# ==================================================================== # # TITLE # # Antimicrobial Resistance (AMR) Analysis # # # # SOURCE # # https://gitlab.com/msberends/AMR # # # # LICENCE # # (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) # # # # This R package is free software; you can freely use and distribute # # it for both personal and commercial purposes under the terms of the # # GNU General Public License version 2.0 (GNU GPL-2), as published by # # the Free Software Foundation. # # # # This R package was created for academic research and was publicly # # released in the hope that it will be useful, but it comes WITHOUT # # ANY WARRANTY OR LIABILITY. # # Visit our website for more info: https://msberends.gitlab.io/AMR. # # ==================================================================== # context("mdro.R") test_that("mdro works", { skip_on_cran() library(dplyr) expect_error(suppressWarnings(mdro(example_isolates, country = "invalid", col_mo = "mo", info = TRUE))) expect_error(suppressWarnings(mdro(example_isolates, country = "fr", info = TRUE))) expect_error(mdro(example_isolates, guideline = c("BRMO", "MRGN"), info = TRUE)) expect_error(mdro(example_isolates, col_mo = "invalid", info = TRUE)) outcome <- mdro(example_isolates) outcome <- eucast_exceptional_phenotypes(example_isolates, info = TRUE) # check class expect_equal(outcome %>% class(), c("ordered", "factor")) outcome <- mdro(example_isolates, "nl", info = TRUE) # check class expect_equal(outcome %>% class(), c("ordered", "factor")) # example_isolates should have these finding using Dutch guidelines expect_equal(outcome %>% freq() %>% pull(count), c(1969, 25, 6)) # 1969 neg, 25 unconfirmed, 6 pos expect_equal(brmo(example_isolates, info = FALSE), mdro(example_isolates, guideline = "BRMO", info = FALSE)) # test Dutch P. aeruginosa MDRO expect_equal( as.character(mdro(data.frame(mo = as.mo("P. aeruginosa"), cfta = "S", cipr = "S", mero = "S", imip = "S", gent = "S", tobr = "S", pita = "S"), guideline = "BRMO", col_mo = "mo", info = FALSE)), "Negative") expect_equal( as.character(mdro(data.frame(mo = as.mo("P. aeruginosa"), cefta = "R", cipr = "R", mero = "R", imip = "R", gent = "R", tobr = "R", pita = "R"), guideline = "BRMO", col_mo = "mo", info = FALSE)), "Positive") # German 3MRGN and 4MRGN expect_equal(as.character(mrgn( data.frame(mo = c("E. coli", "E. coli", "K. pneumoniae", "E. coli", "A. baumannii", "A. baumannii", "A. baumannii", "P. aeruginosa", "P. aeruginosa", "P. aeruginosa"), PIP = c("S", "R", "R", "S", "S", "R", "R", "S", "R", "R"), CTX = c("S", "R", "R", "S", "R", "R", "R", "R", "R", "R"), IPM = c("S", "R", "S", "R", "R", "R", "S", "S", "R", "R"), CIP = c("S", "R", "R", "S", "R", "R", "R", "R", "S", "R"), stringsAsFactors = FALSE))), c("Negative", "4MRGN", "3MRGN", "4MRGN", "4MRGN", "4MRGN", "3MRGN", "Negative", "3MRGN", "4MRGN")) # MDR TB expect_equal( # select only rifampicine, mo will be determined automatically (as M. tuberculosis), # number of mono-resistant strains should be equal to number of rifampicine-resistant strains example_isolates %>% select(RIF) %>% mdr_tb() %>% freq() %>% pull(count) %>% .