mirror of
https://github.com/msberends/AMR.git
synced 2025-07-09 01:22:25 +02:00
unit tests
This commit is contained in:
@ -27,149 +27,105 @@
|
||||
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
|
||||
# ==================================================================== #
|
||||
|
||||
expect_identical(as.mo("Enterobacter asburiae/cloacae"),
|
||||
as.mo("Enterobacter asburiae"))
|
||||
|
||||
suppressMessages(
|
||||
add_custom_microorganisms(
|
||||
data.frame(mo = "ENT_ASB_CLO",
|
||||
genus = "Enterobacter",
|
||||
species = "asburiae/cloacae")
|
||||
)
|
||||
)
|
||||
|
||||
expect_identical(as.character(as.mo("ENT_ASB_CLO")), "ENT_ASB_CLO")
|
||||
expect_identical(mo_name("ENT_ASB_CLO"), "Enterobacter asburiae/cloacae")
|
||||
expect_identical(mo_gramstain("ENT_ASB_CLO", language = NULL), "Gram-negative")
|
||||
# ==================================================================== #
|
||||
# TITLE #
|
||||
# AMR: An R Package for Working with Antimicrobial Resistance Data #
|
||||
# #
|
||||
# SOURCE #
|
||||
# https://github.com/msberends/AMR #
|
||||
# #
|
||||
# CITE AS #
|
||||
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
|
||||
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
|
||||
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
||||
# doi:10.18637/jss.v104.i03 #
|
||||
# #
|
||||
# Developed at the University of Groningen and the University Medical #
|
||||
# Center Groningen in The Netherlands, in collaboration with many #
|
||||
# colleagues from around the world, see our website. #
|
||||
# #
|
||||
# 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. #
|
||||
# We created this package for both routine data analysis and academic #
|
||||
# research and it was publicly released in the hope that it will be #
|
||||
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
|
||||
# #
|
||||
# Visit our website for the full manual and a complete tutorial about #
|
||||
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
|
||||
# ==================================================================== #
|
||||
# Traditional antibiogram ----------------------------------------------
|
||||
|
||||
#
|
||||
#
|
||||
# # Traditional antibiogram ----------------------------------------------
|
||||
#
|
||||
# ab1 <- antibiogram(example_isolates,
|
||||
# antibiotics = c(aminoglycosides(), carbapenems()))
|
||||
#
|
||||
# ab2 <- antibiogram(example_isolates,
|
||||
# antibiotics = aminoglycosides(),
|
||||
# ab_transform = "atc",
|
||||
# mo_transform = "gramstain")
|
||||
#
|
||||
# ab3 <- antibiogram(example_isolates,
|
||||
# antibiotics = carbapenems(),
|
||||
# ab_transform = "name",
|
||||
# mo_transform = "name")
|
||||
#
|
||||
# expect_inherits(ab1, "antibiogram")
|
||||
# expect_inherits(ab2, "antibiogram")
|
||||
# expect_inherits(ab3, "antibiogram")
|
||||
# expect_equal(colnames(ab1), c("Pathogen (N min-max)", "AMK", "GEN", "IPM", "KAN", "MEM", "TOB"))
|
||||
# expect_equal(colnames(ab2), c("Pathogen (N min-max)", "J01GB01", "J01GB03", "J01GB04", "J01GB06"))
|
||||
# expect_equal(colnames(ab3), c("Pathogen (N min-max)", "Imipenem", "Meropenem"))
|
||||
# expect_equal(ab3$Meropenem, c(52, NA, 100, 100, NA))
|
||||
#
|
||||
# # Combined antibiogram -------------------------------------------------
|
||||
#
|
||||
# # combined antibiotics yield higher empiric coverage
|
||||
# ab4 <- antibiogram(example_isolates,
|
||||
# antibiotics = c("TZP", "TZP+TOB", "TZP+GEN"),
|
||||
# mo_transform = "gramstain")
|
||||
