unit tests

2025-01-16 01:21:38 +01:00 · 2022-11-12 22:08:12 +01:00 · 2022-11-12 22:08:12 +01:00 · 1162d1d9b1
commit 1162d1d9b1
parent 8fab745ab1
9 changed files with 302 additions and 121 deletions
--- a/R/ab_property.R
+++ b/R/ab_property.R
@ -59,38 +59,35 @@
 #' @inheritSection AMR Reference Data Publicly Available
 #' @examples
 #' # all properties:
-#' ab_name("AMX") # "Amoxicillin"
-#' ab_atc("AMX") # "J01CA04" (ATC code from the WHO)
-#' ab_cid("AMX") # 33613 (Compound ID from PubChem)
-#' ab_synonyms("AMX") # a list with brand names of amoxicillin
-#' ab_tradenames("AMX") # same
-#' ab_group("AMX") # "Beta-lactams/penicillins"
-#' ab_atc_group1("AMX") # "Beta-lactam antibacterials, penicillins"
-#' ab_atc_group2("AMX") # "Penicillins with extended spectrum"
-#' ab_url("AMX") # link to the official WHO page
+#' ab_name("AMX")
+#' ab_atc("AMX")
+#' ab_cid("AMX")
+#' ab_synonyms("AMX")
+#' ab_tradenames("AMX")
+#' ab_group("AMX")
+#' ab_atc_group1("AMX")
+#' ab_atc_group2("AMX")
+#' ab_url("AMX")
 #'
 #' # smart lowercase tranformation
-#' ab_name(x = c("AMC", "PLB")) # "Amoxicillin/clavulanic acid" "Polymyxin B"
-#' ab_name(
-#'   x = c("AMC", "PLB"),
-#'   tolower = TRUE
-#' ) # "amoxicillin/clavulanic acid" "polymyxin B"
+#' ab_name(x = c("AMC", "PLB"))
+#' ab_name(x = c("AMC", "PLB"), tolower = TRUE)
 #'
 #' # defined daily doses (DDD)
-#' ab_ddd("AMX", "oral") #  1.5
-#' ab_ddd_units("AMX", "oral") # "g"
-#' ab_ddd("AMX", "iv") #  3
-#' ab_ddd_units("AMX", "iv") # "g"
+#' ab_ddd("AMX", "oral")
+#' ab_ddd_units("AMX", "oral")
+#' ab_ddd("AMX", "iv")
+#' ab_ddd_units("AMX", "iv")
 #'
 #' ab_info("AMX") # all properties as a list
 #'
 #' # all ab_* functions use as.ab() internally, so you can go from 'any' to 'any':
-#' ab_atc("AMP") # ATC code of AMP (ampicillin)
-#' ab_group("J01CA01") # Drug group of ampicillins ATC code
-#' ab_loinc("ampicillin") # LOINC codes of ampicillin
-#' ab_name("21066-6") # "Ampicillin" (using LOINC)
-#' ab_name(6249) # "Ampicillin" (using CID)
-#' ab_name("J01CA01") # "Ampicillin" (using ATC)
+#' ab_atc("AMP")
+#' ab_group("J01CA01")
+#' ab_loinc("ampicillin")
+#' ab_name("21066-6")
+#' ab_name(6249)
+#' ab_name("J01CA01")
 #'
 #' # spelling from different languages and dyslexia are no problem
 #' ab_atc("ceftriaxon")
--- a/R/av.R
+++ b/R/av.R
@ -383,13 +383,8 @@ as.av <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
        next
      }

