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(v1.5.0.9007) updated unit tests

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2021-01-18 18:45:43 +01:00
parent 4eab095306
commit 27f084d819
17 changed files with 47 additions and 43 deletions
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13
tests/testthat/test-eucast_rules.R
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@ -50,20 +50,21 @@ test_that("EUCAST rules work", {
expect_warning(eucast_rules(data.frame(mo = "Escherichia coli", vancomycin = "S", stringsAsFactors = TRUE)))
expect_identical(colnames(example_isolates),
colnames(suppressWarnings(eucast_rules(example_isolates))))
colnames(suppressWarnings(eucast_rules(example_isolates, info = FALSE))))
expect_output(suppressMessages(eucast_rules(example_isolates, info = TRUE)))
a <- data.frame(mo = c("Klebsiella pneumoniae",
"Pseudomonas aeruginosa",
"Enterobacter aerogenes"),
"Enterobacter cloacae"),
amox = "-", # Amoxicillin
stringsAsFactors = FALSE)
b <- data.frame(mo = c("Klebsiella pneumoniae",
"Pseudomonas aeruginosa",
"Enterobacter aerogenes"),
"Enterobacter cloacae"),
amox = "R", # Amoxicillin
stringsAsFactors = FALSE)
expect_identical(suppressWarnings(eucast_rules(a, "mo", info = FALSE)), b)
expect_identical(suppressWarnings(eucast_rules(a, "mo", info = TRUE)), b)
expect_output(suppressMessages(suppressWarnings(eucast_rules(a, "mo", info = TRUE))))
a <- data.frame(mo = c("Staphylococcus aureus",
"Streptococcus group A"),
@ -81,8 +82,8 @@ test_that("EUCAST rules work", {
example_isolates %>%
mutate(TIC = as.rsi("R"),
PIP = as.rsi("S")) %>%
eucast_rules(col_mo = "mo", version_expertrules = 3.1) %>%
left_join_microorganisms() %>%
eucast_rules(col_mo = "mo", version_expertrules = 3.1, info = FALSE) %>%
left_join_microorganisms(by = "mo") %>%
filter(family == "Enterobacteriaceae") %>%
pull(PIP) %>%
unique() %>%

13
tests/testthat/test-mdro.R
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@ -34,13 +34,13 @@ test_that("mdro works", {
expect_error(mdro(example_isolates, guideline = c("BRMO", "MRGN"), info = TRUE))
expect_error(mdro(example_isolates, col_mo = "invalid", info = TRUE))
outcome <- suppressWarnings(mdro(example_isolates))
outcome <- mdro(example_isolates, "eucast3.1", info = TRUE)
outcome <- eucast_exceptional_phenotypes(example_isolates, info = TRUE)
expect_output(suppressMessages(suppressWarnings(mdro(example_isolates, info = TRUE))))
expect_output(suppressMessages(suppressWarnings(mdro(example_isolates, "eucast3.1", info = TRUE))))
expect_output(outcome <- suppressMessages(suppressWarnings(eucast_exceptional_phenotypes(example_isolates, info = TRUE))))
# check class
expect_equal(class(outcome), c("ordered", "factor"))
outcome <- mdro(example_isolates, "nl", info = TRUE)
expect_output(outcome <- mdro(example_isolates, "nl", info = TRUE))
# check class
expect_equal(class(outcome), c("ordered", "factor"))
@ -228,15 +228,14 @@ test_that("mdro works", {
"ERY == 'R' & age > 60" ~ "Elderly Type B",
as_factor = TRUE)
expect_output(print(custom))
x <- mdro(example_isolates, guideline = custom, info = TRUE)
expect_equal(as.double(table(x)), c(43, 891, 1066))
expect_output(x <- mdro(example_isolates, guideline = custom, info = TRUE))
expect_equal(as.double(table(x)), c(1066, 43, 891))
expect_output(print(custom_mdro_guideline(AMX == "R" ~ "test", as_factor = FALSE)))
expect_error(custom_mdro_guideline())
expect_error(custom_mdro_guideline("test"))
expect_error(custom_mdro_guideline("test" ~ c(1:3)))
expect_error(custom_mdro_guideline("test" ~ A))
expect_error(custom_mdro_guideline(test ~ "A"))
expect_warning(mdro(example_isolates,
# since `test` gives an error, it will be ignored with a warning
guideline = custom_mdro_guideline(test ~ "A"),

24
tests/testthat/test-resistance_predict.R
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@ -27,25 +27,25 @@ context("resistance_predict.R")
test_that("prediction of rsi works", {
skip_on_cran()
AMX_R <- example_isolates %>%
filter(mo == "B_ESCHR_COLI") %>%
rsi_predict(col_ab = "AMX",
col_date = "date",
model = "binomial",
minimum = 10,
info = TRUE) %>%
pull("value")
library(dplyr)
expect_output(AMX_R <- example_isolates %>%
filter(mo == "B_ESCHR_COLI") %>%
rsi_predict(col_ab = "AMX",
col_date = "date",
model = "binomial",
minimum = 10,
info = TRUE) %>%
pull("value"))
# AMX resistance will increase according to data set `example_isolates`
expect_true(AMX_R[3] < AMX_R[20])
x <- resistance_predict(example_isolates, col_ab = "AMX", year_min = 2010, model = "binomial")
expect_output(x <- suppressMessages(resistance_predict(example_isolates, col_ab = "AMX", year_min = 2010, model = "binomial", info = TRUE)))
pdf(NULL) # prevent Rplots.pdf being created
expect_silent(plot(x))
expect_silent(ggplot_rsi_predict(x))
expect_error(ggplot_rsi_predict(example_isolates))
library(dplyr, warn.conflicts = FALSE)
expect_output(rsi_predict(x = filter(example_isolates, mo == "B_ESCHR_COLI"),
model = "binomial",
col_ab = "AMX",