(v2.1.1.9058) fix hosts, add translations

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 2.1.1.9057
+Version: 2.1.1.9058
 Date: 2024-06-17
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 2.1.1.9057
+# AMR 2.1.1.9058
 
 *(this beta version will eventually become v3.0. We're happy to reach a new major milestone soon, which will be all about the new One Health support! Install this beta using [the instructions here](https://msberends.github.io/AMR/#latest-development-version).)*
 

R/sir.R

@@ -844,6 +844,25 @@ convert_host <- function(x, lang = get_AMR_locale()) {
   x_out[is.na(x_out) & (x %like% "horse|equine" | x %like% translate_AMR("horse|horses|equine", lang))] <- "horse"
   x_out[is.na(x_out) & (x %like% "aqua|fish" | x %like% translate_AMR("aquatic|fish", lang))] <- "aquatic"
   x_out[is.na(x_out) & (x %like% "bird|chicken|poultry|avia" | x %like% translate_AMR("bird|birds|poultry", lang))] <- "poultry"
+  # additional animals, not necessarily currently in breakpoint guidelines:
+  x_out[is.na(x_out) & (x %like% "camel|camelid" | x %like% translate_AMR("camel|camels|camelid", lang))] <- "camels"
+  x_out[is.na(x_out) & (x %like% "deer|cervine" | x %like% translate_AMR("deer|deers|cervine", lang))] <- "deer"
+  x_out[is.na(x_out) & (x %like% "donkey|asinine" | x %like% translate_AMR("donkey|donkeys|asinine", lang))] <- "donkeys"
+  x_out[is.na(x_out) & (x %like% "ferret|musteline" | x %like% translate_AMR("ferret|ferrets|musteline", lang))] <- "ferrets"
+  x_out[is.na(x_out) & (x %like% "goat|caprine" | x %like% translate_AMR("goat|goats|caprine", lang))] <- "goats"
+  x_out[is.na(x_out) & (x %like% "guinea pig|caviine" | x %like% translate_AMR("guinea pig|guinea pigs|caviine", lang))] <- "guinea pigs"
+  x_out[is.na(x_out) & (x %like% "hamster|cricetine" | x %like% translate_AMR("hamster|hamsters|cricetine", lang))] <- "hamsters"
+  x_out[is.na(x_out) & (x %like% "monkey|simian" | x %like% translate_AMR("monkey|monkeys|simian", lang))] <- "monkeys"
+  x_out[is.na(x_out) & (x %like% "mouse|murine" | x %like% translate_AMR("mouse|mice|murine", lang))] <- "mice"
+  x_out[is.na(x_out) & (x %like% "pig|porcine" | x %like% translate_AMR("pig|pigs|porcine", lang))] <- "pigs"
+  x_out[is.na(x_out) & (x %like% "rabbit|leporine" | x %like% translate_AMR("rabbit|rabbits|leporine", lang))] <- "rabbits"
+  x_out[is.na(x_out) & (x %like% "rat|ratine" | x %like% translate_AMR("rat|rats|ratine", lang))] <- "rats"
+  x_out[is.na(x_out) & (x %like% "sheep|ovine" | x %like% translate_AMR("sheep|sheeps|ovine", lang))] <- "sheep"
+  x_out[is.na(x_out) & (x %like% "snake|serpentine" | x %like% translate_AMR("snake|snakes|serpentine", lang))] <- "snakes"
+  x_out[is.na(x_out) & (x %like% "turkey|meleagrine" | x %like% translate_AMR("turkey|turkeys|meleagrine", lang))] <- "turkey"