-      # first 5 except for cephalosporins, then first 7 (those cephalosporins all start quite the same!)
+      # first 5
      found <- suppressWarnings(as.av(substr(x[i], 1, 5), initial_search = FALSE))
-      if (!is.na(found) && av_group(found, initial_search = FALSE) %unlike% "cephalosporins") {
-        x_new[i] <- note_if_more_than_one_found(found, i, from_text)
-        next
-      }
-      found <- suppressWarnings(as.av(substr(x[i], 1, 7), initial_search = FALSE))
      if (!is.na(found)) {
        x_new[i] <- note_if_more_than_one_found(found, i, from_text)
        next
--- a/R/av_property.R
+++ b/R/av_property.R
@ -53,44 +53,33 @@
 #' @inheritSection AMR Reference Data Publicly Available
 #' @examples
 #' # all properties:
-#' av_name("AMX") # "Amoxicillin"
-#' av_atc("AMX") # "J01CA04" (ATC code from the WHO)
-#' av_cid("AMX") # 33613 (Compound ID from PubChem)
-#' av_synonyms("AMX") # a list with brand names of amoxicillin
-#' av_tradenames("AMX") # same
-#' av_group("AMX") # "Beta-lactams/penicillins"
-#' av_atc_group1("AMX") # "Beta-lactam antibacterials, penicillins"
-#' av_atc_group2("AMX") # "Penicillins with extended spectrum"
-#' av_url("AMX") # link to the official WHO page
+#' av_name("ACI")
+#' av_atc("ACI")
+#' av_cid("ACI")
+#' av_synonyms("ACI")
+#' av_tradenames("ACI")
+#' av_group("ACI")
+#' av_url("ACI")
 #'
 #' # smart lowercase tranformation
-#' av_name(x = c("AMC", "PLB")) # "Amoxicillin/clavulanic acid" "Polymyxin B"
-#' av_name(
-#'   x = c("AMC", "PLB"),
-#'   tolower = TRUE
-#' ) # "amoxicillin/clavulanic acid" "polymyxin B"
+#' av_name(x = c("ACI", "VALA"))
+#' av_name(x = c("ACI", "VALA"), tolower = TRUE)
 #'
 #' # defined daily doses (DDD)
-#' av_ddd("AMX", "oral") #  1.5
-#' av_ddd_units("AMX", "oral") # "g"
-#' av_ddd("AMX", "iv") #  3
-#' av_ddd_units("AMX", "iv") # "g"
+#' av_ddd("ACI", "oral")
+#' av_ddd_units("ACI", "oral")
+#' av_ddd("ACI", "iv")
+#' av_ddd_units("ACI", "iv")
 #'
-#' av_info("AMX") # all properties as a list
+#' av_info("ACI") # all properties as a list
 #'
 #' # all av_* functions use as.av() internally, so you can go from 'any' to 'any':
-#' av_atc("AMP") # ATC code of AMP (ampicillin)
-#' av_group("J01CA01") # Drug group of ampicillins ATC code
-#' av_loinc("ampicillin") # LOINC codes of ampicillin
-#' av_name("21066-6") # "Ampicillin" (using LOINC)
-#' av_name(6249) # "Ampicillin" (using CID)
-#' av_name("J01CA01") # "Ampicillin" (using ATC)
-#'
-#' # spelling from different languages and dyslexia are no problem
-#' av_atc("ceftriaxon")
-#' av_atc("cephtriaxone")
-#' av_atc("cephthriaxone")
-#' av_atc("seephthriaaksone")
+#' av_atc("ACI")
+#' av_group("J05AB01")
+#' av_loinc("abacavir")
+#' av_name("29113-8")
+#' av_name(135398513)
+#' av_name("J05AB01")
 av_name <- function(x, language = get_AMR_locale(), tolower = FALSE, ...) {
  meet_criteria(x, allow_NA = TRUE)
  language <- validate_language(language)
@ -137,7 +126,7 @@ av_tradenames <- function(x, ...) {
 av_group <- function(x, language = get_AMR_locale(), ...) {
  meet_criteria(x, allow_NA = TRUE)
  language <- validate_language(language)
-  translate_into_language(av_validate(x = x, property = "group", ...), language = language, only_affect_ab_names = TRUE)
+  translate_into_language(av_validate(x = x, property = "atc_group", ...), language = language, only_affect_ab_names = TRUE)
 }

