(v1.7.1.9055) added EUCAST 3.3 and all LPSN records numbers

.gitignore

@@ -25,3 +25,4 @@ data-raw/taxon.tab
 data-raw/DSMZ_bactnames.xlsx
 data-raw/country_analysis_url_token.R
 data-raw/country_analysis2.R
+data-raw/taxonomy.csv

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 1.7.1.9054
+Version: 1.7.1.9055
-Date: 2021-11-28
+Date: 2021-11-29
 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

@@ -1,5 +1,5 @@
-# `AMR` 1.7.1.9054
+# `AMR` 1.7.1.9055
-## <small>Last updated: 28 November 2021</small>
+## <small>Last updated: 29 November 2021</small>
 
 ### Breaking changes
 * Removed `p_symbol()` and all `filter_*()` functions (except for `filter_first_isolate()`), which were all deprecated in a previous package version
@@ -54,6 +54,7 @@
 * `NA` values of the classes `<mic>`, `<disk>` and `<rsi>` are now exported objects of this package, e.g. `NA_mic_` is an `NA` of class `mic` (just like the base R `NA_character_` is an `NA` of class `character`)
 * The `proportion_df()`, `count_df()` and `rsi_df()` functions now return with the additional S3 class 'rsi_df' so they can be extended by other packages
 * The `mdro()` function now returns `NA` for all rows that have no test results
+* The `species_id` column in the `microorganisms` data set now only contains LPSN record numbers. For this reason, this column is now numeric instead of a character, and `mo_url()` has been updated to reflect this change.
 
 ### Other
 * This package is now being maintained by two epidemiologists and a data scientist from two different non-profit healthcare organisations. All functions in this package are now all considered to be stable. Updates to the AMR interpretation rules (such as by EUCAST and CLSI), the microbial taxonomy, and the antibiotic dosages will all be updated every 6 to 12 months from now on.

R/globals.R

@@ -56,7 +56,7 @@ SNOMED_VERSION <- list(title = "Public Health Information Network Vocabulary Acc
 CATALOGUE_OF_LIFE <- list(
   year = 2019,
   version = "Catalogue of Life: {year} Annual Checklist",
-  url_CoL = "http://www.catalogueoflife.org/col/",
+  url_CoL = "http://www.catalogueoflife.org",
   url_LPSN = "https://lpsn.dsmz.de",
   yearmonth_LPSN = "5 October 2021"
 )

R/mo_property.R

@@ -216,9 +216,9 @@ mo_shortname <- function(x, language = get_locale(), ...) {
   shortnames[shortnames == "S. coagulase-negative"] <- "CoNS"
   shortnames[shortnames == "S. coagulase-positive"] <- "CoPS"
   # exceptions for streptococci: Group A Streptococcus -> GAS
-  shortnames[shortnames %like% "S. group [ABCDFGHK]"] <- paste0("G", gsub("S. group ([ABCDFGHK])", "\\1", shortnames[shortnames %like% "S. group [ABCDFGHK]"]), "S")
+  shortnames[shortnames %like% "S. group [ABCDFGHK]"] <- paste0("G", gsub("S. group ([ABCDFGHK])", "\\1", shortnames[shortnames %like% "S. group [ABCDFGHK]"], perl = TRUE), "S")
   # unknown species etc.
-  shortnames[shortnames %like% "unknown"] <- paste0("(", trimws(gsub("[^a-zA-Z -]", "", shortnames[shortnames %like% "unknown"])), ")")
+  shortnames[shortnames %like% "unknown"] <- paste0("(", trimws(gsub("[^a-zA-Z -]", "", shortnames[shortnames %like% "unknown"], perl = TRUE)), ")")
   
   shortnames[is.na(x.mo)] <- NA_character_
   load_mo_failures_uncertainties_renamed(metadata)
@@ -518,7 +518,7 @@ mo_authors <- function(x, language = get_locale(), ...) {
   
   x <- mo_validate(x = x, property = "ref", language = language, ...)
   # remove last 4 digits and presumably the comma and space that preceed them
-  x[!is.na(x)] <- gsub(",? ?[0-9]{4}", "", x[!is.na(x)])
+  x[!is.na(x)] <- gsub(",? ?[0-9]{4}", "", x[!is.na(x)], perl = TRUE)
   suppressWarnings(x)
 }
 
@@ -534,7 +534,7 @@ mo_year <- function(x, language = get_locale(), ...) {
   
   x <- mo_validate(x = x, property = "ref", language = language, ...)
   # get last 4 digits
-  x[!is.na(x)] <- gsub(".*([0-9]{4})$", "\\1", x[!is.na(x)])
+  x[!is.na(x)] <- gsub(".*([0-9]{4})$", "\\1", x[!is.na(x)], perl = TRUE)
   suppressWarnings(as.integer(x))
 }
 
@@ -564,7 +564,7 @@ mo_taxonomy <- function(x, language = get_locale(),  ...) {
   x <- as.mo(x, language = language, ...)
   metadata <- get_mo_failures_uncertainties_renamed()
   
-  result <- list(kingdom = mo_kingdom(x, language = language),
+  out <- list(kingdom = mo_kingdom(x, language = language),
               phylum = mo_phylum(x, language = language),
               class = mo_class(x, language = language),
               order = mo_order(x, language = language),
@@ -574,7 +574,7 @@ mo_taxonomy <- function(x, language = get_locale(),  ...) {
               subspecies = mo_subspecies(x, language = language))
   
   load_mo_failures_uncertainties_renamed(metadata)
-  result
+  out
 }
 
 #' @rdname mo_property
@@ -652,31 +652,23 @@ mo_url <- function(x, open = FALSE, language = get_locale(), ...) {
   meet_criteria(open, allow_class = "logical", has_length = 1)
   meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
   
-  mo <- as.mo(x = x, language = language, ... = ...)
+  x.mo <- as.mo(x = x, language = language, ... = ...)
-  mo_names <- mo_name(mo)
   metadata <- get_mo_failures_uncertainties_renamed()
   
