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(v0.7.1.9063) septic_patients -> example_isolates

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2019-08-27 16:45:42 +02:00
parent 7a6fce4eb8
commit 93be16484b
92 changed files with 1143 additions and 818 deletions
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2
tests/testthat/test-availability.R
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@ -22,5 +22,5 @@
context("availability.R")
test_that("availability works", {
expect_equal(class(availability(septic_patients)), "data.frame")
expect_equal(class(availability(example_isolates)), "data.frame")
})

2
tests/testthat/test-bug_drug_combinations.R
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@ -22,7 +22,7 @@
context("bug_drug_combinations.R")
test_that("bug_drug_combinations works", {
b <- suppressWarnings(bug_drug_combinations(septic_patients))
b <- suppressWarnings(bug_drug_combinations(example_isolates))
expect_s3_class(b, "bugdrug")
expect_message(print(b))
expect_true(is.data.frame(format(b)))

68
tests/testthat/test-count.R
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@ -22,27 +22,27 @@
context("count.R")
test_that("counts work", {
# AMX resistance in `septic_patients`
expect_equal(count_R(septic_patients$AMX), 683)
expect_equal(count_I(septic_patients$AMX), 3)
expect_equal(count_S(septic_patients$AMX), 543)
expect_equal(count_R(septic_patients$AMX) + count_I(septic_patients$AMX),
count_IR(septic_patients$AMX))
expect_equal(count_S(septic_patients$AMX) + count_I(septic_patients$AMX),
count_SI(septic_patients$AMX))
# AMX resistance in `example_isolates`
expect_equal(count_R(example_isolates$AMX), 683)
expect_equal(count_I(example_isolates$AMX), 3)
expect_equal(count_S(example_isolates$AMX), 543)
expect_equal(count_R(example_isolates$AMX) + count_I(example_isolates$AMX),
count_IR(example_isolates$AMX))
expect_equal(count_S(example_isolates$AMX) + count_I(example_isolates$AMX),
count_SI(example_isolates$AMX))
library(dplyr)
expect_equal(septic_patients %>% count_S(AMC), 1342)
expect_equal(septic_patients %>% count_S(AMC, GEN, only_all_tested = TRUE), 1660)
expect_equal(septic_patients %>% count_S(AMC, GEN, only_all_tested = FALSE), 1728)
expect_equal(septic_patients %>% count_all(AMC, GEN, only_all_tested = TRUE), 1798)
expect_equal(septic_patients %>% count_all(AMC, GEN, only_all_tested = FALSE), 1936)
expect_identical(septic_patients %>% count_all(AMC, GEN, only_all_tested = TRUE),
septic_patients %>% count_S(AMC, GEN, only_all_tested = TRUE) +
septic_patients %>% count_IR(AMC, GEN, only_all_tested = TRUE))
expect_equal(example_isolates %>% count_S(AMC), 1342)
expect_equal(example_isolates %>% count_S(AMC, GEN, only_all_tested = TRUE), 1660)
expect_equal(example_isolates %>% count_S(AMC, GEN, only_all_tested = FALSE), 1728)
expect_equal(example_isolates %>% count_all(AMC, GEN, only_all_tested = TRUE), 1798)
expect_equal(example_isolates %>% count_all(AMC, GEN, only_all_tested = FALSE), 1936)
expect_identical(example_isolates %>% count_all(AMC, GEN, only_all_tested = TRUE),
example_isolates %>% count_S(AMC, GEN, only_all_tested = TRUE) +
example_isolates %>% count_IR(AMC, GEN, only_all_tested = TRUE))
# count of cases
expect_equal(septic_patients %>%
expect_equal(example_isolates %>%
group_by(hospital_id) %>%
summarise(cipro = count_SI(CIP),
genta = count_SI(GEN),
@ -52,29 +52,29 @@ test_that("counts work", {
# count_df
expect_equal(
septic_patients %>% select(AMX) %>% count_df() %>% pull(value),
c(septic_patients$AMX %>% count_SI(),
septic_patients$AMX %>% count_R())
example_isolates %>% select(AMX) %>% count_df() %>% pull(value),
c(example_isolates$AMX %>% count_SI(),
example_isolates$AMX %>% count_R())
)
expect_equal(
septic_patients %>% select(AMX) %>% count_df(combine_IR = TRUE) %>% pull(value),
c(septic_patients$AMX %>% count_S(),
septic_patients$AMX %>% count_IR())
example_isolates %>% select(AMX) %>% count_df(combine_IR = TRUE) %>% pull(value),
c(example_isolates$AMX %>% count_S(),
example_isolates$AMX %>% count_IR())
)
expect_equal(
septic_patients %>% select(AMX) %>% count_df(combine_SI = FALSE) %>% pull(value),
c(septic_patients$AMX %>% count_S(),
septic_patients$AMX %>% count_I(),
septic_patients$AMX %>% count_R())
example_isolates %>% select(AMX) %>% count_df(combine_SI = FALSE) %>% pull(value),
c(example_isolates$AMX %>% count_S(),
example_isolates$AMX %>% count_I(),
example_isolates$AMX %>% count_R())
)
# warning for speed loss
expect_warning(count_R(as.character(septic_patients$AMC)))
expect_warning(count_I(as.character(septic_patients$AMC)))
expect_warning(count_S(as.character(septic_patients$AMC,
septic_patients$GEN)))
expect_warning(count_S(septic_patients$AMC,
as.character(septic_patients$GEN)))
expect_warning(count_R(as.character(example_isolates$AMC)))
expect_warning(count_I(as.character(example_isolates$AMC)))
expect_warning(count_S(as.character(example_isolates$AMC,
example_isolates$GEN)))
expect_warning(count_S(example_isolates$AMC,
as.character(example_isolates$GEN)))
# check for errors
expect_error(count_IR("test", minimum = "test"))
@ -85,6 +85,6 @@ test_that("counts work", {
expect_error(count_S("test", as_percent = "test"))
expect_error(count_df(c("A", "B", "C")))
expect_error(count_df(septic_patients[,"date"]))
expect_error(count_df(example_isolates[,"date"]))
})

