add tests using testthat

tests/testthat.R

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+library(testthat)
+library(AMR)
+
+test_check("AMR")

tests/testthat/test-atc.R

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+context("atc.R")
+
+
+test_that("atc_property works", {
+  expect_equal(tolower(atc_property("J01CA04", property = "Name")), "amoxicillin")
+  expect_equivalent(atc_property("J01CA04", "DDD"), 1)
+})
+
+test_that("abname works", {
+  expect_equal(abname("AMOX"), "Amoxicillin")
+  expect_equal(abname(c("AMOX", "GENT")), c("Amoxicillin", "Gentamicin"))
+  expect_equal(abname("AMOX", from = 'umcg'), "Amoxicillin")
+  expect_equal(abname("amox", from = 'molis'), "Amoxicillin")
+  expect_equal(abname("J01CA04", from = 'atc'), "Amoxicillin")
+})

tests/testthat/test-classes.R

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+context("classes.R")
+
+test_that("rsi works", {
+  expect_true(as.rsi("S") < as.rsi("I"))
+  expect_true(as.rsi("I") < as.rsi("R"))
+  expect_true(as.rsi("R") > as.rsi("S"))
+  expect_true(is.rsi(as.rsi("S")))
+  
+  expect_equal(suppressWarnings(as.logical(as.rsi("INVALID VALUE"))), NA)
+  
+  expect_equal(class(barplot(as.rsi(c("S", "I", "R")))), "numeric")
+  
+  expect_equal(summary(as.rsi(c("S", "R"))), c("Mode" = 'rsi',
+                                               "<NA>" = "0",
+                                               "Sum S" = "1",
+                                               "Sum IR" = "1",
+                                               "Sum R" = "1",
+                                               "Sum I" = "0"))
+})
+
+test_that("mic works", {
+  expect_true(as.mic(8) == as.mic("8"))
+  expect_true(as.mic("1") > as.mic("<=0.0625"))
+  expect_true(as.mic("1") < as.mic(">=32"))
+  expect_true(is.mic(as.mic(8)))
+  
+  expect_equal(as.double(as.mic(">=32")), 32)
+  expect_equal(as.integer(as.mic(">=32")), 32)
+  expect_equal(suppressWarnings(as.logical(as.mic("INVALID VALUE"))), NA)
+  
+  expect_equal(class(plot(as.mic(c(1, 2, 4, 8)))), "numeric")
+  
+  expect_equal(summary(as.mic(c(2, 8))), c("Mode" = 'mic',
+                                           "<NA>" = "0",
+                                           "Min." = "2",
+                                           "Max." = "8"))
+})

tests/testthat/test-clipboard.R

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+context("clipboard.R")
+
+test_that("clipboard works", {
+  # why is the <<- needed? Won't work without it...
+  t1 <<- AMR::antibiotics
+  clipboard_export(t1, info = FALSE)
+  t2 <- clipboard_import()
+  expect_equal(t1, t2)
+})

tests/testthat/test-eucast.R

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+context("EUCAST.R")
+
+test_that("EUCAST rules work", {
+  a <- data.frame(bactid = c("KLEPNE",  # Klebsiella pneumoniae
+                             "PSEAER",  # Pseudomonas aeruginosa
+                             "ENTAER"), # Enterobacter aerogenes
+                  amox = "-",           # Amoxicillin
+                  stringsAsFactors = FALSE)
+  b <- data.frame(bactid = c("KLEPNE",  # Klebsiella pneumoniae
+                             "PSEAER",  # Pseudomonas aeruginosa
+                             "ENTAER"), # Enterobacter aerogenes
+                  amox = "R",           # Amoxicillin
+                  stringsAsFactors = FALSE)
+  expect_equal(EUCAST_rules(a, info = FALSE), b)
+  expect_equal(interpretive_reading(a, info = FALSE), b)
+  
+  a <- data.frame(bactid = c("STAAUR",  # Staphylococcus aureus
+                             "STCGRA"), # Streptococcus pyognenes (Lancefield Group A)
+                  coli = "-",           # Colistin
+                  stringsAsFactors = FALSE)
+  b <- data.frame(bactid = c("STAAUR",  # Staphylococcus aureus
+                             "STCGRA"), # Streptococcus pyognenes (Lancefield Group A)
+                  coli = "R",           # Colistin
+                  stringsAsFactors = FALSE)
+  expect_equal(EUCAST_rules(a, info = FALSE), b)
+})
+
+test_that("MO properties work", {
+  expect_equal(mo_property("ESCCOL"), "Escherichia coli")
+  expect_equal(mo_property("STAAUR"), "Staphylococcus aureus")
+})

