speed improvement for as.mo, more old taxonomic names

.travis.yml

@@ -43,7 +43,7 @@ before_install:
   - if [ $TRAVIS_OS_NAME = osx ]; then brew install libgit2; fi
 
 install:
-  - Rscript -e "install.packages(c('devtools', 'backports', 'clipr', 'curl', 'data.table', 'dplyr', 'hms', 'knitr', 'readr', 'rlang', 'rvest', 'xml2'))"
+  - Rscript -e "install.packages(c('devtools', 'backports', 'clipr', 'curl', 'data.table', 'dplyr', 'hms', 'knitr', 'readr', 'rlang', 'rvest', 'xml2', 'covr', 'ggplot2', 'rmarkdown', 'testthat', 'tidyr'))"
   - if [ $TRAVIS_OS_NAME = osx ]; then Rscript -e "devtools::install_github('r-lib/rlang')"; fi
 
 # postrun

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
 Version: 0.3.0.9009
-Date: 2018-09-24
+Date: 2018-09-27
 Title: Antimicrobial Resistance Analysis
 Authors@R: c(
     person(

R/data.R

@@ -148,9 +148,9 @@
 
 #' Data set with old taxonomic data from ITIS
 #'
-#' A data set containing old, previously valid, taxonomic names. This data set is used internally by \code{\link{as.mo}}.
+#' A data set containing old (previously valid or accepted) taxonomic names according to ITIS. This data set is used internally by \code{\link{as.mo}}.
 #' @inheritSection as.mo ITIS
-#' @format A \code{\link{data.frame}} with 1,682 observations and 5 variables:
+#' @format A \code{\link{data.frame}} with 2,384 observations and 5 variables:
 #' \describe{
 #'   \item{\code{tsn}}{Old Taxonomic Serial Number (TSN), as defined by ITIS}
 #'   \item{\code{name}}{Old taxonomic name of the microorganism as found in ITIS, see Source}
@@ -168,10 +168,21 @@
 #' @format A \code{\link{tibble}} with 1,095 observations and 2 variables:
 #' \describe{
 #'   \item{\code{umcg}}{Code of microorganism according to UMCG MMB}
+#'   \item{\code{certe}}{Code of microorganism according to Certe MMB}
+#' }
+#' @seealso \code{\link{as.mo}} \code{\link{microorganisms.certe}} \code{\link{microorganisms}}
+"microorganisms.umcg"
+
+#' Translation table for Certe
+#'
+#' A data set containing all bacteria codes of Certe MMB. These codes can be joined to data with an ID from \code{\link{microorganisms}$mo} (using \code{\link{left_join_microorganisms}}). GLIMS codes can also be translated to valid \code{MO}s with \code{\link{guess_mo}}.
+#' @format A \code{\link{tibble}} with 2,664 observations and 2 variables:
+#' \describe{
+#'   \item{\code{certe}}{Code of microorganism according to Certe MMB}
 #'   \item{\code{mo}}{Code of microorganism in \code{\link{microorganisms}}}
 #' }
 #' @seealso \code{\link{as.mo}} \code{\link{microorganisms}}
-"microorganisms.umcg"
+"microorganisms.certe"
 
 #' Data set with 2000 blood culture isolates of septic patients
 #'

R/globals.R

@@ -57,6 +57,7 @@ globalVariables(c(".",
                   "real_first_isolate",
                   "S",
                   "septic_patients",
+                  "shortname",
                   "species",
                   "tsn",
                   "tsn_new",

R/mo.R

@@ -60,7 +60,7 @@
 #' \code{guess_mo} is an alias of \code{as.mo}.
 #' @section ITIS:
 #' \if{html}{\figure{itis_logo.jpg}{options: height=60px style=margin-bottom:5px} \cr}
-#' This \code{AMR} package contains the \strong{complete microbial taxonomic data} (with seven taxonomic ranks - from subkingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, https://www.itis.gov). ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic specialists [3]. The complete taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package, as well as all previously accepted names known to ITIS.
+#' This \code{AMR} package contains the \strong{complete microbial taxonomic data} (with seven taxonomic ranks - from subkingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, \url{https://www.itis.gov}). ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic specialists [3]. The complete taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package, as well as all previously accepted names known to ITIS.
 #  (source as section, so it can be inherited by mo_property:)
 #' @section Source:
 #' [1] Becker K \emph{et al.} \strong{Coagulase-Negative Staphylococci}. 2014. Clin Microbiol Rev. 27(4): 870–926. \url{https://dx.doi.org/10.1128/CMR.00109-13}
@@ -69,8 +69,6 @@
 #'
 #' [3] Integrated Taxonomic Information System (ITIS). Retrieved September 2018. \url{http://www.itis.gov}
 #' @export
-#' @importFrom dplyr %>% pull left_join
-#' @importFrom data.table as.data.table setkey
 #' @return Character (vector) with class \code{"mo"}. Unknown values will return \code{NA}.
 #' @seealso \code{\link{microorganisms}} for the \code{data.frame} with ITIS content that is being used to determine ID's. \cr
 #' The \code{\link{mo_property}} functions (like \code{\link{mo_genus}}, \code{\link{mo_gramstain}}) to get properties based on the returned code.
@@ -126,7 +124,25 @@
 #'   mutate(mo = guess_mo(paste(genus, species)))
 #' }
 as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain = FALSE) {
+  exec_as.mo(x = x, Becker = Becker, Lancefield = Lancefield,
+             allow_uncertain = allow_uncertain, property = "mo")
+}
 
+#' @rdname as.mo
+#' @export
+is.mo <- function(x) {
+  # bactid for older releases
+  # remove when is.bactid will be removed
+  identical(class(x), "mo") | identical(class(x), "bactid")
+}
+
+#' @rdname as.mo
+#' @export
+guess_mo <- as.mo
+
+#' @importFrom dplyr %>% pull left_join
+#' @importFrom data.table as.data.table setkey
+exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain = FALSE, property = "mo") {
   if (NCOL(x) == 2) {
     # support tidyverse selection like: df %>% select(colA, colB)
     # paste these columns together
@@ -147,374 +163,362 @@ as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain = FALSE
     }
   }
 
-  MOs <- as.data.table(AMR::microorganisms)
-  setkey(MOs, prevalence, tsn)
-  MOs_mostprevalent <- MOs[prevalence != 9999,]
-  MOs_allothers <- NULL # will be set later, if needed
-  MOs_old <- NULL # will be set later, if needed
-
-
-  if (all(unique(x) %in% MOs[,mo])) {
-    class(x) <- "mo"
-    attr(x, 'package') <- 'AMR'
-    attr(x, 'ITIS') <- TRUE
-    return(x)
-  }
-  if (AMR::is.mo(x) & isTRUE(attributes(x)$ITIS)) {
-    # check for new mo class, data coming from ITIS
-    return(x)
-  }
-
-
   failures <- character(0)
   x_input <- x
-
   # only check the uniques, which is way faster
   x <- unique(x)
 
-  x_backup <- trimws(x, which = "both")
+  MOs <- NULL # will be set later, if needed
-  x_species <- paste(x_backup, "species")
+  MOs_mostprevalent <- NULL # will be set later, if needed
-  # translate to English for supported languages of mo_property
+  MOs_allothers <- NULL # will be set later, if needed
-  x <- gsub("(Gruppe|gruppe|groep|grupo|gruppo|groupe)", "group", x)
+  MOs_old <- NULL # will be set later, if needed
-  # remove 'empty' genus and species values
-  x <- gsub("(no MO)", "", x, fixed = TRUE)
-  # remove dots and other non-text in case of "E. coli" except spaces
-  x <- gsub("[^a-zA-Z0-9/ \\-]+", "", x)
-  # but spaces before and after should be omitted
-  x <- trimws(x, which = "both")
-  x_trimmed <- x
-  x_trimmed_species <- paste(x_trimmed, "species")
-  # replace space by regex sign
-  x_withspaces <- gsub(" ", ".* ", x, fixed = TRUE)
-  x <- gsub(" ", ".*", x, fixed = TRUE)
-  # add start en stop regex
-  x <- paste0('^', x, '$')
-  x_withspaces_all <- x_withspaces
-  x_withspaces_start <- paste0('^', x_withspaces)
-  x_withspaces <- paste0('^', x_withspaces, '$')
 