16
tests/testthat/test-eucast_rules.R
View File

@ -30,15 +30,15 @@ test_that("EUCAST rules work", {
"then_change_these_antibiotics", "to_value",
"reference.rule", "reference.rule_group"))
expect_error(suppressWarnings(eucast_rules(septic_patients, col_mo = "Non-existing")))
expect_error(suppressWarnings(eucast_rules(example_isolates, col_mo = "Non-existing")))
expect_error(eucast_rules(x = "text"))
expect_error(eucast_rules(data.frame(a = "test")))
expect_error(eucast_rules(data.frame(mo = "test"), rules = "invalid rules set"))
expect_warning(eucast_rules(data.frame(mo = "Escherichia coli", vancomycin = "S")))
expect_identical(colnames(septic_patients),
colnames(suppressWarnings(eucast_rules(septic_patients))))
expect_identical(colnames(example_isolates),
colnames(suppressWarnings(eucast_rules(example_isolates))))
a <- data.frame(mo = c("Klebsiella pneumoniae",
"Pseudomonas aeruginosa",
@ -66,7 +66,7 @@ test_that("EUCAST rules work", {
# piperacillin must be R in Enterobacteriaceae when tica is R
library(dplyr)
expect_equal(suppressWarnings(
septic_patients %>%
example_isolates %>%
mutate(TIC = as.rsi("R"),
PIP = as.rsi("S")) %>%
eucast_rules(col_mo = "mo") %>%
@ -79,7 +79,7 @@ test_that("EUCAST rules work", {
# Azithromicin and Clarythromycin must be equal to Erythromycin
a <- suppressWarnings(
septic_patients %>%
example_isolates %>%
transmute(mo,
ERY,
AZM = as.rsi("R"),
@ -87,7 +87,7 @@ test_that("EUCAST rules work", {
eucast_rules(col_mo = "mo") %>%
pull(CLR))
b <- suppressWarnings(
septic_patients %>%
example_isolates %>%
select(mo, ERY) %>%
eucast_rules(col_mo = "mo") %>%
pull(ERY))
@ -108,9 +108,9 @@ test_that("EUCAST rules work", {
"S")
# also test norf
expect_output(suppressWarnings(eucast_rules(septic_patients %>% mutate(NOR = "S", NAL = "S"))))
expect_output(suppressWarnings(eucast_rules(example_isolates %>% mutate(NOR = "S", NAL = "S"))))
# check verbose output
expect_output(suppressWarnings(eucast_rules(septic_patients, verbose = TRUE)))
expect_output(suppressWarnings(eucast_rules(example_isolates, verbose = TRUE)))
})

32
tests/testthat/test-filter_ab_class.R
View File

@ -23,22 +23,22 @@ context("filter_ab_class.R")
test_that("ATC-group filtering works", {
library(dplyr)
expect_gt(septic_patients %>% filter_ab_class("carbapenem") %>% nrow(), 0)
expect_gt(septic_patients %>% filter_aminoglycosides() %>% nrow(), 0)
expect_gt(septic_patients %>% filter_carbapenems() %>% nrow(), 0)
expect_gt(septic_patients %>% filter_cephalosporins() %>% nrow(), 0)
expect_gt(septic_patients %>% filter_1st_cephalosporins() %>% nrow(), 0)
expect_gt(septic_patients %>% filter_2nd_cephalosporins() %>% nrow(), 0)
expect_gt(septic_patients %>% filter_3rd_cephalosporins() %>% nrow(), 0)
expect_gt(septic_patients %>% filter_4th_cephalosporins() %>% nrow(), 0)
expect_gt(septic_patients %>% filter_fluoroquinolones() %>% nrow(), 0)
expect_gt(septic_patients %>% filter_glycopeptides() %>% nrow(), 0)
expect_gt(septic_patients %>% filter_macrolides() %>% nrow(), 0)
expect_gt(septic_patients %>% filter_tetracyclines() %>% nrow(), 0)
expect_gt(example_isolates %>% filter_ab_class("carbapenem") %>% nrow(), 0)
expect_gt(example_isolates %>% filter_aminoglycosides() %>% nrow(), 0)
expect_gt(example_isolates %>% filter_carbapenems() %>% nrow(), 0)
expect_gt(example_isolates %>% filter_cephalosporins() %>% nrow(), 0)
expect_gt(example_isolates %>% filter_1st_cephalosporins() %>% nrow(), 0)
expect_gt(example_isolates %>% filter_2nd_cephalosporins() %>% nrow(), 0)
expect_gt(example_isolates %>% filter_3rd_cephalosporins() %>% nrow(), 0)
expect_gt(example_isolates %>% filter_4th_cephalosporins() %>% nrow(), 0)
expect_gt(example_isolates %>% filter_fluoroquinolones() %>% nrow(), 0)
expect_gt(example_isolates %>% filter_glycopeptides() %>% nrow(), 0)
expect_gt(example_isolates %>% filter_macrolides() %>% nrow(), 0)
expect_gt(example_isolates %>% filter_tetracyclines() %>% nrow(), 0)
expect_gt(septic_patients %>% filter_carbapenems("R", "all") %>% nrow(), 0)
expect_gt(example_isolates %>% filter_carbapenems("R", "all") %>% nrow(), 0)
expect_error(septic_patients %>% filter_carbapenems(result = "test"))
expect_error(septic_patients %>% filter_carbapenems(scope = "test"))
expect_warning(septic_patients %>% select(1:3) %>% filter_carbapenems())
expect_error(example_isolates %>% filter_carbapenems(result = "test"))
expect_error(example_isolates %>% filter_carbapenems(scope = "test"))
expect_warning(example_isolates %>% select(1:3) %>% filter_carbapenems())
})

