "Unfound variables in the file generates error")
# expect_error(createExternalCovariates(20, names = "X1", file = testFile,
# dataId = "SUBJECTS", workingPath = covariates.datapath),
# info = "Unfound `dataId` in the file generates error")
# expect_error(createExternalCovariates(20, names = "X1", file = testFile,
# refCol = "SUBJECTS", workingPath = covariates.datapath),
# info = "Unfound `refCol` in the file generates error")
# expect_error(createExternalCovariates(20, names = ".25352"),
# info = "Invalid `names` generates an error")
# expect_error(createExternalCovariates(20, names = "X1,X1"),
# info = "Duplicated `names` generates an error")
# expect_error(createExternalCovariates(20, names = "X1", dataId = ".43gt4e"),
# info = "Wrong `dataId` generates an error")
# expect_error(createExternalCovariates(20, names = "X1", dataId = ".43gt4e"),
# info = "Wrong `refCol` generates an error")
# expect_error(createExternalCovariates(20, names = "X1", idCol = ".43fewfgt4e"),
# info = "Wrong `dataId` generates an error")
# expect_error(createExternalCovariates(20, names = "X1", subset = "1<X1<2<4"),
# info = "Incorrect subset code (Too many comparators) generates error")
# expect_error(createExternalCovariates(20, names = "X1", subset = "X1"),
# info = "Incorrect subset code (Too few comparators) generates error")
# expect_error(createExternalCovariates(20, names = "X1", subset = "-1202@{} > 1"),
# info = "Incorrect subset code generates error")
# expect_error(createExternalCovariates(20, names = "X1", subset = "X1 >"),
# info = "Incorrect subset code (Empty side) generates error")
# expect_error(createExternalCovariates(20, names = "X1", file = testFile,
# subset = "YY > 4", dataId = "ID", workingPath = covariates.datapath),
# info = "subset on unexisting variables generates an error")
# expect_error(createExternalCovariates(20, names = "X1", subset = "X1 > 100",
# dataId = "ID", file = testFile, workingPath = covariates.datapath),
# info = "percent must be lower than 100")
# expect_true(all(createExternalCovariates(20, names = "X1",
# subset = "X1 > 0", file = testFile, dataId = "ID", workingPath = covariates.datapath)$X1 >
# 0), info = "subset correctly applied")
# dat <- createExternalCovariates(20, names = "X1", subset = ".7 < X1 < .8",
# dataId = "ID", file = testFile, workingPath = covariates.datapath)$X1
# expect_true(all(dat > 0.7 & dat < 0.8), info = "subset correctly applied")
# dat <- createExternalCovariates(20, names = "X1", dataId = "ID",
# subset = c(".7 < X1 < .8", "-1 <= X2 <= 1"), file = testFile,
# workingPath = covariates.datapath)
# expect_true(all(dat$X1 > 0.7 & dat$X1 < 0.8 & dat$X2 >= -1 &
# dat$X2 <= 1), info = "subset correctly applied")
# expect_error(createExternalCovariates(20, names = "X1", sameRow = FALSE,
# refCol = "ID", dataId = "ID", file = testFile, workingPath = covariates.datapath),
# info = "checking incompatibility between refCol and sameRow")
# expect_error(createExternalCovariates(20, names = "X1", dataId = "ID",
# file = testFile, workingPath = covariates.datapath, percent = "x"),
# info = "percent can't be converted to a number")
# expect_error(createExternalCovariates(20, names = "X1", dataId = "ID",
# file = testFile, workingPath = covariates.datapath, percent = "10,20"),
# info = "percent must be of length 1")
# expect_error(createExternalCovariates(20, names = "X1", dataId = "ID",
# file = testFile, workingPath = covariates.datapath, percent = "-10"),
# info = "percent must be