- Added new function guess_bactid to determine the ID of a microorganism based on genus/species

- Renamed `ablist` to `antibiotics`
- Added support for character vector in join functions
- Altered `%like%` to make it case insensitive

.travis.yml

@@ -1,2 +1,21 @@
+# R for travis: see documentation at https://docs.travis-ci.com/user/languages/r
+
 language: r
 cache: packages
+
+r:
+  - 3.0
+
+r_packages:
+  - covr
+
+after_success:
+  - Rscript -e 'covr::codecov()'
+
+notifications:
+  email:
+    recipients:
+      - m.s.berends@umcg.nl
+      - c.f.luz@umcg.nl
+    on_success: change
+    on_failure: always

DESCRIPTION

@@ -1,13 +1,14 @@
 Package: AMR
-Version: 0.1.1
+Version: 0.1.2
-Date: 2018-03-13
+Date: 2018-03-19
 Title: Antimicrobial Resistance Analysis
 Authors@R: c(
     person(
         given = c("Matthijs", "S."),
         family = "Berends",
         email = "m.s.berends@umcg.nl",
-        role = c("aut", "cre")),
+        role = c("aut", "cre"),
+        comment = c(ORCID = "0000-0001-7620-1800")),
     person(
         given = c("Christian", "F."),
         family = "Luz",

NAMESPACE

@@ -19,6 +19,7 @@ export(as.rsi)
 export(atc_property)
 export(first_isolate)
 export(full_join_bactlist)
+export(guess_bactid)
 export(inner_join_bactlist)
 export(interpretive_reading)
 export(is.mic)

NEWS

@@ -1,3 +1,9 @@
+## 0.1.2
+- Added new function `guess_bactid` to determine the ID of a microorganism based on genus/species
+- Renamed `ablist` to `antibiotics`
+- Added support for character vector in join functions
+- Altered `%like%` to make it case insensitive
+
 ## 0.1.1
 - `EUCAST_rules` applies for amoxicillin even if ampicillin is missing
 - Edited column names to comply with GLIMS, the laboratory information system

R/atc.R

@@ -127,13 +127,13 @@ atc_property <- function(atc_code,
 
 #' Name of an antibiotic
 #'
-#' Convert antibiotic codes (from a laboratory information system like MOLIS or GLIMS) to a (trivial) antibiotic name or ATC code, or vice versa. This uses the data from \code{\link{ablist}}.
+#' Convert antibiotic codes (from a laboratory information system like MOLIS or GLIMS) to a (trivial) antibiotic name or ATC code, or vice versa. This uses the data from \code{\link{antibiotics}}.
 #' @param abcode a code or name, like \code{"AMOX"}, \code{"AMCL"} or \code{"J01CA04"}
-#' @param from,to type to transform from and to. See \code{\link{ablist}} for its column names.
+#' @param from,to type to transform from and to. See \code{\link{antibiotics}} for its column names.
 #' @param textbetween text to put between multiple returned texts
 #' @param tolower return output as lower case with function \code{\link{tolower}}.
 #' @keywords ab antibiotics
-#' @source \code{\link{ablist}}
+#' @source \code{\link{antibiotics}}
 #' @export
 #' @importFrom dplyr %>% filter select slice 
 #' @examples
@@ -156,15 +156,15 @@ atc_property <- function(atc_code,
 #' # "AMCL"
 abname <- function(abcode, from = 'umcg', to = 'official', textbetween = ' + ', tolower = FALSE) {
   
-  ablist <- AMR::ablist
+  antibiotics <- AMR::antibiotics
-  colnames(ablist) <- colnames(ablist) %>% tolower()
+  colnames(antibiotics) <- colnames(antibiotics) %>% tolower()
   from <- from %>% tolower()
   to <- to %>% tolower()
   
-  if (!from %in% colnames(ablist) |
+  if (!from %in% colnames(antibiotics) |
-      !to %in% colnames(ablist)) {
+      !to %in% colnames(antibiotics)) {
     stop(paste0('Invalid `from` or `to`. Choose one of ', 
-                colnames(ablist) %>% paste(collapse = ","), '.'), call. = FALSE)
+                colnames(antibiotics) %>% paste(collapse = ","), '.'), call. = FALSE)
   }
   
   abcode <- as.character(abcode)
@@ -173,9 +173,9 @@ abname <- function(abcode, from = 'umcg', to = 'official', textbetween = ' + ',
     drug <- abcode[i]
     if (!grepl('+', drug, fixed = TRUE) & !grepl(' en ', drug, fixed = TRUE)) {
       # bestaat maar uit 1 middel
-      if (any(ablist[, from] == drug)) {
+      if (any(antibiotics[, from] == drug)) {
         abcode[i] <-
-          ablist %>%
+          antibiotics %>%
           filter(.[, from] == drug) %>%
           select(to) %>%
           slice(1) %>%
@@ -205,7 +205,7 @@ abname <- function(abcode, from = 'umcg', to = 'official', textbetween = ' + ',
       
       for (j in 1:length(drug.group)) {
         drug.group[j] <-
-          ablist %>%
+          antibiotics %>%
           filter(.[, from] == drug.group[j]) %>%
           select(to) %>%
           slice(1) %>%