-  # cat(paste0('x                  "', x, '"\n'))
+  if (all(x %in% AMR::microorganisms[, property])) {
-  # cat(paste0('x_species          "', x_species, '"\n'))
+    # already existing mo
-  # cat(paste0('x_withspaces_all   "', x_withspaces_all, '"\n'))
+  } else if (all(x %in% AMR::microorganisms.certe[, "certe"])) {
-  # cat(paste0('x_withspaces_start "', x_withspaces_start, '"\n'))
+    # old Certe codes
-  # cat(paste0('x_withspaces       "', x_withspaces, '"\n'))
+    suppressWarnings(
-  # cat(paste0('x_backup           "', x_backup, '"\n'))
+      x <- data.frame(certe = x, stringsAsFactors = FALSE) %>%
-  # cat(paste0('x_trimmed          "', x_trimmed, '"\n'))
+        left_join(AMR::microorganisms.certe, by = "certe") %>%
-  # cat(paste0('x_trimmed_species  "', x_trimmed_species, '"\n'))
+        left_join(AMR::microorganisms, by = "mo") %>%
+        pull(property)
+    )
+  } else if (all(x %in% AMR::microorganisms.umcg[, "umcg"])) {
+    # old UMCG codes
+    suppressWarnings(
+      x <- data.frame(umcg = x, stringsAsFactors = FALSE) %>%
+        left_join(AMR::microorganisms.umcg, by = "umcg") %>%
+        left_join(AMR::microorganisms.certe, by = "certe") %>%
+        left_join(AMR::microorganisms, by = "mo") %>%
+        pull(property)
+    )
+  } else {
 
-  for (i in 1:length(x)) {
+    MOs <- as.data.table(AMR::microorganisms)
-    if (identical(x_trimmed[i], "") | is.na(x_trimmed[i])) {
+    setkey(MOs, prevalence, tsn)
-      # empty values
+    MOs_mostprevalent <- MOs[prevalence != 9999,]
-      x[i] <- NA
-      next
-    }
 
-    # translate known trivial abbreviations to genus + species ----
+    x_backup <- trimws(x, which = "both")
-    if (!is.na(x_trimmed[i])) {
+    x_species <- paste(x_backup, "species")
-      if (toupper(x_trimmed[i]) == 'MRSA'
+    # translate to English for supported languages of mo_property
-          | toupper(x_trimmed[i]) == 'VISA'
+    x <- gsub("(Gruppe|gruppe|groep|grupo|gruppo|groupe)", "group", x)
-          | toupper(x_trimmed[i]) == 'VRSA') {
+    # remove 'empty' genus and species values
-        x[i] <- 'B_STPHY_AUR'
+    x <- gsub("(no MO)", "", x, fixed = TRUE)
-        next
+    # remove dots and other non-text in case of "E. coli" except spaces
-      }
+    x <- gsub("[^a-zA-Z0-9/ \\-]+", "", x)
-      if (toupper(x_trimmed[i]) == 'MRSE') {
+    # but spaces before and after should be omitted
-        x[i] <- 'B_STPHY_EPI'
+    x <- trimws(x, which = "both")
-        next
+    x_trimmed <- x
-      }
+    x_trimmed_species <- paste(x_trimmed, "species")
-      if (toupper(x_trimmed[i]) == 'VRE') {
+    # replace space by regex sign
-        x[i] <- 'B_ENTRC'
+    x_withspaces <- gsub(" ", ".* ", x, fixed = TRUE)
-        next
+    x <- gsub(" ", ".*", x, fixed = TRUE)
-      }
+    # add start en stop regex
-      if (toupper(x_trimmed[i]) == 'MRPA') {
+    x <- paste0('^', x, '$')
-        # multi resistant P. aeruginosa
+    x_withspaces_all <- x_withspaces
-        x[i] <- 'B_PDMNS_AER'
+    x_withspaces_start <- paste0('^', x_withspaces)
-        next
+    x_withspaces <- paste0('^', x_withspaces, '$')
-      }
-      if (toupper(x_trimmed[i]) %in% c('PISP', 'PRSP', 'VISP', 'VRSP')) {
-        # peni I, peni R, vanco I, vanco R: S. pneumoniae
-        x[i] <- 'B_STRPTC_PNE'
-        next
-      }
-      if (toupper(x_trimmed[i]) %like% '^G[ABCDFGHK]S$') {
-        x[i] <- gsub("G([ABCDFGHK])S", "B_STRPTC_GR\\1", x_trimmed[i])
-        next
-      }
-      # CoNS/CoPS in different languages (support for German, Dutch, Spanish, Portuguese) ----
-      if (tolower(x[i]) %like% '[ck]oagulas[ea] negatie?[vf]'
-          | tolower(x_trimmed[i]) %like% '[ck]oagulas[ea] negatie?[vf]'
-          | tolower(x[i]) %like% '[ck]o?ns[^a-z]?$') {
-        # coerce S. coagulase negative
-        x[i] <- 'B_STPHY_CNS'
-        next
-      }
-      if (tolower(x[i]) %like% '[ck]oagulas[ea] positie?[vf]'
-          | tolower(x_trimmed[i]) %like% '[ck]oagulas[ea] positie?[vf]'
-          | tolower(x[i]) %like% '[ck]o?ps[^a-z]?$') {
-        # coerce S. coagulase positive
-        x[i] <- 'B_STPHY_CPS'
-        next
-      }
-    }
 
