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fortify code with more tests
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5
NEWS
5
NEWS
@ -12,8 +12,9 @@
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- For parameters of functions `first_isolate`, `EUCAST_rules` the column names are now case-insensitive
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- Functions `as.rsi` and `as.mic` now add the package name and version as attribute
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- Expanded README.md
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- Added unit testing with Travis CI (https://travis-ci.org/msberends/AMR)
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- Added code coverage checking with Codecov (https://codecov.io/gh/msberends/AMR/tree/master/R)
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- Added unit testing with the `testthat` package
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- Added build tests for Linux and macOS using Travis CI (https://travis-ci.org/msberends/AMR)
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- Added Line coverage checking using CodeCov (https://codecov.io/gh/msberends/AMR/tree/master/R)
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## 0.1.1
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- `EUCAST_rules` applies for amoxicillin even if ampicillin is missing
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@ -14,18 +14,18 @@ test_that("guess_bactid works", {
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test_that("first isolates work", {
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# septic_patients contains 1960 out of 2000 first isolates
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septic_ptns <- septic_patients
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expect_equal(sum(first_isolate(tbl = septic_ptns,
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#septic_ptns <- septic_patients
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expect_equal(sum(first_isolate(tbl = septic_patients,
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col_date = "date",
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col_patient_id = "patient_id",
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col_bactid = "bactid",
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info = FALSE)), 1960)
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# septic_patients contains 1962 out of 2000 first weighted isolates
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septic_ptns$keyab <- suppressWarnings(key_antibiotics(septic_ptns))
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# septic_patients contains 1962 out of 2000 first *weighted* isolates
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#septic_ptns$keyab <- suppressWarnings(key_antibiotics(septic_ptns))
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expect_equal(
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suppressWarnings(sum(
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first_isolate(tbl = septic_ptns,
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first_isolate(tbl = septic_patients %>% mutate(keyab = key_antibiotics(.)),
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col_date = "date",
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col_patient_id = "patient_id",
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col_bactid = "bactid",
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@ -33,4 +33,20 @@ test_that("first isolates work", {
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type = "keyantibiotics",
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info = TRUE))),
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1962)
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# set 1500 random observations to be of specimen type 'Urine'
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random_rows <- sample(x = 1:2000, size = 1500, replace = FALSE)
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expect_lt(sum(
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first_isolate(tbl = mutate(septic_patients,
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specimen = if_else(row_number() %in% random_rows,
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"Urine",
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"Unknown")),
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col_date = "date",
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col_patient_id = "patient_id",
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col_bactid = "bactid",
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col_specimen = "specimen",
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filter_specimen = "Urine",
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info = TRUE)),
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1501)
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})
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@ -4,15 +4,24 @@ test_that("joins work", {
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unjoined <- septic_patients
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inner <- septic_patients %>% inner_join_microorganisms()
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left <- septic_patients %>% left_join_microorganisms()
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semi <- septic_patients %>% semi_join_microorganisms()
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anti <- septic_patients %>% anti_join_microorganisms()
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suppressWarnings(right <- septic_patients %>% right_join_microorganisms())
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suppressWarnings(full <- septic_patients %>% full_join_microorganisms())
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expect_true(ncol(unjoined) < ncol(inner))
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expect_true(nrow(unjoined) == nrow(inner))
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expect_true(ncol(unjoined) < ncol(left))
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expect_true(nrow(unjoined) == nrow(left))
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expect_true(ncol(semi) == ncol(semi))
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expect_true(nrow(semi) == nrow(semi))
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expect_true(nrow(anti) == 0)
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expect_true(nrow(unjoined) < nrow(right))
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expect_true(nrow(unjoined) < nrow(full))
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expect_equal(nrow(left_join_microorganisms("ESCCOL")), 1)
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})
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@ -2,36 +2,71 @@ context("rsi_analysis.R")
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test_that("rsi works", {
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# amox resistance in `septic_patients` should be around 53.86%
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amox_R <- septic_patients %>% summarise(amox = rsi(amox)) %>% pull(amox)
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expect_equal(amox_R, 0.5386, tolerance = 0.0001)
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expect_equal(rsi_df(septic_patients,
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ab = "amox",
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info = FALSE), 0.5386, tolerance = 0.0001)
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# and pita+genta susceptibility around 98.09%
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expect_equal(rsi(septic_patients$amox), 0.5386, tolerance = 0.0001)
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expect_equal(rsi(septic_patients$amox), 0.5386, tolerance = 0.0001)
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expect_equal(rsi_df(septic_patients,
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ab = c("pita", "gent"),
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interpretation = "S",
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info = FALSE), 0.9809, tolerance = 0.0001)
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ab = "amox",
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info = FALSE),
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0.5386,
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tolerance = 0.0001)
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# pita+genta susceptibility around 98.09%
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expect_equal(rsi(septic_patients$pita,
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septic_patients$gent,
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interpretation = "S",
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info = TRUE),
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0.9809,
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tolerance = 0.0001)
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expect_equal(rsi_df(septic_patients,
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ab = c("pita", "gent"),
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interpretation = "S",
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info = FALSE),
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0.9809,
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tolerance = 0.0001)
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# mero+pita+genta susceptibility around 98.58%
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expect_equal(rsi_df(septic_patients,
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ab = c("mero", "pita", "gent"),
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interpretation = "IS",
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info = FALSE),
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0.9858,
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tolerance = 0.0001)
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})
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test_that("prediction of rsi works", {
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amox_R <- rsi_predict(tbl = septic_patients[which(septic_patients$bactid == "ESCCOL"),],
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col_ab = "amox",
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col_date = "date",
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info = FALSE)
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amox_R <- amox_R %>% pull("probR")
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# amox resistance will decrease according to `septic_patients`
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amox_R <- septic_patients %>%
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filter(bactid == "ESCCOL") %>%
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rsi_predict(col_ab = "amox",
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col_date = "date",
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info = FALSE) %>%
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pull("probR")
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# amox resistance will decrease using dataset `septic_patients`
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expect_true(amox_R[2] > amox_R[20])
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expect_error(rsi_predict(tbl = septic_patients[which(septic_patients$bactid == "ESCCOL"),],
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expect_output(rsi_predict(tbl = filter(septic_patients, bactid == "ESCCOL"),
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model = "binomial",
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col_ab = "amox",
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col_date = "date",
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info = TRUE))
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expect_output(rsi_predict(tbl = filter(septic_patients, bactid == "ESCCOL"),
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model = "loglin",
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col_ab = "amox",
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col_date = "date",
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info = TRUE))
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expect_output(rsi_predict(tbl = filter(septic_patients, bactid == "ESCCOL"),
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model = "lin",
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col_ab = "amox",
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col_date = "date",
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info = TRUE))
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expect_error(rsi_predict(tbl = filter(septic_patients, bactid == "ESCCOL"),
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model = "INVALID MODEL",
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col_ab = "amox",
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col_date = "date",
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info = FALSE))
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expect_error(rsi_predict(tbl = septic_patients[which(septic_patients$bactid == "ESCCOL"),],
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expect_error(rsi_predict(tbl = filter(septic_patients, bactid == "ESCCOL"),
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col_ab = "NOT EXISTING COLUMN",
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col_date = "date",
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info = FALSE))
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expect_error(rsi_predict(tbl = septic_patients[which(septic_patients$bactid == "ESCCOL"),],
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expect_error(rsi_predict(tbl = filter(septic_patients, bactid == "ESCCOL"),
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col_ab = "amox",
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col_date = "NOT EXISTING COLUMN",
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info = FALSE))
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