-  df <- data.frame(mo, stringsAsFactors = FALSE) %pm>%
+  df <- microorganisms[match(x.mo, microorganisms$mo), c("mo", "fullname", "source", "kingdom", "rank")]
-    pm_left_join(pm_select(microorganisms, mo, source, species_id), by = "mo")
+  df$url <- ifelse(df$source == "LPSN",
-  df$url <- ifelse(df$source == "CoL",
+                   paste0(CATALOGUE_OF_LIFE$url_LPSN, "/species/", gsub(" ", "-", tolower(df$fullname), fixed = TRUE)),
-                   paste0(CATALOGUE_OF_LIFE$url_CoL, "details/species/id/", df$species_id, "/"),
+                   paste0(CATALOGUE_OF_LIFE$url_CoL, "/data/search?type=EXACT&q=", gsub(" ", "%20", df$fullname, fixed = TRUE)))
-                   NA_character_)
+  
+  genera <- which(df$kingdom == "Bacteria" & df$rank == "genus")
+  df$url[genera] <- gsub("/species/", "/genus/", df$url[genera], fixed = TRUE)
+  subsp <- which(df$kingdom == "Bacteria" & df$rank %in% c("subsp.", "infraspecies"))
+  df$url[subsp] <- gsub("/species/", "/subspecies/", df$url[subsp], fixed = TRUE)
+  
   u <- df$url
-  u[mo_kingdom(mo) == "Bacteria"] <- paste0(CATALOGUE_OF_LIFE$url_LPSN, "/species/", gsub(" ", "-", tolower(mo_names), fixed = TRUE))
+  names(u) <- df$fullname
-  u[mo_kingdom(mo) == "Bacteria" & mo_rank(mo) == "genus"] <- gsub("/species/",
-                                                                   "/genus/",
-                                                                   u[mo_kingdom(mo) == "Bacteria" & mo_rank(mo) == "genus"],
-                                                                   fixed = TRUE)
-  u[mo_kingdom(mo) == "Bacteria" &
-      mo_rank(mo) %in% c("subsp.", "infraspecies")] <- gsub("/species/",
-                                                            "/subspecies/",
-                                                            u[mo_kingdom(mo) == "Bacteria" &
-                                                                mo_rank(mo) %in% c("subsp.", "infraspecies")],
-                                                            fixed = TRUE)
   
-  names(u) <- mo_names
+  if (isTRUE(open)) {
-  
-  if (open == TRUE) {
     if (length(u) > 1) {
       warning_("Only the first URL will be opened, as `browseURL()` only suports one string.")
     }