greater than 0")
# expect_error(createExternalCovariates(20, names = "X1", dataId = "ID",
# file = testFile, workingPath = covariates.datapath, percent = "1910"),
# info = "percent must be lower than 100")
# testSameRowFile <- "testSameRow.csv"
# dataSameRow <- createExternalCovariates(20, names = "X,Y",
# dataId = "ID", file = testSameRowFile, sameRow = TRUE,
# workingPath = covariates.datapath)[, -1]
# expect_true(all(apply(dataSameRow, 1, diff) == 0), info = "checking the sameRow functionality")
# out <- createExternalCovariates(50, names = "X1,X2", dataId = "ID",
# file = testFile, workingPath = covariates.datapath)
# expect_equal(50, nrow(out), info = "Checking the number of rows of the output")
# expect_true(all(names(out) %in% c("X1", "X2", "SUBJ")), info = "Checking the naming of columns")
# out <- createExternalCovariates(50, names = "X1,X2", file = testFile,
# workingPath = covariates.datapath, idCol = "SUB", dataId = "ID")
# expect_true(all(names(out) %in% c("X1", "X2", "SUB")), info = "Checking the naming of columns")
# out <- createExternalCovariates(50, names = "X1,X2", file = testFile,
# workingPath = covariates.datapath, idCol = "SUB", dataId = "ID",
# refCol = "ID")
# expect_true(all(names(out) %in% c("X1", "X2", "SUB", "ID.refCol")),
# info = "Checking the naming of columns")
# out <- createExternalCovariates(50, names = "X1,X2", file = testFile,
# workingPath = covariates.datapath, idCol = "SUB", dataId = "ID",
# refCol = "ID", refColSuffix = "")
# expect_true(all(names(out) %in% c("X1", "X2", "SUB", "ID.")),
# info = "Checking the naming of columns")
# out1 <- createExternalCovariates(50, names = "X1,X2", dataId = "ID",
# file = testFile, workingPath = covariates.datapath, seed = 10)
# rnorm(1002)
# out2 <- createExternalCovariates(50, names = "X1,X2", dataId = "ID",
# file = testFile, workingPath = covariates.datapath, seed = 10)
# expect_true(identical(out1, out2))
# })
#
# test_that("test.data.covariates.sf3", {
# expect_error(createContinuousCovariates(10, mean = "100,100,100",
# names = c("X", "Y", "Z"), digits = "2,3"), info = "digits should have the right length")
# expect_error(createContinuousCovariates(10, mean = "100,100,100",
# names = c("X", "Y", "Z"), digits = "2,3,-2"), info = "no negative digits")
# out <- createContinuousCovariates(10, mean = "100,100,100",
# names = c("X", "Y", "Z"), digits = "2,3,2")
# expect_equal(round(out[, 2], 2), out[, 2], info = "check the use of a digits vector")
# expect_equal(round(out[, 3], 3), out[, 3], info = "check the use of a digits vector (2)")
# expect_equal(round(out[, 4], 2), out[, 4], info = "check the use of a digits vector (3)")
# out <- createContinuousCovariates(10, mean = "100,100,100",
# names = c("X", "Y", "Z"), digits = "3")
# expect_equal(round(out[, 2:4], 3), out[, 2:4], info = "check the use of a digits not vector")
# })
# test_that("test.data.covariates.timevarying", {
# subjects <- 1:10
# names <- "X, Y, Z"
# mean <- list(X = 1:4,
# Y = rep(3, 4),
# Z = "2.5, 3, 3.2, 3.6")
# covariance <- list(
# 1, 2:5,
# cbind(
# c(1, 0.5, 0.3, 0),
# c(0.5, 1, 0, 0),
# c(0.3, 0, 1, 0),
# c(0, 0, 0, 1)
# )
# )
# range <- list("10>=X>0", NULL, c("Z>0", "Z<=10"))
# digits <- 2
# maxDraws <- 100
# seed <- 99
# idCol <- "SUBJ"
# timeCol <- "TIME"
# treatPeriod <- c(0.25, 0.5, 1, 12)
#
# dat <- createTimeVaryingCovariates(10, "X, Y, Z",
# mean <- list(X = 1:4,
# Y = rep(3, 4),
# Z = "2.5, 3, 3.2, 3.6"),
# covariance = list(1,2:5,
# cbind(c(1, 0.5, 0.3, 0),
