(v2.1.1.9082) algorithm updates

data-raw/_pre_commit_checks.R

@@ -158,6 +158,32 @@ pre_commit_lst$MO_STREP_ABCG <- AMR::microorganisms$mo[which(AMR::microorganisms
     "group a", "group b", "group c", "group g"
   ))]
 pre_commit_lst$MO_LANCEFIELD <- AMR::microorganisms$mo[which(AMR::microorganisms$mo %like% "^(B_STRPT_PYGN(_|$)|B_STRPT_AGLC(_|$)|B_STRPT_(DYSG|EQUI)(_|$)|B_STRPT_ANGN(_|$)|B_STRPT_(DYSG|CANS)(_|$)|B_STRPT_SNGN(_|$)|B_STRPT_SLVR(_|$))")]
+pre_commit_lst$MO_WHO_PRIORITY_GENERA <- c(
+  # World Health Organization's (WHO) Priority Pathogen List
+  "Acinetobacter",
+  "Aspergillus",
+  "Blastomyces",
+  "Campylobacter",
+  "Candida",
+  "Clostridioides",
+  "Coccidioides",
+  "Cryptococcus",
+  "Enterococcus",
+  "Fusarium",
+  "Haemophilus",
+  "Helicobacter",
+  "Histoplasma",
+  "Klebsiella",
+  "Mycobacterium",
+  "Neisseria",
+  "Paracoccidioides",
+  "Pneumocystis",
+  "Pseudomonas",
+  "Salmonella",
+  "Shigella",
+  "Staphylococcus",
+  "Streptococcus"
+)
 pre_commit_lst$MO_RELEVANT_GENERA <- c(
   "Absidia",
   "Acanthamoeba",

data-raw/microorganisms.md5

@@ -1 +1 @@
-f1cbe414851c1eee08ff5440a47af76c
+5b5544d28deade33092925a6758277c4

data-raw/reproduction_of_microorganisms.R

@@ -455,7 +455,7 @@ sort(table(taxonomy_lpsn$status))
 
 # Read MycoBank data ------------------------------------------------------------------------------
 
-taxonomy_mycobank <- readxl::read_excel(file_mycobank, guess_max = 1e5)
+taxonomy_mycobank <- read_excel(file_mycobank, guess_max = 1e5)
 taxonomy_mycobank.bak <- taxonomy_mycobank
 
 taxonomy_mycobank <- taxonomy_mycobank %>%
@@ -1224,10 +1224,12 @@ nonbacterial_genera <- nonbacterial_genera[nonbacterial_genera %unlike% "unknown
 # see https://doi.org/10.1099/mic.0.001269
 taxonomy <- taxonomy %>%
   mutate(prevalence = case_when(
+    # genera of the pathogens mentioned in the World Health Organization's (WHO) Priority Pathogen List
+    genus %in% MO_WHO_PRIORITY_GENERA ~ 1.0,
     # 'established' means 'have infected at least three persons in three or more references'
-    paste(genus, species) %in% established & rank %in% c("species", "subspecies") ~ 1.0,
+    paste(genus, species) %in% established & rank %in% c("species", "subspecies") ~ 1.15,
     # other genera in the 'established' group
-    genus %in% established_genera & rank == "genus" ~ 1.0,
+    genus %in% established_genera & rank == "genus" ~ 1.15,
     
     # 'putative' means 'fewer than three known cases'
     paste(genus, species) %in% putative & rank %in% c("species", "subspecies") ~ 1.25,
@@ -2148,7 +2150,7 @@ microorganisms <- taxonomy
 
 # set class <mo>
 class(microorganisms$mo) <- c("mo", "character")
-microorganisms <- microorganisms %>% arrange(fullname)
+microorganisms <- microorganisms %>% arrange(fullname) %>% df_remove_nonASCII()
 usethis::use_data(microorganisms, overwrite = TRUE, version = 2, compress = "xz")
 rm(microorganisms)
 

data-raw/translations.tsv

@@ -8,6 +8,7 @@ unknown Gram-negatives	TRUE	TRUE	FALSE	TRUE	不明革兰氏阴性菌	neznámé g
 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 protozoan	TRUE	TRUE	FALSE	TRUE	未知原生动物	neznámý prvok	ukendt protozo	onbekend protozoön	tuntematon alkueläin	protozoaire inconnu	unbekanntes Protozoon	άγνωστο πρωτόζωο	protozoo sconosciuto	未知の原生動物	ukjent protozo	nieznany pierwotniak	protozoário desconhecido	protozoar necunoscut	неизвестное простейшее	protozoo desconocido	okänd protozo	bilinmeyen protozoa	невідоме найпростіше
 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