# ==================================================================== # # TITLE # # Antimicrobial Resistance (AMR) Analysis # # # # AUTHORS # # Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) # # # # LICENCE # # This package is free software; you can redistribute it and/or modify # # it under the terms of the GNU General Public License version 2.0, # # as published by the Free Software Foundation. # # # # This R package is distributed in the hope that it will be useful, # # but WITHOUT ANY WARRANTY; without even the implied warranty of # # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # # GNU General Public License version 2.0 for more details. # # ==================================================================== # context("portion.R") test_that("portions works", { # amox resistance in `septic_patients` expect_equal(portion_R(septic_patients$amox), 0.5827645, tolerance = 0.0001) expect_equal(portion_I(septic_patients$amox), 0.0025597, 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$amox)) expect_equal(septic_patients %>% portion_S(amcl), 0.7062363, tolerance = 0.001) expect_equal(septic_patients %>% portion_S(amcl, gent), 0.9210074, tolerance = 0.001) expect_equal(septic_patients %>% portion_S(amcl, gent, also_single_tested = TRUE), 0.9239669, tolerance = 0.001) # amcl+genta susceptibility around 92.1% expect_equal(suppressWarnings(rsi(septic_patients$amcl, septic_patients$gent, interpretation = "S")), 0.9210074, tolerance = 0.000001) # percentages expect_equal(septic_patients %>% group_by(hospital_id) %>% summarise(R = portion_R(cipr, as_percent = TRUE), I = portion_I(cipr, as_percent = TRUE), S = portion_S(cipr, as_percent = TRUE), n = n_rsi(cipr), total = n()) %>% pull(n) %>% sum(), 1409) # count of cases expect_equal(septic_patients %>% group_by(hospital_id) %>% summarise(cipro_p = portion_S(cipr, as_percent = TRUE), cipro_n = n_rsi(cipr), genta_p = portion_S(gent, as_percent = TRUE), genta_n = n_rsi(gent), combination_p = portion_S(cipr, gent, as_percent = TRUE), combination_n = n_rsi(cipr, gent)) %>% pull(combination_n), c(202, 488, 201, 499)) expect_warning(portion_R(as.character(septic_patients$amcl))) expect_warning(portion_S(as.character(septic_patients$amcl))) expect_warning(portion_S(as.character(septic_patients$amcl, septic_patients$gent))) expect_warning(n_rsi(as.character(septic_patients$amcl, septic_patients$gent))) expect_equal(suppressWarnings(n_rsi(as.character(septic_patients$amcl, septic_patients$gent))), 1828) # check for errors expect_error(portion_IR("test", minimum = "test")) expect_error(portion_IR("test", as_percent = "test")) expect_error(portion_I("test", minimum = "test")) expect_error(portion_I("test", as_percent = "test")) expect_error(portion_S("test", minimum = "test")) expect_error(portion_S("test", as_percent = "test")) expect_error(portion_S("test", also_single_tested = "test")) # check too low amount of isolates expect_identical(suppressWarnings(portion_R(septic_patients$amox, minimum = nrow(septic_patients) + 1)), NA) expect_identical(suppressWarnings(portion_I(septic_patients$amox, minimum = nrow(septic_patients) + 1)), NA) expect_identical(suppressWarnings(portion_S(septic_patients$amox, minimum = nrow(septic_patients) + 1)), NA) # warning for speed loss 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))) }) test_that("old rsi works", { # amox resistance in `septic_patients` should be around 58.53% expect_equal(suppressWarnings(rsi(septic_patients$amox)), 0.5853, tolerance = 0.0001) expect_equal(suppressWarnings(rsi(septic_patients$amox, interpretation = "S")), 1 - 0.5853, tolerance = 0.0001) # pita+genta susceptibility around 98.09% expect_equal(suppressWarnings(rsi(septic_patients$pita, septic_patients$gent, interpretation = "S", info = TRUE)), 0.9498886, tolerance = 0.0001) # count of cases expect_equal(septic_patients %>% group_by(hospital_id) %>% summarise(cipro_S = suppressWarnings(rsi(cipr, interpretation = "S", as_percent = TRUE, warning = FALSE)), cipro_n = n_rsi(cipr), genta_S = suppressWarnings(rsi(gent, interpretation = "S", as_percent = TRUE, warning = FALSE)), genta_n = n_rsi(gent), combination_S = suppressWarnings(rsi(cipr, gent, interpretation = "S", as_percent = TRUE, warning = FALSE)), combination_n = n_rsi(cipr, gent)) %>% pull(combination_n), c(202, 488, 201, 499)) # portion_df expect_equal( septic_patients %>% select(amox) %>% portion_df() %>% pull(Value), c(septic_patients$amox %>% portion_S(), septic_patients$amox %>% portion_I(), septic_patients$amox %>% portion_R()) ) expect_equal( septic_patients %>% select(amox) %>% portion_df(combine_IR = TRUE) %>% pull(Value), c(septic_patients$amox %>% portion_S(), septic_patients$amox %>% portion_IR()) ) }) test_that("prediction of rsi works", { amox_R <- septic_patients %>% filter(mo == "B_ESCHR_COL") %>% rsi_predict(col_ab = "amox", col_date = "date", minimum = 10, info = TRUE) %>% pull("value") # amox resistance will increase according to data set `septic_patients` expect_true(amox_R[3] < amox_R[20]) expect_output(rsi_predict(tbl = filter(septic_patients, mo == "B_ESCHR_COL"), model = "binomial", col_ab = "amox", col_date = "date", info = TRUE)) expect_output(rsi_predict(tbl = filter(septic_patients, mo == "B_ESCHR_COL"), model = "loglin", col_ab = "amox", col_date = "date", info = TRUE)) expect_output(rsi_predict(tbl = filter(septic_patients, mo == "B_ESCHR_COL"), model = "lin", col_ab = "amox", col_date = "date", info = TRUE)) expect_error(rsi_predict(tbl = filter(septic_patients, mo == "B_ESCHR_COL"), model = "INVALID MODEL", col_ab = "amox", col_date = "date", info = TRUE)) expect_error(rsi_predict(tbl = filter(septic_patients, mo == "B_ESCHR_COL"), col_ab = "NOT EXISTING COLUMN", col_date = "date", info = TRUE)) expect_error(rsi_predict(tbl = filter(septic_patients, mo == "B_ESCHR_COL"), col_ab = "amox", col_date = "NOT EXISTING COLUMN", info = TRUE)) # almost all E. coli are mero S in the Netherlands :) expect_error(resistance_predict(tbl = filter(septic_patients, mo == "B_ESCHR_COL"), col_ab = "mero", col_date = "date", info = TRUE)) expect_error(portion_df(c("A", "B", "C"))) expect_error(portion_df(septic_patients[,"date"])) })