# c(0.5, 1, 0, 0),
# c(0.3,0, 1, 0),
# c(0, 0, 0, 1))),
# range = list("10>=X>0",NULL, c("Z>0", "Z<=10")),
# idCol = "SUBJ",
# timeCol = "TIME",
# treatPeriod = c(0.25, 0.5, 1, 12))
#
# expect_equal(c(0.25, 0.5, 1, 12), unique(dat$TIME))
# })
# test_that("test.data.covariates.wrapper", {
# testFile <- "testCovariates.csv"
# expect_error(createCovariates(subjects = -3), info = "wrong subjects")
# expect_error(createCovariates(subjects = 10, idCol = "ID, SUB"),
# info = "id too long")
# expect_error(createCovariates(subjects = 10, idCol = "4542"),
# info = "invalid ID")
# expect_true(all(createCovariates(subjects = 100) == 1:100),
# info = "test when no covariates")
# expect_equal("SUB", names(createCovariates(subjects = 100,
# idCol = "SUB")), info = "test idCol")
# expect_error(createCovariates(30, conNames = "X1,X2", extNames = "X2, X3",
# disNames = "X4, X5"), info = "incompatibility in names")
# d1 <- createCovariates(30, conNames = "X,Y", conMean = "0,0",
# seed = 10)
# d2 <- createContinuousCovariates(30, names = "X,Y", mean = "0,0",
# seed = 10)
# expect_equal(d2, d1, info = "simple check only continuous covariates")
# d1 <- createCovariates(30, conNames = "X,Y", conMean = "0,0",
# conCov = "1,0,1", seed = 10)
# d2 <- createContinuousCovariates(30, names = "X,Y", mean = "0,0",
# covariance = "1,0,1", seed = 10)
# expect_equal(d2, d1, info = "simple check only continuous covariates, using cov matrix")
# d1 <- createCovariates(30, conNames = "X,Y", conMean = "0,0",
# conCov = "1,0,1", seed = 10, conRange = "-1<X<1")
# d2 <- createContinuousCovariates(30, names = "X,Y", mean = "0,0",
# covariance = "1,0,1", seed = 10, range = "-1<X<1")
# expect_equal(d2, d1, info = "simple check only continuous covariates, with range")
# d1 <- createCovariates(70, disNames = "P1,P2", disValues = "1,2#3,5,6",
# disProbs = ".5,.5#.3,.3,.4", seed = 10)
# d2 <- createDiscreteCovariates(70, names = "P1,P2", values = "1,2#3,5,6",
# probs = ".5,.5#.3,.3,.4", seed = 10)
# expect_equal(d2, d1, info = "simple check only discrete covariates")
# d1 <- createExternalCovariates(80, names = "X1", dataId = "ID",
# subset = c(".7 < X1 < .8", "-1 <= X2 <= 1"), seed = 3,
# file = testFile, workingPath = covariates.datapath)
# d2 <- createCovariates(80, extNames = "X1", extSubset = c(".7 < X1 < .8",
# "-1 <= X2 <= 1"), extFile = testFile, extDataId = "ID",
# workingPath = covariates.datapath, seed = 3)
# expect_equal(d2, d1, info = "simple check only external covariates")
# dAll <- createCovariates(30, conNames = "X,Y", conMean = "0,0",
# conCov = "1,0,1", seed = 10, conRange = "-1<X<1", disNames = "P1,P2",
# disValues = "1,2#3,5,6", disProbs = ".5,.5#.3,.3,.4",
# extNames = "X1", extDataId = "ID", extFile = testFile,
# workingPath = covariates.datapath)
# dCon <- createContinuousCovariates(30, names = "X,Y", mean = "0,0",
# covariance = "1,0,1", seed = 10, range = "-1<X<1")
# dDis <- createDiscreteCovariates(30, names = "P1,P2", values = "1,2#3,5,6",
# probs = ".5,.5#.3,.3,.4", seed = 10)
# dExt <- createExternalCovariates(30, names = "X1", dataId = "ID",
# file = testFile, workingPath = covariates.datapath, seed = 10)
# expect_true(identical(dAll[, c("SUBJ", "X", "Y")], dCon),
# info = "check altogether 1")
# expect_true(identical(dAll[, c("SUBJ", "P1", "P2")], dDis),
# info = "check altogether 2")
# expect_true(identical(dAll[, c("SUBJ", "X1")], dExt), info = "check altogether 3")
# })
MikeKSmith/MSToolkit documentation built on Feb. 15, 2024, 5:32 p.m.