-    # FIRST TRY FULLNAMES AND CODES
+    # cat(paste0('x                  "', x, '"\n'))
-    # if only genus is available, don't select species
+    # cat(paste0('x_species          "', x_species, '"\n'))
-    if (all(!c(x[i], x_trimmed[i]) %like% " ")) {
+    # cat(paste0('x_withspaces_all   "', x_withspaces_all, '"\n'))
-      found <- MOs[tolower(fullname) %in% tolower(c(x_species[i], x_trimmed_species[i])), mo]
+    # cat(paste0('x_withspaces_start "', x_withspaces_start, '"\n'))
-      if (length(found) > 0) {
+    # cat(paste0('x_withspaces       "', x_withspaces, '"\n'))
-        x[i] <- found[1L]
+    # cat(paste0('x_backup           "', x_backup, '"\n'))
+    # cat(paste0('x_trimmed          "', x_trimmed, '"\n'))
+    # cat(paste0('x_trimmed_species  "', x_trimmed_species, '"\n'))
+
+    for (i in 1:length(x)) {
+      if (identical(x_trimmed[i], "") | is.na(x_trimmed[i])) {
+        # empty values
+        x[i] <- NA
         next
       }
-      if (nchar(x_trimmed[i]) > 4) {
+
-        # not when abbr is esco, stau, klpn, etc.
+      # translate known trivial abbreviations to genus + species ----
-        found <- MOs[tolower(fullname) %like% gsub(" ", ".*", x_trimmed_species[i], fixed = TRUE), mo]
+      if (!is.na(x_trimmed[i])) {
+        if (toupper(x_trimmed[i]) == 'MRSA'
+            | toupper(x_trimmed[i]) == 'VISA'
+            | toupper(x_trimmed[i]) == 'VRSA') {
+          x[i] <- MOs[mo == 'B_STPHY_AUR', ..property][[1]][1L]
+          next
+        }
+        if (toupper(x_trimmed[i]) == 'MRSE') {
+          x[i] <- MOs[mo == 'B_STPHY_EPI', ..property][[1]][1L]
+          next
+        }
+        if (toupper(x_trimmed[i]) == 'VRE') {
+          x[i] <- MOs[mo == 'B_ENTRC', ..property][[1]][1L]
+          next
+        }
+        if (toupper(x_trimmed[i]) == 'MRPA') {
+          # multi resistant P. aeruginosa
+          x[i] <- MOs[mo == 'B_PDMNS_AER', ..property][[1]][1L]
+          next
+        }
+        if (toupper(x_trimmed[i]) %in% c('PISP', 'PRSP', 'VISP', 'VRSP')) {
+          # peni I, peni R, vanco I, vanco R: S. pneumoniae
+          x[i] <- MOs[mo == 'B_STRPTC_PNE', ..property][[1]][1L]
+          next
+        }
+        if (toupper(x_trimmed[i]) %like% '^G[ABCDFGHK]S$') {
+          x[i] <- MOs[mo == gsub("G([ABCDFGHK])S", "B_STRPTC_GR\\1", x_trimmed[i]), ..property][[1]][1L]
+          next
+        }
+        # CoNS/CoPS in different languages (support for German, Dutch, Spanish, Portuguese) ----
+        if (tolower(x[i]) %like% '[ck]oagulas[ea] negatie?[vf]'
+            | tolower(x_trimmed[i]) %like% '[ck]oagulas[ea] negatie?[vf]'
+            | tolower(x[i]) %like% '[ck]o?ns[^a-z]?$') {
+          # coerce S. coagulase negative
+          x[i] <- MOs[mo == 'B_STPHY_CNS', ..property][[1]][1L]
+          next
+        }
+        if (tolower(x[i]) %like% '[ck]oagulas[ea] positie?[vf]'
+            | tolower(x_trimmed[i]) %like% '[ck]oagulas[ea] positie?[vf]'
+            | tolower(x[i]) %like% '[ck]o?ps[^a-z]?$') {
+          # coerce S. coagulase positive
+          x[i] <- MOs[mo == 'B_STPHY_CPS', ..property][[1]][1L]
+          next
+        }
+      }
+
+      # FIRST TRY FULLNAMES AND CODES
+      # if only genus is available, don't select species
+      if (all(!c(x[i], x_trimmed[i]) %like% " ")) {
+        found <- MOs[tolower(fullname) %in% tolower(c(x_species[i], x_trimmed_species[i])), ..property][[1]]
         if (length(found) > 0) {
           x[i] <- found[1L]
           next
         }
+        if (nchar(x_trimmed[i]) > 4) {
+          # not when abbr is esco, stau, klpn, etc.
+          found <- MOs[tolower(fullname) %like% gsub(" ", ".*", x_trimmed_species[i], fixed = TRUE), ..property][[1]]
+          if (length(found) > 0) {
+            x[i] <- found[1L]
+            next
+          }
+        }
       }
-    }
 
-    # search for GLIMS code ----
+      # TRY FIRST THOUSAND MOST PREVALENT IN HUMAN INFECTIONS ----
-    found <- AMR::microorganisms.umcg[which(toupper(AMR::microorganisms.umcg$umcg) == toupper(x_trimmed[i])),]$mo
-    if (length(found) > 0) {
-      x[i] <- MOs[mo.old == found, mo][1L]
-      next
-    }
 
-    # TRY FIRST THOUSAND MOST PREVALENT IN HUMAN INFECTIONS ----
+      found <- MOs_mostprevalent[tolower(fullname) %in% tolower(c(x_backup[i], x_trimmed[i])), ..property][[1]]
+      # most probable: is exact match in fullname
+      if (length(found) > 0) {
+        x[i] <- found[1L]
+        next
+      }
+      found <- MOs_mostprevalent[tsn == x_trimmed[i], ..property][[1]]
+      # is a valid TSN
+      if (length(found) > 0) {
+        x[i] <- found[1L]
+        next
+      }
+      found <- MOs_mostprevalent[mo == toupper(x_backup[i]), ..property][[1]]
+      # is a valid mo
+      if (length(found) > 0) {
+        x[i] <- found[1L]
+        next
+      }
 
-    found <- MOs_mostprevalent[tolower(fullname) %in% tolower(c(x_backup[i], x_trimmed[i])), mo]
+      # try any match keeping spaces ----
-    # most probable: is exact match in fullname
+      found <- MOs_mostprevalent[fullname %like% x_withspaces[i], ..property][[1]]
-    if (length(found) > 0) {
+      if (length(found) > 0) {
-      x[i] <- found[1L]
+        x[i] <- found[1L]
-      next
+        next
-    }
+      }
-    found <- MOs_mostprevalent[tsn == x_trimmed[i], mo]
-    # is a valid TSN
-    if (length(found) > 0) {
-      x[i] <- found[1L]
-      next
-    }
-    found <- MOs_mostprevalent[mo == toupper(x_backup[i]), mo]
-    # is a valid mo
-    if (length(found) > 0) {
-      x[i] <- found[1L]
-      next
-    }
-    found <- MOs_mostprevalent[mo.old == toupper(x_backup[i])
-                               | (substr(x_backup[i], 4, 6) == "SPP" & mo.old == substr(x_backup[i], 1, 3))
-                               | mo.old == substr(x_backup[i], 1, 3), mo]
-    # is a valid old mo
-    if (length(found) > 0) {
-      x[i] <- found[1L]
-      next
-    }
 
-    # try any match keeping spaces ----
+      # try any match keeping spaces, not ending with $ ----
-    found <- MOs_mostprevalent[fullname %like% x_withspaces[i], mo]
+      found <- MOs_mostprevalent[fullname %like% x_withspaces_start[i], ..property][[1]]
-    if (length(found) > 0) {
+      if (length(found) > 0) {
-      x[i] <- found[1L]
+        x[i] <- found[1L]
-      next
+        next
-    }
+      }
 
-    # try any match keeping spaces, not ending with $ ----
+      # try any match diregarding spaces ----
-    found <- MOs_mostprevalent[fullname %like% x_withspaces_start[i], mo]
+      found <- MOs_mostprevalent[fullname %like% x[i], ..property][[1]]
-    if (length(found) > 0) {
+      if (length(found) > 0) {
-      x[i] <- found[1L]
+        x[i] <- found[1L]
-      next
+        next
-    }
+      }
 
-    # try any match diregarding spaces ----
+      # try fullname without start and stop regex, to also find subspecies ----
-    found <- MOs_mostprevalent[fullname %like% x[i], mo]
+      # like "K. pneu rhino" -> "Klebsiella pneumoniae (rhinoscleromatis)" = KLEPNERH
-    if (length(found) > 0) {
+      found <- MOs_mostprevalent[fullname %like% x_withspaces_start[i], ..property][[1]]
-      x[i] <- found[1L]
+      if (length(found) > 0) {
-      next
+        x[i] <- found[1L]
-    }
+        next
+      }
 
-    # try fullname without start and stop regex, to also find subspecies ----
+      # try splitting of characters and then find ID ----
-    # like "K. pneu rhino" -> "Klebsiella pneumoniae (rhinoscleromatis)" = KLEPNERH
+      # like esco = E. coli, klpn = K. pneumoniae, stau = S. aureus
-    found <- MOs_mostprevalent[fullname %like% x_withspaces_start[i], mo]
+      x_split <- x
-    if (length(found) > 0) {
+      x_length <- nchar(x_trimmed[i])
-      x[i] <- found[1L]
+      x_split[i] <- paste0(x_trimmed[i] %>% substr(1, x_length / 2) %>% trimws(),
-      next
+                           '.* ',
-    }
+                           x_trimmed[i] %>% substr((x_length / 2) + 1, x_length) %>% trimws())
+      found <- MOs_mostprevalent[fullname %like% paste0('^', x_split[i]), ..property][[1]]
+      if (length(found) > 0) {
+        x[i] <- found[1L]
+        next
+      }
 