38
tests/testthat/test-first_isolate.R
View File

@ -25,7 +25,7 @@ test_that("first isolates work", {
# first isolates
expect_equal(
sum(
first_isolate(x = septic_patients,
first_isolate(x = example_isolates,
col_date = "date",
col_patient_id = "patient_id",
col_mo = "mo",
@ -37,7 +37,7 @@ test_that("first isolates work", {
expect_equal(
suppressWarnings(
sum(
first_isolate(x = septic_patients %>% mutate(keyab = key_antibiotics(.)),
first_isolate(x = example_isolates %>% mutate(keyab = key_antibiotics(.)),
# let syntax determine these automatically:
# col_date = "date",
# col_patient_id = "patient_id",
@ -51,7 +51,7 @@ test_that("first isolates work", {
expect_equal(
suppressWarnings(
sum(
first_isolate(x = septic_patients %>% dplyr::as_tibble() %>% mutate(keyab = key_antibiotics(.)),
first_isolate(x = example_isolates %>% dplyr::as_tibble() %>% mutate(keyab = key_antibiotics(.)),
# let syntax determine these automatically:
# col_date = "date",
# col_patient_id = "patient_id",
@ -65,7 +65,7 @@ test_that("first isolates work", {
expect_equal(
suppressWarnings(
sum(
first_isolate(x = septic_patients %>% mutate(keyab = key_antibiotics(.)),
first_isolate(x = example_isolates %>% mutate(keyab = key_antibiotics(.)),
col_date = "date",
col_patient_id = "patient_id",
col_mo = "mo",
@ -79,7 +79,7 @@ test_that("first isolates work", {
expect_equal(
suppressWarnings(
sum(
first_isolate(x = septic_patients %>% mutate(keyab = key_antibiotics(.)),
first_isolate(x = example_isolates %>% mutate(keyab = key_antibiotics(.)),
col_date = "date",
col_patient_id = "patient_id",
col_mo = "mo",
@ -92,7 +92,7 @@ test_that("first isolates work", {
# first non-ICU isolates
expect_equal(
sum(
first_isolate(septic_patients,
first_isolate(example_isolates,
col_mo = "mo",
col_date = "date",
col_patient_id = "patient_id",
@ -106,7 +106,7 @@ test_that("first isolates work", {
random_rows <- sample(x = 1:2000, size = 1500, replace = FALSE)
expect_lt(
sum(
first_isolate(x = mutate(septic_patients,
first_isolate(x = mutate(example_isolates,
specimen = if_else(row_number() %in% random_rows,
"Urine",
"Other")),
@ -121,7 +121,7 @@ test_that("first isolates work", {
# same, but now exclude ICU
expect_lt(
sum(
first_isolate(x = mutate(septic_patients,
first_isolate(x = mutate(example_isolates,
specimen = if_else(row_number() %in% random_rows,
"Urine",
"Other")),
@ -137,7 +137,7 @@ test_that("first isolates work", {
1501)
# "No isolates found"
expect_message(septic_patients %>%
expect_message(example_isolates %>%
mutate(specimen = "test") %>%
mutate(first = first_isolate(., "date", "patient_id",
col_mo = "mo",
@ -145,7 +145,7 @@ test_that("first isolates work", {
filter_specimen = "something_unexisting")))
# printing of exclusion message
expect_output(septic_patients %>%
expect_output(example_isolates %>%
first_isolate(col_date = "date",
col_mo = "mo",
col_patient_id = "patient_id",
@ -154,29 +154,29 @@ test_that("first isolates work", {
# errors
expect_error(first_isolate("date", "patient_id", col_mo = "mo"))
expect_error(first_isolate(septic_patients,
expect_error(first_isolate(example_isolates,
col_date = "non-existing col",
col_mo = "mo"))
# look for columns itself
expect_message(first_isolate(septic_patients))
expect_message(first_isolate(septic_patients %>%
expect_message(first_isolate(example_isolates))
expect_message(first_isolate(example_isolates %>%
mutate(mo = as.character(mo)) %>%
left_join_microorganisms()))
# if mo is not an mo class, result should be the same
expect_identical(septic_patients %>%
expect_identical(example_isolates %>%
mutate(mo = as.character(mo)) %>%
first_isolate(col_date = "date",
col_mo = "mo",
col_patient_id = "patient_id"),
septic_patients %>%
example_isolates %>%
first_isolate(col_date = "date",
col_mo = "mo",
col_patient_id = "patient_id"))
# missing dates should be no problem
df <- septic_patients
df <- example_isolates
df[1:100, "date"] <- NA
expect_equal(
sum(
@ -189,19 +189,19 @@ test_that("first isolates work", {
1322)
# unknown MOs
expect_equal(septic_patients %>%
expect_equal(example_isolates %>%
mutate(mo = ifelse(mo == "B_ESCHR_COL", "UNKNOWN", mo)) %>%
mutate(first = first_isolate(., include_unknown = FALSE)) %>%
.$first %>%
sum(),
1062)
expect_equal(septic_patients %>%
expect_equal(example_isolates %>%
mutate(mo = ifelse(mo == "B_ESCHR_COL", "UNKNOWN", mo)) %>%
mutate(first = first_isolate(., include_unknown = TRUE)) %>%
.$first %>%
sum(),
1529)
expect_equal(septic_patients %>%
expect_equal(example_isolates %>%
mutate(mo = ifelse(mo == "B_ESCHR_COL", NA, mo)) %>%
mutate(first = first_isolate(.)) %>%
.$first %>%