#
|
||||
# ab5 <- antibiogram(example_isolates,
|
||||
# antibiotics = c("TZP", "TZP+TOB"),
|
||||
# mo_transform = "gramstain",
|
||||
# ab_transform = "name",
|
||||
# sep = " & ",
|
||||
# add_total_n = FALSE)
|
||||
#
|
||||
# expect_inherits(ab4, "antibiogram")
|
||||
# expect_inherits(ab5, "antibiogram")
|
||||
# expect_equal(colnames(ab4), c("Pathogen (N min-max)", "TZP", "TZP + GEN", "TZP + TOB"))
|
||||
# expect_equal(colnames(ab5), c("Pathogen", "Piperacillin/tazobactam", "Piperacillin/tazobactam & Tobramycin"))
|
||||
#
|
||||
# # Syndromic antibiogram ------------------------------------------------
|
||||
#
|
||||
# # the data set could contain a filter for e.g. respiratory specimens
|
||||
# ab6 <- antibiogram(example_isolates,
|
||||
# antibiotics = c(aminoglycosides(), carbapenems()),
|
||||
# syndromic_group = "ward")
|
||||
#
|
||||
# # with a custom language, though this will be determined automatically
|
||||
# # (i.e., this table will be in Spanish on Spanish systems)
|
||||
# ex1 <- example_isolates[which(mo_genus() == "Escherichia"), ]
|
||||
# ab7 <- antibiogram(ex1,
|
||||
# antibiotics = aminoglycosides(),
|
||||
# ab_transform = "name",
|
||||
# syndromic_group = ifelse(ex1$ward == "ICU",
|
||||
# "UCI", "No UCI"),
|
||||
# language = "es")
|
||||
#
|
||||
# expect_inherits(ab6, "antibiogram")
|
||||
# expect_inherits(ab7, "antibiogram")
|
||||
# expect_equal(colnames(ab6), c("Syndromic Group", "Pathogen (N min-max)", "AMK", "GEN", "IPM", "KAN", "MEM", "TOB"))
|
||||
# expect_equal(colnames(ab7), c("Grupo sindrómico", "Patógeno (N min-max)", "Amikacina", "Gentamicina", "Tobramicina"))
|
||||
#
|
||||
# # Weighted-incidence syndromic combination antibiogram (WISCA) ---------
|
||||
#
|
||||
# # the data set could contain a filter for e.g. respiratory specimens
|
||||
# ab8 <- antibiogram(example_isolates,
|
||||
# antibiotics = c("AMC", "AMC+CIP", "TZP", "TZP+TOB"),
|
||||
# mo_transform = "gramstain",
|
||||
# minimum = 10, # this should be >= 30, but now just as example
|
||||
# syndromic_group = ifelse(example_isolates$age >= 65 &
|
||||
# example_isolates$gender == "M",
|
||||
# "WISCA Group 1", "WISCA Group 2"))
|
||||
#
|
||||
# expect_inherits(ab8, "antibiogram")
|
||||
# expect_equal(colnames(ab8), c("Syndromic Group", "Pathogen (N min-max)", "AMC", "AMC + CIP", "TZP", "TZP + TOB"))
|
||||
#
|
||||
# # Generate plots with ggplot2 or base R --------------------------------
|
||||
#
|
||||
# pdf(NULL) # prevent Rplots.pdf being created
|
||||
#
|
||||
# expect_silent(plot(ab1))
|
||||
# expect_silent(plot(ab2))
|
||||
# expect_silent(plot(ab3))
|
||||
# expect_silent(plot(ab4))
|
||||
# expect_silent(plot(ab5))
|
||||
# expect_silent(plot(ab6))
|
||||
# expect_silent(plot(ab7))
|
||||
# expect_silent(plot(ab8))
|
||||
#
|
||||
# if (AMR:::pkg_is_available("ggplot2")) {
|
||||
# expect_inherits(autoplot(ab1), "gg")
|
||||
# expect_inherits(autoplot(ab2), "gg")
|
||||
# expect_inherits(autoplot(ab3), "gg")
|
||||
# expect_inherits(autoplot(ab4), "gg")
|
||||
# expect_inherits(autoplot(ab5), "gg")
|
||||
# expect_inherits(autoplot(ab6), "gg")
|
||||
# expect_inherits(autoplot(ab7), "gg")
|
||||
# expect_inherits(autoplot(ab8), "gg")
|
||||
# }
|
||||
ab1 <- antibiogram(example_isolates,
|
||||
antibiotics = c(aminoglycosides(), carbapenems()))
|
||||
|
||||
ab2 <- antibiogram(example_isolates,
|
||||
antibiotics = aminoglycosides(),
|
||||
ab_transform = "atc",
|
||||
mo_transform = "gramstain")
|
||||
|
||||
ab3 <- antibiogram(example_isolates,