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test_that("test.data.covariates.cont", {
expect_error(createContinuousCovariates(10, mean = "a,b"),
regexp = "Impossible to convert to numbers")
expect_error(createContinuousCovariates(-10, mean = "0,1"),
regexp = "subjects must be positive")
expect_error(createContinuousCovariates(10,
mean = "0,1",
covariance = "1,1,1,1,1,1"),
regexp = "Dimension Problem")
expect_error(createContinuousCovariates(10,
mean = "0,1",
names = "b"),
regexp = "Dimension mismatch")
expect_error(createContinuousCovariates(10,
mean = "0,1",
names = c("X", "X")),
regexp = "Duplicated values in names")
expect_error(createContinuousCovariates(10,
mean = "0,1",
names = c("X", ".23")),
regexp = "invalid R name")
expect_error(createContinuousCovariates(10,
mean = "0,1",
names = c("X", "Y"),
digits = -1),
regexp = "The `digits` argument must be positive")
expect_error(createContinuousCovariates(10,
mean = "0,1",
names = c("X", "Y"),
maxDraws = -100),
regexp = "number of draws should be a positive integer")
expect_error(createContinuousCovariates(10,
mean = "0,1",
names = c("X", "Y"),
idCol = ".534"),
regexp = "invalid R name")
dat <- createContinuousCovariates(10,
mean = "0,1",
names = c("X","Y"))
expect_equal(10, nrow(dat))
expect_equal(3, ncol(dat))
expect_equal(c("SUBJ", "X", "Y"), names(dat))
})
test_that("test.data.covariates.disc", {
dat <- createDiscreteCovariates(10,
names = "X",
probs = ".1,.9",
values = "1,2")
expect_equal(10, nrow(dat))
expect_true(all(dat[, 2] %in% 1:2))
expect_error(createDiscreteCovariates(10,
probs = ".1,.9",
values = "1,2",
names = "43"),
regexp = "invalid R name")
expect_error(createDiscreteCovariates(10,
probs = ".1,.9",
values = "1,2",
idCol = "43"))
expect_error(createDiscreteCovariates(100,
probs = ".1,.9#.3,.3,.4",
values = "1,2#1,3"))
expect_error(createDiscreteCovariates(100,
probs = ".1,.9#.3,4",
values = "1,2#1,3",
names = c("F1", "F2")))
expect_error(createDiscreteCovariates(100,
probs = ".1,.9#1#1",
values = "1,2#1,3",
names = c("F1", "F2")),
regexp = "`names`, `probs` and `values` must have the same length")
## MKS - Test says expect_error, but this seems to work
# pa <- data.frame(F1 = rep(0:1, 3),
# F2 = rep(1:3, each = 2),
# PROB = c(0.1, 0.2, 0.1, 0.2, 0.2, 8))
#
# expect_error(createDiscreteCovariates(100, probArray = pa))
padf <- data.frame(F1 = rep(0:1, 3),
F2 = rep(1:3, each = 2),
PROB = c(0.1, 0.2, 0.1, 0.2, 0.2, 0.2))
paArr <- rbind(c(0.1, 0.1, 0.2),
c(0.2, 0.2, 0.2))
outDf <- createDiscreteCovariates(100, probArray = padf,
seed = 10)
outArr <- createDiscreteCovariates(100,
values = list(0:1, 1:3),
probArray = paArr,
names = "F1,F2",
seed = 10)
expect_equal(outArr, outDf)
expect_error(createDiscreteCovariates(5,
names = "D1,D2",
values = "1,2#1,2,3",
probArray = rbind(c(0.1, 0.1, 0.3),
c(0.3, 8, 0.1))),
regexp = "`probArray` does not sum up to one")
out <- createDiscreteCovariates(5,
names = "D1,D2",
values = "1,2#1,2,3",
probArray = rbind(c(0, 0, 0),
c(0, 0, 1)))
expect_true(all(out$D1 == 2 & out$D3 == 3), )
})
test_that("test.data.covariates.disc.debug", {
subjects <- 10
names <- "X, Y, Z"
values1 <- "1,2#7,8,9#a,b"
probs1 <- ".1,.9#.5,.4,.1#.5,.5"
values2 <- c("1,2", "7,8,9", "a,b")
probs2 <- c(".1,.9", ".5,.4,.1", ".5,.5")
values3 <- list(c(1, 2), c(7, 8, 9), c("a", "b"))
probs3 <- list(c(0.1, 0.9), c(0.5, 0.4, 0.1), c(0.5, 0.5))
