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replaced bactid by mo

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2018-08-31 13:36:19 +02:00
parent 98ff131680
commit 5965d3c794
41 changed files with 786 additions and 411 deletions
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26
tests/testthat/test-first_isolate.R
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@ -7,7 +7,7 @@ test_that("first isolates work", {
first_isolate(tbl = septic_patients,
col_date = "date",
col_patient_id = "patient_id",
col_bactid = "bactid",
col_mo = "mo",
info = TRUE),
na.rm = TRUE),
1331)
@ -19,7 +19,7 @@ test_that("first isolates work", {
first_isolate(tbl = septic_patients %>% mutate(keyab = key_antibiotics(.)),
col_date = "date",
col_patient_id = "patient_id",
col_bactid = "bactid",
col_mo = "mo",
col_keyantibiotics = "keyab",
type = "keyantibiotics",
info = TRUE),
@ -32,7 +32,7 @@ test_that("first isolates work", {
first_isolate(tbl = septic_patients %>% mutate(keyab = key_antibiotics(.)),
col_date = "date",
col_patient_id = "patient_id",
col_bactid = "bactid",
col_mo = "mo",
col_keyantibiotics = "keyab",
ignore_I = FALSE,
type = "keyantibiotics",
@ -46,7 +46,7 @@ test_that("first isolates work", {
first_isolate(tbl = septic_patients %>% mutate(keyab = key_antibiotics(.)),
col_date = "date",
col_patient_id = "patient_id",
col_bactid = "bactid",
col_mo = "mo",
col_keyantibiotics = "keyab",
type = "points",
info = TRUE),
@ -57,7 +57,7 @@ test_that("first isolates work", {
expect_equal(
sum(
first_isolate(septic_patients,
col_bactid = "bactid",
col_mo = "mo",
col_date = "date",
col_patient_id = "patient_id",
col_icu = "ward_icu",
@ -76,7 +76,7 @@ test_that("first isolates work", {
"Other")),
col_date = "date",
col_patient_id = "patient_id",
col_bactid = "bactid",
col_mo = "mo",
col_specimen = "specimen",
filter_specimen = "Urine",
info = TRUE),
@ -91,7 +91,7 @@ test_that("first isolates work", {
"Other")),
col_date = "date",
col_patient_id = "patient_id",
col_bactid = "bactid",
col_mo = "mo",
col_specimen = "specimen",
filter_specimen = "Urine",
col_icu = "ward_icu",
@ -104,7 +104,7 @@ test_that("first isolates work", {
expect_message(septic_patients %>%
mutate(specimen = "test") %>%
mutate(first = first_isolate(., "date", "patient_id",
col_bactid = "bactid",
col_mo = "mo",
col_specimen = "specimen",
filter_specimen = "something_unexisting",
output_logical = FALSE)))
@ -112,22 +112,22 @@ test_that("first isolates work", {
# printing of exclusion message
expect_output(septic_patients %>%
first_isolate(col_date = "date",
col_bactid = "bactid",
col_mo = "mo",
col_patient_id = "patient_id",
col_testcode = "sex",
testcodes_exclude = "M"))
# errors
expect_error(first_isolate("date", "patient_id", col_bactid = "bactid"))
expect_error(first_isolate("date", "patient_id", col_mo = "mo"))
expect_error(first_isolate(septic_patients))
expect_error(first_isolate(septic_patients,
col_date = "non-existing col",
col_bactid = "bactid"))
col_mo = "mo"))
expect_warning(septic_patients %>%
mutate(bactid = as.character(bactid)) %>%
mutate(mo = as.character(mo)) %>%
first_isolate(col_date = "date",
col_bactid = "bactid",
col_mo = "mo",
col_patient_id = "patient_id"))
})