|
||||
antibiotics = carbapenems(),
|
||||
ab_transform = "name",
|
||||
mo_transform = "name")
|
||||
|
||||
expect_inherits(ab1, "antibiogram")
|
||||
expect_inherits(ab2, "antibiogram")
|
||||
expect_inherits(ab3, "antibiogram")
|
||||
expect_equal(colnames(ab1), c("Pathogen (N min-max)", "AMK", "GEN", "IPM", "KAN", "MEM", "TOB"))
|
||||
expect_equal(colnames(ab2), c("Pathogen (N min-max)", "J01GB01", "J01GB03", "J01GB04", "J01GB06"))
|
||||
expect_equal(colnames(ab3), c("Pathogen (N min-max)", "Imipenem", "Meropenem"))
|
||||
expect_equal(ab3$Meropenem, c(52, NA, 100, 100, NA))
|
||||
|
||||
# Combined antibiogram -------------------------------------------------
|
||||
|
||||
# combined antibiotics yield higher empiric coverage
|
||||
ab4 <- antibiogram(example_isolates,
|
||||
antibiotics = c("TZP", "TZP+TOB", "TZP+GEN"),
|
||||
mo_transform = "gramstain")
|
||||
|
||||
ab5 <- antibiogram(example_isolates,
|
||||
antibiotics = c("TZP", "TZP+TOB"),
|
||||
mo_transform = "gramstain",
|
||||
ab_transform = "name",
|
||||
sep = " & ",
|
||||
add_total_n = FALSE)
|
||||
|
||||
expect_inherits(ab4, "antibiogram")
|
||||
expect_inherits(ab5, "antibiogram")
|
||||
expect_equal(colnames(ab4), c("Pathogen (N min-max)", "TZP", "TZP + GEN", "TZP + TOB"))
|
||||
expect_equal(colnames(ab5), c("Pathogen", "Piperacillin/tazobactam", "Piperacillin/tazobactam & Tobramycin"))
|
||||
|
||||
# Syndromic antibiogram ------------------------------------------------
|
||||
|
||||
# the data set could contain a filter for e.g. respiratory specimens
|
||||
ab6 <- antibiogram(example_isolates,
|
||||
antibiotics = c(aminoglycosides(), carbapenems()),
|
||||
syndromic_group = "ward")
|
||||
|
||||
# with a custom language, though this will be determined automatically
|
||||
# (i.e., this table will be in Spanish on Spanish systems)
|
||||
ex1 <- example_isolates[which(mo_genus() == "Escherichia"), ]
|
||||
ab7 <- antibiogram(ex1,
|
||||
antibiotics = aminoglycosides(),
|
||||
ab_transform = "name",
|
||||
syndromic_group = ifelse(ex1$ward == "ICU",
|
||||
"UCI", "No UCI"),
|
||||
language = "es")
|
||||
|
||||
expect_inherits(ab6, "antibiogram")
|
||||
expect_inherits(ab7, "antibiogram")
|
||||
expect_equal(colnames(ab6), c("Syndromic Group", "Pathogen (N min-max)", "AMK", "GEN", "IPM", "KAN", "MEM", "TOB"))
|
||||
expect_equal(colnames(ab7), c("Grupo sindrómico", "Patógeno (N min-max)", "Amikacina", "Gentamicina", "Tobramicina"))
|
||||
|
||||
# Weighted-incidence syndromic combination antibiogram (WISCA) ---------
|
||||
|
||||
# the data set could contain a filter for e.g. respiratory specimens
|
||||
ab8 <- antibiogram(example_isolates,
|
||||
antibiotics = c("AMC", "AMC+CIP", "TZP", "TZP+TOB"),
|
||||
mo_transform = "gramstain",
|
||||
minimum = 10, # this should be >= 30, but now just as example
|
||||
syndromic_group = ifelse(example_isolates$age >= 65 &
|
||||
example_isolates$gender == "M",
|
||||
"WISCA Group 1", "WISCA Group 2"))
|
||||
|
||||
expect_inherits(ab8, "antibiogram")
|
||||
expect_equal(colnames(ab8), c("Syndromic Group", "Pathogen (N min-max)", "AMC", "AMC + CIP", "TZP", "TZP + TOB"))
|
||||
|
||||
# Generate plots with ggplot2 or base R --------------------------------
|
||||
|
||||
pdf(NULL) # prevent Rplots.pdf being created
|
||||
|
||||
expect_silent(plot(ab1))
|
||||
expect_silent(plot(ab2))
|
||||
expect_silent(plot(ab3))
|
||||
expect_silent(plot(ab4))
|
||||
expect_silent(plot(ab5))
|
||||
expect_silent(plot(ab6))
|
||||