data-raw/eucast_rules.tsv

@@ -303,7 +303,7 @@ fullname	like	^Citrobacter (koseri|amalonaticus|sedlakii|farmeri|rodentium)			am
 fullname	like	^Citrobacter (freundii|braakii|murliniae|werkmanii|youngae)			aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, FOX	R	Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp.	Expert Rules	3.2	
 genus_species	is	Enterobacter cloacae			aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, FOX	R	Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp.	Expert Rules	3.2	
 genus_species	is	Escherichia hermannii			aminopenicillins, TIC	R	Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp.	Expert Rules	3.2	
-genus_species	is	Hafnia alvei			aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, FOX, polymyxins	R	Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp.	Expert Rules	3.2	
+genus_species	is	Hafnia alvei			aminopenicillins, AMC, SAM, CXM, CZO, CEP, LEX, CFR, FOX, polymyxins	R	Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp.	Expert Rules	3.2	
 genus_species	is	Klebsiella aerogenes			aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, FOX	R	Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp.	Expert Rules	3.2	
 genus_species	is	Klebsiella oxytoca			aminopenicillins, TIC	R	Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp.	Expert Rules	3.2	
 fullname	like	^Klebsiella( pneumoniae| quasipneumoniae| variicola)?			aminopenicillins, TIC	R	Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp.	Expert Rules	3.2	
@@ -415,3 +415,121 @@ fullname	like	^(Enterobacter|Klebsiella aerogenes|Citrobacter braakii|Citrobacte
 fullname	like	^(Enterobacter|Klebsiella aerogenes|Citrobacter braakii|Citrobacter freundii|Citrobacter gillenii|Citrobacter murliniae|Citrobacter rodenticum|Citrobacter sedlakii|Citrobacter werkmanii|Citrobacter youngae|Hafnia alvei|Serratia|Morganella morganii|Providencia)	CTX	I	CTX, CRO, CAZ		Expert Rules on Enterobacterales (AmpC de-repressed cephalosporins)	Expert Rules	3.2	This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument
 fullname	like	^(Enterobacter|Klebsiella aerogenes|Citrobacter braakii|Citrobacter freundii|Citrobacter gillenii|Citrobacter murliniae|Citrobacter rodenticum|Citrobacter sedlakii|Citrobacter werkmanii|Citrobacter youngae|Hafnia alvei|Serratia|Morganella morganii|Providencia)	CRO	I	CTX, CRO, CAZ		Expert Rules on Enterobacterales (AmpC de-repressed cephalosporins)	Expert Rules	3.2	This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument
 fullname	like	^(Enterobacter|Klebsiella aerogenes|Citrobacter braakii|Citrobacter freundii|Citrobacter gillenii|Citrobacter murliniae|Citrobacter rodenticum|Citrobacter sedlakii|Citrobacter werkmanii|Citrobacter youngae|Hafnia alvei|Serratia|Morganella morganii|Providencia)	CAZ	I	CTX, CRO, CAZ		Expert Rules on Enterobacterales (AmpC de-repressed cephalosporins)	Expert Rules	3.2	This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument
+order	is	Enterobacterales			PEN, glycopeptides_except_lipo, lipoglycopeptides, FUS, macrolides, lincosamides, streptogramins, RIF, oxazolidinones	R	Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp.	Expert Rules	3.3	
+fullname	like	^Citrobacter (koseri|amalonaticus|sedlakii|farmeri|rodentium)			aminopenicillins, TIC	R	Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp.	Expert Rules	3.3	
+fullname	like	^Citrobacter (freundii|braakii|murliniae|werkmanii|youngae)			aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, FOX	R	Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp.	Expert Rules	3.3	
+genus_species	is	Enterobacter cloacae			aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, FOX	R	Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp.	Expert Rules	3.3	
+genus_species	is	Escherichia hermannii			aminopenicillins, TIC	R	Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp.	Expert Rules	3.3	
+genus_species	is	Hafnia alvei			aminopenicillins, AMC, polymyxins	R	Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp.	Expert Rules	3.3	
+genus_species	is	Klebsiella aerogenes			aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, FOX	R	Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp.	Expert Rules	3.3	
+genus_species	is	Klebsiella oxytoca			aminopenicillins, TIC	R	Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp.	Expert Rules	3.3	
+fullname	like	^Klebsiella( pneumoniae| quasipneumoniae| variicola)?			aminopenicillins, TIC	R	Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp.	Expert Rules	3.3	
+genus_species	is	Leclercia adecarboxylata			FOS	R	Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp.	Expert Rules	3.3	
+genus_species	is	Morganella morganii			aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, DOX, MNO, TCY, polymyxins, NIT	R	Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp.	Expert Rules	3.3	
+genus_species	is	Plesiomonas shigelloides			aminopenicillins, AMC, SAM	R	Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp.	Expert Rules	3.3	
+genus_species	is	Proteus mirabilis			DOX, MNO, TCY, TGC, polymyxins, NIT	R	Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp.	Expert Rules	3.3	
+genus_species	is	Proteus penneri			aminopenicillins, CZO, CEP, LEX, CFR, CXM, DOX, MNO, TCY, TGC, polymyxins, NIT	R	Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp.	Expert Rules	3.3	
+genus_species	is	Proteus vulgaris			aminopenicillins, CZO, CEP, LEX, CFR, CXM, DOX, MNO, TCY, TGC, polymyxins, NIT	R	Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp.	Expert Rules	3.3	
+genus_species	is	Providencia rettgeri			aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, DOX, MNO, TCY, polymyxins, NIT	R	Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp.	Expert Rules	3.3	
+genus_species	is	Providencia stuartii			aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, DOX, MNO, TCY, polymyxins, NIT	R	Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp.	Expert Rules	3.3	
+genus	is	Raoultella			aminopenicillins, TIC	R	Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp.	Expert Rules	3.3	
+genus_species	is	Serratia marcescens			aminopenicillins, AMC, SAM, CZO, CEP, LEX, CFR, FOX, CXM, DOX, TCY, polymyxins, NIT	R	Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp.	Expert Rules	3.3	
+genus_species	is	Yersinia enterocolitica			aminopenicillins, AMC, SAM, TIC, CZO, CEP, LEX, CFR, FOX	R	Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp.	Expert Rules	3.3	
