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https://github.com/msberends/AMR.git
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update to septic_patients, speed improvements
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@ -37,8 +37,8 @@ test_that("as.bactid works", {
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select(genus) %>%
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as.bactid() %>%
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as.character(),
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c("STC", "STC", "NEI", "STA", "STA",
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"NEI", "ENT", "ENT", "ESC", "KLE"))
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c("ESC", "ESC", "STA", "STA", "STA",
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"STA", "STA", "STA", "STA", "STA"))
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# select with two columns
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expect_identical(
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@ -8,9 +8,9 @@ test_that("first isolates work", {
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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),
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info = TRUE),
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na.rm = TRUE),
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1959)
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1326)
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# septic_patients contains 1962 out of 2000 first *weighted* isolates
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expect_equal(
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@ -24,8 +24,8 @@ test_that("first isolates work", {
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type = "keyantibiotics",
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info = TRUE),
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na.rm = TRUE)),
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1962)
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# and 1997 when using points
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1421)
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# and 1961 when using points
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expect_equal(
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suppressWarnings(
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sum(
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@ -37,7 +37,7 @@ test_that("first isolates work", {
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type = "points",
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info = TRUE),
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na.rm = TRUE)),
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1997)
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1425)
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# septic_patients contains 1732 out of 2000 first non-ICU isolates
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expect_equal(
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@ -50,7 +50,7 @@ test_that("first isolates work", {
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info = TRUE,
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icu_exclude = TRUE),
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na.rm = TRUE),
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1732)
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1171)
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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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@ -59,7 +59,7 @@ test_that("first isolates work", {
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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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"Other")),
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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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@ -74,7 +74,7 @@ test_that("first isolates work", {
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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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"Other")),
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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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@ -4,8 +4,8 @@ test_that("frequency table works", {
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expect_equal(nrow(freq(c(1, 1, 2, 2, 3, 3, 4, 4, 5, 5))), 5)
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expect_equal(nrow(frequency_tbl(c(1, 1, 2, 2, 3, 3, 4, 4, 5, 5))), 5)
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# date column of septic_patients should contain 1662 unique dates
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expect_equal(nrow(freq(septic_patients$date)), 1662)
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# date column of septic_patients should contain 1151 unique dates
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expect_equal(nrow(freq(septic_patients$date)), 1151)
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expect_equal(nrow(freq(septic_patients$date)),
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length(unique(septic_patients$date)))
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@ -2,12 +2,12 @@ context("kurtosis.R")
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test_that("kurtosis works", {
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expect_equal(kurtosis(septic_patients$age),
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6.423118,
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3.57781,
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tolerance = 0.00001)
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expect_equal(unname(kurtosis(data.frame(septic_patients$age))),
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6.423118,
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3.57781,
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tolerance = 0.00001)
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expect_equal(kurtosis(matrix(septic_patients$age)),
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6.423118,
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3.57781,
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tolerance = 0.00001)
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})
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@ -13,7 +13,8 @@ test_that("MDRO works", {
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expect_equal(outcome %>% class(), c('ordered', 'factor'))
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# septic_patients should have these finding using Dutch guidelines
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expect_equal(outcome %>% freq() %>% pull(count), c(3, 21))
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expect_equal(outcome %>% freq() %>% pull(count),
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c(2, 14)) # 2 unconfirmed, 14 positive
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expect_equal(BRMO(septic_patients, info = FALSE), MDRO(septic_patients, "nl", info = FALSE))
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@ -1,19 +1,19 @@
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context("resistance.R")
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test_that("resistance works", {
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# amox resistance in `septic_patients` should be around 57.56%
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expect_equal(resistance(septic_patients$amox, include_I = TRUE), 0.5756, tolerance = 0.0001)
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expect_equal(susceptibility(septic_patients$amox, include_I = FALSE), 1 - 0.5756, tolerance = 0.0001)
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# amox resistance in `septic_patients` should be around 66.33%
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expect_equal(resistance(septic_patients$amox, include_I = TRUE), 0.6633, tolerance = 0.0001)
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expect_equal(susceptibility(septic_patients$amox, include_I = FALSE), 1 - 0.6633, tolerance = 0.0001)
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# pita+genta susceptibility around 98.09%
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expect_equal(susceptibility(septic_patients$pita,
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septic_patients$gent),
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0.9809,
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0.9535,
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tolerance = 0.0001)
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expect_equal(suppressWarnings(rsi(septic_patients$pita,
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septic_patients$gent,
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interpretation = "S")),
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0.9809,
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0.9535,
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tolerance = 0.0001)
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# count of cases
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@ -26,7 +26,7 @@ test_that("resistance works", {
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combination_p = susceptibility(cipr, gent, as_percent = TRUE),
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combination_n = n_rsi(cipr, gent)) %>%
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pull(combination_n),
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c(138, 474, 170, 464, 183))
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c(202, 482, 201, 499))
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expect_warning(resistance(as.character(septic_patients$amcl)))
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expect_warning(susceptibility(as.character(septic_patients$amcl)))
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@ -36,26 +36,26 @@ test_that("resistance works", {
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})
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test_that("old rsi works", {
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# amox resistance in `septic_patients` should be around 53.86%
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expect_equal(rsi(septic_patients$amox), 0.5756, tolerance = 0.0001)
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expect_equal(rsi(septic_patients$amox), 0.5756, tolerance = 0.0001)
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# amox resistance in `septic_patients` should be around 66.33%
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expect_equal(rsi(septic_patients$amox), 0.6633, tolerance = 0.0001)
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expect_equal(rsi(septic_patients$amox, interpretation = "S"), 1 - 0.6633, tolerance = 0.0001)
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expect_equal(rsi_df(septic_patients,
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ab = "amox",
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info = TRUE),
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0.5756,
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0.6633,
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tolerance = 0.0001)
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# pita+genta susceptibility around 98.09%
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expect_equal(rsi(septic_patients$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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0.9535,
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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 = TRUE),
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0.9809,
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0.9535,
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tolerance = 0.0001)
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# more than 2 not allowed
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expect_error(rsi_df(septic_patients,
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@ -76,7 +76,7 @@ test_that("old rsi works", {
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as_percent = TRUE, warning = FALSE),
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combination_n = n_rsi(cipr, gent)) %>%
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pull(combination_n),
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c(138, 474, 170, 464, 183))
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c(202, 482, 201, 499))
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})
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test_that("prediction of rsi works", {
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@ -86,8 +86,8 @@ test_that("prediction of rsi works", {
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col_date = "date",
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info = TRUE) %>%
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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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# amox resistance will increase according to data set `septic_patients`
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expect_true(amox_R[3] < amox_R[20])
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expect_output(rsi_predict(tbl = filter(septic_patients, bactid == "ESCCOL"),
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model = "binomial",
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@ -2,12 +2,12 @@ context("skewness.R")
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test_that("skewness works", {
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expect_equal(skewness(septic_patients$age),
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-1.637164,
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-0.90624,
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tolerance = 0.00001)
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expect_equal(unname(skewness(data.frame(septic_patients$age))),
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-1.637164,
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-0.90624,
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tolerance = 0.00001)
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expect_equal(skewness(matrix(septic_patients$age)),
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-1.637164,
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-0.90624,
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tolerance = 0.00001)
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})
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