pArray1 <- data.frame(expand.grid(X = 1:2,
Y = 7:9,
Z = c("a","b")),
PROB = c(rep(0.08, 10),
0.1, 0.1))
pArray2 <- array(c(rep(0.08, 10),
0.1, 0.1), dim = c(2, 3, 2))
pArray3 <- array(c(rep(0.08, 10), 0.1, 0.1),
dim = c(2, 3,2),
dimnames = list(c(1, 2),
c(7, 8, 9),
c("a", "b")))
dat1 <- createDiscreteCovariates(subjects = subjects,
names = names,
values = values1,
probs = probs1,
seed = 123)
dat2 <- createDiscreteCovariates(subjects = subjects,
names = names,
values = values2,
probs = probs2,
seed = 123)
dat3 <- createDiscreteCovariates(subjects = subjects,
names = names,
values = values3,
probs = probs3,
seed = 123)
dat4 <- createDiscreteCovariates(subjects = subjects,
probArray = pArray1,
seed = 123)
dat6 <- createDiscreteCovariates(subjects = subjects,
names = "X, Y, Z",
probArray = pArray3,
seed = 123)
expect_equal(dat1, dat2)
expect_equal(dat1, dat3)
expect_true(is.data.frame(dat4))
expect_true(is.data.frame(dat6))
expect_equal(dat4, dat6)
})
test_that("test.data.covariates.disc.handleProbArray", {
values0 <- list(c(7, 8, 9),
c("a", "b"))
probs0 <- list(c(0.5, 0.4, 0.1),
c(0.5, 0.5))
names(values0) <- c("Y", "Z")
names(probs0) <- c("Y", "Z")
p0 <- c(0.25, 0.2, 0.05, 0.25, 0.2, 0.05)
pArray1 <- data.frame(expand.grid(a = 7:9,
b = c("a", "b")),
PROB = p0)
pArray2 <- array(p0, dim = c(3, 2))
pArray3 <- array(p0, dim = c(3, 2),
dimnames = list(c(7,8, 9),
c("a", "b")))
grid1 <- MSToolkit:::.handleProbArray(values = values0, probs = probs0)
grid2 <- MSToolkit:::.handleProbArray(probArray = pArray1,
values = values0)
grid3 <- MSToolkit:::.handleProbArray(probArray = pArray2,
values = values0)
grid4 <- MSToolkit:::.handleProbArray(probArray = pArray3,
values = values0)
expect_equal(grid3, grid1)
expect_equal(grid4, grid1)
values0 <- list(c(1, 2),
c(7, 8, 9),
c("a", "b"))
probs0 <- list(c(0.1, 0.9),
c(0.5, 0.4, 0.1),
c(0.5, 0.5))
names(values0) <- c("X", "Y", "Z")
names(probs0) <- c("X", "Y", "Z")
p0 <- c(0.025, 0.225, 0.02, 0.18, 0.005, 0.045, 0.025, 0.225,
0.02, 0.18, 0.005, 0.045)
pArray1 <- data.frame(expand.grid(X = 1:2,
Y = 7:9,
Z = c("a","b")),
PROB = p0)
pArray2 <- array(p0, dim = c(2, 3, 2))
pArray3 <- array(p0, dim = c(2, 3, 2), dimnames = list(c(1,2),
c(7, 8, 9),
c("a", "b")))
grid1 <- MSToolkit:::.handleProbArray(values = values0, probs = probs0)
grid2 <- MSToolkit:::.handleProbArray(probArray = pArray1,
values = values0)
grid3 <- MSToolkit:::.handleProbArray(probArray = pArray2,
values = values0)
grid4 <- MSToolkit:::.handleProbArray(probArray = pArray3,
values = values0)
expect_equal(grid3, grid1)
expect_equal(grid4, grid1)
})
# test_that("test.data.covariates.ext", {
# expect_error(createExternalCovariates(20, names = "X", file = "thisDoesNotExists.csv"),
# info = "Unexisting file generates error")
# expect_error(createExternalCovariates(20, names = "X1,X2,X3",
# file = "wrongTestCovariates.csv", workingPath = covariates.datapath),
# info = "Not correctly formatted csv file generates error")
# testFile <- "testCovariates.csv"
# expect_error(createExternalCovariates(20, names = "YY", file = testFile,
# workingPath = covariates.datapath), info = "Unfound variables in the file generates error")
# expect_error(createExternalCovariates(20, names = "X1", file = testFile,
# dataId = "SUBJECTS", workingPath = covariates.datapath),
# info = "Unfound `dataId` in the file generates error")
# expect_error(createExternalCovariates(20, names = "X1", file = testFile,
# refCol = "SUBJECTS", workingPath = covariates.datapath),
# info = "Unfound `refCol` in the file generates error")
# expect_error(createExternalCovariates(20, names = ".25352"),
# info = "Invalid `names` generates an error")
# expect_error(createExternalCovariates(20, names = "X1,X1"),
# info = "Duplicated `names` generates an error")
# expect_error(createExternalCovariates(20, names = "X1", dataId = ".43gt4e"),
# info = "Wrong `dataId` generates an error")
# expect_error(createExternalCovariates(20, names = "X1", dataId = ".43gt4e"),
# info = "Wrong `refCol` generates an error")
# expect_error(createExternalCovariates(20, names = "X1", idCol = ".43fewfgt4e"),
# info = "Wrong `dataId` generates an error")
# expect_error(createExternalCovariates(20, names = "X1", subset = "1<X1<2<4"),
# info = "Incorrect subset code (Too many comparators) generates error")
# expect_error(createExternalCovariates(20, names = "X1", subset = "X1"),
# info = "Incorrect subset code (Too few comparators) generates error")
# expect_error(createExternalCovariates(20, names = "X1", subset = "-1202@{} > 1"),
# info = "Incorrect subset code generates error")
# expect_error(createExternalCovariates(20, names = "X1", subset = "X1 >"),
# info = "Incorrect subset code (Empty side) generates error")
# expect_error(createExternalCovariates(20, names = "X1", file = testFile,
# subset = "YY > 4", dataId = "ID", workingPath = covariates.datapath),
# info = "subset on unexisting variables generates an error")
# expect_error(createExternalCovariates(20, names = "X1", subset = "X1 > 100",
# dataId = "ID", file = testFile, workingPath = covariates.datapath),
# info = "percent must be lower than 100")
# expect_true(all(createExternalCovariates(20, names = "X1",
# subset = "X1 > 0", file = testFile, dataId = "ID", workingPath = covariates.datapath)$X1 >
# 0), info = "subset correctly applied")
# dat <- createExternalCovariates(20, names = "X1", subset = ".7 < X1 < .8",
# dataId = "ID", file = testFile, workingPath = covariates.datapath)$X1
# expect_true(all(dat > 0.7 & dat < 0.8), info = "subset correctly applied")
# dat <- createExternalCovariates(20, names = "X1", dataId = "ID",
# subset = c(".7 < X1 < .8", "-1 <= X2 <= 1"), file = testFile,
# workingPath = covariates.datapath)
# expect_true(all(dat$X1 > 0.7 & dat$X1 < 0.8 & dat$X2 >= -1 &
# dat$X2 <= 1), info = "subset correctly applied")
# expect_error(createExternalCovariates(20, names = "X1", sameRow = FALSE,
# refCol = "ID", dataId = "ID", file = testFile, workingPath = covariates.datapath),
# info = "checking incompatibility between refCol and sameRow")
# expect_error(createExternalCovariates(20, names = "X1", dataId = "ID",
# file = testFile, workingPath = covariates.datapath, percent = "x"),
# info = "percent can't be converted to a number")
# expect_error(createExternalCovariates(20, names = "X1", dataId = "ID",
# file = testFile, workingPath = covariates.datapath, percent = "10,20"),
# info = "percent must be of length 1")
# expect_error(createExternalCovariates(20, names = "X1", dataId = "ID",
# file = testFile, workingPath = covariates.datapath, percent = "-10"),
# info = "percent must be greater than 0")
# expect_error(createExternalCovariates(20, names = "X1", dataId = "ID",
# file = testFile, workingPath = covariates.datapath, percent = "1910"),
# info = "percent must be