R/data.R

@@ -18,36 +18,53 @@
 
 #' Dataset with 420 antibiotics
 #'
-#' A dataset containing all antibiotics with a J0 code, with their DDD's.
+#' A dataset containing all antibiotics with a J0 code, with their DDD's. Properties were downloaded from the WHO, see Source.
-#' @format A data.frame with 420 observations and 12 variables:
+#' @format A data.frame with 420 observations and 16 variables:
 #' \describe{
 #'   \item{\code{atc}}{ATC code, like \code{J01CR02}}
 #'   \item{\code{molis}}{MOLIS code, like \code{amcl}}
 #'   \item{\code{umcg}}{UMCG code, like \code{AMCL}}
-#'   \item{\code{official}}{Official name by the WHO, like \code{"amoxicillin and enzyme inhibitor"}}
+#'   \item{\code{official}}{Official name by the WHO, like \code{"Amoxicillin and enzyme inhibitor"}}
 #'   \item{\code{official_nl}}{Official name in the Netherlands, like \code{"Amoxicilline met enzymremmer"}}
 #'   \item{\code{trivial_nl}}{Trivial name in Dutch, like \code{"Amoxicilline/clavulaanzuur"}}
-#'   \item{\code{oral_ddd}}{Defined Daily Dose (DDD) according to the WHO, oral treatment}
+#'   \item{\code{oral_ddd}}{Defined Daily Dose (DDD), oral treatment}
 #'   \item{\code{oral_units}}{Units of \code{ddd_units}}
-#'   \item{\code{iv_ddd}}{Defined Daily Dose (DDD) according to the WHO, parenteral treatment}
+#'   \item{\code{iv_ddd}}{Defined Daily Dose (DDD), parenteral treatment}
 #'   \item{\code{iv_units}}{Units of \code{iv_ddd}}
-#'   \item{\code{atc_group1}}{ATC group in Dutch, like \code{"Macroliden, lincosamiden en streptograminen"}}
+#'   \item{\code{atc_group1}}{ATC group, like \code{"Macrolides, lincosamides and streptogramins"}}
-#'   \item{\code{atc_group2}}{Subgroup of \code{atc_group1} in Dutch, like \code{"Macroliden"}}
+#'   \item{\code{atc_group2}}{Subgroup of \code{atc_group1}, like \code{"Macrolides"}}
+#'   \item{\code{atc_group1_nl}}{ATC group in Dutch, like \code{"Macroliden, lincosamiden en streptograminen"}}
+#'   \item{\code{atc_group2_nl}}{Subgroup of \code{atc_group1} in Dutch, like \code{"Macroliden"}}
+#'   \item{\code{useful_gramnegative}}{\code{FALSE} if not useful according to EUCAST, \code{NA} otherwise (see Source)}
+#'   \item{\code{useful_grampositive}}{\code{FALSE} if not useful according to EUCAST, \code{NA} otherwise (see Source)}
 #' }
-#' @source MOLIS (LIS of Certe) - \url{https://www.certe.nl} \cr \cr GLIMS (LIS of UMCG) - \url{https://www.umcg.nl} \cr \cr World Health Organization - \url{https://www.whocc.no/atc_ddd_index/}
+#' @source - World Health Organization: \url{https://www.whocc.no/atc_ddd_index/} \cr - EUCAST - Expert rules intrinsic exceptional V3.1 \cr - MOLIS (LIS of Certe): \url{https://www.certe.nl} \cr - GLIMS (LIS of UMCG): \url{https://www.umcg.nl}
 #' @seealso \code{\link{bactlist}}
-# todo:
+# last two columns created with:
-# ablist <- ablist %>% mutate(useful_gramnegative = if_else(atc_group2 == 'Tetracyclines', FALSE, TRUE))
+# antibiotics %>%
-# ablist <- ablist %>% mutate(useful_gramnegative = if_else(atc_group2 %like% 'Glycopept', FALSE, useful_gramnegative))
+#   mutate(useful_gramnegative = 
-# Tbl1 Enterobacteriaceae are also intrinsically resistant to benzylpenicillin, glycopeptides, fusidic acid, macrolides (with some exceptions1), lincosamides, streptogramins, rifampicin, daptomycin and linezolid.
+#            if_else(
-# Tbl2 Non-fermentative Gram-negative bacteria are also generally intrinsically resistant to benzylpenicillin, first and second generation cephalosporins, glycopeptides, fusidic acid, macrolides, lincosamides, streptogramins, rifampicin, daptomycin and linezolid
+#              atc_group1 %like% '(fusidic|glycopeptide|macrolide|lincosamide|daptomycin|linezolid)' |
-# Tbl3 Gram-negative bacteria other than Enterobacteriaceae and non-fermentative Gram-negative bacteria listed are also intrinsically resistant to glycopeptides, lincosamides, daptomycin and linezolid.
+#                atc_group2 %like% '(fusidic|glycopeptide|macrolide|lincosamide|daptomycin|linezolid)' |
-"ablist"
+#                official %like% '(fusidic|glycopeptide|macrolide|lincosamide|daptomycin|linezolid)',
+#              FALSE,
+#              NA
+#            ),
+#          useful_grampositive =
+#            if_else(
+#              atc_group1 %like% '(aztreonam|temocillin|polymyxin|colistin|nalidixic)' |
+#                atc_group2 %like% '(aztreonam|temocillin|polymyxin|colistin|nalidixic)' |
+#                official %like% '(aztreonam|temocillin|polymyxin|colistin|nalidixic)',
+#              FALSE,
+#              NA
+#            )
+#   )
+"antibiotics"
 
