(v1.7.1.9054) mdro() update - fixes #49, first_isolate() speedup

data-raw/ab.md5

@@ -1 +1 @@
-9f708801889d2eaf974c6eb85c83a8e7
+f7c99b5734e4cdf37f51c55faca6ac2b

data-raw/antibiotics.txt

@@ -214,7 +214,7 @@
 "GAT"	5379	"Gatifloxacin"	"Quinolones"	"c(\"J01MA16\", \"S01AE06\")"	"Quinolone antibacterials"	"Fluoroquinolones"	"c(\"\", \"gati\")"	"c(\"gatiflo\", \"gatifloxacin\", \"gatifloxacine\", \"gatifloxcin\", \"gatilox\", \"gatiquin\", \"gatispan\", \"tequin\", \"tequin and zymar\", \"zymaxid\")"	0.4	"g"	0.4	"g"	"character(0)"
 "GEM"	9571107	"Gemifloxacin"	"Quinolones"	"J01MA15"	"Quinolone antibacterials"	"Fluoroquinolones"	""	"c(\"factiv\", \"factive\", \"gemifioxacin\", \"gemifloxacin\", \"gemifloxacine\", \"gemifloxacino\", \"gemifloxacinum\")"	0.32	"g"			"character(0)"
 "GEN"	3467	"Gentamicin"	"Aminoglycosides"	"c(\"D06AX07\", \"J01GB03\", \"S01AA11\", \"S02AA14\", \"S03AA06\")"	"Aminoglycoside antibacterials"	"Other aminoglycosides"	"c(\"cn\", \"gen\", \"gent\", \"gm\")"	"c(\"apogen\", \"centicin\", \"cidomycin\", \"garasol\", \"genoptic liquifilm\", \"genoptic s.o.p.\", \"gentacycol\", \"gentafair\", \"gentak\", \"gentamar\", \"gentamcin sulfate\", \"gentamicin\", \"gentamicina\", \"gentamicine\", \"gentamicins\", \"gentamicinum\", \"gentamycin\", \"gentamycins\", \"gentamycinum\", \"gentavet\", \"gentocin\", \"jenamicin\", \"lyramycin\", \"oksitselanim\", \"refobacin\", \"refobacin tm\", \"septigen\", \"uromycine\")"			0.24	"g"	"c(\"13561-6\", \"13562-4\", \"15106-8\", \"22746-2\", \"22747-0\", \"31091-2\", \"31092-0\", \"31093-8\", \"35668-3\", \"3663-2\", \"3664-0\", \"3665-7\", \"39082-3\", \"47109-4\", \"59379-8\", \"80971-5\", \"88111-0\")"
-"GEH"		"Gentamicin-high"	"Aminoglycosides"				"c(\"g_h\", \"gehl\", \"genta high\", \"gentamicin high\")"	""					""
+"GEH"		"Gentamicin-high"	"Aminoglycosides"				"c(\"gehi\", \"gehl\", \"genta high\", \"gentamicin high\")"	""					""
 "GEP"	25101874	"Gepotidacin"	"Other antibacterials"				""	"gepotidacin"					"character(0)"
 "GRX"	72474	"Grepafloxacin"	"Quinolones"	"J01MA11"	"Quinolone antibacterials"	"Fluoroquinolones"	"c(\"\", \"grep\")"	"grepafloxacin"	0.4	"g"			"character(0)"
 "GRI"	441140	"Griseofulvin"	"Antifungals/antimycotics"	"c(\"D01AA08\", \"D01BA01\")"			""	"c(\"amudane\", \"curling factor\", \"delmofulvina\", \"fulcin\", \"fulcine\", \"fulvican grisactin\", \"fulvicin\", \"fulvicin bolus\", \"fulvidex\", \"fulvina\", \"fulvinil\", \"fulvistatin\", \"fungivin\", \"greosin\", \"gresfeed\", \"gricin\", \"grifulin\", \"grifulvin\", \"grifulvin v\", \"grisactin\", \"grisactin ultra\", \"grisactin v\", \"griscofulvin\", \"grise ostatin\", \"grisefuline\", \"griseo\", \"griseofulvin\", \"griseofulvin forte\", \"griseofulvina\", \"griseofulvine\", \"griseofulvinum\", \"griseomix\", \"griseostatin\", \"grisetin\", \"grisofulvin\", 
@@ -403,7 +403,7 @@
 "SPM"		"Spiramycin/metronidazole"	"Other antibacterials"	"J01RA04"	"Combinations of antibacterials"	"Combinations of antibacterials"	""	""					""
 "STR"		"Streptoduocin"	"Aminoglycosides"	"J01GA02"	"Aminoglycoside antibacterials"	"Streptomycins"	""	""			1	"g"	""
 "STR1"	19649	"Streptomycin"	"Aminoglycosides"	"c(\"A07AA04\", \"J01GA01\")"	"Aminoglycoside antibacterials"	"Streptomycins"	"c(\"s\", \"stm\", \"str\", \"stre\")"	"c(\"agrept\", \"agrimycin\", \"chemform\", \"estreptomicina\", \"neodiestreptopab\", \"strepcen\", \"streptomicina\", \"streptomycin\", \"streptomycin a\", \"streptomycin spx\", \"streptomycin sulfate\", \"streptomycine\", \"streptomyzin\", \"vetstrep\")"			1	"g"	"4039-4"
-"STH"		"Streptomycin-high"	"Aminoglycosides"				"c(\"s_h\", \"sthl\", \"strepto high\", \"streptomycin high\")"	""					""
+"STH"		"Streptomycin-high"	"Aminoglycosides"				"c(\"sthi\", \"sthl\", \"strepto high\", \"streptomycin high\")"	""					""
 "STI"		"Streptomycin/isoniazid"	"Antimycobacterials"	"J04AM01"	"Drugs for treatment of tuberculosis"	"Combinations of drugs for treatment of tuberculosis"	""	""					""
 "SUL"	130313	"Sulbactam"	"Beta-lactams/penicillins"	"J01CG01"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase inhibitors"	""	"c(\"betamaze\", \"sulbactam\", \"sulbactam acid\", \"sulbactam free acid\", \"sulbactamum\")"			1	"g"	"character(0)"
 "SBC"	20055036	"Sulbenicillin"	"Beta-lactams/penicillins"	"J01CA16"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	""	"c(\"kedacillina\", \"sulbenicilina\", \"sulbenicilline\", \"sulbenicillinum\")"			15	"g"	"character(0)"