 #' @rdname av_property
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@ -102,9 +102,9 @@ navbar:
      - text: "Get properties of an antibiotic"
        icon: "fa-capsules"
        href: "reference/ab_property.html" # reference instead of an article
-      # - text: "Other: benchmarks"
-      #   icon: "fa-shipping-fast"
-      #   href: "articles/benchmarks.html"
+      - text: "Get properties of an antiviral agent"
+        icon: "fa-capsules"
+        href: "reference/av_property.html" # reference instead of an article
    - text: "Manual"
      icon: "fa-book-open"
      href: "reference/index.html"
@ -175,8 +175,19 @@ reference:
    - "`mean_amr_distance`"
    - "`resistance_predict`"
    - "`guess_ab_col`"
+    
+  - title: "Other: antiviral drugs"
+    desc: >
+      This package also provides extensive support for antiviral agents, even though it is not the primary
+      scope of this package. Working with data containing information about antiviral drugs was never easier.
+      Use these functions to get valid properties of antiviral drugs from any input or to clean your input.
+      You can even retrieve drug names and doses from clinical text records, using `av_from_text()`.
+    contents:
+    - "`as.av`"
+    - "`av_property`"
+    - "`av_from_text`"

-  - title: "Background information on included data"
+  - title: "Other: background information on included data"
    desc: >
      Some pages about our package and its external sources. Be sure to read our [How To's](./../articles/index.html)
      for more information about how to work with functions in this package.
--- a/inst/tinytest/test-av.R
+++ b/inst/tinytest/test-av.R
@ -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"))
--- a/inst/tinytest/test-av_from_text.R
+++ b/inst/tinytest/test-av_from_text.R
@ -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_ab = 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"
+)
--- a/inst/tinytest/test-av_property.R
+++ b/inst/tinytest/test-av_property.R
@ -0,0 +1,65 @@
+# ==================================================================== #
+# 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_warning(av_ddd("ACI", "oral", units = TRUE)) # old behaviour
+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"))
--- a/man/ab_property.Rd
+++ b/man/ab_property.Rd
@ -109,38 +109,35 @@ All data sets in this \code{AMR} package (about microorganisms, antibiotics, R/S

 \examples{
 # all properties:
-ab_name("AMX") # "Amoxicillin"
-ab_atc("AMX") # "J01CA04" (ATC code from the WHO)
-ab_cid("AMX") # 33613 (Compound ID from PubChem)
-ab_synonyms("AMX") # a list with brand names of amoxicillin
-ab_tradenames("AMX") # same
-ab_group("AMX") # "Beta-lactams/penicillins"
-ab_atc_group1("AMX") # "Beta-lactam antibacterials, penicillins"
-ab_atc_group2("AMX") # "Penicillins with extended spectrum"
-ab_url("AMX") # link to the official WHO page
+ab_name("AMX")
+ab_atc("AMX")
+ab_cid("AMX")
+ab_synonyms("AMX")
+ab_tradenames("AMX")
+ab_group("AMX")
+ab_atc_group1("AMX")
+ab_atc_group2("AMX")
+ab_url("AMX")

 # smart lowercase tranformation
-ab_name(x = c("AMC", "PLB")) # "Amoxicillin/clavulanic acid" "Polymyxin B"
-ab_name(
-  x = c("AMC", "PLB"),
-  tolower = TRUE
-) # "amoxicillin/clavulanic acid" "polymyxin B"
+ab_name(x = c("AMC", "PLB"))
+ab_name(x = c("AMC", "PLB"), tolower = TRUE)