6
tests/testthat/test-freq.R
View File

@ -24,10 +24,10 @@ context("freq.R")
test_that("frequency table works", {
library(clean)
# mo
expect_true(is.freq(freq(septic_patients$mo)))
expect_true(is.freq(freq(example_isolates$mo)))
# rsi
expect_true(is.freq(freq(septic_patients$AMX)))
expect_true(is.freq(freq(example_isolates$AMX)))
library(dplyr)
expect_true(is.freq(septic_patients %>% freq(mo)))
expect_true(is.freq(example_isolates %>% freq(mo)))
})

20
tests/testthat/test-ggplot_rsi.R
View File

@ -30,34 +30,34 @@ test_that("ggplot_rsi works", {
# data should be equal
expect_equal(
(septic_patients %>% select(AMC, CIP) %>% ggplot_rsi())$data %>%
(example_isolates %>% select(AMC, CIP) %>% ggplot_rsi())$data %>%
summarise_all(portion_IR) %>% as.double(),
septic_patients %>% select(AMC, CIP) %>%
example_isolates %>% select(AMC, CIP) %>%
summarise_all(portion_IR) %>% as.double()
)
print(septic_patients %>% select(AMC, CIP) %>% ggplot_rsi(x = "interpretation", facet = "antibiotic"))
print(septic_patients %>% select(AMC, CIP) %>% ggplot_rsi(x = "antibiotic", facet = "interpretation"))
print(example_isolates %>% select(AMC, CIP) %>% ggplot_rsi(x = "interpretation", facet = "antibiotic"))
print(example_isolates %>% select(AMC, CIP) %>% ggplot_rsi(x = "antibiotic", facet = "interpretation"))
expect_equal(
(septic_patients %>% select(AMC, CIP) %>% ggplot_rsi(x = "interpretation", facet = "antibiotic"))$data %>%
(example_isolates %>% select(AMC, CIP) %>% ggplot_rsi(x = "interpretation", facet = "antibiotic"))$data %>%
summarise_all(portion_IR) %>% as.double(),
septic_patients %>% select(AMC, CIP) %>%
example_isolates %>% select(AMC, CIP) %>%
summarise_all(portion_IR) %>% as.double()
)
expect_equal(
(septic_patients %>% select(AMC, CIP) %>% ggplot_rsi(x = "antibiotic", facet = "interpretation"))$data %>%
(example_isolates %>% select(AMC, CIP) %>% ggplot_rsi(x = "antibiotic", facet = "interpretation"))$data %>%
summarise_all(portion_IR) %>% as.double(),
septic_patients %>% select(AMC, CIP) %>%
example_isolates %>% select(AMC, CIP) %>%
summarise_all(portion_IR) %>% as.double()
)
expect_equal(
(septic_patients %>% select(AMC, CIP) %>% ggplot_rsi(x = "antibiotic",
(example_isolates %>% select(AMC, CIP) %>% ggplot_rsi(x = "antibiotic",
facet = "interpretation"))$data %>%
summarise_all(count_IR) %>% as.double(),
septic_patients %>% select(AMC, CIP) %>%
example_isolates %>% select(AMC, CIP) %>%
summarise_all(count_IR) %>% as.double()
)

10
tests/testthat/test-guess_ab_col.R
View File

@ -23,15 +23,15 @@ context("guess_ab_col.R")
test_that("guess_ab_col works", {
expect_equal(guess_ab_col(septic_patients, "amox"),
expect_equal(guess_ab_col(example_isolates, "amox"),
"AMX")
expect_equal(guess_ab_col(septic_patients, "amoxicillin"),
expect_equal(guess_ab_col(example_isolates, "amoxicillin"),
"AMX")
expect_equal(guess_ab_col(septic_patients, "J01AA07"),
expect_equal(guess_ab_col(example_isolates, "J01AA07"),
"TCY")
expect_equal(guess_ab_col(septic_patients, "tetracycline"),
expect_equal(guess_ab_col(example_isolates, "tetracycline"),
"TCY")
expect_equal(guess_ab_col(septic_patients, "TETR"),
expect_equal(guess_ab_col(example_isolates, "TETR"),
"TCY")
df <- data.frame(AMP_ND10 = "R",