+  if (message_not_thrown_before("convert_host", x) && any(is.na(x_out) & !is.na(x))) {
+    warning_("The following host(s) are invalid: ", vector_and(x[is.na(x_out) & !is.na(x)]), call = FALSE, immediate = TRUE)
+  }
   x_out[x_out == "ecoff"] <- "ECOFF"
   x_out
 }
@@ -912,18 +931,21 @@ as_sir_method <- function(method_short,
       host <- breakpoint_type
     }
   }
-  if (!is.null(current_df) && length(host) == 1 && host %in% colnames(current_df) && any(current_df[[host]] %like% "[A-Z]", na.rm = TRUE)) {
+  if (!is.null(host) && !all(toupper(as.character(host)) %in% c("HUMAN", "ECOFF"))) {
-    host <- current_df[[host]]
+    if (!is.null(current_df) && length(host) == 1 && host %in% colnames(current_df) && any(current_df[[host]] %like% "[A-Z]", na.rm = TRUE)) {
-  } else if (length(host) != length(x)) {
+      host <- current_df[[host]]
-    # for dplyr's across()
+    } else if (length(host) != length(x)) {
-    cur_column_dplyr <- import_fn("cur_column", "dplyr", error_on_fail = FALSE)
+      # for dplyr's across()
-    if (!is.null(cur_column_dplyr) && is.data.frame(current_df)) {
+      cur_column_dplyr <- import_fn("cur_column", "dplyr", error_on_fail = FALSE)
-      # try to get current column, which will only be available when in across()
+      if (!is.null(cur_column_dplyr) && is.data.frame(current_df)) {
-      host <- tryCatch(cur_column_dplyr(),
+        # try to get current column, which will only be available when in across()
-                     error = function(e) host
+        host <- tryCatch(cur_column_dplyr(),
-      )
+                         error = function(e) host
+        )
+      }
     }
   }
+  host.bak <- host
   host <- convert_host(host)
   if (breakpoint_type == "animal" && message_not_thrown_before("as.sir", "host_preferred_order")) {
     message_("Please note that in the absence of specific veterinary breakpoints for certain animal hosts, breakpoints for dogs, cattle, swine, cats, horse, aquatic, and poultry, in that order, are used as substitutes.\n\n")
@@ -1169,6 +1191,10 @@ as_sir_method <- function(method_short,
     mo_current <- df_unique[i, "mo", drop = TRUE]
     ab_current <- df_unique[i, "ab", drop = TRUE]
     host_current <- df_unique[i, "host", drop = TRUE]
+    if (is.na(host_current)) {
+      # fall back to human
+      host_current <- "human"
+    }
     uti_current <- df_unique[i, "uti", drop = TRUE]
     notes_current <- character(0)
     if (isFALSE(uti_current)) {
@@ -1229,7 +1255,7 @@ as_sir_method <- function(method_short,
           index = rows,
           ab_given = vectorise_log_entry(ab.bak[match(ab_current, df$ab)][1], length(rows)),
           mo_given = vectorise_log_entry(mo.bak[match(mo_current, df$mo)][1], length(rows)),