-    # try splitting of characters and then find ID ----
+      # try any match with text before and after original search string ----
-    # like esco = E. coli, klpn = K. pneumoniae, stau = S. aureus
+      # so "negative rods" will be "GNR"
-    x_split <- x
+      # if (x_trimmed[i] %like% "^Gram") {
-    x_length <- nchar(x_trimmed[i])
+      #   x_trimmed[i] <- gsub("^Gram", "", x_trimmed[i], ignore.case = TRUE)
-    x_split[i] <- paste0(x_trimmed[i] %>% substr(1, x_length / 2) %>% trimws(),
+      #   # remove leading and trailing spaces again
-                         '.* ',
+      #   x_trimmed[i] <- trimws(x_trimmed[i], which = "both")
-                         x_trimmed[i] %>% substr((x_length / 2) + 1, x_length) %>% trimws())
+      # }
-    found <- MOs_mostprevalent[fullname %like% paste0('^', x_split[i]), mo]
+      # if (!is.na(x_trimmed[i])) {
-    if (length(found) > 0) {
+      #   found <- MOs_mostprevalent[fullname %like% x_trimmed[i], ..property][[1]]
-      x[i] <- found[1L]
+      #   if (length(found) > 0) {
-      next
+      #     x[i] <- found[1L]
-    }
+      #     next
+      #   }
+      # }
 
-    # try any match with text before and after original search string ----
+      # THEN TRY ALL OTHERS ----
-    # so "negative rods" will be "GNR"
+      if (is.null(MOs_allothers)) {
-    # if (x_trimmed[i] %like% "^Gram") {
+        MOs_allothers <- MOs[prevalence == 9999,]
-    #   x_trimmed[i] <- gsub("^Gram", "", x_trimmed[i], ignore.case = TRUE)
+      }
-    #   # remove leading and trailing spaces again
-    #   x_trimmed[i] <- trimws(x_trimmed[i], which = "both")
-    # }
-    # if (!is.na(x_trimmed[i])) {
-    #   found <- MOs_mostprevalent[fullname %like% x_trimmed[i], mo]
-    #   if (length(found) > 0) {
-    #     x[i] <- found[1L]
-    #     next
-    #   }
-    # }
 
-    # THEN TRY ALL OTHERS ----
+      found <- MOs_allothers[tolower(fullname) == tolower(x_backup[i]), ..property][[1]]
-    if (is.null(MOs_allothers)) {
+      # most probable: is exact match in fullname
-      MOs_allothers <- MOs[prevalence == 9999,]
+      if (length(found) > 0) {
-    }
+        x[i] <- found[1L]
+        next
+      }
+      found <- MOs_allothers[tolower(fullname) == tolower(x_trimmed[i]), ..property][[1]]
+      # most probable: is exact match in fullname
+      if (length(found) > 0) {
+        x[i] <- found[1L]
+        next
+      }
+      found <- MOs_allothers[tsn == x_trimmed[i], ..property][[1]]
+      # is a valid TSN
+      if (length(found) > 0) {
+        x[i] <- found[1L]
+        next
+      }
+      found <- MOs_allothers[mo == toupper(x_backup[i]), ..property][[1]]
+      # is a valid mo
+      if (length(found) > 0) {
+        x[i] <- found[1L]
+        next
+      }
 
-    found <- MOs_allothers[tolower(fullname) == tolower(x_backup[i]), mo]
+      # try any match keeping spaces ----
-    # most probable: is exact match in fullname
+      found <- MOs_allothers[fullname %like% x_withspaces[i], ..property][[1]]
-    if (length(found) > 0) {
+      if (length(found) > 0) {
-      x[i] <- found[1L]
+        x[i] <- found[1L]
-      next
+        next
-    }
+      }
-    found <- MOs_allothers[tolower(fullname) == tolower(x_trimmed[i]), mo]
-    # most probable: is exact match in fullname
-    if (length(found) > 0) {
-      x[i] <- found[1L]
-      next
-    }
-    found <- MOs_allothers[tsn == x_trimmed[i], mo]
-    # is a valid TSN
-    if (length(found) > 0) {
-      x[i] <- found[1L]
-      next
-    }
-    found <- MOs_allothers[mo == toupper(x_backup[i]), mo]
-    # is a valid mo
-    if (length(found) > 0) {
-      x[i] <- found[1L]
-      next
-    }
-    found <- MOs_allothers[mo.old == toupper(x_backup[i])
-                           | (substr(x_backup[i], 4, 6) == "SPP" & mo.old == substr(x_backup[i], 1, 3))
-                           | mo.old == substr(x_backup[i], 1, 3), mo]
-    # is a valid old mo
-    if (length(found) > 0) {
-      x[i] <- found[1L]
-      next
-    }
 
-    # try any match keeping spaces ----
+      # try any match keeping spaces, not ending with $ ----
-    found <- MOs_allothers[fullname %like% x_withspaces[i], mo]
+      found <- MOs_allothers[fullname %like% x_withspaces_start[i], ..property][[1]]
-    if (length(found) > 0) {
+      if (length(found) > 0) {
-      x[i] <- found[1L]
+        x[i] <- found[1L]
-      next
+        next
-    }
+      }
 
-    # try any match keeping spaces, not ending with $ ----
+      # try any match diregarding spaces ----
-    found <- MOs_allothers[fullname %like% x_withspaces_start[i], mo]
+      found <- MOs_allothers[fullname %like% x[i], ..property][[1]]
-    if (length(found) > 0) {
+      if (length(found) > 0) {
-      x[i] <- found[1L]
+        x[i] <- found[1L]
-      next
+        next
-    }
+      }
 
-    # try any match diregarding spaces ----
+      # try fullname without start and stop regex, to also find subspecies ----
-    found <- MOs_allothers[fullname %like% x[i], mo]
+      # like "K. pneu rhino" -> "Klebsiella pneumoniae (rhinoscleromatis)" = KLEPNERH
-    if (length(found) > 0) {
+      found <- MOs_allothers[fullname %like% x_withspaces_start[i], ..property][[1]]
-      x[i] <- found[1L]
+      if (length(found) > 0) {
-      next
+        x[i] <- found[1L]
-    }
+        next
+      }
 
-    # try fullname without start and stop regex, to also find subspecies ----
+      # try splitting of characters and then find ID ----
-    # like "K. pneu rhino" -> "Klebsiella pneumoniae (rhinoscleromatis)" = KLEPNERH
+      # like esco = E. coli, klpn = K. pneumoniae, stau = S. aureus
-    found <- MOs_allothers[fullname %like% x_withspaces_start[i], mo]
+      x_split <- x
-    if (length(found) > 0) {
+      x_length <- nchar(x_trimmed[i])
-      x[i] <- found[1L]
+      x_split[i] <- paste0(x_trimmed[i] %>% substr(1, x_length / 2) %>% trimws(),
-      next
+                           '.* ',
-    }
+                           x_trimmed[i] %>% substr((x_length / 2) + 1, x_length) %>% trimws())
+      found <- MOs_allothers[fullname %like% paste0('^', x_split[i]), ..property][[1]]
+      if (length(found) > 0) {
+        x[i] <- found[1L]
+        next
+      }
 
-    # try splitting of characters and then find ID ----
+      # # try any match with text before and after original search string ----
-    # like esco = E. coli, klpn = K. pneumoniae, stau = S. aureus
+      # # so "negative rods" will be "GNR"
-    x_split <- x
+      # if (x_trimmed[i] %like% "^Gram") {
-    x_length <- nchar(x_trimmed[i])
+      #   x_trimmed[i] <- gsub("^Gram", "", x_trimmed[i], ignore.case = TRUE)
-    x_split[i] <- paste0(x_trimmed[i] %>% substr(1, x_length / 2) %>% trimws(),
+      #   # remove leading and trailing spaces again
-                         '.* ',
+      #   x_trimmed[i] <- trimws(x_trimmed[i], which = "both")
-                         x_trimmed[i] %>% substr((x_length / 2) + 1, x_length) %>% trimws())
+      # }
-    found <- MOs_allothers[fullname %like% paste0('^', x_split[i]), mo]
+      # if (!is.na(x_trimmed[i])) {
-    if (length(found) > 0) {
+      #   found <- MOs_allothers[fullname %like% x_trimmed[i], ..property][[1]]
-      x[i] <- found[1L]
+      #   if (length(found) > 0) {
-      next
+      #     x[i] <- found[1L]
-    }
+      #     next
+      #   }
+      # }
 