14
tests/testthat/test-join_microorganisms.R
View File

@ -22,13 +22,13 @@
context("join_microorganisms.R")
test_that("joins work", {
unjoined <- septic_patients
inner <- septic_patients %>% inner_join_microorganisms()
left <- septic_patients %>% left_join_microorganisms()
semi <- septic_patients %>% semi_join_microorganisms()
anti <- septic_patients %>% anti_join_microorganisms()
suppressWarnings(right <- septic_patients %>% right_join_microorganisms())
suppressWarnings(full <- septic_patients %>% full_join_microorganisms())
unjoined <- example_isolates
inner <- example_isolates %>% inner_join_microorganisms()
left <- example_isolates %>% left_join_microorganisms()
semi <- example_isolates %>% semi_join_microorganisms()
anti <- example_isolates %>% anti_join_microorganisms()
suppressWarnings(right <- example_isolates %>% right_join_microorganisms())
suppressWarnings(full <- example_isolates %>% full_join_microorganisms())
expect_true(ncol(unjoined) < ncol(inner))
expect_true(nrow(unjoined) == nrow(inner))

4
tests/testthat/test-key_antibiotics.R
View File

@ -22,8 +22,8 @@
context("key_antibiotics.R")
test_that("keyantibiotics work", {
expect_equal(length(key_antibiotics(septic_patients, warnings = FALSE)), nrow(septic_patients))
expect_false(all(is.na(key_antibiotics(septic_patients))))
expect_equal(length(key_antibiotics(example_isolates, warnings = FALSE)), nrow(example_isolates))
expect_false(all(is.na(key_antibiotics(example_isolates))))
expect_true(key_antibiotics_equal("SSS", "SSS"))
expect_false(key_antibiotics_equal("SSS", "SRS"))
expect_true(key_antibiotics_equal("SSS", "SIS", ignore_I = TRUE))

6
tests/testthat/test-kurtosis.R
View File

@ -22,13 +22,13 @@
context("kurtosis.R")
test_that("kurtosis works", {
expect_equal(kurtosis(septic_patients$age),
expect_equal(kurtosis(example_isolates$age),
3.549319,
tolerance = 0.00001)
expect_equal(unname(kurtosis(data.frame(septic_patients$age))),
expect_equal(unname(kurtosis(data.frame(example_isolates$age))),
3.549319,
tolerance = 0.00001)
expect_equal(kurtosis(matrix(septic_patients$age)),
expect_equal(kurtosis(matrix(example_isolates$age)),
3.549319,
tolerance = 0.00001)
})

26
tests/testthat/test-mdro.R
View File

@ -24,29 +24,29 @@ context("mdro.R")
test_that("mdro works", {
library(dplyr)
expect_error(suppressWarnings(mdro(septic_patients, country = "invalid", col_mo = "mo", info = TRUE)))
expect_error(suppressWarnings(mdro(septic_patients, country = "fr", info = TRUE)))
expect_error(mdro(septic_patients, guideline = c("BRMO", "MRGN"), info = TRUE))
expect_error(mdro(septic_patients, col_mo = "invalid", info = TRUE))
expect_error(suppressWarnings(mdro(example_isolates, country = "invalid", col_mo = "mo", info = TRUE)))
expect_error(suppressWarnings(mdro(example_isolates, country = "fr", info = TRUE)))
expect_error(mdro(example_isolates, guideline = c("BRMO", "MRGN"), info = TRUE))
expect_error(mdro(example_isolates, col_mo = "invalid", info = TRUE))
outcome <- mdro(septic_patients)
outcome <- eucast_exceptional_phenotypes(septic_patients, info = TRUE)
outcome <- mdro(example_isolates)
outcome <- eucast_exceptional_phenotypes(example_isolates, info = TRUE)
# check class
expect_equal(outcome %>% class(), c('ordered', 'factor'))
outcome <- mdro(septic_patients, "nl", info = TRUE)
outcome <- mdro(example_isolates, "nl", info = TRUE)
# check class
expect_equal(outcome %>% class(), c('ordered', 'factor'))
# septic_patients should have these finding using Dutch guidelines
# example_isolates should have these finding using Dutch guidelines
expect_equal(outcome %>% freq() %>% pull(count),
c(1969, 25, 6)) # 1969 neg, 25 unconfirmed, 6 pos
expect_equal(brmo(septic_patients, info = FALSE),
mdro(septic_patients, guideline = "BRMO", info = FALSE))
expect_equal(brmo(example_isolates, info = FALSE),
mdro(example_isolates, guideline = "BRMO", info = FALSE))
# still working on German guidelines
expect_error(suppressWarnings(mrgn(septic_patients, info = TRUE)))
expect_error(suppressWarnings(mrgn(example_isolates, info = TRUE)))
# test Dutch P. aeruginosa MDRO
expect_equal(
@ -80,8 +80,8 @@ test_that("mdro works", {
expect_equal(
# select only rifampicine, mo will be determined automatically (as M. tuberculosis),
# number of mono-resistant strains should be equal to number of rifampicine-resistant strains
septic_patients %>% select(RIF) %>% mdr_tb() %>% freq() %>% pull(count) %>% .[2],
count_R(septic_patients$RIF))
example_isolates %>% select(RIF) %>% mdr_tb() %>% freq() %>% pull(count) %>% .[2],
count_R(example_isolates$RIF))
sample_rsi <- function() {
sample(c("S", "I", "R"),

