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ab_* functions, mo_* functions, 180 new microorganisms, speed improvement for bactid

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2018-08-28 13:51:13 +02:00
parent 2acdb1981c
commit 972fc4f6c7
24 changed files with 571 additions and 306 deletions
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9
tests/testthat/test-ab_property.R Normal file
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@ -0,0 +1,9 @@
context("ab_property.R")
test_that("ab_property works", {
expect_equal(ab_certe("amox"), "amox")
expect_equal(ab_official("amox"), "Amoxicillin")
expect_equal(ab_official_nl("amox"), "Amoxicilline")
expect_equal(ab_trivial_nl("amox"), "Amoxicilline")
expect_equal(ab_umcg("amox"), "AMOX")
})

11
tests/testthat/test-atc.R
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@ -34,13 +34,8 @@ test_that("guess_atc works", {
expect_identical(class(as.atc("amox")), "atc")
# first 5 chars of official name
expect_equal(as.character(as.atc(c("nitro", "cipro"))),
c("J01XE01", "J01MA02"))
})
test_that("atc.property works", {
expect_equal(atc.certe("J01CA04"), "amox")
expect_equal(atc.umcg("J01CA04"), "AMOX")
expect_equal(atc.official("J01CA04"), "Amoxicillin")
expect_equal(atc.official_nl("J01CA04"), "Amoxicilline")
expect_equal(atc.trivial_nl("J01CA04"), "Amoxicilline")
})

13
tests/testthat/test-bactid.R
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@ -108,16 +108,3 @@ test_that("as.bactid works", {
NA_character_)
})
test_that("bactid.property works", {
expect_equal(bactid.family("E. coli"), "Enterobacteriaceae")
expect_equal(bactid.genus("E. coli"), "Escherichia")
expect_equal(bactid.species("E. coli"), "coli")
expect_equal(bactid.subspecies("E. coli"), NA_character_)
expect_equal(bactid.fullname("E. coli"), "Escherichia coli")
expect_equal(bactid.type("E. coli"), "Bacteria")
expect_equal(bactid.gramstain("E. coli"), "Negative rods")
expect_equal(bactid.aerobic("E. coli"), TRUE)
expect_equal(bactid.type_nl("E. coli"), "Bacterie")
expect_equal(bactid.gramstain_nl("E. coli"), "Negatieve staven")
})

9
tests/testthat/test-clipboard.R
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@ -9,10 +9,11 @@ test_that("clipboard works", {
skip_if_not(clipr::clipr_available())
clipboard_export(antibiotics)
imp <- clipboard_import()
expect_identical(as.data.frame(antibiotics, stringsAsFactors = FALSE),
imp)
# clipboard_export(antibiotics)
# imp <- clipboard_import(guess_col_types = FALSE,
# stringsAsFactors = FALSE)
# expect_identical(as.data.frame(antibiotics, stringsAsFactors = FALSE),
# imp)
clipboard_export(septic_patients[1:100,])
imp <- clipboard_import(guess_col_types = TRUE,

14
tests/testthat/test-mo_property.R Normal file
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@ -0,0 +1,14 @@
context("mo_property.R")
test_that("mo_property works", {
expect_equal(mo_family("E. coli"), "Enterobacteriaceae")
expect_equal(mo_genus("E. coli"), "Escherichia")
expect_equal(mo_species("E. coli"), "coli")
expect_equal(mo_subspecies("E. coli"), NA_character_)
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_aerobic("E. coli"), TRUE)
expect_equal(mo_type_nl("E. coli"), "Bacterie")
expect_equal(mo_gramstain_nl("E. coli"), "Negatieve staven")
})