-    # # try any match with text before and after original search string ----
+      # MISCELLANEOUS ----
-    # # so "negative rods" will be "GNR"
-    # if (x_trimmed[i] %like% "^Gram") {
-    #   x_trimmed[i] <- gsub("^Gram", "", x_trimmed[i], ignore.case = TRUE)
-    #   # remove leading and trailing spaces again
-    #   x_trimmed[i] <- trimws(x_trimmed[i], which = "both")
-    # }
-    # if (!is.na(x_trimmed[i])) {
-    #   found <- MOs_allothers[fullname %like% x_trimmed[i], mo]
-    #   if (length(found) > 0) {
-    #     x[i] <- found[1L]
-    #     next
-    #   }
-    # }
 
-    # MISCELLANEOUS ----
+      # look for old taxonomic names ----
-
+      if (is.null(MOs_old)) {
-    # look for old taxonomic names ----
+        MOs_old <- as.data.table(AMR::microorganisms.old)
-    if (is.null(MOs_old)) {
+        setkey(MOs_old, name, tsn_new)
-      MOs_old <- as.data.table(AMR::microorganisms.old)
+      }
-      setkey(MOs_old, name, tsn_new)
+      found <- MOs_old[tolower(name) == tolower(x_backup[i]) |
-    }
+                         tsn == x_trimmed[i],]
-    found <- MOs_old[tolower(name) == tolower(x_backup[i]) |
-                       tsn == x_trimmed[i],]
-    if (NROW(found) > 0) {
-      x[i] <- MOs[tsn == found[1, tsn_new], mo]
-      renamed_note(name_old = found[1, name],
-                   name_new = MOs[tsn == found[1, tsn_new], fullname],
-                   authors = found[1, authors],
-                   year = found[1, year])
-      next
-    }
-
-    # check for uncertain results ----
-    if (allow_uncertain == TRUE) {
-      # (1) look again for old taxonomic names, now for G. species ----
-      found <- MOs_old[name %like% x_withspaces[i]
-                       | name %like% x_withspaces_start[i]
-                       | name %like% x[i],]
       if (NROW(found) > 0) {
-        x[i] <- MOs[tsn == found[1, tsn_new], mo]
+        x[i] <- MOs[tsn == found[1, tsn_new], ..property][[1]]
-        warning("Uncertain interpretation: '",
-                x_backup[i], "' -> '", found[1, name], "'",
-                call. = FALSE, immediate. = TRUE)
         renamed_note(name_old = found[1, name],
                      name_new = MOs[tsn == found[1, tsn_new], fullname],
                      authors = found[1, authors],
                      year = found[1, year])
-
         next
       }
 
-      # (2) try to strip off one element and check the remains
+      # check for uncertain results ----
-      x_strip <- x_backup[i] %>% strsplit(" ") %>% unlist()
+      if (allow_uncertain == TRUE) {
-      x_strip <- x_strip[1:length(x_strip) - 1]
+        # (1) look again for old taxonomic names, now for G. species ----
-      x[i] <- suppressWarnings(suppressMessages(as.mo(x_strip)))
+        found <- MOs_old[name %like% x_withspaces[i]
-      if (!is.na(x[i])) {
+                         | name %like% x_withspaces_start[i]
-        warning("Uncertain interpretation: '",
+                         | name %like% x[i],]
-                x_backup[i], "' -> '", MOs[mo == x[i], fullname], "' (", x[i], ")",
+        if (NROW(found) > 0) {
-                call. = FALSE, immediate. = TRUE)
+          x[i] <- MOs[tsn == found[1, tsn_new], ..property][[1]]
-        next
+          warning("Uncertain interpretation: '",
+                  x_backup[i], "' -> '", found[1, name], "'",
+                  call. = FALSE, immediate. = TRUE)
+          renamed_note(name_old = found[1, name],
+                       name_new = MOs[tsn == found[1, tsn_new], fullname],
+                       authors = found[1, authors],
+                       year = found[1, year])
+
+          next
+        }
+
+        # (2) try to strip off one element and check the remains
+        x_strip <- x_backup[i] %>% strsplit(" ") %>% unlist()
+        x_strip <- x_strip[1:length(x_strip) - 1]
+        x[i] <- suppressWarnings(suppressMessages(as.mo(x_strip)))
+        if (!is.na(x[i])) {
+          warning("Uncertain interpretation: '",
+                  x_backup[i], "' -> '", MOs[mo == x[i], fullname], "' (", x[i], ")",
+                  call. = FALSE, immediate. = TRUE)
+          next
+        }
       }
+
+      # not found ----
+      x[i] <- NA_character_
+      failures <- c(failures, x_backup[i])
+
     }
-
-    # not found ----
-    x[i] <- NA_character_
-    failures <- c(failures, x_backup[i])
-
   }
 
   failures <- failures[!failures %in% c(NA, NULL, NaN)]
@@ -529,6 +533,10 @@ as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain = FALSE
   if (Becker == TRUE | Becker == "all") {
     # See Source. It's this figure:
     # https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4187637/figure/F3/
+    if (is.null(MOs)) {
+      MOs <- as.data.table(AMR::microorganisms)
+      setkey(MOs, prevalence, tsn)
+    }
     MOs_staph <- MOs[genus == "Staphylococcus"]
     setkey(MOs_staph, species)
     CoNS <- MOs_staph[species %in% c("arlettae", "auricularis", "capitis",
@@ -541,65 +549,66 @@ as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain = FALSE
                                      "pettenkoferi", "piscifermentans", "rostri",
                                      "saccharolyticus", "saprophyticus", "sciuri",
                                      "stepanovicii", "simulans", "succinus",
-                                     "vitulinus", "warneri", "xylosus"), mo]
+                                     "vitulinus", "warneri", "xylosus"), ..property][[1]]
     CoPS <- MOs_staph[species %in% c("simiae", "agnetis", "chromogenes",
                                      "delphini", "felis", "lutrae",
                                      "hyicus", "intermedius",
                                      "pseudintermedius", "pseudointermedius",
-                                     "schleiferi"), mo]
+                                     "schleiferi"), ..property][[1]]
-    x[x %in% CoNS] <- "B_STPHY_CNS"
+    x[x %in% CoNS] <- MOs[mo == 'B_STPHY_CNS', ..property][[1]][1L]
-    x[x %in% CoPS] <- "B_STPHY_CPS"
+    x[x %in% CoPS] <- MOs[mo == 'B_STPHY_CPS', ..property][[1]][1L]
     if (Becker == "all") {
-      x[x == "B_STPHY_AUR"] <- "B_STPHY_CPS"
+      x[x == MOs[mo == 'B_STPHY_AUR', ..property][[1]][1L]] <- MOs[mo == 'B_STPHY_CPS', ..property][[1]][1L]
     }
   }
 