-          host_given = vectorise_log_entry(host_current, length(rows)),
+          host_given = vectorise_log_entry(host.bak[match(host_current, df$host)][1], length(rows)),
           ab = vectorise_log_entry(ab_current, length(rows)),
           mo = vectorise_log_entry(mo_current, length(rows)),
           host = vectorise_log_entry(host_current, length(rows)),
@@ -1353,7 +1379,7 @@ as_sir_method <- function(method_short,
           index = rows,
           ab_given = vectorise_log_entry(ab.bak[match(ab_current, df$ab)][1], length(rows)),
           mo_given = vectorise_log_entry(mo.bak[match(mo_current, df$mo)][1], length(rows)),
-          host_given = vectorise_log_entry(host_current, length(rows)),
+          host_given = vectorise_log_entry(host.bak[match(host_current, df$host)][1], length(rows)),
           ab = vectorise_log_entry(breakpoints_current[, "ab", drop = TRUE], length(rows)),
           mo = vectorise_log_entry(breakpoints_current[, "mo", drop = TRUE], length(rows)),
           host = vectorise_log_entry(breakpoints_current[, "host", drop = TRUE], length(rows)),

data-raw/translations.tsv

@@ -306,3 +306,16 @@ dog|dogs|canine	FALSE	FALSE	FALSE	FALSE	狗|狗|犬类	pes|psi|psí	hund|hunde	h
 horse|horses|equine	FALSE	FALSE	FALSE	FALSE	马|马|马	kůň|koně|koně	hest|heste	paard|paarden	hevonen|hevoset|hevoset	cheval|chevaux|équine	pferd|pferde	άλογο|άλογα|ιπποειδή	cavallo|cavalli|equino	馬|馬|馬	hest	koń|konie|koń	cavalo|cavalos|equinos	cal|cai|ecvideu	лошадь|лошади|лошадь	caballo|caballos|equino	häst|hästar|häst	at|atlar|atçılık	кінь|коні|конячий
 bird|birds|poultry	FALSE	FALSE	FALSE	FALSE	鸟类|鸟类|家禽	ptáci|ptáci|drůbež	fugl|fugle|fjerkræ	vogel|vogels|pluimvee	lintu|linnut|siipikarja	oiseaux|oiseaux|volaille	vogel|vögel|geflügel	πουλιά|πουλιά|πουλερικά	uccello|uccelli|pollame	鳥|鳥|家禽	fugl|fugler|fjørfe	ptak|ptaki|drób	aves|aves|aves de capoeira	pasăre|păsări|păsări de curte	птица|птицы|домашняя птица	aves|aves|aves de corral	fågel|fåglar|fjäderfä	kuş|kuşlar|kümes hayvanları	птах|птахів|птиця
 swine|swines	FALSE	FALSE	FALSE	FALSE	猪|猪	prasata|prasata	svin	varken|varkens	sika|sikaa	porcine|porcs	schwein|schweine	χοίροι|χοίροι	suino|suini	豚|豚|頭	svin	trzoda chlewna|świnie	suínos	porc|porcine	свинья|свиньи	porcino|porcinos	svin	domuz|domuz	свиня|свині
+camel|camels|camelid	FALSE	FALSE	FALSE	FALSE	骆驼|骆驼|骆驼科	velbloud|velbloudi|velbloudí	kamel|kameler|kamelid	kameel|kamelen|kameelachtig	kameli|kamelit|kamelidi	chameau|chameaux|camélidé	Kamel|Kamele|Kameliden	καμήλα|καμήλες|καμηλίδιο	cammello|camelli|camelide	ラクダ|ラクダ|ラクダ科	kamel|kameler|kamelid	wielbłąd|wielbłądy|wielbłądowate	camelo|camelos|camelídeo	camel|cămila|camelidă	верблюд|верблюды|верблюдовые	camello|camellos|camélido	kamel|kameler|kamelid	deve|develer|devegiller	верблюд|верблюди|верблюдовий