expect_silent(plot(ab7))
|
||||
expect_silent(plot(ab8))
|
||||
|
||||
if (AMR:::pkg_is_available("ggplot2")) {
|
||||
expect_inherits(autoplot(ab1), "gg")
|
||||
expect_inherits(autoplot(ab2), "gg")
|
||||
expect_inherits(autoplot(ab3), "gg")
|
||||
expect_inherits(autoplot(ab4), "gg")
|
||||
expect_inherits(autoplot(ab5), "gg")
|
||||
expect_inherits(autoplot(ab6), "gg")
|
||||
expect_inherits(autoplot(ab7), "gg")
|
||||
expect_inherits(autoplot(ab8), "gg")
|
||||
}
|
||||
|
||||
@ -123,7 +123,7 @@ expect_identical(as.character(as.mo(" ")), NA_character_)
|
||||
# too few characters
|
||||
expect_warning(as.mo("ab"))
|
||||
|
||||
expect_equal(
|
||||
expect_identical(
|
||||
suppressWarnings(as.character(as.mo(c("Qq species", "", "MRSA", "K. pneu rhino", "esco")))),
|
||||
c("UNKNOWN", NA_character_, "B_STPHY_AURS", "B_KLBSL_PNMN_RHNS", "B_ESCHR_COLI")
|
||||
)
|
||||
@ -317,7 +317,7 @@ expect_warning(x[[1]] <- "invalid code")
|
||||
expect_warning(c(x[1], "test"))
|
||||
|
||||
# ignoring patterns
|
||||
expect_equal(
|
||||
expect_identical(
|
||||
as.character(as.mo(c("E. coli", "E. coli ignorethis"), ignore_pattern = "this")),
|
||||
c("B_ESCHR_COLI", NA)
|
||||
)
|
||||
|
||||
@ -28,9 +28,26 @@
|
||||
# ==================================================================== #
|
||||
|
||||
expect_identical(mo_genus("B_GRAMP", language = "pt"), "(Gram positivos desconhecidos)")
|
||||
expect_identical(mo_fullname("CoNS", "en"), "Coagulase-negative Staphylococcus (CoNS)")
|
||||
|
||||
expect_identical(mo_fullname("CoNS", "cs"), "Koaguláza-negativní stafylokok (KNS)")
|
||||
expect_identical(mo_fullname("CoNS", "da"), "Koagulase-negative stafylokokker (KNS)")
|
||||
expect_identical(mo_fullname("CoNS", "de"), "Koagulase-negative Staphylococcus (KNS)")
|
||||
expect_identical(mo_fullname("CoNS", "nl"), "Coagulase-negatieve Staphylococcus (CNS)")
|
||||
expect_identical(mo_fullname("CoNS", "el"), "Σταφυλόκοκκος με αρνητική πηκτικότητα (CoNS)")
|
||||
expect_identical(mo_fullname("CoNS", "en"), "Coagulase-negative Staphylococcus (CoNS)")
|
||||
expect_identical(mo_fullname("CoNS", "es"), "Staphylococcus coagulasa negativo (SCN)")
|
||||
expect_identical(mo_fullname("CoNS", "fi"), "Koagulaasinegatiivinen stafylokokki (KNS)")
|
||||
expect_identical(mo_fullname("CoNS", "fr"), "Staphylococcus à coagulase négative (CoNS)")
|
||||
expect_identical(mo_fullname("CoNS", "it"), "Staphylococcus negativo coagulasi (CoNS)")
|
||||
expect_identical(mo_fullname("CoNS", "ja"), "コアグラーゼ陰性ブドウ球菌 (グラム陰性)")
|
||||
expect_identical(mo_fullname("CoNS", "nl"), "Coagulase-negatieve Staphylococcus (CNS)")
|
||||
expect_identical(mo_fullname("CoNS", "no"), "Koagulase-negative stafylokokker (KNS)")
|
||||
expect_identical(mo_fullname("CoNS", "pl"), "Staphylococcus koagulazoujemny (CoNS)")
|
||||
expect_identical(mo_fullname("CoNS", "pt"), "Staphylococcus coagulase negativo (CoNS)")
|
||||
expect_identical(mo_fullname("CoNS", "ro"), "Stafilococ coagulazo-negativ (SCN)")
|
||||
expect_identical(mo_fullname("CoNS", "ru"), "Коагулазоотрицательный стафилококк (КОС)")
|
||||
expect_identical(mo_fullname("CoNS", "sv"), "Koagulasnegativa stafylokocker (KNS)")
|
||||
expect_identical(mo_fullname("CoNS", "tr"), "Koagülaz-negatif Stafilokok (KNS)")
|
||||
expect_identical(mo_fullname("CoNS", "uk"), "Коагулазонегативний стафілокок (КНС)")
|
||||
expect_identical(mo_fullname("CoNS", "zh"), "凝固酶阴性葡萄球菌 (CoNS)")
|
||||
|
||||
expect_error(mo_fullname("CoNS", "aa"))
|
||||
Reference in New Issue
Block a user