 #' Dataset with ~2500 microorganisms
 #'
 #' A dataset containing all microorganisms of MOLIS. MO codes of the UMCG can be looked up using \code{\link{bactlist.umcg}}.
-#' @format A data.frame with 2507 observations and 10 variables:
+#' @format A data.frame with 2507 observations and 12 variables:
 #' \describe{
 #'   \item{\code{bactid}}{ID of microorganism}
 #'   \item{\code{bactsys}}{Bactsyscode of microorganism}
@@ -56,12 +73,14 @@
 #'   \item{\code{species}}{Species name of microorganism, like \code{"coli"}}
 #'   \item{\code{subspecies}}{Subspecies name of bio-/serovar of microorganism, like \code{"EHEC"}}
 #'   \item{\code{fullname}}{Full name, like \code{"Echerichia coli (EHEC)"}}
-#'   \item{\code{type}}{Type of microorganism in Dutch, like \code{"Bacterie"} and \code{"Schimmel/gist"}}
+#'   \item{\code{type}}{Type of microorganism, like \code{"Bacteria"} and \code{"Fungus/yeast"}}
-#'   \item{\code{gramstain}}{Gram of microorganism in Dutch, like \code{"Negatieve staven"}}
+#'   \item{\code{gramstain}}{Gram of microorganism, like \code{"Negative rods"}}
-#'   \item{\code{aerobic}}{Type aerobe/anaerobe of bacteria}
+#'   \item{\code{aerobic}}{Logical whether bacteria is aerobic}
+#'   \item{\code{type_nl}}{Type of microorganism in Dutch, like \code{"Bacterie"} and \code{"Schimmel/gist"}}
+#'   \item{\code{gramstain_nl}}{Gram of microorganism in Dutch, like \code{"Negatieve staven"}}
 #' }
 #' @source MOLIS (LIS of Certe) - \url{https://www.certe.nl}
-#' @seealso \code{\link{ablist}} \code{\link{bactlist.umcg}}
+#' @seealso \code{\link{guess_bactid}} \code{\link{antibiotics}} \code{\link{bactlist.umcg}}
 "bactlist"
 
 #' Translation table for UMCG with ~1100 microorganisms
@@ -90,7 +109,7 @@
 #'   \item{\code{sex}}{sex of the patient}
 #'   \item{\code{patient_id}}{ID of the patient, first 10 characters of an SHA hash containing irretrievable information}
 #'   \item{\code{bactid}}{ID of microorganism, see \code{\link{bactlist}}}
-#'   \item{\code{peni:mupi}}{38 different antibiotics with class \code{rsi} (see \code{\link{as.rsi}}), these column names occur in \code{\link{ablist}} and can be translated with \code{\link{abname}}}
+#'   \item{\code{peni:mupi}}{38 different antibiotics with class \code{rsi} (see \code{\link{as.rsi}}), these column names occur in \code{\link{antibiotics}} and can be translated with \code{\link{abname}}}
 #' }
 #' @source MOLIS (LIS of Certe) - \url{https://www.certe.nl}
 "septic_patients"

R/first_isolates.R

@@ -357,7 +357,7 @@ first_isolate <- function(tbl,
 #' @export
 #' @importFrom dplyr %>% mutate if_else 
 #' @return Character of length 1.
-#' @seealso \code{\link{mo_property}} \code{\link{ablist}}
+#' @seealso \code{\link{mo_property}} \code{\link{antibiotics}}
 #' @examples 
 #' \donttest{
 #' #' # set key antibiotics to a new variable
@@ -403,7 +403,7 @@ key_antibiotics <- function(tbl,
     }
   }
   
-  # bactlist aan vastknopen
+  # join bactlist
   tbl <- tbl %>% left_join_bactlist(col_bactcode)
   