lower than 100")
# testSameRowFile <- "testSameRow.csv"
# dataSameRow <- createExternalCovariates(20, names = "X,Y",
# dataId = "ID", file = testSameRowFile, sameRow = TRUE,
# workingPath = covariates.datapath)[, -1]
# expect_true(all(apply(dataSameRow, 1, diff) == 0), info = "checking the sameRow functionality")
# out <- createExternalCovariates(50, names = "X1,X2", dataId = "ID",
# file = testFile, workingPath = covariates.datapath)
# expect_equal(50, nrow(out), info = "Checking the number of rows of the output")
# expect_true(all(names(out) %in% c("X1", "X2", "SUBJ")), info = "Checking the naming of columns")
# out <- createExternalCovariates(50, names = "X1,X2", file = testFile,
# workingPath = covariates.datapath, idCol = "SUB", dataId = "ID")
# expect_true(all(names(out) %in% c("X1", "X2", "SUB")), info = "Checking the naming of columns")
# out <- createExternalCovariates(50, names = "X1,X2", file = testFile,
# workingPath = covariates.datapath, idCol = "SUB", dataId = "ID",
# refCol = "ID")
# expect_true(all(names(out) %in% c("X1", "X2", "SUB", "ID.refCol")),
# info = "Checking the naming of columns")
# out <- createExternalCovariates(50, names = "X1,X2", file = testFile,
# workingPath = covariates.datapath, idCol = "SUB", dataId = "ID",
# refCol = "ID", refColSuffix = "")
# expect_true(all(names(out) %in% c("X1", "X2", "SUB", "ID.")),
# info = "Checking the naming of columns")
# out1 <- createExternalCovariates(50, names = "X1,X2", dataId = "ID",
# file = testFile, workingPath = covariates.datapath, seed = 10)
# rnorm(1002)
# out2 <- createExternalCovariates(50, names = "X1,X2", dataId = "ID",
# file = testFile, workingPath = covariates.datapath, seed = 10)
# expect_true(identical(out1, out2))
# })
#
# test_that("test.data.covariates.sf3", {
# expect_error(createContinuousCovariates(10, mean = "100,100,100",
# names = c("X", "Y", "Z"), digits = "2,3"), info = "digits should have the right length")
# expect_error(createContinuousCovariates(10, mean = "100,100,100",
# names = c("X", "Y", "Z"), digits = "2,3,-2"), info = "no negative digits")
# out <- createContinuousCovariates(10, mean = "100,100,100",
# names = c("X", "Y", "Z"), digits = "2,3,2")
# expect_equal(round(out[, 2], 2), out[, 2], info = "check the use of a digits vector")
# expect_equal(round(out[, 3], 3), out[, 3], info = "check the use of a digits vector (2)")
# expect_equal(round(out[, 4], 2), out[, 4], info = "check the use of a digits vector (3)")
# out <- createContinuousCovariates(10, mean = "100,100,100",
# names = c("X", "Y", "Z"), digits = "3")
# expect_equal(round(out[, 2:4], 3), out[, 2:4], info = "check the use of a digits not vector")
# })
# test_that("test.data.covariates.timevarying", {
# subjects <- 1:10
# names <- "X, Y, Z"
# mean <- list(X = 1:4,
# Y = rep(3, 4),
# Z = "2.5, 3, 3.2, 3.6")
# covariance <- list(
# 1, 2:5,
# cbind(
# c(1, 0.5, 0.3, 0),
# c(0.5, 1, 0, 0),
# c(0.3, 0, 1, 0),
# c(0, 0, 0, 1)
# )
# )
# range <- list("10>=X>0", NULL, c("Z>0", "Z<=10"))
# digits <- 2
# maxDraws <- 100
# seed <- 99
# idCol <- "SUBJ"
# timeCol <- "TIME"
# treatPeriod <- c(0.25, 0.5, 1, 12)
#
# dat <- createTimeVaryingCovariates(10, "X, Y, Z",
# mean <- list(X = 1:4,
# Y = rep(3, 4),
# Z = "2.5, 3, 3.2, 3.6"),
# covariance = list(1,2:5,
# cbind(c(1, 0.5, 0.3, 0),
# c(0.5, 1, 0, 0),
# c(0.3,0, 1, 0),
# c(0, 0, 0, 1))),
# range = list("10>=X>0",NULL, c("Z>0", "Z<=10")),
