anaerobic codes

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 2.0.0.9008
-Date: 2023-04-15
+Version: 2.0.0.9009
+Date: 2023-04-17
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)
   data analysis and to work with microbial and antimicrobial properties by

NEWS.md

@@ -1,8 +1,9 @@
-# AMR 2.0.0.9008
+# AMR 2.0.0.9009
 
 ## Changed
 * formatting fix for `sir_interpretation_history()`
 * Fixed some WHONET codes for microorganisms and consequently a couple of entries in `clinical_breakpoints`
+* Added microbial codes for Gram-negative/positive anaerobic bacteria
 
 
 # AMR 2.0.0

R/mo.R

@@ -995,8 +995,10 @@ out[x %like_case% "^g[abcdefghijkl]s$"] <- gsub("g([abcdefghijkl])s",
   out[x %like_case% "( |^)gram[-]( |$)"] <- "B_GRAMN"
   out[x %like_case% "gram[ -]?pos.*"] <- "B_GRAMP"
   out[x %like_case% "( |^)gram[+]( |$)"] <- "B_GRAMP"
+  out[x %like_case% "anaerob[a-z]+ .*gram[ -]?neg.*"] <- "B_ANAER-NEG"
+  out[x %like_case% "anaerob[a-z]+ .*gram[ -]?pos.*"] <- "B_ANAER-POS"
   out[is.na(out) & x %like_case% "anaerob[a-z]+ (micro)?.*organism"] <- "B_ANAER"
-
+  
   # yeasts and fungi
   out[x %like_case% "^yeast?"] <- "F_YEAST"
   out[x %like_case% "^fung(us|i)"] <- "F_FUNGUS"
@@ -1006,7 +1008,7 @@ out[x %like_case% "^g[abcdefghijkl]s$"] <- gsub("g([abcdefghijkl])s",
   out[x %like_case% "gono[ck]o[ck]"] <- "B_NESSR_GNRR"
   out[x %like_case% "pneumo[ck]o[ck]"] <- "B_STRPT_PNMN"
 
-  # unexisting names (xxx and con are WHONET codes)
+  # unexisting names (con is the WHONET code for contamination)
   out[x %in% c("con", "other", "none", "unknown") | x %like_case% "virus"] <- "UNKNOWN"
 
   # WHONET has a lot of E. coli and Vibrio cholerae names
@@ -1017,18 +1019,23 @@ out[x %like_case% "^g[abcdefghijkl]s$"] <- gsub("g([abcdefghijkl])s",
 }
 
 italicise <- function(x) {
+  if (!has_colour()) {
+    return(x)
+  }
   out <- font_italic(x, collapse = NULL)
+  # city-like serovars of Salmonella (start with a capital)
   out[x %like_case% "Salmonella [A-Z]"] <- paste(
     font_italic("Salmonella"),
     gsub("Salmonella ", "", x[x %like_case% "Salmonella [A-Z]"])
   )
+  # streptococcal groups
   out[x %like_case% "Streptococcus [A-Z]"] <- paste(
     font_italic("Streptococcus"),
     gsub("Streptococcus ", "", x[x %like_case% "Streptococcus [A-Z]"])
   )
-  if (has_colour()) {
-    out <- gsub("(Group|group|Complex|complex)(\033\\[23m)?", "\033[23m\\1", out, perl = TRUE)
-  }
+  # be sure not to make these italic
+  out <- gsub("([ -]*)(Group|group|Complex|complex)(\033\\[23m)?", "\033[23m\\1\\2", out, perl = TRUE)
+  out <- gsub("(\033\\[3m)?(Beta[-]haemolytic|Coagulase[-](postive|negative)) ", "\\2 \033[3m", out, perl = TRUE)
   out
 }
 