+genus_species	is	Yersinia pseudotuberculosis			polymyxins	R	Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp.	Expert Rules	3.3	
+genus_species	is	Aeromonas hydrophila			aminopenicillins, SAM	R	Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp.	Expert Rules	3.3	
+genus_species	is	Aeromonas veronii			aminopenicillins, SAM, TIC	R	Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp.	Expert Rules	3.3	
+genus_species	is	Aeromonas dhakensis			aminopenicillins, SAM, FOX	R	Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp.	Expert Rules	3.3	
+genus_species	is	Aeromonas caviae			aminopenicillins, SAM	R	Table 1: Intrinsic resistance in Enterobacterales and Aeromonas spp.	Expert Rules	3.3	
+genus	one_of	Achromobacter, Acinetobacter, Alcaligenes, Bordetella, Burkholderia, Elizabethkingia, Flavobacterium, Ochrobactrum, Pseudomonas, Stenotrophomonas			PEN, cephalosporins_1st, cephalosporins_2nd, glycopeptides_except_lipo, lipoglycopeptides, FUS, macrolides, lincosamides, streptogramins, RIF, oxazolidinones	R	Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria	Expert Rules	3.3	
+fullname	like	^Acinetobacter (baumannii|pittii|nosocomialis)			aminopenicillins, AMC, CRO, CTX, ATM, ETP, TMP, FOS, DOX, TCY	R	Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria	Expert Rules	3.3	Additional rules from header added in separate rule (genus is one of…)
+genus	is	Acinetobacter			DOX, TCY	R	Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria	Expert Rules	3.3	Additional rules from header added in separate rule (genus is one of…)
+genus_species	is	Achromobacter xylosoxidans 			aminopenicillins, CRO, CTX, ETP, ATM	R	Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria	Expert Rules	3.3	Additional rules from header added in separate rule (genus is one of…)
+fullname	like	^Burkholderia (ambifaria|anthina|arboris|cepacia|cenocepacia|contaminans|diffusa|dolosa|lata|latens|metallica|multivorans|paludis|pseudomultivorans|pyrrocinia|pseudomultivorans|seminalis|stabilis|stagnalis|territorii|ubonensis|vietnamiensis)			aminopenicillins, AMC, SAM, TIC, TCC, PIP, TZP, CRO, CTX, ATM, ETP, CIP, CHL, aminoglycosides, TMP, FOS, polymyxins	R	Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria	Expert Rules	3.3	Additional rules from header added in separate rule (genus is one of…)
+genus_species	is	Elizabethkingia meningoseptica			aminopenicillins, AMC, SAM, TIC, TCC, CTX, CRO, CAZ, FEP, ATM, ETP, IPM, MEM, polymyxins	R	Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria	Expert Rules	3.3	Additional rules from header added in separate rule (genus is one of…)
+genus_species	is	Elizabethkingia anophelis			aminopenicillins, AMC, SAM, TIC, TCC, CTX, CRO, CAZ, FEP, ATM, ETP, IPM, MEM	R	Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria	Expert Rules	3.3	Additional rules from header added in separate rule (genus is one of…)
+genus_species	is	Brucella anthropi			aminopenicillins, AMC, SAM, TIC, TCC, PIP, TZP, CZO, CTX, CRO, CAZ, FEP, ATM, ETP	R	Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria	Expert Rules	3.3	Additional rules from header added in separate rule (genus is one of…)
+genus_species	is	Pseudomonas aeruginosa			aminopenicillins, AMC, SAM, CTX, CRO, ETP, CHL, KAN, NEO, TMP, DOX, MNO, TCY, TGC	R	Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria	Expert Rules	3.3	Additional rules from header added in separate rule (genus is one of…)
+genus_species	is	Stenotrophomonas maltophilia			aminopenicillins, AMC, SAM, TIC, PIP, TZP, CRO, CTX, ATM, ETP, IPM, MEM, aminoglycosides, TMP, FOS, TCY	R	Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria	Expert Rules	3.3	Additional rules from header added in separate rule (genus is one of…)
+genus	is	Chryseobacterium			aminopenicillins, AMC, SAM, TIC, TCC, CRO, CTX, CAZ, ATM, ETP, IPM, MEM, aminoglycosides, polymyxins	R	Table 2: Intrinsic resistance in non-fermentative gram-negative bacteria	Expert Rules	3.3	Additional rules from header added in separate rule (genus is one of…)
+genus_species	is	Haemophilus influenzae			FUS, streptogramins, glycopeptides_except_lipo, lipoglycopeptides, lincosamides, oxazolidinones	R	Table 3: Intrinsic resistance in other gram-negative bacteria	Expert Rules	3.3	
+genus_species	is	Moraxella catarrhalis			TMP, glycopeptides_except_lipo, lipoglycopeptides, lincosamides, oxazolidinones	R	Table 3: Intrinsic resistance in other gram-negative bacteria	Expert Rules	3.3	
+genus	is	Neisseria			TMP, glycopeptides_except_lipo, lipoglycopeptides, lincosamides, oxazolidinones	R	Table 3: Intrinsic resistance in other gram-negative bacteria	Expert Rules	3.3	
+genus_species	is	Campylobacter fetus			FUS, streptogramins, TMP, NAL, glycopeptides_except_lipo, lipoglycopeptides, lincosamides, oxazolidinones	R	Table 3: Intrinsic resistance in other gram-negative bacteria	Expert Rules	3.3	
+fullname	like	^Campylobacter (jejuni|coli)			FUS, streptogramins, TMP, glycopeptides_except_lipo, lipoglycopeptides, lincosamides, oxazolidinones	R	Table 3: Intrinsic resistance in other gram-negative bacteria	Expert Rules	3.3	
+gramstain	is	Gram-positive			ATM, TEM, polymyxins, NAL	R	Table 4: Intrinsic resistance in gram-positive bacteria	Expert Rules	3.3	
+genus_species	is	Staphylococcus saprophyticus			FUS, CAZ, FOS, NOV	R	Table 4: Intrinsic resistance in gram-positive bacteria	Expert Rules	3.3	
+genus_species	is	Staphylococcus cohnii			CAZ, NOV	R	Table 4: Intrinsic resistance in gram-positive bacteria	Expert Rules	3.3	
+genus_species	is	Staphylococcus xylosus			CAZ, NOV	R	Table 4: Intrinsic resistance in gram-positive bacteria	Expert Rules	3.3	
+genus_species	is	Staphylococcus capitis			CAZ, FOS	R	Table 4: Intrinsic resistance in gram-positive bacteria	Expert Rules	3.3	
+genus_species	is	Staphylococcus aureus			CAZ	R	Table 4: Intrinsic resistance in gram-positive bacteria	Expert Rules	3.3	
+genus_species	is	Staphylococcus coagulase-negative			CAZ	R	Table 4: Intrinsic resistance in gram-positive bacteria	Expert Rules	3.3	
+genus	is	Streptococcus			FUS, CAZ, aminoglycosides	R	Table 4: Intrinsic resistance in gram-positive bacteria	Expert Rules	3.3	
+genus_species	is	Enterococcus faecalis			FUS, CAZ, cephalosporins_except_CAZ, aminoglycosides, macrolides, CLI, QDA, SDI, SUD, SDM, SLF, SLF1, SLF2, SZO, SLF3, SLF4, SMX, SLF5, SLF6, SLF7, SLF8, SLF9, SLF10, SLF11, SLF12, SUT, SLF13	R	Table 4: Intrinsic resistance in gram-positive bacteria	Expert Rules	3.3	These last ones are all true sulfonamides