   tbl$key_ab <- NA_character_
@@ -422,7 +422,7 @@ key_antibiotics <- function(tbl,
   list_ab <- c(peni, amox, teic, vanc, clin, line, clar, trsu)
   list_ab <- list_ab[list_ab %in% colnames(tbl)]
   tbl <- tbl %>% mutate(key_ab =
-                          if_else(gramstain %like% '^Positi[e]?ve',
+                          if_else(gramstain %like% '^Positive ',
                                   apply(X = tbl[, list_ab],
                                         MARGIN = 1,
                                         FUN = function(x) paste(x, collapse = "")),
@@ -432,7 +432,7 @@ key_antibiotics <- function(tbl,
   list_ab <- c(amox, amcl, pita, cfur, cfot, cfta, cftr, mero, cipr, trsu, gent)
   list_ab <- list_ab[list_ab %in% colnames(tbl)]
   tbl <- tbl %>% mutate(key_ab =
-                          if_else(gramstain %like% '^Negati[e]?ve',
+                          if_else(gramstain %like% '^Negative ',
                                   apply(X = tbl[, list_ab],
                                         MARGIN = 1,
                                         FUN = function(x) paste(x, collapse = "")),
@@ -502,3 +502,95 @@ key_antibiotics_equal <- function(x, y, points_threshold = 2, info = FALSE) {
   }
   result
 }
+
+#' Find bacteria ID based on genus/species
+#'
+#' Use this function to determine a valid ID based on a genus (and species). This input could be a full name (like \code{"Staphylococcus aureus"}), an abbreviated name (like \code{"S. aureus"}), or just a genus. You could also use a \code{\link{paste}} of a genus and species column to use the full name as input: \code{x = paste(df$genus, df$species)}, where \code{df} is your dataframe.
+#' @param x character vector to determine \code{bactid}
+#' @export
+#' @importFrom dplyr %>% filter slice pull
+#' @return Character (vector).
+#' @seealso \code{\link{bactlist}} for the dataframe that is being used to determine ID's.
+#' @examples 
+#' # These examples all return "STAAUR", the ID of S. aureus:
+#' guess_bactid("stau")
+#' guess_bactid("STAU")
+#' guess_bactid("staaur")
+#' guess_bactid("S. aureus")
+#' guess_bactid("S aureus")
+#' guess_bactid("Staphylococcus aureus")
+#' guess_bactid("MRSA") # Methicillin-resistant S. aureus
+#' guess_bactid("VISA") # Vancomycin Intermediate S. aureus
+guess_bactid <- function(x) {
+  # remove dots and other non-text in case of "E. coli" except spaces
+  x <- gsub("[^a-zA-Z ]+", "", x)
+  x.bak <- x
+  # replace space by regex sign
+  x <- gsub(" ", ".*", x, fixed = TRUE)
+  # add start and stop
+  x_species <- paste(x, 'species')
+  x <- paste0('^', x, '$')
+  
+  for (i in 1:length(x)) {
+    if (tolower(x[i]) == '^e.*coli$') {
+      # avoid detection of Entamoeba coli in case of Escherichia coli
+      x[i] <- 'Escherichia coli'
+    }
+    if (tolower(x[i]) == '^st.*au$'
+        | tolower(x[i]) == '^stau$'
+        | tolower(x[i]) == '^staaur$') {
+      # avoid detection of Staphylococcus auricularis in case of S. aureus
+      x[i] <- 'Staphylococcus aureus'
+    }
+    if (tolower(x[i]) == '^p.*aer$') {
+      # avoid detection of Pasteurella aerogenes in case of Pseudomonas aeruginosa
+      x[i] <- 'Pseudomonas aeruginosa'
+    }
+    # translate known trivial names to genus+species
+    if (toupper(x.bak[i]) == 'MRSA'
+        | toupper(x.bak[i]) == 'VISA'
+        | toupper(x.bak[i]) == 'VRSA') {
+      x[i] <- 'Staphylococcus aureus'
+    }
+    if (toupper(x.bak[i]) == 'MRSE') {
+      x[i] <- 'Staphylococcus epidermidis'
+    }
+    if (toupper(x.bak[i]) == 'VRE') {
+      x[i] <- 'Enterococcus'
+    }
+
+    # let's try the ID's first
+    found <- AMR::bactlist %>% filter(bactid == x.bak[i])
+    
+    if (nrow(found) == 0) {
+      # now try exact match
+      found <- AMR::bactlist %>% filter(fullname == x[i])
+    }
+    if (nrow(found) == 0) {
+      # try any match
+      found <- AMR::bactlist %>% filter(fullname %like% x[i])
+    }
+    if (nrow(found) == 0) {
+      # try only genus, with 'species' attached
+      found <- AMR::bactlist %>% filter(fullname %like% x_species[i])
+    }
+    if (nrow(found) == 0) {
+      # try splitting of characters and then find ID
+      # like esco = E. coli, klpn = K. pneumoniae, stau = S. aureus
+      x_length <- nchar(x.bak[i])
+      x[i] <- paste0(x.bak[i] %>% substr(1, x_length / 2) %>% trimws(),
+                     '.* ',
+                     x.bak[i] %>% substr((x_length / 2) + 1, x_length) %>% trimws())
+      found <- AMR::bactlist %>% filter(fullname %like% paste0('^', x[i]))
+    }
+    
+    if (nrow(found) != 0) {
+      x[i] <- found %>% 
+        slice(1) %>% 
+        pull(bactid)
+    } else {
+      x[i] <- ""
+    }
+  }
+  x
+}

R/globals.R

@@ -23,6 +23,7 @@ globalVariables(c('.',
                   'date_lab',
                   'days_diff',
                   'first_isolate_row_index',
+                  'fullname',
                   'genus',
                   'gramstain',
                   'key_ab',