8
tests/testthat/test-misc.R
View File

@ -42,8 +42,8 @@ test_that("functions missing in older R versions work", {
test_that("looking up ab columns works", {
expect_warning(generate_warning_abs_missing(c("AMP", "AMX")))
expect_warning(generate_warning_abs_missing(c("AMP", "AMX"), any = TRUE))
expect_warning(get_column_abx(septic_patients, hard_dependencies = "FUS"))
expect_message(get_column_abx(septic_patients, soft_dependencies = "FUS"))
expect_message(get_column_abx(dplyr::rename(septic_patients, thisone = AMX), amox = "thisone", tmp = "thisone", verbose = TRUE))
expect_warning(get_column_abx(dplyr::rename(septic_patients, thisone = AMX), amox = "thisone", tmp = "thisone", verbose = FALSE))
expect_warning(get_column_abx(example_isolates, hard_dependencies = "FUS"))
expect_message(get_column_abx(example_isolates, soft_dependencies = "FUS"))
expect_message(get_column_abx(dplyr::rename(example_isolates, thisone = AMX), amox = "thisone", tmp = "thisone", verbose = TRUE))
expect_warning(get_column_abx(dplyr::rename(example_isolates, thisone = AMX), amox = "thisone", tmp = "thisone", verbose = FALSE))
})

16
tests/testthat/test-mo.R
View File

@ -147,7 +147,7 @@ test_that("as.mo works", {
# select with one column
expect_identical(
septic_patients[1:10,] %>%
example_isolates[1:10,] %>%
left_join_microorganisms() %>%
select(genus) %>%
as.mo() %>%
@ -157,9 +157,9 @@ test_that("as.mo works", {
# select with two columns
expect_identical(
septic_patients[1:10,] %>%
example_isolates[1:10,] %>%
pull(mo),
septic_patients[1:10,] %>%
example_isolates[1:10,] %>%
left_join_microorganisms() %>%
select(genus, species) %>%
as.mo())
@ -168,13 +168,13 @@ test_that("as.mo works", {
expect_warning(as.mo(c("INVALID", "Yeah, unknown")))
# too many columns
expect_error(septic_patients %>% select(1:3) %>% as.mo())
expect_error(example_isolates %>% select(1:3) %>% as.mo())
# print
expect_output(print(as.mo(c("B_ESCHR_COL", NA))))
# test pull
expect_equal(nrow(septic_patients %>% mutate(mo = as.mo(mo))),
expect_equal(nrow(example_isolates %>% mutate(mo = as.mo(mo))),
2000)
# test data.frame
@ -248,7 +248,7 @@ test_that("as.mo works", {
expect_warning(as.mo("Virus"))
# summary
expect_equal(length(summary(septic_patients$mo)), 6)
expect_equal(length(summary(example_isolates$mo)), 6)
# WHONET codes and NA/NaN
expect_equal(as.character(as.mo(c("xxx", "na", "nan"), debug = TRUE)),
@ -260,7 +260,7 @@ test_that("as.mo works", {
rep("UNKNOWN", 3))
expect_null(mo_failures())
expect_true(septic_patients %>% pull(mo) %>% is.mo())
expect_true(example_isolates %>% pull(mo) %>% is.mo())
# expect_equal(get_mo_code("test", "mo"), "test")
# expect_equal(length(get_mo_code("Escherichia", "genus")),
@ -286,7 +286,7 @@ test_that("as.mo works", {
expect_output(print(tibble(mo = as.mo("B_STRPT_PNE"))))
# assigning and subsetting
x <- septic_patients$mo
x <- example_isolates$mo
expect_s3_class(x[1], "mo")
expect_s3_class(x[[1]], "mo")
expect_s3_class(c(x[1], x[9]), "mo")

