scientific notation for MICs

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 2.1.0.9003
+Version: 2.1.0.9004
 Date: 2023-10-20
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)

NEWS.md

@@ -1,10 +1,10 @@
-# AMR 2.1.0.9003
+# AMR 2.1.0.9004
 
 * Fix for selecting first isolates using the phenotype-based method
  * This included too many isolates when patients had altering antibiograms within the same bacterial species
  * See for more info [our issue #122](https://github.com/msberends/AMR/issues/122)
 * Added 1,366 LOINC codes to the `antibiotics` data set and updated to the latest version (LOINC v2.76)
-* MICs can now be used in complex number calculations
+* MICs can now be used in complex number calculations and allow scientific number format as input (e.g., `as.mic("1.28e-2")`)
 * Fix rounding MICs on latest R beta ('R-devel')
 * Removed unneeded note about the used language when option `AMR_locale` is set
 * Fixed non-ASCII characters in documentation, according to CRAN maintainers

R/aa_globals.R

@@ -102,7 +102,7 @@ TAXONOMY_VERSION <- list(
  ),
  SNOMED = list(
  accessed_date = as.Date("2021-07-01"),
- citation = "Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS). US Edition of SNOMED CT from 1 September 2020. Value Set Name 'Microoganism', OID 2.16.840.1.114222.4.11.1009 (v12).",
+ citation = "Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS). US Edition of SNOMED CT from 1 September 2020. Value Set Name 'Microorganism', OID 2.16.840.1.114222.4.11.1009 (v12).",
  url = "https://phinvads.cdc.gov"
  ),
  LOINC = list(
@@ -113,6 +113,7 @@ TAXONOMY_VERSION <- list(
 )
 
 globalVariables(c(
+ ".GenericCallEnv",
  ".mo",
  ".rowid",
  ".syndromic_group",

R/mic.R

@@ -184,6 +184,8 @@ as.mic <- function(x, na.rm = FALSE) {
 
  # comma to period
  x <- gsub(",", ".", x, fixed = TRUE)
+ # transform scientific notation
+ x[x %like% "[-]?[0-9]+([.][0-9]+)?e[-]?[0-9]+"] <- as.double(x[x %like% "[-]?[0-9]+([.][0-9]+)?e[-]?[0-9]+"])
  # transform Unicode for >= and <=
  x <- gsub("\u2264", "<=", x, fixed = TRUE)
  x <- gsub("\u2265", ">=", x, fixed = TRUE)

inst/tinytest/test-first_isolate.R

@@ -45,6 +45,19 @@ expect_equal(
  1373
 )
 
+# for phenotype determination
+expect_equal(AMR:::duplicated_antibiogram("SSSS", points_threshold = 2, ignore_I = TRUE, type = "points"),
+ FALSE)
+expect_equal(AMR:::duplicated_antibiogram(c("RRR", "SSS"),
+ points_threshold = 2, ignore_I = TRUE, type = "points"),
+ c(FALSE, FALSE))
+expect_equal(AMR:::duplicated_antibiogram(c("RRR", "RRR", "SSS"),
+ points_threshold = 2, ignore_I = TRUE, type = "points"),
+ c(FALSE, TRUE, FALSE))
+expect_equal(AMR:::duplicated_antibiogram(c("RRR", "RSS", "SSS", "RSS", "RRR", "RRR", "SSS", "RSS", "RSR", "RRR"),
+ points_threshold = 2, ignore_I = TRUE, type = "points"),
+ c(FALSE, FALSE, FALSE, TRUE, TRUE, TRUE, TRUE, TRUE, FALSE, TRUE))
+
 # Phenotype-based, using key antimicrobials
 expect_equal(
  sum(first_isolate(