   # Lancefield ----
   if (Lancefield == TRUE | Lancefield == "all") {
-    # group A
+    if (is.null(MOs)) {
-    x[x == "B_STRPTC_PYO"] <- "B_STRPTC_GRA" # S. pyogenes
+      MOs <- as.data.table(AMR::microorganisms)
-    # group B
+      setkey(MOs, prevalence, tsn)
-    x[x == "B_STRPTC_AGA"] <- "B_STRPTC_GRB" # S. agalactiae
+    }
+    # group A - S. pyogenes
+    x[x == MOs[mo == 'B_STRPTC_PYO', ..property][[1]][1L]] <- MOs[mo == 'B_STRPTC_GRA', ..property][[1]][1L]
+    # group B - S. agalactiae
+    x[x == MOs[mo == 'B_STRPTC_AGA', ..property][[1]][1L]] <- MOs[mo == 'B_STRPTC_GRB', ..property][[1]][1L]
     # group C
     S_groupC <- MOs %>% filter(genus == "Streptococcus",
                                species %in% c("equisimilis", "equi",
                                               "zooepidemicus", "dysgalactiae")) %>%
-      pull(mo)
+      pull(property)
-    x[x %in% S_groupC] <- "B_STRPTC_GRC" # S. agalactiae
+    x[x %in% S_groupC] <- MOs[mo == 'B_STRPTC_GRC', ..property][[1]][1L]
     if (Lancefield == "all") {
-      x[substr(x, 1, 7) == "B_ENTRC"] <- "B_STRPTC_GRD" # all Enterococci
+      # all Enterococci
+      x[x %like% "^(Enterococcus|B_ENTRC)"] <- MOs[mo == 'B_STRPTC_GRD', ..property][[1]][1L]
     }
-    # group F
+    # group F - S. anginosus
-    x[x == "B_STRPTC_ANG"] <- "B_STRPTC_GRF" # S. anginosus
+    x[x == MOs[mo == 'B_STRPTC_ANG', ..property][[1]][1L]] <- MOs[mo == 'B_STRPTC_GRF', ..property][[1]][1L]
-    # group H
+    # group H - S. sanguinis
-    x[x == "B_STRPTC_SAN"] <- "B_STRPTC_GRH" # S. sanguinis
+    x[x == MOs[mo == 'B_STRPTC_SAN', ..property][[1]][1L]] <- MOs[mo == 'B_STRPTC_GRH', ..property][[1]][1L]
-    # group K
+    # group K - S. salivarius
-    x[x == "B_STRPTC_SAL"] <- "B_STRPTC_GRK" # S. salivarius
+    x[x == MOs[mo == 'B_STRPTC_SAL', ..property][[1]][1L]] <- MOs[mo == 'B_STRPTC_GRK', ..property][[1]][1L]
   }
 
   # left join the found results to the original input values (x_input)
-  DT_found <- data.table(input = as.character(unique(x_input)),
+  df_found <- data.frame(input = as.character(unique(x_input)),
                          found = x,
-                         key = "input",
                          stringsAsFactors = FALSE)
-  DT_input <- data.table(input = as.character(x_input),
+  df_input <- data.frame(input = as.character(x_input),
-                         key = "input",
                          stringsAsFactors = FALSE)
-  x <- DT_found[DT_input, on = "input", found]
+  x <- df_input %>%
+    left_join(df_found,
+              by = "input") %>%
+    pull(found)
 
-  # df_found <- data.frame(input = as.character(unique(x_input)),
+  if (property == "mo") {
-  #                        found = x,
+    class(x) <- "mo"
-  #                        stringsAsFactors = FALSE)
+    attr(x, 'package') <- 'AMR'
-  # df_input <- data.frame(input = as.character(x_input),
+    attr(x, 'ITIS') <- TRUE
-  #                        stringsAsFactors = FALSE)
+  } else if (property == "tsn") {
-  # x <- df_input %>%
+    x <- as.integer(x)
-  #   left_join(df_found,
+  }
-  #             by = "input") %>%
-  #   pull(found)
 
-  class(x) <- "mo"
-  attr(x, 'package') <- 'AMR'
-  attr(x, 'ITIS') <- TRUE
   x
 }
 
@@ -614,19 +623,6 @@ renamed_note <- function(name_old, name_new, authors, year) {
   base::message(msg)
 }
 
-
-#' @rdname as.mo
-#' @export
-is.mo <- function(x) {
-  # bactid for older releases
-  # remove when is.bactid will be removed
-  identical(class(x), "mo") | identical(class(x), "bactid")
-}
-
-#' @rdname as.mo
-#' @export
-guess_mo <- as.mo
-
 #' @exportMethod print.mo
 #' @export
 #' @noRd

R/mo_property.R

@@ -27,7 +27,7 @@
 #' @inheritSection as.mo Source
 #' @rdname mo_property
 #' @name mo_property
-#' @return A logical (in case of \code{mo_aerobic}), a list (in case of \code{mo_taxonomy}), a character otherwise
+#' @return A \code{list} (in case of \code{mo_taxonomy}) or a \code{character} otherwise
 #' @export
 #' @seealso \code{\link{microorganisms}}
 #' @examples
@@ -39,7 +39,7 @@
 #' mo_family("E. coli")          # "Enterobacteriaceae"
 #' mo_genus("E. coli")           # "Escherichia"
 #' mo_species("E. coli")         # "coli"
-#' mo_subspecies("E. coli")      # ""
+#' mo_subspecies("E. coli")      # NA
 #' mo_fullname("E. coli")        # "Escherichia coli"
 #' mo_shortname("E. coli")       # "E. coli"
 #' mo_gramstain("E. coli")       # "Gram negative"
@@ -98,15 +98,17 @@
 #' # Complete taxonomy up to Subkingdom, returns a list
 #' mo_taxonomy("E. coli")
 mo_fullname <- function(x, Becker = FALSE, Lancefield = FALSE, language = NULL) {
-  mo_property(x, "fullname", Becker = Becker, Lancefield = Lancefield, language = language)
+  x <- mo_validate(x = x, property = "fullname", Becker = Becker, Lancefield = Lancefield)
+  mo_translate(x, language = language)
 }
 
 #' @rdname mo_property
+#' @importFrom dplyr %>% left_join mutate pull
 #' @export
 mo_shortname <- function(x, Becker = FALSE, Lancefield = FALSE, language = NULL) {
   if (Becker %in% c(TRUE, "all") | Lancefield == TRUE) {
-    res1 <- as.mo(x)
+    res1 <- AMR::as.mo(x)
-    res2 <- suppressWarnings(as.mo(x, Becker = Becker, Lancefield = Lancefield))
+    res2 <- suppressWarnings(AMR::as.mo(res1, Becker = Becker, Lancefield = Lancefield))
     res2_fullname <- mo_fullname(res2)
     res2_fullname[res2_fullname %like% "\\(CoNS\\)"] <- "CoNS"
     res2_fullname[res2_fullname %like% "\\(CoPS\\)"] <- "CoPS"
@@ -115,8 +117,8 @@ mo_shortname <- function(x, Becker = FALSE, Lancefield = FALSE, language = NULL)
                           res2_fullname) # turn "Streptococcus group A" and "Streptococcus grupo A" to "GAS"
     res2_fullname_vector <- res2_fullname[res2_fullname == mo_fullname(res1)]
     res2_fullname[res2_fullname == mo_fullname(res1)] <- paste0(substr(mo_genus(res2_fullname_vector), 1, 1),
-                                                             ". ",
+                                                                ". ",
-                                                             suppressWarnings(mo_species(res2_fullname_vector)))
+                                                                suppressWarnings(mo_species(res2_fullname_vector)))
     if (sum(res1 == res2, na.rm = TRUE) > 0) {
       res1[res1 == res2] <- paste0(substr(mo_genus(res1[res1 == res2]), 1, 1),
                                    ". ",
@@ -126,112 +128,115 @@ mo_shortname <- function(x, Becker = FALSE, Lancefield = FALSE, language = NULL)
     result <- as.character(res1)
   } else {
     x <- AMR::as.mo(x)
-    # return G. species
+    result <- data.frame(mo = x) %>%
-    result <- paste0(substr(mo_genus(x), 1, 1), ". ", suppressWarnings(mo_species(x)))
+      left_join(AMR::microorganisms, by = "mo") %>%
+      mutate(shortname = ifelse(!is.na(genus) & !is.na(species), paste0(substr(genus, 1, 1), ". ", species), NA_character_)) %>%
+      pull(shortname)
   }
-  result[result %in% c(". ", "(. ")] <- ""
   mo_translate(result, language = language)
 }
 