R/join.R

@@ -4,23 +4,28 @@
 #' @rdname join
 #' @name join
 #' @aliases join inner_join
-#' @param x existing table to join
+#' @param x existing table to join, also supports character vectors
 #' @param by a variable to join by - could be a column name of \code{x} with values that exist in \code{bactlist$bactid} (like \code{by = "bacteria_id"}), or another column in \code{\link{bactlist}} (but then it should be named, like \code{by = c("my_genus_species" = "fullname")})
+#' @param suffix if there are non-joined duplicate variables in \code{x} and \code{y}, these suffixes will be added to the output to disambiguate them. Should be a character vector of length 2.
 #' @param ... other parameters to pass on to \code{dplyr::\link[dplyr]{join}}.
-#' @details As opposed to the \code{\link[dplyr]{join}} functions of \code{dplyr}, at default existing columns will get a suffix \code{"2"} and the newly joined columns will not get a suffix. See \code{\link[dplyr]{join}} for more information.
+#' @details As opposed to the \code{\link[dplyr]{join}} functions of \code{dplyr}, characters vectors are supported and at default existing columns will get a suffix \code{"2"} and the newly joined columns will not get a suffix. See \code{\link[dplyr]{join}} for more information.
 #' @export
 #' @examples 
+#' left_join_bactlist("STAAUR")
+#' 
 #' df <- data.frame(date = seq(from = as.Date("2018-01-01"),
 #'                             to = as.Date("2018-01-07"),
 #'                             by = 1),
 #'                  bacteria_id = c("STAAUR", "STAAUR", "STAAUR", "STAAUR",
 #'                                  "ESCCOL", "ESCCOL", "ESCCOL"),
 #'                  stringsAsFactors = FALSE)
-#'                  
 #' colnames(df)
 #' df2 <- left_join_bactlist(df, "bacteria_id")
 #' colnames(df2)
-inner_join_bactlist <- function(x, by = 'bactid', ...) {
+inner_join_bactlist <- function(x, by = 'bactid', suffix = c("2", ""), ...) {
+  if (any(class(x) %in% c('character', 'factor'))) {
+    x <- data.frame(bactid = x, stringsAsFactors = FALSE)
+  }
   # no name set to `by` parameter
   if (is.null(names(by))) {
     joinby <- colnames(AMR::bactlist)[1]
@@ -37,7 +42,10 @@ inner_join_bactlist <- function(x, by = 'bactid', ...) {
 
 #' @rdname join
 #' @export
-left_join_bactlist <- function(x, by = 'bactid', ...) {
+left_join_bactlist <- function(x, by = 'bactid', suffix = c("2", ""), ...) {
+  if (any(class(x) %in% c('character', 'factor'))) {
+    x <- data.frame(bactid = x, stringsAsFactors = FALSE)
+  }
   # no name set to `by` parameter
   if (is.null(names(by))) {
     joinby <- colnames(AMR::bactlist)[1]
@@ -54,7 +62,10 @@ left_join_bactlist <- function(x, by = 'bactid', ...) {
 
 #' @rdname join
 #' @export
-right_join_bactlist <- function(x, by = 'bactid', ...) {
+right_join_bactlist <- function(x, by = 'bactid', suffix = c("2", ""), ...) {
+  if (any(class(x) %in% c('character', 'factor'))) {
+    x <- data.frame(bactid = x, stringsAsFactors = FALSE)
+  }
   # no name set to `by` parameter
   if (is.null(names(by))) {
     joinby <- colnames(AMR::bactlist)[1]
@@ -71,7 +82,10 @@ right_join_bactlist <- function(x, by = 'bactid', ...) {
 
 #' @rdname join
 #' @export
-full_join_bactlist <- function(x, by = 'bactid', ...) {
+full_join_bactlist <- function(x, by = 'bactid', suffix = c("2", ""), ...) {
+  if (any(class(x) %in% c('character', 'factor'))) {
+    x <- data.frame(bactid = x, stringsAsFactors = FALSE)
+  }
   # no name set to `by` parameter
   if (is.null(names(by))) {
     joinby <- colnames(AMR::bactlist)[1]
@@ -85,6 +99,9 @@ full_join_bactlist <- function(x, by = 'bactid', ...) {
 #' @rdname join
 #' @export
 semi_join_bactlist <- function(x, by = 'bactid', ...) {
+  if (any(class(x) %in% c('character', 'factor'))) {
+    x <- data.frame(bactid = x, stringsAsFactors = FALSE)
+  }
   # no name set to `by` parameter
   if (is.null(names(by))) {
     joinby <- colnames(AMR::bactlist)[1]
@@ -98,6 +115,9 @@ semi_join_bactlist <- function(x, by = 'bactid', ...) {
 #' @rdname join
 #' @export
 anti_join_bactlist <- function(x, by = 'bactid', ...) {
+  if (any(class(x) %in% c('character', 'factor'))) {
+    x <- data.frame(bactid = x, stringsAsFactors = FALSE)
+  }
   # no name set to `by` parameter
   if (is.null(names(by))) {
     joinby <- colnames(AMR::bactlist)[1]