+deer|deers|cervine	FALSE	FALSE	FALSE	FALSE	鹿|鹿|鹿科	jelen|jeleni|jelení	hjort|hjorte|hjortedyr	hert|herten|hertachtig	peura|peurat|peura	cerf|cerfs|cervidé	Hirsch|Hirsche|Hirschartige	ελάφι|ελάφια|ελαφίδι	cervo|cervi|cervino	鹿|鹿|鹿科	hjort|hjorter|hjortedyr	jelen|jelenie|jeleniowate	cervo|cervos|cervídeo	cer|cerbi|cervină	олень|олени|оленевые	ciervo|ciervos|cervino	hjort|hjortar|hjortdjur	geyik|geyikler|geyikgiller	олень|олені|оленячий
+donkey|donkeys|asinine	FALSE	FALSE	FALSE	FALSE	驴|驴|驴科	osel|osli|oslovitý	æsel|æsler|æselagtig	ezel|ezels|ezelachtig	aasi|aasit|aasimainen	âne|ânes|asinin	Esel|Esel|asinisch	γάιδαρος|γάιδαροι|γαιδουρίνο	asino|asini|asinino	ロバ|ロバ|ロバ科	esel|esler|eselaktig	osioł|osły|osiołowate	burro|burros|asinino	măgar|măgari|asinin	осел|ослы|ослиный	burro|burros|asnal	åsna|åsnor|åsne	esek|eşekler|eşekgiller	осел|осли|ослячий
+ferret|ferrets|musteline	FALSE	FALSE	FALSE	FALSE	雪貂|雪貂|鼬科	tchoř|tchoři|tchořovitý	fritte|fritter|mårhund	fret|fretten|fretachtig	viiru|viirut|näätäeläin	furet|furets|mustélidé	Frettchen|Frettchen|Marderartige	νεράιδα|νεράιδες|μουστελίδα	furetto|furetti|mustelide	フェレット|フェレット|イタチ科	frett|fretter|mårhund	szop|szopy|szopowate	furão|furões|mustelídeo	jder|jderi|mustelidă	хорек|хорьки|хорьковые	hurón|hurones|mustélido	iller|iller|marten	göründü|göründüler|göründü	хорек|хорки|хорьковий
+goat|goats|caprine	FALSE	FALSE	FALSE	FALSE	山羊|山羊|山羊科	koza|kozy|kozí	ged|geder|gede	geit|geiten|geitachtig	vuohi|vuohet|vuohi	chèvre|chèvres|caprin	Ziege|Ziegen|ziegenartig	κατσίκα|κατσίκες|κατσικίσιο	capra|capre|caprino	ヤギ|ヤギ|ヤギ科	geit|geiter|geite	koza|kozy|kozowate	cabra|cabras|caprino	capră|capre|caprină	коза|козы|козий	cabra|cabras|caprino	get|getter|getdjur	keçi|keçiler|keçi	коза|кози|козячий
+guinea pig|guinea pigs|caviine	FALSE	FALSE	FALSE	FALSE	豚鼠|豚鼠|豚鼠科	morce|morče|morčecovitý	marsvin|marsvin|marsvin	cavia	merisika|merisikat|merisika	cobaye|cobayes|cobaye	Meerschweinchen|Meerschweinchen|Meerschweinchenartige	τσιντσιλά|τσιντσιλάδες|τσιντσιλίδι	cavia|cavie|cavino	モルモット|モルモット|モルモット科	marsvin|marsvin|marsvin	swinka morska|swinki morskie|świnka morska	porquinho-da-índia|porquinhos-da-índia|caviíneo	porcușor de Guineea|porcușori de Guineea|caviină	морская свинка|морские свинки|морская свинка	cobaya|cobayas|cavino	marsvin|marsvin|marsvin	yaban domuzu|yaban domuzları|yaban domuzu	морська свинка|морські свинки|морська свинка
+hamster|hamsters|cricetine	FALSE	FALSE	FALSE	FALSE	仓鼠|仓鼠|仓鼠科	křeček|křečci|křečkovitý	hamster|hamstere|hamster	hamster|hamsters|hamsterachtig	hamsteri|hamsterit|hamsteri	hamster|hamsters|cricétidé	Hamster|Hamster|Hamsterartige	χάμστερ|χάμστερ|χαμστερίδι	criceto|criceti|cricetino	ハムスター|ハムスター|ハムスター科	hamster|hamstere|hamster	chomik|chomiki|chomikowate	hamster|hamsters|cricetídeo	hamster|hamsteri|cricetină	хомяк|хомяки|хомячий	hamster|hamsters|cricetino	hamster|hamstrar|hamster	hamster|hamsterler|hamster	хом'як|хом'яки|хом'ячий