 #' @rdname mo_property
 #' @export
 mo_subspecies <- function(x, Becker = FALSE, Lancefield = FALSE, language = NULL) {
-  mo_property(x, "subspecies", Becker = Becker, Lancefield = Lancefield, language = language)
+  mo_translate(exec_as.mo(x,
+                          Becker = Becker,
+                          Lancefield = Lancefield,
+                          property = "subspecies"),
+               language = language)
 }
 
 #' @rdname mo_property
 #' @export
 mo_species <- function(x, Becker = FALSE, Lancefield = FALSE, language = NULL) {
-  mo_property(x, "species", Becker = Becker, Lancefield = Lancefield, language = language)
+  x <- mo_validate(x = x, property = "species", Becker = Becker, Lancefield = Lancefield)
+  mo_translate(x, language = language)
 }
 
 #' @rdname mo_property
 #' @export
 mo_genus <- function(x, language = NULL) {
-  mo_property(x, "genus", language = language)
+  x <- mo_validate(x = x, property = "genus")
+  mo_translate(x, language = language)
 }
 
 #' @rdname mo_property
 #' @export
 mo_family <- function(x) {
-  mo_property(x, "family")
+  mo_validate(x = x, property = "family")
 }
 
 #' @rdname mo_property
 #' @export
 mo_order <- function(x) {
-  mo_property(x, "order")
+  mo_validate(x = x, property = "order")
 }
 
 #' @rdname mo_property
 #' @export
 mo_class <- function(x) {
-  mo_property(x, "class")
+  mo_validate(x = x, property = "class")
 }
 
 #' @rdname mo_property
 #' @export
 mo_phylum <- function(x) {
-  mo_property(x, "phylum")
+  mo_validate(x = x, property = "phylum")
 }
 
 #' @rdname mo_property
 #' @export
 mo_subkingdom  <- function(x) {
-  mo_property(x, "subkingdom")
+  mo_validate(x = x, property = "subkingdom")
 }
 
 #' @rdname mo_property
 #' @export
 mo_type <- function(x, language = NULL) {
-  mo_property(x, "type", language = language)
+  x <- mo_validate(x = x, property = "type")
+  mo_translate(x, language = language)
 }
 
 #' @rdname mo_property
 #' @export
 mo_TSN  <- function(x) {
-  mo_property(x, "tsn")
+  mo_validate(x = x, property = "tsn")
 }
 
 #' @rdname mo_property
 #' @export
 mo_gramstain <- function(x, language = NULL) {
-  mo_property(x, "gramstain", language = language)
+  x <- mo_validate(x = x, property = "gramstain")
+  mo_translate(x, language = language)
 }
 
 #' @rdname mo_property
 #' @importFrom data.table data.table as.data.table setkey
 #' @export
 mo_property <- function(x, property = 'fullname', Becker = FALSE, Lancefield = FALSE, language = NULL) {
-  property <- tolower(property[1])
+  if (length(property) != 1L) {
+    stop("'property' must be of length 1.")
+  }
   if (!property %in% colnames(AMR::microorganisms)) {
-    stop("invalid property: ", property, " - use a column name of the `microorganisms` data set")
+    stop("invalid property: '", property, "' - use a column name of the `microorganisms` data set")
   }
-  if (Becker == TRUE | Lancefield == TRUE | !is.mo(x)) {
-    # this will give a warning if x cannot be coerced
-    x <- AMR::as.mo(x = x, Becker = Becker, Lancefield = Lancefield)
-  }
-  A <- data.table(mo = x, stringsAsFactors = FALSE)
-  B <- as.data.table(AMR::microorganisms)
-  setkey(B, mo)
-  result2 <- B[A, on = 'mo', ..property][[1]]
 
-  if (property == "tsn") {
+  # this will give a warning if x cannot be coerced
-    result2 <- as.integer(result2)
+  res <- exec_as.mo(x = x, Becker = Becker, Lancefield = Lancefield, property = property)
-  } else {
+
-    # will else not retain `logical` class
+  if (property != "tsn") {
-    result2[x %in% c("", NA) | result2 %in% c("", NA, "(no MO)")] <- ""
+    res[x %in% c("", NA) | res %in% c("", NA, "(no MO)")] <- ""
     if (property %in% c("fullname", "shortname", "genus", "species", "subspecies", "type", "gramstain")) {
-      result2 <- mo_translate(result2, language = language)
+      res <- mo_translate(res, language = language)
     }
   }
-  result2
+  res
 }
 
 #' @rdname mo_property
 #' @export
 mo_taxonomy <- function(x) {
-  x <- as.mo(x)
+  x <- AMR::as.mo(x)
   base::list(subkingdom = mo_subkingdom(x),
              phylum = mo_phylum(x),
              class = mo_class(x),
@@ -247,7 +252,7 @@ mo_translate <- function(x, language) {
   if (is.null(language)) {
     language <- getOption("AMR_locale", default = "en")[1L]
   } else {
-    language <- tolower(language[1])
+    language <- tolower(language[1L])
   }
   if (language %in% c("en", "")) {
     return(x)
@@ -364,3 +369,14 @@ mo_translate <- function(x, language) {
   )
 
 }
+
+mo_validate <- function(x, property, Becker = FALSE, Lancefield = FALSE) {
+  if (!all(x %in% AMR::microorganisms[, property]) | Becker %in% c(TRUE, "all") | Lancefield == TRUE) {
+    exec_as.mo(x,
+               Becker = Becker,
+               Lancefield = Lancefield,
+               property = property)
+  } else {
+    x
+  }
+}

man/as.mo.Rd

@@ -65,7 +65,7 @@ This means that looking up human non-pathogenic microorganisms takes a longer ti
 \section{ITIS}{
 
 \if{html}{\figure{itis_logo.jpg}{options: height=60px style=margin-bottom:5px} \cr}
-This \code{AMR} package contains the \strong{complete microbial taxonomic data} (with seven taxonomic ranks - from subkingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, https://www.itis.gov). ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic specialists [3]. The complete taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package, as well as all previously accepted names known to ITIS.
+This \code{AMR} package contains the \strong{complete microbial taxonomic data} (with seven taxonomic ranks - from subkingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, \url{https://www.itis.gov}). ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic specialists [3]. The complete taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package, as well as all previously accepted names known to ITIS.
 }
 
 \section{Source}{

man/microorganisms.Rd

@@ -34,7 +34,7 @@ A data set containing the complete microbial taxonomy of the kingdoms Bacteria,
 \section{ITIS}{
 
 \if{html}{\figure{itis_logo.jpg}{options: height=60px style=margin-bottom:5px} \cr}
-This \code{AMR} package contains the \strong{complete microbial taxonomic data} (with seven taxonomic ranks - from subkingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, https://www.itis.gov). ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic specialists [3]. The complete taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package, as well as all previously accepted names known to ITIS.
+This \code{AMR} package contains the \strong{complete microbial taxonomic data} (with seven taxonomic ranks - from subkingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, \url{https://www.itis.gov}). ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic specialists [3]. The complete taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package, as well as all previously accepted names known to ITIS.
 }
 