+genus_species	is	Enterococcus faecalis	TMP	S	SXT, SLT1, SLT2, SLT3, SLT4, SLT5	S	Table 4: Intrinsic resistance in gram-positive bacteria	Expert Rules	3.3	Since R to sulfonamides - TMP result is equal with combinations
+genus_species	is	Enterococcus faecalis	TMP	I	SXT, SLT1, SLT2, SLT3, SLT4, SLT5	I	Table 4: Intrinsic resistance in gram-positive bacteria	Expert Rules	3.3	Since R to sulfonamides - TMP result is equal with combinations
+genus_species	is	Enterococcus faecalis	TMP	R	SXT, SLT1, SLT2, SLT3, SLT4, SLT5	R	Table 4: Intrinsic resistance in gram-positive bacteria	Expert Rules	3.3	Since R to sulfonamides - TMP result is equal with combinations
+fullname	like	^Enterococcus (gallinarum|casseliflavus)			FUS, CAZ, cephalosporins_except_CAZ, aminoglycosides, macrolides, CLI, QDA, VAN, SDI, SUD, SDM, SLF, SLF1, SLF2, SZO, SLF3, SLF4, SMX, SLF5, SLF6, SLF7, SLF8, SLF9, SLF10, SLF11, SLF12, SUT, SLF13	R	Table 4: Intrinsic resistance in gram-positive bacteria	Expert Rules	3.3	These last ones are all true sulfonamides
+fullname	like	^Enterococcus (gallinarum|casseliflavus)	TMP	S	SXT, SLT1, SLT2, SLT3, SLT4, SLT5	S	Table 4: Intrinsic resistance in gram-positive bacteria	Expert Rules	3.3	Since R to sulfonamides - TMP result is equal with combinations
+fullname	like	^Enterococcus (gallinarum|casseliflavus)	TMP	I	SXT, SLT1, SLT2, SLT3, SLT4, SLT5	I	Table 4: Intrinsic resistance in gram-positive bacteria	Expert Rules	3.3	Since R to sulfonamides - TMP result is equal with combinations
+fullname	like	^Enterococcus (gallinarum|casseliflavus)	TMP	R	SXT, SLT1, SLT2, SLT3, SLT4, SLT5	R	Table 4: Intrinsic resistance in gram-positive bacteria	Expert Rules	3.3	Since R to sulfonamides - TMP result is equal with combinations
+genus_species	is	Enterococcus faecium			FUS, CAZ, cephalosporins_except_CAZ, aminoglycosides, macrolides, SDI, SUD, SDM, SLF, SLF1, SLF2, SZO, SLF3, SLF4, SMX, SLF5, SLF6, SLF7, SLF8, SLF9, SLF10, SLF11, SLF12, SUT, SLF13	R	Table 4: Intrinsic resistance in gram-positive bacteria	Expert Rules	3.3	These last ones are all true sulfonamides
+genus_species	is	Enterococcus faecium	TMP	S	SXT, SLT1, SLT2, SLT3, SLT4, SLT5	S	Table 4: Intrinsic resistance in gram-positive bacteria	Expert Rules	3.3	Since R to sulfonamides - TMP result is equal with combinations
+genus_species	is	Enterococcus faecium	TMP	I	SXT, SLT1, SLT2, SLT3, SLT4, SLT5	I	Table 4: Intrinsic resistance in gram-positive bacteria	Expert Rules	3.3	Since R to sulfonamides - TMP result is equal with combinations
+genus_species	is	Enterococcus faecium	TMP	R	SXT, SLT1, SLT2, SLT3, SLT4, SLT5	R	Table 4: Intrinsic resistance in gram-positive bacteria	Expert Rules	3.3	Since R to sulfonamides - TMP result is equal with combinations
+genus	is	Corynebacterium			FOS	R	Table 4: Intrinsic resistance in gram-positive bacteria	Expert Rules	3.3	
+genus_species	is	Listeria monocytogenes			CAZ, cephalosporins_except_CAZ	R	Table 4: Intrinsic resistance in gram-positive bacteria	Expert Rules	3.3	
+genus	one_of	Leuconostoc, Pediococcus			VAN, TEC	R	Table 4: Intrinsic resistance in gram-positive bacteria	Expert Rules	3.3	
+genus	is	Lactobacillus			VAN, TEC	R	Table 4: Intrinsic resistance in gram-positive bacteria	Expert Rules	3.3	
+fullname	like	^Clostridium (ramosum|innocuum)			VAN	R	Table 4: Intrinsic resistance in gram-positive bacteria	Expert Rules	3.3	
+genus_species	one_of	Escherichia coli, Proteus mirabilis	AMP	R	PIP	R	Expert Rules on Enterobacterales	Expert Rules	3.3	
+genus_species	one_of	Escherichia coli, Proteus mirabilis	AMP	S	PIP	S	Expert Rules on Enterobacterales	Expert Rules	3.3	
+fullname	like	^(Klebsiella(?! aerogenes)|Raoultella)			PIP	R	Expert Rules on Enterobacterales	Expert Rules	3.3	
+fullname	like	^(Enterobacter|Klebsiella aerogenes|Citrobacter freundii|Serratia|Morganella morganii|Hafnia alvei|Providencia)	CXM	S	CXM, cephalosporins_2nd	R	Expert Rules on Enterobacterales	Expert Rules	3.3	
+genus	one_of	Arsenophonus, Biostraticola, Brenneria, Buchnera, Budvicia, Buttiauxella, Cedecea, Citrobacter, Cosenzaea, Cronobacter, Dickeya, Edwardsiella, Enterobacillus, Enterobacter, Erwinia, Escherichia, Ewingella, Franconibacter, Gibbsiella, Hafnia, Izhakiella, Klebsiella, Kluyvera, Kosakonia, Leclercia, Lelliottia, Leminorella, Lonsdalea, Mangrovibacter, Mixta, Moellerella, Morganella, Obesumbacterium, Pantoea, Pectobacterium, Phaseolibacter, Photorhabdus, Phytobacter, Plesiomonas, Pluralibacter, Pragia, Proteus, Providencia, Pseudescherichia, Pseudocitrobacter, Rahnella, Raoultella, Rosenbergiella, Rouxiella, Saccharobacter, Samsonia, Serratia, Shigella, Shimwellia, Siccibacter, Sodalis, Tatumella, Thorsellia, Trabulsiella, Wigglesworthia, Xenorhabdus, Yersinia, Yokenella	CIP	R	fluoroquinolones	R	Expert Rules on Enterobacterales	Expert Rules	3.3	This is Enterobacterales except Salmonella spp.
+fullname	like	^(Serratia|Providencia|Morganella morganii)			TGC	R	Expert Rules on Enterobacterales	Expert Rules	3.3	
+genus	is	Salmonella			cephalosporins_2nd	R	Expert Rules on Salmonella	Expert Rules	3.3	
+genus	is	Salmonella			aminoglycosides	R	Expert Rules on Salmonella	Expert Rules	3.3	
+genus	is	Salmonella	PEF	R	CIP	R	Expert Rules on Salmonella	Expert Rules	3.3	
+genus_species	is	Staphylococcus aureus	FOX1	R	betalactams	R	Expert Rules on Staphylococcus	Expert Rules	3.3	
+genus_species	is	Staphylococcus aureus	FOX1	S	betalactams	S	Expert Rules on Staphylococcus	Expert Rules	3.3	
+genus_species	one_of	Staphylococcus aureus, Staphylococcus lugdunensis	PEN	R	AMP, AMX, AZL, BAM, CRB, CRN, EPC, HET, MEC, MEZ, MTM, PIP, PME, PVM, SBC, TAL, TEM, TIC	R	Expert Rules on Staphylococcus	Expert Rules	3.3	all penicillins without beta-lactamse inhibitor
+genus	is	Staphylococcus	ERY, CLI	S	macrolides, lincosamides	S	Expert Rules on Staphylococcus	Expert Rules	3.3	
+genus	is	Staphylococcus	NOR	S	CIP, LVX, MFX, OFX	S	Expert Rules on Staphylococcus	Expert Rules	3.3	
+genus	is	Staphylococcus	LVX	R	fluoroquinolones	R	Expert Rules on Staphylococcus	Expert Rules	3.3	
+genus	is	Staphylococcus	MFX	R	fluoroquinolones	R	Expert Rules on Staphylococcus	Expert Rules	3.3	
+genus	is	Staphylococcus	TCY	S	DOX, MNO, TGC	S	Expert Rules on Staphylococcus	Expert Rules	3.3	
+genus	is	Staphylococcus	TCY	R	DOX, MNO	R	Expert Rules on Staphylococcus	Expert Rules	3.3	
+genus	is	Staphylococcus	VAN	S	lipoglycopeptides	S	Expert Rules on Staphylococcus	Expert Rules	3.3	