R/misc.R

@@ -19,17 +19,20 @@
 # No export, no Rd
 "%like%" <- function(vector, pattern) {
   # Source: https://github.com/Rdatatable/data.table/blob/master/R/like.R
+  # But made it case insensitive
   if (is.factor(vector)) {
-    as.integer(vector) %in% grep(pattern, levels(vector))
+    as.integer(vector) %in% grep(pattern, levels(vector), ignore.case = TRUE)
   } else {
-    grepl(pattern, vector)
+    grepl(pattern, vector, ignore.case = TRUE)
   }
 }
 
+# No export, no Rd
 percent <- function(x, round = 1, ...) {
   base::paste0(base::round(x * 100, digits = round), "%")
 }
 
+# No export, no Rd
 quasiquotate <- function(deparsed, parsed) {
   # when text: remove first and last "
   if (any(deparsed %like% '^".+"$' | deparsed %like% "^'.+'$")) {

README.md

@@ -28,7 +28,7 @@ This package is available on CRAN and also here on GitHub.
 
 ### From GitHub (latest development version)
 [![Travis_Build](https://travis-ci.org/msberends/AMR.svg?branch=master)](https://travis-ci.org/msberends/AMR)
-[![Since_Release](https://img.shields.io/github/commits-since/msberends/AMR/latest.svg?colorB=3679BC)](https://github.com/msberends/AMR/releases)
+[![Since_Release](https://img.shields.io/github/commits-since/msberends/AMR/latest.svg?colorB=3679BC)](https://github.com/msberends/AMR/commits/master)
 [![Last_Commit](https://img.shields.io/github/last-commit/msberends/AMR.svg?colorB=3679BC)](https://github.com/msberends/AMR/commits/master)
 
 ```r
@@ -116,7 +116,14 @@ A plot of `rsi_data`:
 plot(rsi_data)
 ```
 
-![example](man/figures/rsi_example.png)
+![example1](man/figures/rsi_example.png)
+
+A plot of `mic_data` (defaults to bar plot):
+```r
+plot(mic_data)
+```
+
+![example2](man/figures/mic_example.png)
 
 Other epidemiological functions:
 

man/ablist.Rd

@@ -1,34 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/data.R
-\docType{data}
-\name{ablist}
-\alias{ablist}
-\title{Dataset with 420 antibiotics}
-\format{A data.frame with 420 observations and 12 variables:
-\describe{
-  \item{\code{atc}}{ATC code, like \code{J01CR02}}
-  \item{\code{molis}}{MOLIS code, like \code{amcl}}
-  \item{\code{umcg}}{UMCG code, like \code{AMCL}}
-  \item{\code{official}}{Official name by the WHO, like \code{"amoxicillin and enzyme inhibitor"}}
-  \item{\code{official_nl}}{Official name in the Netherlands, like \code{"Amoxicilline met enzymremmer"}}
-  \item{\code{trivial_nl}}{Trivial name in Dutch, like \code{"Amoxicilline/clavulaanzuur"}}
-  \item{\code{oral_ddd}}{Defined Daily Dose (DDD) according to the WHO, oral treatment}
-  \item{\code{oral_units}}{Units of \code{ddd_units}}
-  \item{\code{iv_ddd}}{Defined Daily Dose (DDD) according to the WHO, parenteral treatment}
-  \item{\code{iv_units}}{Units of \code{iv_ddd}}
-  \item{\code{atc_group1}}{ATC group in Dutch, like \code{"Macroliden, lincosamiden en streptograminen"}}
-  \item{\code{atc_group2}}{Subgroup of \code{atc_group1} in Dutch, like \code{"Macroliden"}}
-}}
-\source{
-MOLIS (LIS of Certe) - \url{https://www.certe.nl} \cr \cr GLIMS (LIS of UMCG) - \url{https://www.umcg.nl} \cr \cr World Health Organization - \url{https://www.whocc.no/atc_ddd_index/}
-}
-\usage{
-ablist
-}
-\description{
-A dataset containing all antibiotics with a J0 code, with their DDD's.
-}
-\seealso{
-\code{\link{bactlist}}
-}
-\keyword{datasets}

man/abname.Rd

@@ -4,7 +4,7 @@
 \alias{abname}
 \title{Name of an antibiotic}
 \source{
-\code{\link{ablist}}
+\code{\link{antibiotics}}
 }
 \usage{
 abname(abcode, from = "umcg", to = "official", textbetween = " + ",
@@ -13,14 +13,14 @@ abname(abcode, from = "umcg", to = "official", textbetween = " + ",
 \arguments{
 \item{abcode}{a code or name, like \code{"AMOX"}, \code{"AMCL"} or \code{"J01CA04"}}
 
-\item{from, to}{type to transform from and to. See \code{\link{ablist}} for its column names.}
+\item{from, to}{type to transform from and to. See \code{\link{antibiotics}} for its column names.}
 
