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support for portuguese, language determination based on system

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2018-09-08 16:06:47 +02:00
parent b8a6c9af19
commit 26f5be0033
19 changed files with 307 additions and 106 deletions
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7
tests/testthat/test-data.R Normal file
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@ -0,0 +1,7 @@
context("data.R")
test_that("data sets are valid", {
# IDs should always be unique
expect_identical(nrow(antibiotics), length(unique(antibiotics$atc)))
expect_identical(nrow(microorganisms), length(unique(microorganisms$mo)))
})

8
tests/testthat/test-first_isolate.R
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@ -10,7 +10,7 @@ test_that("first isolates work", {
col_mo = "mo",
info = TRUE),
na.rm = TRUE),
1331)
1330)
# septic_patients contains 1426 out of 2000 first *weighted* isolates
expect_equal(
@ -24,7 +24,7 @@ test_that("first isolates work", {
type = "keyantibiotics",
info = TRUE),
na.rm = TRUE)),
1426)
1425)
# and 1449 when not ignoring I
expect_equal(
suppressWarnings(
@ -38,7 +38,7 @@ test_that("first isolates work", {
type = "keyantibiotics",
info = TRUE),
na.rm = TRUE)),
1449)
1448)
# and 1430 when using points
expect_equal(
suppressWarnings(
@ -64,7 +64,7 @@ test_that("first isolates work", {
info = TRUE,
icu_exclude = TRUE),
na.rm = TRUE),
1176)
1175)
# set 1500 random observations to be of specimen type 'Urine'
random_rows <- sample(x = 1:2000, size = 1500, replace = FALSE)

1
tests/testthat/test-mo.R
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@ -13,6 +13,7 @@ test_that("as.mo works", {
expect_equal(as.character(as.mo("Klebsiella")), "KLE")
expect_equal(as.character(as.mo("K. pneu rhino")), "KLEPNERH") # K. pneumoniae subspp. rhinoscleromatis
expect_equal(as.character(as.mo("Bartonella")), "BAR")
expect_equal(as.character(as.mo("C. difficile")), "CLODIF")
expect_equal(as.character(as.mo("S. pyo")), "STCPYO") # not Actinomyces pyogenes

8
tests/testthat/test-mo_property.R
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@ -6,8 +6,8 @@ test_that("mo_property works", {
expect_equal(mo_species("E. coli"), "coli")
expect_equal(mo_subspecies("E. coli"), "")
expect_equal(mo_fullname("E. coli"), "Escherichia coli")
expect_equal(mo_type("E. coli"), "Bacteria")
expect_equal(mo_gramstain("E. coli"), "Negative rods")
expect_equal(mo_type("E. coli", language = "en"), "Bacteria")
expect_equal(mo_gramstain("E. coli", language = "en"), "Negative rods")
expect_equal(mo_aerobic("E. coli"), TRUE)
expect_equal(mo_shortname("MRSA"), "S. aureus")
@ -16,8 +16,8 @@ test_that("mo_property works", {
expect_equal(mo_shortname("S. aga"), "S. agalactiae")
expect_equal(mo_shortname("S. aga", Lancefield = TRUE), "GBS")
expect_equal(mo_type("E. coli", language = "de"), "Bakterien")
expect_equal(mo_gramstain("E. coli", language = "de"), "Negative Staebchen")
expect_equal(mo_type("E. coli", language = "de"), "Bakterium")
expect_equal(mo_gramstain("E. coli", language = "de"), "Negative St\u00e4bchen")
expect_equal(mo_type("E. coli", language = "nl"), "Bacterie")
expect_equal(mo_gramstain("E. coli", language = "nl"), "Negatieve staven")