(v0.9.0.9012) Support for LOINC codes

R/ab.R

@@ -143,6 +143,19 @@ as.ab <- function(x, ...) {
       x_new[i] <- found[1L]
       next
     }
+    
+    # exact LOINC code
+    loinc_found <- unlist(lapply(AMR::antibiotics$loinc,
+                                   function(s) if (x[i] %in% s) {
+                                     TRUE
+                                   } else {
+                                     FALSE
+                                   }))
+    found <- AMR::antibiotics$ab[loinc_found == TRUE]
+    if (length(found) > 0) {
+      x_new[i] <- found[1L]
+      next
+    }
 
     # exact synonym
     synonym_found <- unlist(lapply(AMR::antibiotics$synonyms,

R/ab_property.R

@@ -47,18 +47,18 @@
 #' 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"
 #'
+#' # 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"
 #'
+#' # defined daily doses (DDD)
 #' ab_ddd("AMX", "oral")               #  1
 #' ab_ddd("AMX", "oral", units = TRUE) # "g"
 #' ab_ddd("AMX", "iv")                 #  1
@@ -66,12 +66,13 @@
 #'
 #' ab_info("AMX")       # all properties as a list
 #'
-#' # all ab_* functions use as.ab() internally:
-#' ab_name("Fluclox")   # "Flucloxacillin"
-#' ab_name("fluklox")   # "Flucloxacillin"
-#' ab_name("floxapen")  # "Flucloxacillin"
-#' ab_name(21319)       # "Flucloxacillin" (using CID)
-#' ab_name("J01CF05")   # "Flucloxacillin" (using ATC)
+#' # 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)
 #' 
 #' # spelling from different languages and dyslexia are no problem
 #' ab_atc("ceftriaxon")
@@ -137,6 +138,18 @@ ab_atc_group2 <- function(x, language = get_locale(), ...) {
   translate_AMR(ab_validate(x = x, property = "atc_group2", ...), language = language)
 }
 
+#' @rdname ab_property
+#' @export
+ab_loinc <- function(x, ...) {
+  loincs <- ab_validate(x = x, property = "loinc", ...)
+  names(loincs) <- x
+  if (length(loincs) == 1) {
+    unname(unlist(loincs))
+  } else {
+    loincs
+  }
+}
+
 #' @rdname ab_property
 #' @export
 ab_ddd <- function(x, administration = "oral", units = FALSE, ...) {

R/data.R

@@ -23,7 +23,7 @@
 #'
 #' Two data sets containing all antibiotics/antimycotics and antivirals. Use [as.ab()] or one of the [ab_property()] functions to retrieve values from the [antibiotics] data set. Three identifiers are included in this data set: an antibiotic ID (`ab`, primarily used in this package) as defined by WHONET/EARS-Net, an ATC code (`atc`) as defined by the WHO, and a Compound ID (`cid`) as found in PubChem. Other properties in this data set are derived from one or more of these codes.
 #' @format
-#' ### For the [antibiotics] data set: a [`data.frame`] with 452 observations and 13 variables:
+#' ### For the [antibiotics] data set: a [`data.frame`] with 452 observations and 14 variables:
 #' - `ab`\cr Antibiotic ID as used in this package (like `AMC`), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available
 #' - `atc`\cr ATC code (Anatomical Therapeutic Chemical) as defined by the WHOCC, like `J01CR02`
 #' - `cid`\cr Compound ID as found in PubChem
@@ -37,6 +37,7 @@
 #' - `oral_units`\cr Units of `oral_ddd`
 #' - `iv_ddd`\cr Defined Daily Dose (DDD), parenteral treatment
 #' - `iv_units`\cr Units of `iv_ddd`
+#' - `loinc`\cr All LOINC codes (Logical Observation Identifiers Names and Codes) associated with the antimicrobial name of the drug. Use [ab_loic()] to retrieve them quickly, see [ab_property()].
 #' 
 #' ### For the [antivirals] data set: a [`data.frame`] with 102 observations and 9 variables:
 #' - `atc`\cr ATC code (Anatomical Therapeutic Chemical) as defined by the WHOCC

R/eucast_rules.R

@@ -23,7 +23,7 @@
 EUCAST_VERSION_BREAKPOINTS <- "9.0, 2019"
 EUCAST_VERSION_EXPERT_RULES <- "3.1, 2016"
 
-#' EUCAST rules
+#' Apply EUCAST rules
 #' 
 #' @description
 #' Apply susceptibility rules as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, <http://eucast.org>), see *Source*. This includes (1) expert rules, (2) intrinsic resistance and (3) inferred resistance as defined in their breakpoint tables. 
@@ -49,6 +49,7 @@ EUCAST_VERSION_EXPERT_RULES <- "3.1, 2016"
 #' - Set amoxicillin/clavulanic acid (AMC) = S where amoxicillin (AMX) = S;
 #' - Set piperacillin/tazobactam (TZP) = S where piperacillin (PIP) = S;
 #' - Set trimethoprim/sulfamethoxazole (SXT) = S where trimethoprim (TMP) = S.
+#' 
 #' To *not* use these rules, please use `eucast_rules(..., rules = c("breakpoints", "expert"))`.
 #'
 #' The file containing all EUCAST rules is located here: <https://gitlab.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv>.

R/mo.R

@@ -922,8 +922,10 @@ exec_as.mo <- function(x,
               set_mo_history(x_backup[i], get_mo_code(x[i], property), 0, force = force_mo_history, disable = disable_mo_history)
             }
             next
-          } else if (grepl("[sS]almonella [A-Z][a-z]+ ?.*", x_backup[i], ignore.case = FALSE)) {
+          } else if (grepl("[sS]almonella [A-Z][a-z]+ ?.*", x_backup[i], ignore.case = FALSE) &
+                       !x_backup[i] %like% "t[iy](ph|f)[iy]") {
             # Salmonella with capital letter species like "Salmonella Goettingen" - they're all S. enterica
+            # except for S. typhi, S. paratyphi, S. typhimurium
             x[i] <- microorganismsDT[mo == "B_SLMNL_ENTR",
                                      ..property][[1]][1L]
             if (initial_search == TRUE) {