+genus	is	Staphylococcus	LNZ	S	TZD	S	Expert Rules on Staphylococcus	Expert Rules	3.3	
+fullname	like	^Enterococcus (faecalis|faecium)	AMP	R	ureidopenicillins, IPM	R	Expert Rules on Enterococcus	Expert Rules	3.3	
+fullname	like	^Enterococcus (faecalis|faecium)	AMX	R	ureidopenicillins, IPM	R	Expert Rules on Enterococcus	Expert Rules	3.3	
+genus	is	Enterococcus	NOR	S	CIP, LVX	S	Expert Rules on Enterococcus	Expert Rules	3.3	
+genus	is	Enterococcus	VAN	S	lipoglycopeptides	S	Expert Rules on Enterococcus	Expert Rules	3.3	
+genus_species	is	Enterococcus faecium			CLI	R	Expert Rules on Enterococcus	Expert Rules	3.3	
+genus_species	one_of	Streptococcus group A, Streptococcus group B, Streptococcus group C, Streptococcus group G	PEN	S	aminopenicillins, cephalosporins, carbapenems	S	Expert Rules on Streptococcus A, B, C and G	Expert Rules	3.3	
+genus_species	one_of	Streptococcus group A, Streptococcus group B, Streptococcus group C, Streptococcus group G	NOR	S	LVX, MFX	S	Expert Rules on Streptococcus A, B, C and G	Expert Rules	3.3	
+genus_species	one_of	Streptococcus group A, Streptococcus group B, Streptococcus group C, Streptococcus group G	NOR	R	LVX, MFX	R	Expert Rules on Streptococcus A, B, C and G	Expert Rules	3.3	
+genus_species	is	Streptococcus pneumoniae	OXA	S	PHN, PEN, aminopenicillins, cephalosporins_except_CAZ, carbapenems	S	Expert Rules on Streptococcus pneumoniae	Expert Rules	3.3	
+genus_species	is	Streptococcus pneumoniae	NOR	S	LVX, MFX	S	Expert Rules on Streptococcus pneumoniae	Expert Rules	3.3	
+genus_species	is	Streptococcus pneumoniae	NOR	R	LVX, MFX	R	Expert Rules on Streptococcus pneumoniae	Expert Rules	3.3	
+genus_species	is	Streptococcus pneumoniae	LVX	R	fluoroquinolones	R	Expert Rules on Streptococcus pneumoniae	Expert Rules	3.3	
+genus_species	is	Streptococcus pneumoniae	MFX	R	fluoroquinolones	R	Expert Rules on Streptococcus pneumoniae	Expert Rules	3.3	
+genus_species	is	Streptococcus pneumoniae	TCY	S	DOX, MNO	S	Expert Rules on Streptococcus pneumoniae	Expert Rules	3.3	
+genus_species	is	Streptococcus pneumoniae	TCY	R	DOX, MNO	R	Expert Rules on Streptococcus pneumoniae	Expert Rules	3.3	
+genus_species	is	Streptococcus pneumoniae	VAN	S	lipoglycopeptides	S	Expert Rules on Streptococcus pneumoniae	Expert Rules	3.3	
+fullname	like	^Streptococcus (anginosus|australis|bovis|constellatus|cristatus|equinus|gallolyticus|gordonii|infantarius|infantis|intermedius|mitis|mutans|oligofermentans|oralis|parasanguinis|peroris|pseudopneumoniae|salivarius|sanguinis|sinensis|sobrinus|thermophilus|vestibularis|viridans)$	PEN	S	aminopenicillins, CTX, CRO	S	Expert Rules on Viridans Group Streptococci	Expert Rules	3.3	
+genus_species	is	Haemophilus influenzae 	PEN	S	betalactams	S	Expert Rules on Haemophilus influenzae	Expert Rules	3.3	
+genus_species	is	Haemophilus influenzae 	NAL	S	fluoroquinolones	S	Expert Rules on Haemophilus influenzae	Expert Rules	3.3	
+genus_species	is	Haemophilus influenzae 	NAL	R	CIP, LVX, MFX	R	Expert Rules on Haemophilus influenzae	Expert Rules	3.3	
+genus_species	is	Haemophilus influenzae 	TCY	S	DOX, MNO	S	Expert Rules on Haemophilus influenzae	Expert Rules	3.3	
+genus_species	is	Haemophilus influenzae 	TCY	R	DOX, MNO	R	Expert Rules on Haemophilus influenzae	Expert Rules	3.3	
+genus_species	is	Moraxella catarrhalis	NAL	S	fluoroquinolones	S	Expert Rules on Moraxella catarrhalis	Expert Rules	3.3	
+genus_species	is	Moraxella catarrhalis	NAL	R	fluoroquinolones	R	Expert Rules on Moraxella catarrhalis	Expert Rules	3.3	
+genus	is	Campylobacter	ERY	S	CLR, AZM	S	Expert Rules on Campylobacter	Expert Rules	3.3	
+genus_species	is	Campylobacter	ERY	R	CLR, AZM	R	Expert Rules on Campylobacter	Expert Rules	3.3	
+fullname	like	^(Enterobacter|Klebsiella aerogenes|Citrobacter braakii|Citrobacter freundii|Citrobacter gillenii|Citrobacter murliniae|Citrobacter rodenticum|Citrobacter sedlakii|Citrobacter werkmanii|Citrobacter youngae|Hafnia alvei|Serratia|Morganella morganii|Providencia)	CTX	S	CTX, CRO, CAZ		Expert Rules on Enterobacterales (AmpC de-repressed cephalosporins)	Expert Rules	3.3	This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument
+fullname	like	^(Enterobacter|Klebsiella aerogenes|Citrobacter braakii|Citrobacter freundii|Citrobacter gillenii|Citrobacter murliniae|Citrobacter rodenticum|Citrobacter sedlakii|Citrobacter werkmanii|Citrobacter youngae|Hafnia alvei|Serratia|Morganella morganii|Providencia)	CRO	S	CTX, CRO, CAZ		Expert Rules on Enterobacterales (AmpC de-repressed cephalosporins)	Expert Rules	3.3	This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument
+fullname	like	^(Enterobacter|Klebsiella aerogenes|Citrobacter braakii|Citrobacter freundii|Citrobacter gillenii|Citrobacter murliniae|Citrobacter rodenticum|Citrobacter sedlakii|Citrobacter werkmanii|Citrobacter youngae|Hafnia alvei|Serratia|Morganella morganii|Providencia)	CAZ	S	CTX, CRO, CAZ		Expert Rules on Enterobacterales (AmpC de-repressed cephalosporins)	Expert Rules	3.3	This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument
+fullname	like	^(Enterobacter|Klebsiella aerogenes|Citrobacter braakii|Citrobacter freundii|Citrobacter gillenii|Citrobacter murliniae|Citrobacter rodenticum|Citrobacter sedlakii|Citrobacter werkmanii|Citrobacter youngae|Hafnia alvei|Serratia|Morganella morganii|Providencia)	CTX	I	CTX, CRO, CAZ		Expert Rules on Enterobacterales (AmpC de-repressed cephalosporins)	Expert Rules	3.3	This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument
+fullname	like	^(Enterobacter|Klebsiella aerogenes|Citrobacter braakii|Citrobacter freundii|Citrobacter gillenii|Citrobacter murliniae|Citrobacter rodenticum|Citrobacter sedlakii|Citrobacter werkmanii|Citrobacter youngae|Hafnia alvei|Serratia|Morganella morganii|Providencia)	CRO	I	CTX, CRO, CAZ		Expert Rules on Enterobacterales (AmpC de-repressed cephalosporins)	Expert Rules	3.3	This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument
+fullname	like	^(Enterobacter|Klebsiella aerogenes|Citrobacter braakii|Citrobacter freundii|Citrobacter gillenii|Citrobacter murliniae|Citrobacter rodenticum|Citrobacter sedlakii|Citrobacter werkmanii|Citrobacter youngae|Hafnia alvei|Serratia|Morganella morganii|Providencia)	CAZ	I	CTX, CRO, CAZ		Expert Rules on Enterobacterales (AmpC de-repressed cephalosporins)	Expert Rules	3.3	This is rule 3 and 4 of EUCAST Expert Rules v3.2 on Enterobacterales, result will be set with the 'ampc_derepressed_cephalosporins' argument

