context("create sdc object from the yaml configuration file")
ccd <<- xml2Data("../data/test_data_anonym.xml")
demg <- suppressWarnings(sql.demographic.table(ccd))
conf <- yaml.load_file('../data/test.yaml')
keyvar <- conf$keyVars
keydt <- names(conf$datetimeVars)
numvar <- names(conf$numVars)
var <- c(keydt, keyvar, numvar)
test_that("create sdc object", {
demg <- data.frame(demg)
sdc <<- suppressWarnings(sdc.trial(ccd, '../data/test.yaml'))
})
test_that("remove unique columns", {
tdata <- data.frame(a=rep(1, 10))
expect_true(is.null(non.unique.columns(tdata, "a")))
tdata <- data.frame(a=seq(1, 10))
expect_equal(non.unique.columns(tdata, "a"), "a")
tdata <- data.frame(a=c(1, 2, 3 ,NA, NA))
expect_equal(non.unique.columns(tdata, "a"), "a")
tdata <- data.frame(a=c(1, 1, 1 ,NA, NA))
expect_true(is.null(non.unique.columns(tdata, "a")))
tdata <- data.frame(a=as.numeric(c(NA ,NA, NA)))
expect_true(is.null(non.unique.columns(tdata, "a")))
# tdata <- data.frame(a=c("x", "y"))
# expect_error(non.unique.columns(tdata, "a"))
})
test_that("get all the 2d data from a selected episodes but not the demographic
data",
{
cl <- clinic.data.list(ccd, 2, sdc$conf$nidentify)
expect_false(all(stname2code(var) %in% names(cl)))
cl <- clinic.data.list(ccd, 1, sdc$conf$nidentify)
expect_false(all(stname2code(var) %in% names(cl)))
})
test_that("anonymisation from cleanEHR", {
suppressWarnings(anonymisation(ccd, conf))
})
test_that("appending age column", {
age <- append.age(demg)$AGE
expect_true(is.numeric(age))
expect_identical(age, c(25, 33, 44, 37, 59, 25, 25, NA, NA, NA, NA, NA))
})
test_that("Microaggregation on numeric variables", {
demg$AGE <- runif(nrow(demg))
microaggregation.numvar(demg, conf)
})
test_that("check l-diversity suppression", {
sdc.l <- suppressWarnings(sdc.trial(ccd, conf, l.div=2, verbose=T))
})
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