tests/testthat/test-first_isolates.R

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+context("first_isolates.R")
+
+test_that("keyantibiotics work", {
+  expect_equal(length(key_antibiotics(septic_patients, info = FALSE)), nrow(septic_patients))
+  expect_true(key_antibiotics_equal("SSS", "SSS"))
+  expect_true(key_antibiotics_equal("SSS", "SIS", ignore_I = TRUE))
+  expect_false(key_antibiotics_equal("SSS", "SIS", ignore_I = FALSE))
+})
+
+
+test_that("guess_bactid works", {
+  expect_equal(guess_bactid("E. coli"), "ESCCOL")
+  expect_equal(guess_bactid("Escherichia coli"), "ESCCOL")
+})
+
+test_that("first isolates work", {
+  # septic_patients contains 1960 out of 2000 first isolates
+  expect_equal(sum(first_isolate(septic_patients,
+                             "date",
+                             "patient_id",
+                             "bactid",
+                             info = FALSE)), 1960)
+})

tests/testthat/test-joins.R

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+context("joins.R")
+
+test_that("joins work", {
+  unjoined <- septic_patients
+  inner <- septic_patients %>% inner_join_microorganisms()
+  left <- septic_patients %>% left_join_microorganisms()
+  suppressWarnings(right <- septic_patients %>% right_join_microorganisms())
+  suppressWarnings(full <- septic_patients %>% full_join_microorganisms())
+  
+  expect_true(ncol(unjoined) < ncol(inner))
+  expect_true(nrow(unjoined) == nrow(inner))
+  
+  expect_true(ncol(unjoined) < ncol(left))
+  expect_true(nrow(unjoined) == nrow(left))
+  
+  expect_true(nrow(unjoined) < nrow(right))
+  expect_true(nrow(unjoined) < nrow(full))
+})

tests/testthat/test-misc.R

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+context("misc.R")
+
+test_that("`like` works", {
+  expect_true("test" %like% "^t")
+  expect_true("test" %like% "test")
+  expect_true("test" %like% "TEST")
+  expect_true(as.factor("test") %like% "TEST")
+})
+
+test_that("percentages works", {
+  expect_equal(percent(0.25), "25%")
+  expect_equal(percent(0.5), "50%")
+  expect_equal(percent(0.1234), "12.3%")
+})
+
+test_that("quasiquotation works", {
+  expect_equal(quasiquotate(deparse(substitute("test")), "test"), "test")
+  expect_equal(quasiquotate(deparse(substitute('test')), "'test'"), "test")
+  expect_equal(quasiquotate(deparse(substitute(test)), test), "test")
+})

tests/testthat/test-rsi_analysis.R

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+context("rsi_analysis.R")
+
+test_that("rsi works", {
+  # amox resistance in `septic_patients` should be around 53.86%
+  amox_R <- septic_patients %>% summarise(amox = rsi(amox)) %>% pull(amox)
+  expect_equal(amox_R, 0.5386, tolerance = 0.0001)
+  expect_equal(rsi_df(septic_patients, 
+                      ab = "amox",
+                      info = FALSE), 0.5386, tolerance = 0.0001)
+  # and pita+genta susceptibility around 98.09%
+  expect_equal(rsi_df(septic_patients,
+                      ab = c("pita", "gent"), 
+                      interpretation = "S", 
+                      info = FALSE), 0.9809, tolerance = 0.0001)
+})
+
+test_that("prediction of rsi works", {
+  amox_R <- rsi_predict(tbl = septic_patients[which(septic_patients$bactid == "ESCCOL"),], 
+                        col_ab = "amox",
+                        col_date = "date",
+                        info = FALSE)
+  amox_R <- amox_R %>% pull("probR")
+  # amox resistance will decrease according to `septic_patients`
+  expect_true(amox_R[2] > amox_R[20])
+  expect_error(rsi_predict(tbl = septic_patients[which(septic_patients$bactid == "ESCCOL"),], 
+                           model = "INVALID MODEL",
+                           col_ab = "amox",
+                           col_date = "date",
+                           info = FALSE))
+  expect_error(rsi_predict(tbl = septic_patients[which(septic_patients$bactid == "ESCCOL"),], 
+                           col_ab = "NOT EXISTING COLUMN",
+                           col_date = "date",
+                           info = FALSE))
+  expect_error(rsi_predict(tbl = septic_patients[which(septic_patients$bactid == "ESCCOL"),], 
+                           col_ab = "amox",
+                           col_date = "NOT EXISTING COLUMN",
+                           info = FALSE))
+})