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(v1.6.0.9010) big first_isolate() update

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dr. M.S. (Matthijs) Berends
2021-04-26 23:57:37 +02:00
parent 5f9e7bd3ee
commit 93683a4ae2
38 changed files with 1134 additions and 933 deletions
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99
tests/testthat/test-first_isolate.R
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@ -28,58 +28,29 @@ context("first_isolate.R")
test_that("first isolates work", {
skip_on_cran()
# first isolates
expect_equal(
sum(
first_isolate(x = example_isolates,
col_date = "date",
col_patient_id = "patient_id",
col_mo = "mo",
info = TRUE),
na.rm = TRUE),
1300)
# first weighted isolates
ex_iso_with_keyab <- example_isolates
ex_iso_with_keyab$keyab <- key_antibiotics(example_isolates, warnings = FALSE)
expect_equal(
suppressWarnings(
sum(
first_isolate(x = ex_iso_with_keyab,
# let syntax determine arguments automatically
type = "keyantibiotics",
info = TRUE),
na.rm = TRUE)),
1398)
# when not ignoring I
expect_equal(
suppressWarnings(
sum(
first_isolate(x = ex_iso_with_keyab,
col_date = "date",
col_patient_id = "patient_id",
col_mo = "mo",
col_keyantibiotics = "keyab",
ignore_I = FALSE,
type = "keyantibiotics",
info = TRUE),
na.rm = TRUE)),
1421)
# when using points
expect_equal(
suppressWarnings(
sum(
first_isolate(x = ex_iso_with_keyab,
col_date = "date",
col_patient_id = "patient_id",
col_mo = "mo",
col_keyantibiotics = "keyab",
type = "points",
info = TRUE),
na.rm = TRUE)),
1348)
# all four methods
expect_equal(sum(first_isolate(x = example_isolates, method = "isolate-based", info = TRUE), na.rm = TRUE),
1984)
expect_equal(sum(first_isolate(x = example_isolates, method = "patient-based", info = TRUE), na.rm = TRUE),
1265)
expect_equal(sum(first_isolate(x = example_isolates, method = "episode-based", info = TRUE), na.rm = TRUE),
1300)
expect_equal(sum(first_isolate(x = example_isolates, method = "phenotype-based", info = TRUE), na.rm = TRUE),
1379)
# Phenotype-based, using key antimicrobials
expect_equal(sum(first_isolate(x = example_isolates,
method = "phenotype-based",
type = "keyantimicrobials",
antifungal = NULL, info = TRUE), na.rm = TRUE),
1395)
expect_equal(sum(first_isolate(x = example_isolates,
method = "phenotype-based",
type = "keyantimicrobials",
antifungal = NULL, info = TRUE, ignore_I = FALSE), na.rm = TRUE),
1418)
# first non-ICU isolates
expect_equal(
sum(
@ -91,7 +62,7 @@ test_that("first isolates work", {
info = TRUE,
icu_exclude = TRUE),
na.rm = TRUE),
881)
941)
# set 1500 random observations to be of specimen type 'Urine'
random_rows <- sample(x = 1:2000, size = 1500, replace = FALSE)
@ -157,11 +128,13 @@ test_that("first isolates work", {
mutate(mo = as.character(mo)) %>%
first_isolate(col_date = "date",
col_mo = "mo",
col_patient_id = "patient_id"),
col_patient_id = "patient_id",
info = FALSE),
example_isolates %>%
first_isolate(col_date = "date",
col_mo = "mo",
col_patient_id = "patient_id"))
col_patient_id = "patient_id",
info = FALSE))
# support for WHONET
expect_message(example_isolates %>%
@ -182,31 +155,29 @@ test_that("first isolates work", {
col_mo = "mo",
info = TRUE),
na.rm = TRUE),
1305)
1382)
# unknown MOs
test_unknown <- example_isolates
test_unknown$mo <- ifelse(test_unknown$mo == "B_ESCHR_COLI", "UNKNOWN", test_unknown$mo)
expect_equal(sum(first_isolate(test_unknown, include_unknown = FALSE)),
1045)
1108)
expect_equal(sum(first_isolate(test_unknown, include_unknown = TRUE)),
1528)
1591)
test_unknown$mo <- ifelse(test_unknown$mo == "UNKNOWN", NA, test_unknown$mo)
expect_equal(sum(first_isolate(test_unknown)),
1045)
1108)
# empty rsi results
expect_equal(sum(first_isolate(example_isolates, include_untested_rsi = FALSE)),
1287)
1366)
# shortcuts
expect_identical(filter_first_isolate(example_isolates),
subset(example_isolates, first_isolate(example_isolates)))
ex <- example_isolates
ex$keyab <- key_antibiotics(ex)
subset(example_isolates, first_isolate(example_isolates, method = "episode-based")))
expect_identical(filter_first_weighted_isolate(example_isolates),
subset(example_isolates, first_isolate(ex)))
subset(example_isolates, first_isolate(example_isolates, method = "phenotype-based")))
# notice that all mo's are distinct, so all are TRUE
expect_true(all(example_isolates %pm>%