78
tests/testthat/test-portion.R
View File

@ -22,28 +22,28 @@
context("portion.R")
test_that("portions works", {
# AMX resistance in `septic_patients`
expect_equal(portion_R(septic_patients$AMX), 0.5557364, tolerance = 0.0001)
expect_equal(portion_I(septic_patients$AMX), 0.002441009, tolerance = 0.0001)
expect_equal(1 - portion_R(septic_patients$AMX) - portion_I(septic_patients$AMX),
portion_S(septic_patients$AMX))
expect_equal(portion_R(septic_patients$AMX) + portion_I(septic_patients$AMX),
portion_IR(septic_patients$AMX))
expect_equal(portion_S(septic_patients$AMX) + portion_I(septic_patients$AMX),
portion_SI(septic_patients$AMX))
# AMX resistance in `example_isolates`
expect_equal(portion_R(example_isolates$AMX), 0.5557364, tolerance = 0.0001)
expect_equal(portion_I(example_isolates$AMX), 0.002441009, tolerance = 0.0001)
expect_equal(1 - portion_R(example_isolates$AMX) - portion_I(example_isolates$AMX),
portion_S(example_isolates$AMX))
expect_equal(portion_R(example_isolates$AMX) + portion_I(example_isolates$AMX),
portion_IR(example_isolates$AMX))
expect_equal(portion_S(example_isolates$AMX) + portion_I(example_isolates$AMX),
portion_SI(example_isolates$AMX))
expect_equal(septic_patients %>% portion_SI(AMC),
expect_equal(example_isolates %>% portion_SI(AMC),
0.7626397,
tolerance = 0.0001)
expect_equal(septic_patients %>% portion_SI(AMC, GEN),
expect_equal(example_isolates %>% portion_SI(AMC, GEN),
0.9408,
tolerance = 0.0001)
expect_equal(septic_patients %>% portion_SI(AMC, GEN, only_all_tested = TRUE),
expect_equal(example_isolates %>% portion_SI(AMC, GEN, only_all_tested = TRUE),
0.9382647,
tolerance = 0.0001)
# percentages
expect_equal(septic_patients %>%
expect_equal(example_isolates %>%
group_by(hospital_id) %>%
summarise(R = portion_R(CIP, as_percent = TRUE),
I = portion_I(CIP, as_percent = TRUE),
@ -55,7 +55,7 @@ test_that("portions works", {
1409)
# count of cases
expect_equal(septic_patients %>%
expect_equal(example_isolates %>%
group_by(hospital_id) %>%
summarise(cipro_p = portion_SI(CIP, as_percent = TRUE),
cipro_n = n_rsi(CIP),
@ -66,14 +66,14 @@ test_that("portions works", {
pull(combination_n),
c(305, 617, 241, 711))
expect_warning(portion_R(as.character(septic_patients$AMC)))
expect_warning(portion_S(as.character(septic_patients$AMC)))
expect_warning(portion_S(as.character(septic_patients$AMC,
septic_patients$GEN)))
expect_warning(n_rsi(as.character(septic_patients$AMC,
septic_patients$GEN)))
expect_equal(suppressWarnings(n_rsi(as.character(septic_patients$AMC,
septic_patients$GEN))),
expect_warning(portion_R(as.character(example_isolates$AMC)))
expect_warning(portion_S(as.character(example_isolates$AMC)))
expect_warning(portion_S(as.character(example_isolates$AMC,
example_isolates$GEN)))
expect_warning(n_rsi(as.character(example_isolates$AMC,
example_isolates$GEN)))
expect_equal(suppressWarnings(n_rsi(as.character(example_isolates$AMC,
example_isolates$GEN))),
1879)
# check for errors
@ -86,36 +86,36 @@ test_that("portions works", {
expect_error(portion_S("test", also_single_tested = TRUE))
# check too low amount of isolates
expect_identical(suppressWarnings(portion_R(septic_patients$AMX, minimum = nrow(septic_patients) + 1)),
expect_identical(suppressWarnings(portion_R(example_isolates$AMX, minimum = nrow(example_isolates) + 1)),
NA)
expect_identical(suppressWarnings(portion_I(septic_patients$AMX, minimum = nrow(septic_patients) + 1)),
expect_identical(suppressWarnings(portion_I(example_isolates$AMX, minimum = nrow(example_isolates) + 1)),
NA)
expect_identical(suppressWarnings(portion_S(septic_patients$AMX, minimum = nrow(septic_patients) + 1)),
expect_identical(suppressWarnings(portion_S(example_isolates$AMX, minimum = nrow(example_isolates) + 1)),
NA)
# warning for speed loss
expect_warning(portion_R(as.character(septic_patients$GEN)))
expect_warning(portion_I(as.character(septic_patients$GEN)))
expect_warning(portion_S(septic_patients$AMC, as.character(septic_patients$GEN)))
expect_warning(portion_R(as.character(example_isolates$GEN)))
expect_warning(portion_I(as.character(example_isolates$GEN)))
expect_warning(portion_S(example_isolates$AMC, as.character(example_isolates$GEN)))
# portion_df
expect_equal(
septic_patients %>% select(AMX) %>% portion_df() %>% pull(value),
c(septic_patients$AMX %>% portion_SI(),
septic_patients$AMX %>% portion_R())
example_isolates %>% select(AMX) %>% portion_df() %>% pull(value),
c(example_isolates$AMX %>% portion_SI(),
example_isolates$AMX %>% portion_R())
)
expect_equal(
septic_patients %>% select(AMX) %>% portion_df(combine_IR = TRUE) %>% pull(value),
c(septic_patients$AMX %>% portion_S(),
septic_patients$AMX %>% portion_IR())
example_isolates %>% select(AMX) %>% portion_df(combine_IR = TRUE) %>% pull(value),
c(example_isolates$AMX %>% portion_S(),
example_isolates$AMX %>% portion_IR())
)
expect_equal(
septic_patients %>% select(AMX) %>% portion_df(combine_SI = FALSE) %>% pull(value),
c(septic_patients$AMX %>% portion_S(),
septic_patients$AMX %>% portion_I(),
septic_patients$AMX %>% portion_R())
example_isolates %>% select(AMX) %>% portion_df(combine_SI = FALSE) %>% pull(value),
c(example_isolates$AMX %>% portion_S(),
example_isolates$AMX %>% portion_I(),
example_isolates$AMX %>% portion_R())
)
expect_error(portion_df(c("A", "B", "C")))
expect_error(portion_df(septic_patients[,"date"]))
expect_error(portion_df(example_isolates[,"date"]))
})