data-raw/ex2.R

@@ -0,0 +1,13 @@
+ex2 <- example_isolates
+for (extra_id in seq_len(50)) {
+  ex2 <- ex2 %>% 
+    bind_rows(example_isolates %>% mutate(patient_id = paste0(patient_id, extra_id)))
+}
+# randomly clear antibibiograms of 2%
+clr <- sort(sample(x = seq_len(nrow(ex2)),
+                   size = nrow(ex2) * 0.02))
+for (row in which(is.rsi(ex2))) {
+  ex2[clr, row] <- NA_rsi_
+}
+
+

data-raw/reproduction_of_antibiotics.R

@@ -546,8 +546,8 @@ antibiotics[which(antibiotics$ab == "FEP"), "abbreviations"][[1]] <- list(c(anti
 antibiotics[which(antibiotics$ab == "CTC"), "abbreviations"][[1]] <- list(c("xctl"))
 antibiotics[which(antibiotics$ab == "CTX"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CTX"), "abbreviations"][[1]], "xct"))
 # High level Gentamcin and Streptomycin
-antibiotics[which(antibiotics$ab == "GEH"), "abbreviations"][[1]] <- list(c("gehl", "gentamicin high", "genta high"))
-antibiotics[which(antibiotics$ab == "STH"), "abbreviations"][[1]] <- list(c("sthl", "streptomycin high", "strepto high"))
+antibiotics[which(antibiotics$ab == "GEH"), "abbreviations"][[1]] <- list(c("gehl", "gentamicin high", "genta high", "gehi"))
+antibiotics[which(antibiotics$ab == "STH"), "abbreviations"][[1]] <- list(c("sthl", "streptomycin high", "strepto high", "sthi"))
 # add imi and "imipenem/cilastatine" to imipenem
 antibiotics[which(antibiotics$ab == "IPM"), "abbreviations"][[1]] <- list(c("imip", "imi", "imp"))
 antibiotics[which(antibiotics$ab == "IPM"), "synonyms"][[1]] <- list(sort(c(antibiotics[which(antibiotics$ab == "IPM"), "synonyms"][[1]], "imipenem/cilastatin")))