data-raw/mo.md5

@@ -1 +1 @@
-e8251824eec0b72d037b3dbfcdbe444a
+dbe572abad4a2dc85db8cb146b74beb9

data-raw/reproduction_of_microorganisms_update.R

@@ -25,6 +25,8 @@
 
 # Go to https://lpsn.dsmz.de/downloads (register first) and download the latest CSV file.
 
+file_location <- "data-raw/taxonomy.csv"
+
 library(tidyverse)
 library(AMR)
 
@@ -111,7 +113,7 @@ abbreviate_mo <- function(x, minlength = 5, prefix = "", ...) {
 
 # Read data ---------------------------------------------------------------
 
-taxonomy <- read_csv("~/Downloads/taxonomy.csv")
+taxonomy <- read_csv(file_location)
 
 # Create synonyms ---------------------------------------------------------
 
@@ -129,8 +131,7 @@ new_synonyms <- taxonomy %>%
   filter(fullname != fullname_new) %>% 
   # this part joins this table to itself to correct for entries that had >1 renames, 
   # such as:
-  # Bacteroides tectum -> Bacteroides tectus
+  # Bacteroides tectum -> Bacteroides tectus -> Bacteroides pyogenes
-  # Bacteroides tectus -> Bacteroides pyogenes
   left_join(., ., 
             by = c("fullname_new" = "fullname"), 
             suffix = c("", ".2")) %>%
@@ -359,6 +360,20 @@ MOs <- MOs %>%
 MOs <- MOs %>% 
   df_remove_nonASCII()
 
+# Add LPSN record IDs -----------------------------------------------------
+
+records_ids <- taxonomy %>%
+  mutate(across(1:3, function(x) { x[is.na(x)] <- ""; x}),
+         fullname = trimws(paste(genus_name, sp_epithet, subsp_epithet))) %>%
+  transmute(fullname, species_id = as.numeric(record_no))
+message("Adding ", sum(records_ids$fullname %in% microorganisms$fullname), " LPSN record IDs")
+MOs <- MOs %>%
+  select(-species_id) %>% 
+  left_join(records_ids, by = "fullname") %>%
+  relocate(species_id, .after = ref) %>% 
+  mutate(source = case_when(!is.na(species_id) ~ "LPSN",
+                            source %unlike% "manual" ~ "CoL",
+                            TRUE ~ source))
 
 # Merge synonyms ----------------------------------------------------------
 

docs/LICENSE-text.html

@@ -84,7 +84,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9054</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9055</span>
       </span>
     </div>
 

docs/articles/datasets.html

@@ -42,7 +42,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9054</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9055</span>
       </span>
     </div>
 
@@ -188,7 +188,7 @@
     <div class="page-header toc-ignore">
       <h1 data-toc-skip>Data sets for download / own use</h1>
             
-            <h4 class="date">28 November 2021</h4>
+            <h4 class="date">29 November 2021</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/datasets.Rmd"><code>vignettes/datasets.Rmd</code></a></small>
       <div class="hidden name"><code>datasets.Rmd</code></div>
@@ -207,20 +207,20 @@ If you are reading this page from within R, please <a href="https://msberends.gi
 <a href="#microorganisms-currently-accepted-names" class="anchor"></a>Microorganisms (currently accepted names)</h2>
 <p>A data set with 70,760 rows and 16 columns, containing the following column names:<br><em>mo</em>, <em>fullname</em>, <em>kingdom</em>, <em>phylum</em>, <em>class</em>, <em>order</em>, <em>family</em>, <em>genus</em>, <em>species</em>, <em>subspecies</em>, <em>rank</em>, <em>ref</em>, <em>species_id</em>, <em>source</em>, <em>prevalence</em> and <em>snomed</em>.</p>
 <p>This data set is in R available as <code>microorganisms</code>, after you load the <code>AMR</code> package.</p>
-<p>It was last updated on 6 October 2021 14:38:29 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
+<p>It was last updated on 29 November 2021 09:21:53 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
 <p><strong>Direct download links:</strong></p>
 <ul>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.rds">R file</a> (2.2 MB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.rds">R file</a> (1.3 MB)<br>
 </li>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.xlsx">Excel file</a> (6.4 MB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.txt">plain text file</a> (14.9 MB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.txt">plain text file</a> (13.1 MB)<br>
 </li>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.sas">SAS file</a> (30.7 MB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.sav">SPSS file</a> (18 MB)<br>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.sav">SPSS file</a> (16.3 MB)<br>
 </li>
-<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.dta">Stata file</a> (29.2 MB)</li>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.dta">Stata file</a> (27.6 MB)</li>
 </ul>
 <p><strong>NOTE: The exported files for SAS, SPSS and Stata do not contain SNOMED codes, as their file size would exceed 100 MB; the file size limit of GitHub.</strong> Advice? Use R instead.</p>
 <div id="source" class="section level3">

docs/authors.html

@@ -84,7 +84,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9054</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9055</span>
       </span>
     </div>
 

docs/index.html

@@ -45,7 +45,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9054</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9055</span>
       </span>
     </div>
 
@@ -193,7 +193,7 @@
 <a href="#amr-for-r-" class="anchor"></a><code>AMR</code> (for R) <img src="./logo.png" align="right" height="120px">
 </h1></div>
 <blockquote>
-<p>Update: The latest EUCAST guideline for intrinsic resistance (v3.3, October 2021) is now supported, and our taxonomy tables has been updated as well (5 October 2021).</p>
+<p>Update: The latest EUCAST guideline for intrinsic resistance (v3.3, October 2021) is now supported, and our taxonomy tables has been updated as well (LPSN, 5 October 2021).</p>
 </blockquote>
 <div id="what-is-amr-for-r" class="section level3">
 <h3 class="hasAnchor">

docs/news/index.html

@@ -84,7 +84,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9054</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9055</span>
       </span>
     </div>
 