26
tests/testthat/test-resistance_predict.R
View File

@ -22,7 +22,7 @@
context("resistance_predict.R")
test_that("prediction of rsi works", {
AMX_R <- septic_patients %>%
AMX_R <- example_isolates %>%
filter(mo == "B_ESCHR_COL") %>%
rsi_predict(col_ab = "AMX",
col_date = "date",
@ -30,57 +30,57 @@ test_that("prediction of rsi works", {
minimum = 10,
info = TRUE) %>%
pull("value")
# AMX resistance will increase according to data set `septic_patients`
# AMX resistance will increase according to data set `example_isolates`
expect_true(AMX_R[3] < AMX_R[20])
x <- resistance_predict(septic_patients, col_ab = "AMX", year_min = 2010, model = "binomial")
x <- resistance_predict(example_isolates, col_ab = "AMX", year_min = 2010, model = "binomial")
plot(x)
ggplot_rsi_predict(x)
expect_error(ggplot_rsi_predict(septic_patients))
expect_error(ggplot_rsi_predict(example_isolates))
library(dplyr)
expect_output(rsi_predict(x = filter(septic_patients, mo == "B_ESCHR_COL"),
expect_output(rsi_predict(x = filter(example_isolates, mo == "B_ESCHR_COL"),
model = "binomial",
col_ab = "AMX",
col_date = "date",
info = TRUE))
expect_output(rsi_predict(x = filter(septic_patients, mo == "B_ESCHR_COL"),
expect_output(rsi_predict(x = filter(example_isolates, mo == "B_ESCHR_COL"),
model = "loglin",
col_ab = "AMX",
col_date = "date",
info = TRUE))
expect_output(rsi_predict(x = filter(septic_patients, mo == "B_ESCHR_COL"),
expect_output(rsi_predict(x = filter(example_isolates, mo == "B_ESCHR_COL"),
model = "lin",
col_ab = "AMX",
col_date = "date",
info = TRUE))
expect_error(rsi_predict(x = filter(septic_patients, mo == "B_ESCHR_COL"),
expect_error(rsi_predict(x = filter(example_isolates, mo == "B_ESCHR_COL"),
model = "INVALID MODEL",
col_ab = "AMX",
col_date = "date",
info = TRUE))
expect_error(rsi_predict(x = filter(septic_patients, mo == "B_ESCHR_COL"),
expect_error(rsi_predict(x = filter(example_isolates, mo == "B_ESCHR_COL"),
model = "binomial",
col_ab = "NOT EXISTING COLUMN",
col_date = "date",
info = TRUE))
expect_error(rsi_predict(x = filter(septic_patients, mo == "B_ESCHR_COL"),
expect_error(rsi_predict(x = filter(example_isolates, mo == "B_ESCHR_COL"),
model = "binomial",
col_ab = "AMX",
col_date = "NOT EXISTING COLUMN",
info = TRUE))
expect_error(rsi_predict(x = filter(septic_patients, mo == "B_ESCHR_COL"),
expect_error(rsi_predict(x = filter(example_isolates, mo == "B_ESCHR_COL"),
col_ab = "AMX",
col_date = "NOT EXISTING COLUMN",
info = TRUE))
expect_error(rsi_predict(x = filter(septic_patients, mo == "B_ESCHR_COL"),
expect_error(rsi_predict(x = filter(example_isolates, mo == "B_ESCHR_COL"),
col_ab = "AMX",
col_date = "date",
info = TRUE))
# almost all E. coli are MEM S in the Netherlands :)
expect_error(resistance_predict(x = filter(septic_patients, mo == "B_ESCHR_COL"),
expect_error(resistance_predict(x = filter(example_isolates, mo == "B_ESCHR_COL"),
model = "binomial",
col_ab = "MEM",
col_date = "date",

10
tests/testthat/test-rsi.R
View File

@ -41,12 +41,12 @@ test_that("rsi works", {
"-Sum R" = "1",
"-Sum I" = "0"))
expect_identical(as.logical(lapply(septic_patients, is.rsi.eligible)),
rep(FALSE, length(septic_patients)))
expect_identical(as.logical(lapply(example_isolates, is.rsi.eligible)),
rep(FALSE, length(example_isolates)))
library(dplyr)
# 40 rsi columns
expect_equal(septic_patients %>%
expect_equal(example_isolates %>%
mutate_at(vars(PEN:RIF), as.character) %>%
lapply(is.rsi.eligible) %>%
as.logical() %>%
@ -69,7 +69,7 @@ test_that("mic2rsi works", {
guideline = "EUCAST")),
"R")
expect_true(septic_patients %>%
expect_true(example_isolates %>%
mutate(amox_mic = as.mic(2)) %>%
select(mo, amox_mic) %>%
as.rsi() %>%
@ -97,7 +97,7 @@ test_that("disk2rsi works", {
guideline = "CLSI")),
"R")
expect_true(septic_patients %>%
expect_true(example_isolates %>%
mutate(amox_disk = as.disk(15)) %>%
select(mo, amox_disk) %>%
as.rsi(guideline = "CLSI") %>%

6
tests/testthat/test-skewness.R
View File

@ -22,13 +22,13 @@
context("skewness.R")
test_that("skewness works", {
expect_equal(skewness(septic_patients$age),
expect_equal(skewness(example_isolates$age),
-0.8958019,
tolerance = 0.00001)
expect_equal(unname(skewness(data.frame(septic_patients$age))),
expect_equal(unname(skewness(data.frame(example_isolates$age))),
-0.8958019,
tolerance = 0.00001)
expect_equal(skewness(matrix(septic_patients$age)),
expect_equal(skewness(matrix(example_isolates$age)),
-0.8958019,
tolerance = 0.00001)
})