 \item{textbetween}{text to put between multiple returned texts}
 
 \item{tolower}{return output as lower case with function \code{\link{tolower}}.}
 }
 \description{
-Convert antibiotic codes (from a laboratory information system like MOLIS or GLIMS) to a (trivial) antibiotic name or ATC code, or vice versa. This uses the data from \code{\link{ablist}}.
+Convert antibiotic codes (from a laboratory information system like MOLIS or GLIMS) to a (trivial) antibiotic name or ATC code, or vice versa. This uses the data from \code{\link{antibiotics}}.
 }
 \examples{
 abname("AMCL")

man/antibiotics.Rd

@@ -0,0 +1,38 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/data.R
+\docType{data}
+\name{antibiotics}
+\alias{antibiotics}
+\title{Dataset with 420 antibiotics}
+\format{A data.frame with 420 observations and 16 variables:
+\describe{
+  \item{\code{atc}}{ATC code, like \code{J01CR02}}
+  \item{\code{molis}}{MOLIS code, like \code{amcl}}
+  \item{\code{umcg}}{UMCG code, like \code{AMCL}}
+  \item{\code{official}}{Official name by the WHO, like \code{"Amoxicillin and enzyme inhibitor"}}
+  \item{\code{official_nl}}{Official name in the Netherlands, like \code{"Amoxicilline met enzymremmer"}}
+  \item{\code{trivial_nl}}{Trivial name in Dutch, like \code{"Amoxicilline/clavulaanzuur"}}
+  \item{\code{oral_ddd}}{Defined Daily Dose (DDD), oral treatment}
+  \item{\code{oral_units}}{Units of \code{ddd_units}}
+  \item{\code{iv_ddd}}{Defined Daily Dose (DDD), parenteral treatment}
+  \item{\code{iv_units}}{Units of \code{iv_ddd}}
+  \item{\code{atc_group1}}{ATC group, like \code{"Macrolides, lincosamides and streptogramins"}}
+  \item{\code{atc_group2}}{Subgroup of \code{atc_group1}, like \code{"Macrolides"}}
+  \item{\code{atc_group1_nl}}{ATC group in Dutch, like \code{"Macroliden, lincosamiden en streptograminen"}}
+  \item{\code{atc_group2_nl}}{Subgroup of \code{atc_group1} in Dutch, like \code{"Macroliden"}}
+  \item{\code{useful_gramnegative}}{\code{FALSE} if not useful according to EUCAST, \code{NA} otherwise (see Source)}
+  \item{\code{useful_grampositive}}{\code{FALSE} if not useful according to EUCAST, \code{NA} otherwise (see Source)}
+}}
+\source{
+- World Health Organization: \url{https://www.whocc.no/atc_ddd_index/} \cr - EUCAST - Expert rules intrinsic exceptional V3.1 \cr - MOLIS (LIS of Certe): \url{https://www.certe.nl} \cr - GLIMS (LIS of UMCG): \url{https://www.umcg.nl}
+}
+\usage{
+antibiotics
+}
+\description{
+A dataset containing all antibiotics with a J0 code, with their DDD's. Properties were downloaded from the WHO, see Source.
+}
+\seealso{
+\code{\link{bactlist}}
+}
+\keyword{datasets}

man/bactlist.Rd

@@ -4,7 +4,7 @@
 \name{bactlist}
 \alias{bactlist}
 \title{Dataset with ~2500 microorganisms}
-\format{A data.frame with 2507 observations and 10 variables:
+\format{A data.frame with 2507 observations and 12 variables:
 \describe{
   \item{\code{bactid}}{ID of microorganism}
   \item{\code{bactsys}}{Bactsyscode of microorganism}
@@ -13,9 +13,11 @@
   \item{\code{species}}{Species name of microorganism, like \code{"coli"}}
   \item{\code{subspecies}}{Subspecies name of bio-/serovar of microorganism, like \code{"EHEC"}}
   \item{\code{fullname}}{Full name, like \code{"Echerichia coli (EHEC)"}}
-  \item{\code{type}}{Type of microorganism in Dutch, like \code{"Bacterie"} and \code{"Schimmel/gist"}}
+  \item{\code{type}}{Type of microorganism, like \code{"Bacteria"} and \code{"Fungus/yeast"}}
-  \item{\code{gramstain}}{Gram of microorganism in Dutch, like \code{"Negatieve staven"}}
+  \item{\code{gramstain}}{Gram of microorganism, like \code{"Negative rods"}}
-  \item{\code{aerobic}}{Type aerobe/anaerobe of bacteria}
+  \item{\code{aerobic}}{Logical whether bacteria is aerobic}
+  \item{\code{type_nl}}{Type of microorganism in Dutch, like \code{"Bacterie"} and \code{"Schimmel/gist"}}
+  \item{\code{gramstain_nl}}{Gram of microorganism in Dutch, like \code{"Negatieve staven"}}
 }}
 \source{
 MOLIS (LIS of Certe) - \url{https://www.certe.nl}
@@ -27,6 +29,6 @@ bactlist
 A dataset containing all microorganisms of MOLIS. MO codes of the UMCG can be looked up using \code{\link{bactlist.umcg}}.
 }
 \seealso{
-\code{\link{ablist}} \code{\link{bactlist.umcg}}
+\code{\link{guess_bactid}} \code{\link{antibiotics}} \code{\link{bactlist.umcg}}
 }
 \keyword{datasets}

