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unit tests
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80
inst/tinytest/test-av.R
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80
inst/tinytest/test-av.R
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# ==================================================================== #
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# TITLE #
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# AMR: An R Package for Working with Antimicrobial Resistance Data #
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# #
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# SOURCE #
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# https://github.com/msberends/AMR #
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# #
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# CITE AS #
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# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
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# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
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# Data. Journal of Statistical Software, 104(3), 1-31. #
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# doi:10.18637/jss.v104.i03 #
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# #
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# Developed at the University of Groningen, the Netherlands, in #
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# collaboration with non-profit organisations Certe Medical #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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# #
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# This R package is free software; you can freely use and distribute #
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# it for both personal and commercial purposes under the terms of the #
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# GNU General Public License version 2.0 (GNU GPL-2), as published by #
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# the Free Software Foundation. #
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# We created this package for both routine data analysis and academic #
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# research and it was publicly released in the hope that it will be #
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# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
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# #
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# Visit our website for the full manual and a complete tutorial about #
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# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
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# ==================================================================== #
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expect_equal(
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as.character(as.av(c(
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"J05AB01",
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"J 05 AB 01",
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"Aciclovir",
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"aciclo",
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" aciclo 123",
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"ACICL",
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"ACI",
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"Virorax",
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"Zovirax"
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))),
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rep("ACI", 9)
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)
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expect_identical(class(as.av("acic")), c("av", "character"))
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expect_identical(class(antivirals$av), c("av", "character"))
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expect_true(is.av(as.av("acic")))
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expect_stdout(print(as.av("acic")))
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expect_stdout(print(data.frame(a = as.av("acic"))))
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expect_warning(as.av("J00AA00")) # ATC not yet available in data set
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expect_warning(as.av("UNKNOWN"))
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expect_stdout(print(as.av("acic")))
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expect_equal(
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as.character(as.av("zovirax")),
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"ACI"
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)
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expect_equal(
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as.character(as.av(c("Abacaivr", "Celvudine"))),
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c("ABA", "CLE")
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)
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expect_warning(as.av("Abacavir Clevudine"))
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# based on Levenshtein distance
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expect_identical(av_name("adevofir dypifo", language = NULL), "Adefovir dipivoxil")
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# assigning and subsetting
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x <- antivirals$av
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expect_inherits(x[1], "av")
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expect_inherits(x[[1]], "av")
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expect_inherits(c(x[1], x[9]), "av")
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expect_inherits(unique(x[1], x[9]), "av")
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expect_inherits(rep(x[1], 2), "av")
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expect_warning(x[1] <- "invalid code")
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expect_warning(x[[1]] <- "invalid code")
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expect_warning(c(x[1], "test"))
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58
inst/tinytest/test-av_from_text.R
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58
inst/tinytest/test-av_from_text.R
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# ==================================================================== #
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# TITLE #
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# AMR: An R Package for Working with Antimicrobial Resistance Data #
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# #
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# SOURCE #
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# https://github.com/msberends/AMR #
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# #
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# CITE AS #
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# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
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# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
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# Data. Journal of Statistical Software, 104(3), 1-31. #
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# doi:10.18637/jss.v104.i03 #
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# #
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# Developed at the University of Groningen, the Netherlands, in #
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# collaboration with non-profit organisations Certe Medical #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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# #
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# This R package is free software; you can freely use and distribute #
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# it for both personal and commercial purposes under the terms of the #
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# GNU General Public License version 2.0 (GNU GPL-2), as published by #
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# the Free Software Foundation. #
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# We created this package for both routine data analysis and academic #
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# research and it was publicly released in the hope that it will be #
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# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
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# #
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# Visit our website for the full manual and a complete tutorial about #
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# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
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# ==================================================================== #
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expect_identical(
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av_from_text("28/03/2020 regular aciclovir 500mg po tds")[[1]],
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as.av("Aciclovir")
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)
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expect_identical(
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av_from_text("28/03/2020 regular aciclovir 500mg po tds", thorough_search = TRUE)[[1]],
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as.av("Aciclovir")
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)
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expect_identical(
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av_from_text("28/03/2020 regular aciclovir 500mg po tds", thorough_search = FALSE)[[1]],
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as.av("Aciclovir")
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)
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expect_identical(
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av_from_text("28/03/2020 regular aciclovir 500mg po tds", translate_ab = TRUE)[[1]],
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"Aciclovir"
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)
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expect_identical(
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av_from_text("administered aciclo and valaciclo", collapse = ", ")[[1]],
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"ACI, VALA"
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)
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expect_identical(
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av_from_text("28/03/2020 regular aciclo 500mg po tds", type = "dose")[[1]],
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500
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)
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expect_identical(
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av_from_text("28/03/2020 regular aciclo 500mg po tds", type = "admin")[[1]],
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"oral"
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)
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65
inst/tinytest/test-av_property.R
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65
inst/tinytest/test-av_property.R
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# ==================================================================== #
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# TITLE #
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# AMR: An R Package for Working with Antimicrobial Resistance Data #
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# #
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# SOURCE #
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# https://github.com/msberends/AMR #
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# #
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# CITE AS #
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# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
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# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
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# Data. Journal of Statistical Software, 104(3), 1-31. #
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# doi:10.18637/jss.v104.i03 #
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# #
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# Developed at the University of Groningen, the Netherlands, in #
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# collaboration with non-profit organisations Certe Medical #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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# #
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# This R package is free software; you can freely use and distribute #
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# it for both personal and commercial purposes under the terms of the #
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# GNU General Public License version 2.0 (GNU GPL-2), as published by #
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# the Free Software Foundation. #
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# We created this package for both routine data analysis and academic #
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# research and it was publicly released in the hope that it will be #
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# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
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# #
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# Visit our website for the full manual and a complete tutorial about #
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# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
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# ==================================================================== #
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expect_identical(av_name("ACI", language = NULL), "Aciclovir")
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expect_identical(av_atc("ACI"), "J05AB01")
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expect_identical(av_cid("ACI"), as.integer(135398513))
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expect_inherits(av_tradenames("ACI"), "character")
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expect_inherits(av_tradenames(c("ACI", "ACI")), "list")
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expect_identical(av_group("ACI", language = NULL),"Nucleosides and nucleotides excl. reverse transcriptase inhibitors")
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expect_identical(av_name(135398513, language = NULL), "Aciclovir")
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expect_identical(av_name("J05AB01", language = NULL), "Aciclovir")
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expect_identical(av_ddd("ACI", "oral"), 4)
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expect_warning(av_ddd("ACI", "oral", units = TRUE)) # old behaviour
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expect_identical(av_ddd_units("ACI", "iv"), "g")
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expect_identical(av_ddd("ACI", "iv"), 4)
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expect_identical(
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av_name(x = c("ACI", "VALA"), tolower = TRUE, language = NULL),
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c("aciclovir", "valaciclovir")
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)
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expect_inherits(av_info("ACI"), "list")
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expect_error(av_property("acic", "invalid property"))
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expect_error(av_name("acic", language = "INVALID"))
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expect_stdout(print(av_name("acic", language = NULL)))
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expect_equal(av_name("29113-8", language = NULL), "Abacavir")
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expect_equal(
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av_loinc("Abacavir"),
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c("29113-8", "78772-1", "78773-9", "79134-3", "80118-3")
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)
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expect_true(av_url("ACI") %like% "whocc.no")
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expect_warning(av_url("ASP"))
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