Nothing
test_that("get_target_column_names works with
target_columns = 'linelist_tags'", {
target_columns <- get_target_column_names(
data = readRDS(system.file("extdata",
"test_linelist.RDS",
package = "cleanepi")),
target_columns = "linelist_tags",
cols = NULL
)
expect_type(target_columns, "character")
expect_length(target_columns, 4L)
expect_identical(target_columns, c("dt_onset", "dt_report", "sex",
"outcome"))
})
test_that("get_target_column_names works with
target_columns as a vector of column names", {
target_columns <- get_target_column_names(
data = readRDS(system.file("extdata",
"test_df.RDS",
package = "cleanepi")),
target_columns = c("dateOfBirth", "sex"),
cols = NULL
)
expect_type(target_columns, "character")
expect_length(target_columns, 2L)
expect_identical(target_columns, c("dateOfBirth", "sex"))
})
test_that("get_target_column_names works with
target_columns as a vector of numeric values", {
target_columns <- get_target_column_names(
data = readRDS(system.file("extdata",
"test_df.RDS",
package = "cleanepi")),
target_columns = c(6L, 8L),
cols = NULL
)
expect_type(target_columns, "character")
expect_length(target_columns, 2L)
expect_identical(target_columns, c("dateOfBirth", "sex"))
})
test_that("get_target_column_names works with target_columns and cols", {
target_columns <- get_target_column_names(
data = readRDS(system.file("extdata",
"test_df.RDS",
package = "cleanepi")),
target_columns = c("dateOfBirth", "sex", "country_name"),
cols = "country_name"
)
expect_type(target_columns, "character")
expect_length(target_columns, 2L)
expect_identical(target_columns, c("dateOfBirth", "sex"))
})
test_that("get_target_column_names fails as expected", {
expect_error(
get_target_column_names(
data = readRDS(system.file("extdata",
"test_df.RDS",
package = "cleanepi")),
target_columns = "country_name",
cols = "country_name"
),
regexp = cat("Assertion on',target_columns,'failed: all specified target
columns will be ignored because they are either empty or
constant.")
)
})
test_that("get_target_column_names fails as expected", {
expect_error(
get_target_column_names(
data = readRDS(system.file("extdata",
"test_df.RDS",
package = "cleanepi")),
target_columns = "linelist_tags",
cols = NULL
),
regexp = cat("Assertion on',keep,'failed: usage of 'linelist_tags'
is only reserved for 'linelist' type of data.")
)
})
data <- readRDS(system.file("extdata", "test_df.RDS", package = "cleanepi"))
scan_res <- scan_data(data)
# Perform data cleaning
cleaned_data <- data |>
replace_missing_values(target_columns = "sex", na_strings = "-99") |>
convert_to_numeric(target_columns = "sex", lang = "en")
test_that("add_to_report works as expected", {
cleaned_data <- add_to_report(x = cleaned_data,
key = "scanning_result",
value = scan_res)
report <- attr(cleaned_data, "report")
expect_type(report, "list")
expect_length(report, 3L)
expect_named(report, c("missing_values_replaced_at", "converted_into_numeric",
"scanning_result"))
expect_identical(report[["missing_values_replaced_at"]], "sex")
expect_identical(report[["converted_into_numeric"]], "sex")
data <- add_to_report(x = data,
key = "scanning_result",
value = scan_res)
report <- attr(data, "report")
expect_type(report, "list")
expect_length(report, 1L)
expect_named(report, "scanning_result")
expect_named(report[["scanning_result"]], c("Field_names", "missing",
"numeric", "date", "character",
"logical"))
expect_identical(nrow(report[["scanning_result"]]), ncol(data))
})
# test internal function
test_that("date_get_part1 works as expected", {
res <- date_get_part1(NA, sep = "/")
expect_identical(res, NA)
res <- date_get_part1("2024/03/28", sep = "/")
expect_identical(res, "2024")
})
test_that("date_get_part2 works as expected", {
res <- date_get_part2(NA, sep = "/")
expect_identical(res, NA)
res <- date_get_part2("2024/03/28", sep = "/")
expect_identical(res, "03")
})
test_that("date_get_part3 works as expected", {
res <- date_get_part3(NA, sep = "/")
expect_identical(res, NA)
res <- date_get_part3("2024/03/28", sep = "/")
expect_identical(res, "28")
})
test_that("get_sum works as expected", {
res <- get_sum("28")
expect_identical(res, 10)
})
test_that("get_target_column_names fails as expected", {
data <- readRDS(system.file("extdata", "test_df.RDS", package = "cleanepi"))
expect_error(
get_target_column_names(data, target_columns = c(2L, 3L, 10L), cols = NULL),
regexp = cat("Some specified column names indices are out of bound.")
)
})
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