 # defined daily doses (DDD)
-ab_ddd("AMX", "oral") #  1.5
-ab_ddd_units("AMX", "oral") # "g"
-ab_ddd("AMX", "iv") #  3
-ab_ddd_units("AMX", "iv") # "g"
+ab_ddd("AMX", "oral")
+ab_ddd_units("AMX", "oral")
+ab_ddd("AMX", "iv")
+ab_ddd_units("AMX", "iv")

 ab_info("AMX") # all properties as a list

 # all ab_* functions use as.ab() internally, so you can go from 'any' to 'any':
-ab_atc("AMP") # ATC code of AMP (ampicillin)
-ab_group("J01CA01") # Drug group of ampicillins ATC code
-ab_loinc("ampicillin") # LOINC codes of ampicillin
-ab_name("21066-6") # "Ampicillin" (using LOINC)
-ab_name(6249) # "Ampicillin" (using CID)
-ab_name("J01CA01") # "Ampicillin" (using ATC)
+ab_atc("AMP")
+ab_group("J01CA01")
+ab_loinc("ampicillin")
+ab_name("21066-6")
+ab_name(6249)
+ab_name("J01CA01")

 # spelling from different languages and dyslexia are no problem
 ab_atc("ceftriaxon")
--- a/man/av_property.Rd
+++ b/man/av_property.Rd
@ -85,44 +85,33 @@ All data sets in this \code{AMR} package (about microorganisms, antibiotics, R/S

 \examples{
 # all properties:
-av_name("AMX") # "Amoxicillin"
-av_atc("AMX") # "J01CA04" (ATC code from the WHO)
-av_cid("AMX") # 33613 (Compound ID from PubChem)
-av_synonyms("AMX") # a list with brand names of amoxicillin
-av_tradenames("AMX") # same
-av_group("AMX") # "Beta-lactams/penicillins"
-av_atc_group1("AMX") # "Beta-lactam antibacterials, penicillins"
-av_atc_group2("AMX") # "Penicillins with extended spectrum"
-av_url("AMX") # link to the official WHO page
+av_name("ACI")
+av_atc("ACI")
+av_cid("ACI")
+av_synonyms("ACI")
+av_tradenames("ACI")
+av_group("ACI")
+av_url("ACI")

 # smart lowercase tranformation
-av_name(x = c("AMC", "PLB")) # "Amoxicillin/clavulanic acid" "Polymyxin B"
-av_name(
-  x = c("AMC", "PLB"),
-  tolower = TRUE
-) # "amoxicillin/clavulanic acid" "polymyxin B"
+av_name(x = c("ACI", "VALA"))
+av_name(x = c("ACI", "VALA"), tolower = TRUE)

 # defined daily doses (DDD)
-av_ddd("AMX", "oral") #  1.5
-av_ddd_units("AMX", "oral") # "g"
-av_ddd("AMX", "iv") #  3
-av_ddd_units("AMX", "iv") # "g"
+av_ddd("ACI", "oral")
+av_ddd_units("ACI", "oral")
+av_ddd("ACI", "iv")
+av_ddd_units("ACI", "iv")

-av_info("AMX") # all properties as a list
+av_info("ACI") # all properties as a list

 # all av_* functions use as.av() internally, so you can go from 'any' to 'any':
-av_atc("AMP") # ATC code of AMP (ampicillin)
-av_group("J01CA01") # Drug group of ampicillins ATC code
-av_loinc("ampicillin") # LOINC codes of ampicillin
-av_name("21066-6") # "Ampicillin" (using LOINC)
-av_name(6249) # "Ampicillin" (using CID)
-av_name("J01CA01") # "Ampicillin" (using ATC)
-
-# spelling from different languages and dyslexia are no problem
-av_atc("ceftriaxon")
-av_atc("cephtriaxone")
-av_atc("cephthriaxone")
-av_atc("seephthriaaksone")
+av_atc("ACI")
+av_group("J05AB01")
+av_loinc("abacavir")
+av_name("29113-8")
+av_name(135398513)
+av_name("J05AB01")
 }
 \seealso{
 \link{antivirals}