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https://github.com/msberends/AMR.git
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new portion functions
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@ -1,29 +1,17 @@
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context("rsi_IR.R")
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context("portion.R")
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test_that("resistance works", {
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# check shortcuts
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expect_equal(resistance(septic_patients$amox, include_I = TRUE),
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rsi_IR(septic_patients$amox))
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expect_equal(resistance(septic_patients$amox, include_I = FALSE),
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rsi_R(septic_patients$amox))
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expect_equal(intermediate(septic_patients$amox),
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rsi_I(septic_patients$amox))
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expect_equal(susceptibility(septic_patients$amox, include_I = TRUE),
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rsi_SI(septic_patients$amox))
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expect_equal(susceptibility(septic_patients$amox, include_I = FALSE),
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rsi_S(septic_patients$amox))
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# amox resistance in `septic_patients`
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expect_equal(rsi_R(septic_patients$amox), 0.6603, tolerance = 0.0001)
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expect_equal(rsi_I(septic_patients$amox), 0.0030, tolerance = 0.0001)
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expect_equal(1 - rsi_R(septic_patients$amox) - rsi_I(septic_patients$amox),
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rsi_S(septic_patients$amox))
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expect_equal(portion_R(septic_patients$amox), 0.6603, tolerance = 0.0001)
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expect_equal(portion_I(septic_patients$amox), 0.0030, tolerance = 0.0001)
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expect_equal(1 - portion_R(septic_patients$amox) - portion_I(septic_patients$amox),
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portion_S(septic_patients$amox))
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expect_equal(portion_R(septic_patients$amox) + portion_I(septic_patients$amox),
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portion_IR(septic_patients$amox))
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expect_equal(portion_S(septic_patients$amox) + portion_I(septic_patients$amox),
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portion_SI(septic_patients$amox))
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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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0.9535,
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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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@ -33,10 +21,10 @@ test_that("resistance works", {
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# percentages
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expect_equal(septic_patients %>%
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group_by(hospital_id) %>%
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summarise(R = rsi_R(cipr, as_percent = TRUE),
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I = rsi_I(cipr, as_percent = TRUE),
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S = rsi_S(cipr, as_percent = TRUE),
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n = rsi_n(cipr),
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summarise(R = portion_R(cipr, as_percent = TRUE),
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I = portion_I(cipr, as_percent = TRUE),
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S = portion_S(cipr, as_percent = TRUE),
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n = n_rsi(cipr),
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total = n()) %>%
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pull(n) %>%
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sum(),
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@ -45,45 +33,45 @@ test_that("resistance works", {
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# count of cases
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expect_equal(septic_patients %>%
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group_by(hospital_id) %>%
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summarise(cipro_p = susceptibility(cipr, as_percent = TRUE),
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summarise(cipro_p = portion_S(cipr, as_percent = TRUE),
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cipro_n = n_rsi(cipr),
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genta_p = susceptibility(gent, as_percent = TRUE),
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genta_p = portion_S(gent, as_percent = TRUE),
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genta_n = n_rsi(gent),
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combination_p = susceptibility(cipr, gent, as_percent = TRUE),
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combination_n = rsi_n(cipr, gent)) %>%
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combination_p = portion_S(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(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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expect_warning(susceptibility(as.character(septic_patients$amcl,
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expect_warning(portion_R(as.character(septic_patients$amcl)))
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expect_warning(portion_S(as.character(septic_patients$amcl)))
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expect_warning(portion_S(as.character(septic_patients$amcl,
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septic_patients$gent)))
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# check for errors
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expect_error(rsi_IR(septic_patients %>% select(amox, amcl)))
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expect_error(rsi_IR("test", minimum = "test"))
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expect_error(rsi_IR("test", as_percent = "test"))
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expect_error(rsi_I(septic_patients %>% select(amox, amcl)))
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expect_error(rsi_I("test", minimum = "test"))
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expect_error(rsi_I("test", as_percent = "test"))
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expect_error(rsi_S("test", minimum = "test"))
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expect_error(rsi_S("test", as_percent = "test"))
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expect_error(rsi_S(septic_patients %>% select(amox, amcl)))
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expect_error(rsi_S("R", septic_patients %>% select(amox, amcl)))
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expect_error(portion_IR(septic_patients %>% select(amox, amcl)))
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expect_error(portion_IR("test", minimum = "test"))
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expect_error(portion_IR("test", as_percent = "test"))
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expect_error(portion_I(septic_patients %>% select(amox, amcl)))
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expect_error(portion_I("test", minimum = "test"))
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expect_error(portion_I("test", as_percent = "test"))
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expect_error(portion_S("test", minimum = "test"))
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expect_error(portion_S("test", as_percent = "test"))
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expect_error(portion_S(septic_patients %>% select(amox, amcl)))
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expect_error(portion_S("R", septic_patients %>% select(amox, amcl)))
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# check too low amount of isolates
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expect_identical(rsi_R(septic_patients$amox, minimum = nrow(septic_patients) + 1),
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expect_identical(portion_R(septic_patients$amox, minimum = nrow(septic_patients) + 1),
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NA)
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expect_identical(rsi_I(septic_patients$amox, minimum = nrow(septic_patients) + 1),
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expect_identical(portion_I(septic_patients$amox, minimum = nrow(septic_patients) + 1),
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NA)
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expect_identical(rsi_S(septic_patients$amox, minimum = nrow(septic_patients) + 1),
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expect_identical(portion_S(septic_patients$amox, minimum = nrow(septic_patients) + 1),
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NA)
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# warning for speed loss
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expect_warning(rsi_R(as.character(septic_patients$gent)))
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expect_warning(rsi_I(as.character(septic_patients$gent)))
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expect_warning(rsi_S(septic_patients$amcl, as.character(septic_patients$gent)))
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expect_warning(portion_R(as.character(septic_patients$gent)))
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expect_warning(portion_I(as.character(septic_patients$gent)))
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expect_warning(portion_S(septic_patients$amcl, as.character(septic_patients$gent)))
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})
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@ -91,11 +79,7 @@ test_that("old rsi works", {
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# amox resistance in `septic_patients` should be around 66.33%
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expect_equal(suppressWarnings(rsi(septic_patients$amox)), 0.6633, tolerance = 0.0001)
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expect_equal(suppressWarnings(rsi(septic_patients$amox, interpretation = "S")), 1 - 0.6633, tolerance = 0.0001)
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expect_equal(rsi_df(septic_patients,
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ab = "amox",
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info = TRUE),
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0.6633,
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tolerance = 0.0001)
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# pita+genta susceptibility around 98.09%
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expect_equal(suppressWarnings(rsi(septic_patients$pita,
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septic_patients$gent,
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@ -103,17 +87,6 @@ test_that("old rsi works", {
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info = TRUE)),
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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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0.9535,
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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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ab = c("mero", "pita", "gent"),
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interpretation = "IS",
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info = TRUE))
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# count of cases
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expect_equal(septic_patients %>%
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