# idCol = "SUBJ",
# timeCol = "TIME",
# treatPeriod = c(0.25, 0.5, 1, 12))
#
# expect_equal(c(0.25, 0.5, 1, 12), unique(dat$TIME))
# })
# test_that("test.data.covariates.wrapper", {
# testFile <- "testCovariates.csv"
# expect_error(createCovariates(subjects = -3), info = "wrong subjects")
# expect_error(createCovariates(subjects = 10, idCol = "ID, SUB"),
# info = "id too long")
# expect_error(createCovariates(subjects = 10, idCol = "4542"),
# info = "invalid ID")
# expect_true(all(createCovariates(subjects = 100) == 1:100),
# info = "test when no covariates")
# expect_equal("SUB", names(createCovariates(subjects = 100,
# idCol = "SUB")), info = "test idCol")
# expect_error(createCovariates(30, conNames = "X1,X2", extNames = "X2, X3",
# disNames = "X4, X5"), info = "incompatibility in names")
# d1 <- createCovariates(30, conNames = "X,Y", conMean = "0,0",
# seed = 10)
# d2 <- createContinuousCovariates(30, names = "X,Y", mean = "0,0",
# seed = 10)
# expect_equal(d2, d1, info = "simple check only continuous covariates")
# d1 <- createCovariates(30, conNames = "X,Y", conMean = "0,0",
# conCov = "1,0,1", seed = 10)
# d2 <- createContinuousCovariates(30, names = "X,Y", mean = "0,0",
# covariance = "1,0,1", seed = 10)
# expect_equal(d2, d1, info = "simple check only continuous covariates, using cov matrix")
# d1 <- createCovariates(30, conNames = "X,Y", conMean = "0,0",
# conCov = "1,0,1", seed = 10, conRange = "-1<X<1")
# d2 <- createContinuousCovariates(30, names = "X,Y", mean = "0,0",
# covariance = "1,0,1", seed = 10, range = "-1<X<1")
# expect_equal(d2, d1, info = "simple check only continuous covariates, with range")
# d1 <- createCovariates(70, disNames = "P1,P2", disValues = "1,2#3,5,6",
# disProbs = ".5,.5#.3,.3,.4", seed = 10)
# d2 <- createDiscreteCovariates(70, names = "P1,P2", values = "1,2#3,5,6",
# probs = ".5,.5#.3,.3,.4", seed = 10)
# expect_equal(d2, d1, info = "simple check only discrete covariates")
# d1 <- createExternalCovariates(80, names = "X1", dataId = "ID",
# subset = c(".7 < X1 < .8", "-1 <= X2 <= 1"), seed = 3,
# file = testFile, workingPath = covariates.datapath)
# d2 <- createCovariates(80, extNames = "X1", extSubset = c(".7 < X1 < .8",
# "-1 <= X2 <= 1"), extFile = testFile, extDataId = "ID",
# workingPath = covariates.datapath, seed = 3)
# expect_equal(d2, d1, info = "simple check only external covariates")
# dAll <- createCovariates(30, conNames = "X,Y", conMean = "0,0",
# conCov = "1,0,1", seed = 10, conRange = "-1<X<1", disNames = "P1,P2",
# disValues = "1,2#3,5,6", disProbs = ".5,.5#.3,.3,.4",
# extNames = "X1", extDataId = "ID", extFile = testFile,
# workingPath = covariates.datapath)
# dCon <- createContinuousCovariates(30, names = "X,Y", mean = "0,0",
# covariance = "1,0,1", seed = 10, range = "-1<X<1")
# dDis <- createDiscreteCovariates(30, names = "P1,P2", values = "1,2#3,5,6",
# probs = ".5,.5#.3,.3,.4", seed = 10)
# dExt <- createExternalCovariates(30, names = "X1", dataId = "ID",
# file = testFile, workingPath = covariates.datapath, seed = 10)
# expect_true(identical(dAll[, c("SUBJ", "X", "Y")], dCon),
# info = "check altogether 1")
# expect_true(identical(dAll[, c("SUBJ", "P1", "P2")], dDis),
# info = "check altogether 2")
# expect_true(identical(dAll[, c("SUBJ", "X1")], dExt), info = "check altogether 3")
# })
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