[2], count_R(example_isolates$RIF)) sample_rsi <- function() { sample(c("S", "I", "R"), size = 5000, prob = c(0.5, 0.1, 0.4), replace = TRUE) } expect_gt( #suppressWarnings( data.frame(rifampicin = sample_rsi(), inh = sample_rsi(), gatifloxacin = sample_rsi(), eth = sample_rsi(), pza = sample_rsi(), MFX = sample_rsi(), KAN = sample_rsi()) %>% mdr_tb() %>% n_distinct() #) , 2) # check the guideline by Magiorakos et al. (2012), the default guideline stau <- tribble( ~mo, ~GEN, ~RIF, ~CPT, ~OXA, ~CIP, ~MFX, ~SXT, ~FUS, ~VAN, ~TEC, ~TLV, ~TGC, ~CLI, ~DAP, ~ERY, ~LNZ, ~CHL, ~FOS, ~QDA, ~TCY, ~DOX, ~MNO, "S. aureus", "R", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S. aureus", "R", "R", "R", "R", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S. aureus", "S", "S", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "S. aureus", "R", "R", "I", "I", "I", "I", "I", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R" ) expect_equal(as.integer(mdro(stau)), c(1:4)) expect_s3_class(mdro(stau, verbose = TRUE), "data.frame") ente <- tribble( ~mo, ~GEH, ~STH, ~IPM, ~MEM, ~DOR, ~CIP, ~LVX, ~MFX, ~VAN, ~TEC, ~TGC, ~DAP, ~LNZ, ~AMP, ~QDA, ~DOX, ~MNO, "Enterococcus", "R", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "Enterococcus", "R", "R", "R", "R", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "Enterococcus", "S", "S", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "Enterococcus", "R", "R", "I", "I", "I", "I", "I", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R" ) expect_equal(as.integer(mdro(ente)), c(1:4)) expect_s3_class(mdro(ente, verbose = TRUE), "data.frame") entero <- tribble( ~mo, ~GEN, ~TOB, ~AMK, ~NET, ~CPT, ~TCC, ~TZP, ~ETP, ~IPM, ~MEM, ~DOR, ~CZO, ~CXM, ~CTX, ~CAZ, ~FEP, ~FOX, ~CTT, ~CIP, ~SXT, ~TGC, ~ATM, ~AMP, ~AMC, ~SAM, ~CHL, ~FOS, ~COL, ~TCY, ~DOX, ~MNO, "E. coli", "R", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "E. coli", "R", "R", "R", "R", "R", "R", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "E. coli", "S", "S", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "E. coli", "R", "R", "I", "I", "I", "I", "I", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R" ) expect_equal(as.integer(mdro(entero)), c(1:4)) expect_s3_class(mdro(entero, verbose = TRUE), "data.frame") pseud <- tribble( ~mo, ~GEN, ~TOB, ~AMK, ~NET, ~IPM, ~MEM, ~DOR, ~CAZ, ~FEP, ~CIP, ~LVX, ~TCC, ~TZP, ~ATM, ~FOS, ~COL, ~PLB, "P. aeruginosa", "R", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "P. aeruginosa", "R", "S", "S", "S", "R", "S", "S", "S", "R", "S", "S", "S", "S", "S", "S", "S", "S", "P. aeruginosa", "S", "S", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "P. aeruginosa", "R", "R", "I", "I", "I", "I", "I", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R" ) expect_equal(as.integer(mdro(pseud)), c(1:4)) expect_s3_class(mdro(pseud, verbose = TRUE), "data.frame") acin <- tribble( ~mo, ~GEN, ~TOB, ~AMK, ~NET, ~IPM, ~MEM, ~DOR, ~CIP, ~LVX, ~TZP, ~TCC, ~CTX, ~CRO, ~CAZ, ~FEP, ~SXT, ~SAM, ~COL, ~PLB, ~TCY, ~DOX, ~MNO, "A. baumannii", "R", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "A. baumannii", "R", "R", "R", "R", "S", "R", "S", "S", "S", "S", "S", "S", "S", "S", "R", "S", "S", "S", "S", "S", "S", "S", "A. baumannii", "S", "S", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "A. baumannii", "R", "R", "I", "I", "I", "I", "I", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R", "R" ) expect_equal(as.integer(mdro(acin)), c(1:4)) expect_s3_class(mdro(acin, verbose = TRUE), "data.frame") })