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AI improvements

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2018-12-07 12:04:55 +01:00
parent 87ad6da745
commit 8e8a9cd190
19 changed files with 199 additions and 140 deletions
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40
tests/testthat/test-atc.R
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@ -1,25 +1,25 @@
context("atc.R")
test_that("atc_property works", {
#skip_on_cran() # relies on internet connection of server, don't test
#skip_on_appveyor() # security error on AppVeyor
if (!is.null(curl::nslookup("www.whocc.no", error = FALSE))) {
expect_equal(tolower(atc_property("J01CA04", property = "Name")), "amoxicillin")
expect_equal(atc_property("J01CA04", property = "unit"), "g")
expect_equal(atc_property("J01CA04", property = "DDD"),
atc_ddd("J01CA04"))
expect_identical(atc_property("J01CA04", property = "Groups"),
atc_groups("J01CA04"))
expect_warning(atc_property("ABCDEFG", property = "DDD"))
expect_error(atc_property("J01CA04", property = c(1:5)))
expect_error(atc_property("J01CA04", property = "test"))
expect_error(atc_property("J01CA04", property = "test", administration = c(1:5)))
}
})
# test_that("atc_property works", {
# skip_on_cran() # relies on internet connection of server, don't test
# skip_on_appveyor() # security error on AppVeyor
#
# if (!is.null(curl::nslookup("www.whocc.no", error = FALSE))) {
# expect_equal(tolower(atc_property("J01CA04", property = "Name")), "amoxicillin")
# expect_equal(atc_property("J01CA04", property = "unit"), "g")
# expect_equal(atc_property("J01CA04", property = "DDD"),
# atc_ddd("J01CA04"))
#
# expect_identical(atc_property("J01CA04", property = "Groups"),
# atc_groups("J01CA04"))
#
# expect_warning(atc_property("ABCDEFG", property = "DDD"))
#
# expect_error(atc_property("J01CA04", property = c(1:5)))
# expect_error(atc_property("J01CA04", property = "test"))
# expect_error(atc_property("J01CA04", property = "test", administration = c(1:5)))
# }
# })
test_that("guess_atc works", {
expect_equal(as.character(guess_atc(c("J01FA01",

2
tests/testthat/test-mic.R
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@ -21,7 +21,7 @@ test_that("mic works", {
plot(as.mic(c(1, 2, 4, 8)))
print(as.mic(c(1, 2, 4, 8)))
expect_equal(summary(as.mic(c(2, 8))), c("Mode" = 'mic',
expect_equal(summary(as.mic(c(2, 8))), c("Class" = "mic",
"<NA>" = "0",
"Min." = "2",
"Max." = "8"))

4
tests/testthat/test-mo.R
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@ -214,10 +214,10 @@ test_that("as.mo works", {
expect_equal(as.character(suppressWarnings(as.mo(
c("Microbacterium paraoxidans",
"Streptococcus suis (bovis gr)",
"Raoultella (here some text) terrigena"), allow_uncertain = TRUE))),
"Raoultella (here some text) terrigena")))),
c("B_MCRBC", "B_STRPTC_SUI", "B_RLTLL_TER"))
# Salmonella (City) are all actually Salmonella enterica spp (City)
expect_equal(as.character(suppressMessages(as.mo("Salmonella Goettingen", allow_uncertain = TRUE))),
expect_equal(as.character(suppressMessages(as.mo("Salmonella Goettingen"))),
"B_SLMNL_ENT")
})

2
tests/testthat/test-rsi.R
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@ -13,7 +13,7 @@ test_that("rsi works", {
expect_equal(suppressWarnings(as.logical(as.rsi("INVALID VALUE"))), NA)
expect_equal(summary(as.rsi(c("S", "R"))), c("Mode" = 'rsi',
expect_equal(summary(as.rsi(c("S", "R"))), c("Class" = "rsi",
"<NA>" = "0",
"Sum S" = "1",
"Sum IR" = "1",