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Implement extensive support for antiviral agents support (#77)

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Dr. Matthijs Berends
2022-11-13 08:46:10 +01:00
committed by GitHub
parent d2edcf51ad
commit 496c08d851
46 changed files with 1966 additions and 1563 deletions
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2
inst/tinytest/test-ab_property.R
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@ -45,10 +45,8 @@ expect_identical(ab_name(21319, language = NULL), "Flucloxacillin")
expect_identical(ab_name("J01CF05", language = NULL), "Flucloxacillin")
expect_identical(ab_ddd("AMX", "oral"), 1.5)
expect_warning(ab_ddd("AMX", "oral", units = TRUE)) # old behaviour
expect_identical(ab_ddd_units("AMX", "iv"), "g")
expect_identical(ab_ddd("AMX", "iv"), 3)
expect_identical(ab_ddd_units("AMX", "iv"), "g")
expect_identical(ab_name(x = c("AMC", "PLB"), language = NULL), c("Amoxicillin/clavulanic acid", "Polymyxin B"))
expect_identical(

80
inst/tinytest/test-av.R Executable file
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@ -0,0 +1,80 @@
# ==================================================================== #
# 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, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #
# #
# 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/ #
# ==================================================================== #
expect_equal(
as.character(as.av(c(
"J05AB01",
"J 05 AB 01",
"Aciclovir",
"aciclo",
" aciclo 123",
"ACICL",
"ACI",
"Virorax",
"Zovirax"
))),
rep("ACI", 9)
)
expect_identical(class(as.av("acic")), c("av", "character"))
expect_identical(class(antivirals$av), c("av", "character"))
expect_true(is.av(as.av("acic")))
expect_stdout(print(as.av("acic")))
expect_stdout(print(data.frame(a = as.av("acic"))))
expect_warning(as.av("J00AA00")) # ATC not yet available in data set
expect_warning(as.av("UNKNOWN"))
expect_stdout(print(as.av("acic")))
expect_equal(
as.character(as.av("zovirax")),
"ACI"
)
expect_equal(
as.character(as.av(c("Abacaivr", "Celvudine"))),
c("ABA", "CLE")
)
expect_warning(as.av("Abacavir Clevudine"))
# based on Levenshtein distance
expect_identical(av_name("adevofir dypifo", language = NULL), "Adefovir dipivoxil")
# assigning and subsetting
x <- antivirals$av
expect_inherits(x[1], "av")
expect_inherits(x[[1]], "av")
expect_inherits(c(x[1], x[9]), "av")
expect_inherits(unique(x[1], x[9]), "av")
expect_inherits(rep(x[1], 2), "av")
expect_warning(x[1] <- "invalid code")
expect_warning(x[[1]] <- "invalid code")
expect_warning(c(x[1], "test"))

58
inst/tinytest/test-av_from_text.R Normal file
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@ -0,0 +1,58 @@
# ==================================================================== #
# 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, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #
# #
# 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/ #
# ==================================================================== #
expect_identical(
av_from_text("28/03/2020 regular aciclovir 500mg po tds")[[1]],
as.av("Aciclovir")
)
expect_identical(
av_from_text("28/03/2020 regular aciclovir 500mg po tds", thorough_search = TRUE)[[1]],
as.av("Aciclovir")
)
expect_identical(
av_from_text("28/03/2020 regular aciclovir 500mg po tds", thorough_search = FALSE)[[1]],
as.av("Aciclovir")
)
expect_identical(
av_from_text("28/03/2020 regular aciclovir 500mg po tds", translate_av = TRUE)[[1]],
"Aciclovir"
)
expect_identical(
av_from_text("administered aciclo and valaciclo", collapse = ", ")[[1]],
"ACI, VALA"
)
expect_identical(
av_from_text("28/03/2020 regular aciclo 500mg po tds", type = "dose")[[1]],
500
)
expect_identical(
av_from_text("28/03/2020 regular aciclo 500mg po tds", type = "admin")[[1]],
"oral"
)

64
inst/tinytest/test-av_property.R Normal file
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@ -0,0 +1,64 @@
# ==================================================================== #
# 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, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #
# #
# 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/ #
# ==================================================================== #
expect_identical(av_name("ACI", language = NULL), "Aciclovir")
expect_identical(av_atc("ACI"), "J05AB01")
expect_identical(av_cid("ACI"), as.integer(135398513))
expect_inherits(av_tradenames("ACI"), "character")
expect_inherits(av_tradenames(c("ACI", "ACI")), "list")
expect_identical(av_group("ACI", language = NULL),"Nucleosides and nucleotides excl. reverse transcriptase inhibitors")
expect_identical(av_name(135398513, language = NULL), "Aciclovir")
expect_identical(av_name("J05AB01", language = NULL), "Aciclovir")
expect_identical(av_ddd("ACI", "oral"), 4)
expect_identical(av_ddd_units("ACI", "iv"), "g")
expect_identical(av_ddd("ACI", "iv"), 4)
expect_identical(
av_name(x = c("ACI", "VALA"), tolower = TRUE, language = NULL),
c("aciclovir", "valaciclovir")
)
expect_inherits(av_info("ACI"), "list")
expect_error(av_property("acic", "invalid property"))
expect_error(av_name("acic", language = "INVALID"))
expect_stdout(print(av_name("acic", language = NULL)))
expect_equal(av_name("29113-8", language = NULL), "Abacavir")
expect_equal(
av_loinc("Abacavir"),
c("29113-8", "78772-1", "78773-9", "79134-3", "80118-3")
)
expect_true(av_url("ACI") %like% "whocc.no")
expect_warning(av_url("ASP"))

2
inst/tinytest/test-mdro.R
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@ -27,8 +27,6 @@
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
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))