R/mo_property.R

@@ -480,7 +480,7 @@ mo_gramstain <- function(x, language = get_AMR_locale(), keep_synonyms = getOpti
     # but class Negativicutes (of phylum Bacillota) are Gram-negative!
     mo_class(x.mo, language = NULL, keep_synonyms = keep_synonyms) != "Negativicutes")
   # and of course our own ID for Gram-positives
-  | x.mo == "B_GRAMP"] <- "Gram-positive"
+  | x.mo %in% c("B_GRAMP", "B_ANAER-POS")] <- "Gram-positive"
 
   load_mo_uncertainties(metadata)
   translate_into_language(x, language = language, only_unknown = FALSE)

data-raw/translations.tsv

@@ -6,6 +6,8 @@ Coagulase-positive Staphylococcus	TRUE	TRUE	FALSE	TRUE	凝固酶阳性葡萄球
 Beta-haemolytic Streptococcus	TRUE	TRUE	FALSE	TRUE	β-溶血性链球菌	Beta-hemolytický streptokok	Beta-haemolytiske streptokokker	Beta-hemolytische Streptococcus	Beeta-hemolyyttinen streptokokki	Streptococcus Bêta-hémolytique	Beta-hämolytischer Streptococcus	Β-αιμολυτικός στρεπτόκοκκος	Streptococcus Beta-emolitico	ベータ溶血性レンサ球菌	Beta-hemolytiske streptokokker	Streptococcus beta-hemolityczny	Streptococcus Beta-hemolítico	Streptococ beta-hemolitic	Бета-гемолитический стрептококк	Streptococcus Beta-hemolítico	Beta-hemolytiska streptokocker	Beta-hemolitik Streptokok	Бета-гемолітичний стрептокок
 unknown Gram-negatives	TRUE	TRUE	FALSE	TRUE	不明革兰氏阴性菌	neznámé gramnegativní	ukendte Gram-negative	onbekende Gram-negatieven	tuntemattomat gramnegatiiviset	Gram négatifs inconnus	unbekannte Gramnegativen	άγνωστοι αρνητικοί κατά Gram	Gram negativi sconosciuti	不明なグラム陰性菌	ukjent Gram-negative	Nieznane bakterie Gram-ujemne	Gram negativos desconhecidos	Gram-negative necunoscute	неизвестные грамотрицательные	Gram negativos desconocidos	okända gramnegativa bakterier	bilinmeyen Gram-negatifler	невідомі грамнегативні
 unknown Gram-positives	TRUE	TRUE	FALSE	TRUE	不明革兰氏阳性菌	neznámé grampozitivní	ukendte Gram-positive	onbekende Gram-positieven	tuntemattomat grampositiiviset	Gram positifs inconnus	unbekannte Grampositiven	άγνωστοι θετικοί κατά Gram	Gram positivi sconosciuti	未知のグラム陽性菌	ukjent Gram-positive	Nieznane bakterie Gram-dodatnie	Gram positivos desconhecidos	Gram-pozitive necunoscute	неизвестные грамположительные	Gram positivos desconocidos	okända Gram-positiva	bilinmeyen Gram-pozitifler	невідомі грампозитивні
+unknown anaerobic Gram-negatives	TRUE	TRUE	FALSE	TRUE			ukendte anaerobe Gram-negative	onbekende anaerobe Gram-negatieven			unbekannte anaerobe Gramnegativen												
+unknown anaerobic Gram-positives	TRUE	TRUE	FALSE	TRUE			ukendte anaerobe Gram-positive	onbekende anaerobe Gram-positieven			unbekannte anaerobe Grampositiven												
 unknown fungus	TRUE	TRUE	FALSE	TRUE	未知真菌	neznámé houby	ukendt svamp	onbekende schimmel	tuntematon sieni	champignon inconnu	unbekannter Pilze	άγνωστος μύκητας	fungo sconosciuto	未知真菌	ukjent sopp	Nieznany grzyb	fungo desconhecido	ciuperci necunoscute	неизвестный грибок	hongo desconocido	Okänd svamp	bilinmeyen mantar	невідомий гриб
 unknown yeast	TRUE	TRUE	FALSE	TRUE	未知酵母菌	neznámé kvasinky	ukendt gær	onbekende gist	tuntematon hiiva	levure inconnue	unbekannte Hefe	άγνωστος ζυμομύκητας	lievito sconosciuto	未知酵母	ukjent gjær	Nieznany drożdżak	levedura desconhecida	drojdie necunoscută	неизвестные дрожжи	levadura desconocida	Okänd jäst	bilinmeyen maya	невідомі дріжджі
 unknown name	TRUE	TRUE	FALSE	TRUE	不明名称	neznámý název	ukendt navn	onbekende naam	tuntematon nimi	nom inconnu	unbekannte Name	άγνωστο όνομα	nome sconosciuto	名称未知	ukjent navn	nieznana nazwa	nome desconhecido	nume necunoscut	неизвестное название	nombre desconocido	okänt namn	bilinmeyen isim	невідома назва