man/guess_bactid.Rd

@@ -0,0 +1,31 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/first_isolates.R
+\name{guess_bactid}
+\alias{guess_bactid}
+\title{Find bacteria ID based on genus/species}
+\usage{
+guess_bactid(x)
+}
+\arguments{
+\item{x}{character vector to determine \code{bactid}}
+}
+\value{
+Character (vector).
+}
+\description{
+Use this function to determine a valid ID based on a genus (and species). This input could be a full name (like \code{"Staphylococcus aureus"}), an abbreviated name (like \code{"S. aureus"}), or just a genus. You could also use a \code{\link{paste}} of a genus and species column to use the full name as input: \code{x = paste(df$genus, df$species)}, where \code{df} is your dataframe.
+}
+\examples{
+# These examples all return "STAAUR", the ID of S. aureus:
+guess_bactid("stau")
+guess_bactid("STAU")
+guess_bactid("staaur")
+guess_bactid("S. aureus")
+guess_bactid("S aureus")
+guess_bactid("Staphylococcus aureus")
+guess_bactid("MRSA") # Methicillin-resistant S. aureus
+guess_bactid("VISA") # Vancomycin Intermediate S. aureus
+}
+\seealso{
+\code{\link{bactlist}} for the dataframe that is being used to determine ID's.
+}

man/join.Rd

@@ -11,39 +11,42 @@
 \alias{anti_join_bactlist}
 \title{Join a table with \code{bactlist}}
 \usage{
-inner_join_bactlist(x, by = "bactid", ...)
+inner_join_bactlist(x, by = "bactid", suffix = c("2", ""), ...)
 
-left_join_bactlist(x, by = "bactid", ...)
+left_join_bactlist(x, by = "bactid", suffix = c("2", ""), ...)
 
-right_join_bactlist(x, by = "bactid", ...)
+right_join_bactlist(x, by = "bactid", suffix = c("2", ""), ...)
 
-full_join_bactlist(x, by = "bactid", ...)
+full_join_bactlist(x, by = "bactid", suffix = c("2", ""), ...)
 
 semi_join_bactlist(x, by = "bactid", ...)
 
 anti_join_bactlist(x, by = "bactid", ...)
 }
 \arguments{
-\item{x}{existing table to join}
+\item{x}{existing table to join, also supports character vectors}
 
 \item{by}{a variable to join by - could be a column name of \code{x} with values that exist in \code{bactlist$bactid} (like \code{by = "bacteria_id"}), or another column in \code{\link{bactlist}} (but then it should be named, like \code{by = c("my_genus_species" = "fullname")})}
 
+\item{suffix}{if there are non-joined duplicate variables in \code{x} and \code{y}, these suffixes will be added to the output to disambiguate them. Should be a character vector of length 2.}
+
 \item{...}{other parameters to pass on to \code{dplyr::\link[dplyr]{join}}.}
 }
 \description{
 Join the list of microorganisms \code{\link{bactlist}} easily to an existing table.
 }
 \details{
-As opposed to the \code{\link[dplyr]{join}} functions of \code{dplyr}, at default existing columns will get a suffix \code{"2"} and the newly joined columns will not get a suffix. See \code{\link[dplyr]{join}} for more information.
+As opposed to the \code{\link[dplyr]{join}} functions of \code{dplyr}, characters vectors are supported and at default existing columns will get a suffix \code{"2"} and the newly joined columns will not get a suffix. See \code{\link[dplyr]{join}} for more information.
 }
 \examples{
+left_join_bactlist("STAAUR")
+
 df <- data.frame(date = seq(from = as.Date("2018-01-01"),
                             to = as.Date("2018-01-07"),
                             by = 1),
                  bacteria_id = c("STAAUR", "STAAUR", "STAAUR", "STAAUR",
                                  "ESCCOL", "ESCCOL", "ESCCOL"),
                  stringsAsFactors = FALSE)
-                 
 colnames(df)
 df2 <- left_join_bactlist(df, "bacteria_id")
 colnames(df2)

man/key_antibiotics.Rd

@@ -33,5 +33,5 @@ tbl$keyab <- key_antibiotics(tbl)
 }
 }
 \seealso{
-\code{\link{mo_property}} \code{\link{ablist}}
+\code{\link{mo_property}} \code{\link{antibiotics}}
 }

man/septic_patients.Rd

@@ -15,7 +15,7 @@
   \item{\code{sex}}{sex of the patient}
   \item{\code{patient_id}}{ID of the patient, first 10 characters of an SHA hash containing irretrievable information}
   \item{\code{bactid}}{ID of microorganism, see \code{\link{bactlist}}}
-  \item{\code{peni:mupi}}{38 different antibiotics with class \code{rsi} (see \code{\link{as.rsi}}), these column names occur in \code{\link{ablist}} and can be translated with \code{\link{abname}}}
+  \item{\code{peni:mupi}}{38 different antibiotics with class \code{rsi} (see \code{\link{as.rsi}}), these column names occur in \code{\link{antibiotics}} and can be translated with \code{\link{abname}}}
 }}
 \source{
 MOLIS (LIS of Certe) - \url{https://www.certe.nl}