context("resistance.R") test_that("resistance works", { # amox resistance in `septic_patients` should be around 57.56% expect_equal(resistance(septic_patients$amox, include_I = TRUE), 0.5756, tolerance = 0.0001) expect_equal(susceptibility(septic_patients$amox, include_I = FALSE), 1 - 0.5756, tolerance = 0.0001) # pita+genta susceptibility around 98.09% expect_equal(susceptibility(septic_patients$pita, septic_patients$gent), 0.9809, tolerance = 0.0001) expect_equal(suppressWarnings(rsi(septic_patients$pita, septic_patients$gent, interpretation = "S")), 0.9809, tolerance = 0.0001) # count of cases expect_equal(septic_patients %>% group_by(hospital_id) %>% summarise(cipro_p = susceptibility(cipr, as_percent = TRUE), cipro_n = n_rsi(cipr), genta_p = susceptibility(gent, as_percent = TRUE), genta_n = n_rsi(gent), combination_p = susceptibility(cipr, gent, as_percent = TRUE), combination_n = n_rsi(cipr, gent)) %>% pull(combination_n), c(138, 474, 170, 464, 183)) }) test_that("prediction of rsi works", { amox_R <- septic_patients %>% filter(bactid == "ESCCOL") %>% rsi_predict(col_ab = "amox", col_date = "date", info = FALSE) %>% pull("probR") # amox resistance will decrease using dataset `septic_patients` expect_true(amox_R[2] > amox_R[20]) 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"), model = "INVALID MODEL", col_ab = "amox", col_date = "date", info = FALSE)) expect_error(rsi_predict(tbl = filter(septic_patients, bactid == "ESCCOL"), col_ab = "NOT EXISTING COLUMN", col_date = "date", info = FALSE)) expect_error(rsi_predict(tbl = filter(septic_patients, bactid == "ESCCOL"), col_ab = "amox", col_date = "NOT EXISTING COLUMN", info = FALSE)) })