 \seealso{

man/microorganisms.certe.Rd

@@ -0,0 +1,21 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/data.R
+\docType{data}
+\name{microorganisms.certe}
+\alias{microorganisms.certe}
+\title{Translation table for Certe}
+\format{A \code{\link{tibble}} with 2,664 observations and 2 variables:
+\describe{
+  \item{\code{certe}}{Code of microorganism according to Certe MMB}
+  \item{\code{mo}}{Code of microorganism in \code{\link{microorganisms}}}
+}}
+\usage{
+microorganisms.certe
+}
+\description{
+A data set containing all bacteria codes of Certe MMB. These codes can be joined to data with an ID from \code{\link{microorganisms}$mo} (using \code{\link{left_join_microorganisms}}). GLIMS codes can also be translated to valid \code{MO}s with \code{\link{guess_mo}}.
+}
+\seealso{
+\code{\link{as.mo}} \code{\link{microorganisms}}
+}
+\keyword{datasets}

man/microorganisms.old.Rd

@@ -4,7 +4,7 @@
 \name{microorganisms.old}
 \alias{microorganisms.old}
 \title{Data set with old taxonomic data from ITIS}
-\format{A \code{\link{data.frame}} with 1,682 observations and 5 variables:
+\format{A \code{\link{data.frame}} with 2,384 observations and 5 variables:
 \describe{
   \item{\code{tsn}}{Old Taxonomic Serial Number (TSN), as defined by ITIS}
   \item{\code{name}}{Old taxonomic name of the microorganism as found in ITIS, see Source}
@@ -19,12 +19,12 @@
 microorganisms.old
 }
 \description{
-A data set containing old, previously valid, taxonomic names. This data set is used internally by \code{\link{as.mo}}.
+A data set containing old (previously valid or accepted) taxonomic names according to ITIS. This data set is used internally by \code{\link{as.mo}}.
 }
 \section{ITIS}{
 
 \if{html}{\figure{itis_logo.jpg}{options: height=60px style=margin-bottom:5px} \cr}
-This \code{AMR} package contains the \strong{complete microbial taxonomic data} (with seven taxonomic ranks - from subkingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, https://www.itis.gov). ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic specialists [3]. The complete taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package, as well as all previously accepted names known to ITIS.
+This \code{AMR} package contains the \strong{complete microbial taxonomic data} (with seven taxonomic ranks - from subkingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, \url{https://www.itis.gov}). ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic specialists [3]. The complete taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package, as well as all previously accepted names known to ITIS.
 }
 
 \seealso{

man/microorganisms.umcg.Rd

@@ -7,7 +7,7 @@
 \format{A \code{\link{tibble}} with 1,095 observations and 2 variables:
 \describe{
   \item{\code{umcg}}{Code of microorganism according to UMCG MMB}
-  \item{\code{mo}}{Code of microorganism in \code{\link{microorganisms}}}
+  \item{\code{certe}}{Code of microorganism according to Certe MMB}
 }}
 \usage{
 microorganisms.umcg
@@ -16,6 +16,6 @@ microorganisms.umcg
 A data set containing all bacteria codes of UMCG MMB. These codes can be joined to data with an ID from \code{\link{microorganisms}$mo} (using \code{\link{left_join_microorganisms}}). GLIMS codes can also be translated to valid \code{MO}s with \code{\link{guess_mo}}.
 }
 \seealso{
-\code{\link{as.mo}} \code{\link{microorganisms}}
+\code{\link{as.mo}} \code{\link{microorganisms.certe}} \code{\link{microorganisms}}
 }
 \keyword{datasets}

man/mo_property.Rd

@@ -65,7 +65,7 @@ mo_taxonomy(x)
 \item{property}{one of the column names of one of the \code{\link{microorganisms}} data set or \code{"shortname"}}
 }
 \value{
-A logical (in case of \code{mo_aerobic}), a list (in case of \code{mo_taxonomy}), a character otherwise
+A \code{list} (in case of \code{mo_taxonomy}) or a \code{character} otherwise
 }
 \description{
 Use these functions to return a specific property of a microorganism from the \code{\link{microorganisms}} data set. All input values will be evaluated internally with \code{\link{as.mo}}.
@@ -73,7 +73,7 @@ Use these functions to return a specific property of a microorganism from the \c
 \section{ITIS}{
 
 \if{html}{\figure{itis_logo.jpg}{options: height=60px style=margin-bottom:5px} \cr}
-This \code{AMR} package contains the \strong{complete microbial taxonomic data} (with seven taxonomic ranks - from subkingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, https://www.itis.gov). ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic specialists [3]. The complete taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package, as well as all previously accepted names known to ITIS.
+This \code{AMR} package contains the \strong{complete microbial taxonomic data} (with seven taxonomic ranks - from subkingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, \url{https://www.itis.gov}). ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic specialists [3]. The complete taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package, as well as all previously accepted names known to ITIS.
 }
 
 \section{Source}{
@@ -94,7 +94,7 @@ mo_order("E. coli")           # "Enterobacteriales"
 mo_family("E. coli")          # "Enterobacteriaceae"
 mo_genus("E. coli")           # "Escherichia"
 mo_species("E. coli")         # "coli"
-mo_subspecies("E. coli")      # ""
+mo_subspecies("E. coli")      # NA
 mo_fullname("E. coli")        # "Escherichia coli"
 mo_shortname("E. coli")       # "E. coli"
 mo_gramstain("E. coli")       # "Gram negative"

tests/testthat/test-mo.R

@@ -15,7 +15,7 @@ test_that("as.mo works", {
   expect_equal(as.character(as.mo("Escherichia  species")), "B_ESCHR")
   expect_equal(as.character(as.mo("Escherichia")), "B_ESCHR")
   expect_equal(as.character(as.mo(" B_ESCHR_COL ")), "B_ESCHR_COL")
-  #expect_equal(as.character(as.mo("coli")), "B_ESCHR_COL") # not Campylobacter
+  expect_equal(as.character(as.mo("e coli")), "B_ESCHR_COL") # not Campylobacter
   expect_equal(as.character(as.mo("klpn")), "B_KLBSL_PNE")
   expect_equal(as.character(as.mo("Klebsiella")), "B_KLBSL")
   expect_equal(as.character(as.mo("K. pneu rhino")), "B_KLBSL_PNE_RHI") # K. pneumoniae subspp. rhinoscleromatis
@@ -34,9 +34,6 @@ test_that("as.mo works", {
 
   expect_equal(as.character(as.mo("P. aer")), "B_PDMNS_AER") # not Pasteurella aerogenes
 
-  # expect_equal(as.character(as.mo("Negative rods")), "GNR")
-  # expect_equal(as.character(as.mo("Gram negative rods")), "GNR")
-
   # GLIMS
   expect_equal(as.character(as.mo("bctfgr")), "B_BCTRD_FRA")
 

tests/testthat/test-mo_property.R

@@ -8,11 +8,13 @@ test_that("mo_property works", {
   expect_equal(mo_family("E. coli"), "Enterobacteriaceae")
   expect_equal(mo_genus("E. coli"), "Escherichia")
   expect_equal(mo_species("E. coli"), "coli")
-  expect_equal(mo_subspecies("E. coli"), "")
+  expect_equal(mo_subspecies("E. coli"), NA_character_)
   expect_equal(mo_fullname("E. coli"), "Escherichia coli")
   expect_equal(mo_type("E. coli", language = "en"), "Bacteria")
   expect_equal(mo_gramstain("E. coli", language = "en"), "Gram negative")
   expect_equal(class(mo_taxonomy("E. coli")), "list")
+  expect_equal(names(mo_taxonomy("E. coli")), c("subkingdom", "phylum", "class", "order",
+                                                "family", "genus", "species", "subspecies"))
 
   expect_equal(mo_shortname("MRSA"), "S. aureus")
   expect_equal(mo_shortname("MRSA", Becker = TRUE), "S. aureus")
@@ -21,12 +23,8 @@ test_that("mo_property works", {
   expect_equal(mo_shortname("S. aga", Lancefield = TRUE), "GBS")
 
   # test integrity
-  # library(dplyr)
+  MOs <- AMR::microorganisms
-  # rnd <- sample(1:nrow(AMR::microorganisms), 500, replace = FALSE) # random 500 rows
+  expect_identical(MOs$fullname, mo_fullname(MOs$fullname, language = "en"))
-  # MOs <- AMR::microorganisms %>% filter(!is.na(mo),
-  #                                       species != "species",
-  #                                       dplyr::row_number() %in% rnd)
-  # expect_identical(MOs$fullname, mo_fullname(MOs$fullname, language = "en"))
 
   # check languages
   expect_equal(mo_type("E. coli", language = "de"), "Bakterien")