@@ -232,12 +232,12 @@
       <small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
     </div>
 
-    <div id="amr-1719054" class="section level1">
+    <div id="amr-1719055" class="section level1">
-<h1 class="page-header" data-toc-text="1.7.1.9054">
+<h1 class="page-header" data-toc-text="1.7.1.9055">
-<a href="#amr-1719054" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9054</h1>
+<a href="#amr-1719055" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9055</h1>
-<div id="last-updated-28-november-2021" class="section level2">
+<div id="last-updated-29-november-2021" class="section level2">
 <h2 class="hasAnchor">
-<a href="#last-updated-28-november-2021" class="anchor"></a><small>Last updated: 28 November 2021</small>
+<a href="#last-updated-29-november-2021" class="anchor"></a><small>Last updated: 29 November 2021</small>
 </h2>
 <div id="breaking-changes" class="section level3">
 <h3 class="hasAnchor">
@@ -324,6 +324,7 @@
 <code>NA</code> values of the classes <code>&lt;mic&gt;</code>, <code>&lt;disk&gt;</code> and <code>&lt;rsi&gt;</code> are now exported objects of this package, e.g. <code>NA_mic_</code> is an <code>NA</code> of class <code>mic</code> (just like the base R <code>NA_character_</code> is an <code>NA</code> of class <code>character</code>)</li>
 <li>The <code><a href="../reference/proportion.html">proportion_df()</a></code>, <code><a href="../reference/count.html">count_df()</a></code> and <code><a href="../reference/proportion.html">rsi_df()</a></code> functions now return with the additional S3 class ‘rsi_df’ so they can be extended by other packages</li>
 <li>The <code><a href="../reference/mdro.html">mdro()</a></code> function now returns <code>NA</code> for all rows that have no test results</li>
+<li>The <code>species_id</code> column in the <code>microorganisms</code> data set now only contains LPSN record numbers. For this reason, this column is now numeric instead of a character, and <code><a href="../reference/mo_property.html">mo_url()</a></code> has been updated to reflect this change.</li>
 </ul>
 </div>
 <div id="other" class="section level3">

docs/reference/index.html

@@ -84,7 +84,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9054</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9055</span>
       </span>
     </div>
 
@@ -464,7 +464,7 @@
         <td>
           <p><code><a href="microorganisms.html">microorganisms</a></code> </p>
         </td>
-        <td><p>Data Set with 70,760 Microorganisms</p></td>
+        <td><p>Data Set with 70,791 Microorganisms</p></td>
       </tr><tr>
         
         <td>

docs/reference/microorganisms.html

@@ -6,7 +6,7 @@
 <meta http-equiv="X-UA-Compatible" content="IE=edge">
 <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-<title>Data Set with 70,760 Microorganisms — microorganisms • AMR (for R)</title>
+<title>Data Set with 70,791 Microorganisms — microorganisms • AMR (for R)</title>
 
 <!-- favicons -->
 <link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
@@ -48,7 +48,7 @@
   <link href="../extra.css" rel="stylesheet">
   <script src="../extra.js"></script>
 
-<meta property="og:title" content="Data Set with 70,760 Microorganisms — microorganisms" />
+<meta property="og:title" content="Data Set with 70,791 Microorganisms — microorganisms" />
 <meta property="og:description" content="A data set containing the full microbial taxonomy (last updated: 5 October 2021) of six kingdoms from the Catalogue of Life (CoL) and the List of Prokaryotic names with Standing in Nomenclature (LPSN). MO codes can be looked up using as.mo()." />
 <meta property="og:image" content="https://msberends.github.io/AMR/logo.png" />
 <meta name="twitter:card" content="summary_large_image" />
@@ -85,7 +85,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9053</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9055</span>
       </span>
     </div>
 
@@ -229,7 +229,7 @@
 <div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
-    <h1>Data Set with 70,760 Microorganisms</h1>
+    <h1>Data Set with 70,791 Microorganisms</h1>
     <small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/data.R'><code>R/data.R</code></a></small>
     <div class="hidden name"><code>microorganisms.Rd</code></div>
     </div>
@@ -243,7 +243,7 @@
 
     <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
 
-    <p>A <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 70,760 observations and 16 variables:</p><ul>
+    <p>A <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 70,791 observations and 16 variables:</p><ul>
 <li><p><code>mo</code><br /> ID of microorganism as used by this package</p></li>
 <li><p><code>fullname</code><br /> Full name, like <code>"Escherichia coli"</code></p></li>
 <li><p><code>kingdom</code>, <code>phylum</code>, <code>class</code>, <code>order</code>, <code>family</code>, <code>genus</code>, <code>species</code>, <code>subspecies</code><br /> Taxonomic rank of the microorganism</p></li>
@@ -342,7 +342,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
 
       <footer>
       <div class="copyright">
-  <p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, Dennis Souverein, Erwin E. A. Hassing, Christian F. Luz.</p>
+  <p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, Christian F. Luz, Dennis Souverein, Erwin E. A. Hassing.</p>
 </div>
 
 <div class="pkgdown">

docs/survey.html

@@ -84,7 +84,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9054</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9055</span>
       </span>
     </div>
 

index.md

@@ -1,6 +1,6 @@
 # `AMR` (for R) <img src="./logo.png" align="right" height="120px" />
 
-> Update: The latest EUCAST guideline for intrinsic resistance (v3.3, October 2021) is now supported, and our taxonomy tables has been updated as well (5 October 2021).
+> Update: The latest EUCAST guideline for intrinsic resistance (v3.3, October 2021) is now supported, and our taxonomy tables has been updated as well (LPSN, 5 October 2021).
 
 ### What is `AMR` (for R)?
 

man/microorganisms.Rd

@@ -3,9 +3,9 @@
 \docType{data}
 \name{microorganisms}
 \alias{microorganisms}
-\title{Data Set with 70,760 Microorganisms}
+\title{Data Set with 70,791 Microorganisms}
 \format{
-A \link{data.frame} with 70,760 observations and 16 variables:
+A \link{data.frame} with 70,791 observations and 16 variables:
 \itemize{
 \item \code{mo}\cr ID of microorganism as used by this package
 \item \code{fullname}\cr Full name, like \code{"Escherichia coli"}