+monkey|monkeys|simian	FALSE	FALSE	FALSE	FALSE	猴子|猴子|猴科	opice|opice|opičí	abe|aber|abe	aap|apen|aapachtig	apina|apinat|apina	singe|singes|simien	Affe|Affen|affenartig	πίθηκος|πίθηκοι|πιθηκίδι	scimmia|scimmie|scimmia	猿|猿|サル	ape|aper|ape	małpa|małpy|małpia	macaco|macacos|símio	maimută|maimuțe|simeză	обезьяна|обезьяны|обезьяньи	mono|monos|simio	apa|apor|apa	maymun|maymunlar|maymun	мавпа|мавпи|мавпячий
+mouse|mice|murine	FALSE	FALSE	FALSE	FALSE	老鼠|老鼠|鼠科	myš|myši|myšovitý	mus|mus|mus	muis|muizen|muisachtig	hiiri|hiiret|hiiri	souris|souris|murin	Maus|Mäuse|Mäuseartig	ποντίκι|ποντίκια|μυοειδές	topo|topi|murino	ネズミ|ネズミ|ネズミ科	mus|mus|muse	mysz|myszy|myszowate	rato|ratos|murino	șoarece|șoareci|murină	мышь|мыши|мышиный	ratón|ratones|murino	mus|möss|mus	fare|fareler|fare	миша|миші|мишачий
+pig|pigs|porcine	FALSE	FALSE	FALSE	FALSE	猪|猪|猪科	prase|prasata|prasatovitý	gris|grise|svin	varken|varkens|varkenachtig	sika|siat|sika	cochon|cochons|porcin	Schwein|Schweine|schweineartig	γουρούνι|γουρούνια|χοιρίδι	maiale|maiali|suino	豚|豚|豚科	gris|griser|svin	świnia|świnie|świński	porco|porcos|porcino	porc|porci|porcină	свинья|свиньи|свиный	cerdo|cerdos|porcino	gris|grisar|svin	domuz|domuzlar|domuz	свиня|свині|свинячий
+rat|rats|ratine	FALSE	FALSE	FALSE	FALSE	鼠|鼠|鼠科	krysa|krysy|krysí	rat|rotter|rotte	rat|ratten|ratachtig	rotta|rotat|rotta	rat|rats|raté	Ratte|Ratten|Rattenartig	αρουραίος|αρουραίοι|αρουραίδι	ratto|ratti|rattino	ラット|ラット|ラット科	ratte|rotter|rotte	szczur|szczury|szczurzy	rato|ratos|rato	șobolan|șobolani|șobolănesc	крыса|крысы|крысиный	rata|ratas|rata	råtta|råttor|råtta	sıçan|sıçanlar|sıçan	щур|щури|щурячий
+snake|snakes|serpentine	FALSE	FALSE	FALSE	FALSE	蛇|蛇|蛇科	had|hadi|hadí	slange|slanger|slange	slang|slangen|slangachtig	käärme|käärmeet|käärme	serpent|serpents|serpentin	Schlange|Schlangen|schlangenartig	φίδι|φίδια|οφιειδές	serpente|serpenti|serpentino	ヘビ|ヘビ|ヘビ科	slange|slanger|slange	wąż|węże|wężowy	cobra|cobras|serpentina	șarpe|șerpi|șerpuitor	змея|змеи|змеиный	serpiente|serpientes|serpentina	orm|ormar|orm	yılan|yılanlar|yılan	змія|змії|змієвий
+turkey|turkeys|meleagrine	FALSE	FALSE	FALSE	FALSE	火鸡|火鸡|火鸡科	krocan|krocany|krocanovitý	kalkun|kalkuner|kalkun	kalkoen|kalkoenen|kalkoenachtig	kalkkuna|kalkkunat|kalkkuna	dinde|dindes|meleagrin	Pute|Puten|Truthuhn	γαλοπούλα|γαλοπούλες|μελεαγρίδιο	tacchino|tacchini|meleagride	七面鳥|七面鳥|七面鳥科	kalkun|kalkuner|kalkun	indyk|indyki|indykowy	peru|perus|meleagrina	curcan|curcani|meleagrină	индейка|индейки|индейковый	pavo|pavos|meleagrina	kalkon|kalkoner|kalkon	hindi|hindiler|hindi	індик|індики|індиковий