AMR/tests/testthat/test-portion.R

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context("portion.R")
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test_that("portions works", {
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# amox resistance in `septic_patients`
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expect_equal(portion_R(septic_patients$amox), 0.6603, tolerance = 0.0001)
expect_equal(portion_I(septic_patients$amox), 0.0030, tolerance = 0.0001)
expect_equal(1 - portion_R(septic_patients$amox) - portion_I(septic_patients$amox),
portion_S(septic_patients$amox))
expect_equal(portion_R(septic_patients$amox) + portion_I(septic_patients$amox),
portion_IR(septic_patients$amox))
expect_equal(portion_S(septic_patients$amox) + portion_I(septic_patients$amox),
portion_SI(septic_patients$amox))
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expect_equal(septic_patients %>% portion_S(amcl),
0.673,
tolerance = 0.001)
expect_equal(septic_patients %>% portion_S(amcl, gent),
0.921,
tolerance = 0.001)
# amcl+genta susceptibility around 92.1%
expect_equal(suppressWarnings(rsi(septic_patients$amcl,
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septic_patients$gent,
interpretation = "S")),
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0.9208777,
tolerance = 0.000001)
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# percentages
expect_equal(septic_patients %>%
group_by(hospital_id) %>%
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summarise(R = portion_R(cipr, as_percent = TRUE),
I = portion_I(cipr, as_percent = TRUE),
S = portion_S(cipr, as_percent = TRUE),
n = n_rsi(cipr),
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total = n()) %>%
pull(n) %>%
sum(),
1404)
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# count of cases
expect_equal(septic_patients %>%
group_by(hospital_id) %>%
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summarise(cipro_p = portion_S(cipr, as_percent = TRUE),
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cipro_n = n_rsi(cipr),
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genta_p = portion_S(gent, as_percent = TRUE),
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genta_n = n_rsi(gent),
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combination_p = portion_S(cipr, gent, as_percent = TRUE),
combination_n = n_rsi(cipr, gent)) %>%
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pull(combination_n),
c(202, 482, 201, 499))
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expect_warning(portion_R(as.character(septic_patients$amcl)))
expect_warning(portion_S(as.character(septic_patients$amcl)))
expect_warning(portion_S(as.character(septic_patients$amcl,
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septic_patients$gent)))
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expect_warning(n_rsi(as.character(septic_patients$amcl,
septic_patients$gent)))
expect_equal(suppressWarnings(n_rsi(as.character(septic_patients$amcl,
septic_patients$gent))),
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1570)
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# check for errors
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expect_error(portion_IR("test", minimum = "test"))
expect_error(portion_IR("test", as_percent = "test"))
expect_error(portion_I("test", minimum = "test"))
expect_error(portion_I("test", as_percent = "test"))
expect_error(portion_S("test", minimum = "test"))
expect_error(portion_S("test", as_percent = "test"))
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# check too low amount of isolates
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expect_identical(portion_R(septic_patients$amox, minimum = nrow(septic_patients) + 1),
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NA)
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expect_identical(portion_I(septic_patients$amox, minimum = nrow(septic_patients) + 1),
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NA)
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expect_identical(portion_S(septic_patients$amox, minimum = nrow(septic_patients) + 1),
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NA)
# warning for speed loss
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expect_warning(portion_R(as.character(septic_patients$gent)))
expect_warning(portion_I(as.character(septic_patients$gent)))
expect_warning(portion_S(septic_patients$amcl, as.character(septic_patients$gent)))
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})
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test_that("old rsi works", {
# amox resistance in `septic_patients` should be around 66.33%
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expect_equal(suppressWarnings(rsi(septic_patients$amox)), 0.6633, tolerance = 0.0001)
expect_equal(suppressWarnings(rsi(septic_patients$amox, interpretation = "S")), 1 - 0.6633, tolerance = 0.0001)
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# pita+genta susceptibility around 98.09%
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expect_equal(suppressWarnings(rsi(septic_patients$pita,
septic_patients$gent,
interpretation = "S",
info = TRUE)),
0.9535,
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tolerance = 0.0001)
# count of cases
expect_equal(septic_patients %>%
group_by(hospital_id) %>%
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summarise(cipro_S = suppressWarnings(rsi(cipr, interpretation = "S",
as_percent = TRUE, warning = FALSE)),
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cipro_n = n_rsi(cipr),
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genta_S = suppressWarnings(rsi(gent, interpretation = "S",
as_percent = TRUE, warning = FALSE)),
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genta_n = n_rsi(gent),
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combination_S = suppressWarnings(rsi(cipr, gent, interpretation = "S",
as_percent = TRUE, warning = FALSE)),
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combination_n = n_rsi(cipr, gent)) %>%
pull(combination_n),
c(202, 482, 201, 499))
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# portion_df
expect_equal(
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septic_patients %>% select(amox) %>% portion_df() %>% pull(Percentage),
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c(septic_patients$amox %>% portion_S(),
septic_patients$amox %>% portion_I(),
septic_patients$amox %>% portion_R())
)
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})
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test_that("prediction of rsi works", {
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amox_R <- septic_patients %>%
filter(bactid == "ESCCOL") %>%
rsi_predict(col_ab = "amox",
col_date = "date",
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minimum = 10,
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info = TRUE) %>%
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pull("value")
# amox resistance will increase according to data set `septic_patients`
expect_true(amox_R[3] < amox_R[20])
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expect_output(rsi_predict(tbl = filter(septic_patients, bactid == "ESCCOL"),
model = "binomial",
col_ab = "amox",
col_date = "date",
info = TRUE))
expect_output(rsi_predict(tbl = filter(septic_patients, bactid == "ESCCOL"),
model = "loglin",
col_ab = "amox",
col_date = "date",
info = TRUE))
expect_output(rsi_predict(tbl = filter(septic_patients, bactid == "ESCCOL"),
model = "lin",
col_ab = "amox",
col_date = "date",
info = TRUE))
expect_error(rsi_predict(tbl = filter(septic_patients, bactid == "ESCCOL"),
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model = "INVALID MODEL",
col_ab = "amox",
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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col_ab = "NOT EXISTING COLUMN",
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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col_ab = "amox",
col_date = "NOT EXISTING COLUMN",
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info = TRUE))
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# almost all E. coli are mero S in the Netherlands :)
expect_error(resistance_predict(tbl = filter(septic_patients, bactid == "ESCCOL"),
col_ab = "mero",
col_date = "date",
info = TRUE))
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})