misc

R/EUCAST.R

@@ -45,10 +45,10 @@
 #'                 stringsAsFactors = FALSE)
 #' a
 #' 
-#' b <- EUCAST_rules(a)
+#' b <- EUCAST_rules(a, "bactid")
 #' b
 EUCAST_rules <- function(tbl,
-                         col_bactcode = 'bactid',
+                         col_bactcode,
                          info = TRUE,
                          amcl = 'amcl',
                          amik = 'amik',

R/atc.R

@@ -128,7 +128,7 @@ 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}}.
-#' @param abcode a code or name, like \code{"amox"}, \code{"cftr"} or \code{"J01CA04"}
+#' @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 textbetween text to put between multiple returned texts
 #' @param tolower return output as lower case with function \code{\link{tolower}}.
@@ -146,7 +146,7 @@ atc_property <- function(atc_code,
 #' abname(c("AMCL", "GENT"))
 #' # "amoxicillin and enzyme inhibitor" "gentamicin" 
 #'
-#' abname("AMCL", to = "trivial")
+#' abname("AMCL", to = "trivial_nl")
 #' # "Amoxicilline/clavulaanzuur"
 #'
 #' abname("AMCL", to = "atc")
@@ -210,7 +210,7 @@ abname <- function(abcode, from = 'umcg', to = 'official', textbetween = ' + ',
           select(to) %>%
           slice(1) %>%
           as.character()
-        if (j > 1 & to %in% c('official', 'trivial')) {
+        if (j > 1 & to %in% c('official', 'trivial_nl')) {
           drug.group[j] <- drug.group[j] %>% tolower()
         }
       }

R/data.R

@@ -26,7 +26,7 @@
 #'   \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}}{Trivial name in Dutch, like \code{"Amoxicilline/clavulaanzuur"}}
+#'   \item{\code{trivial_nl}}{Trivial name in Dutch, like \code{"Amoxicilline/clavulaanzuur"}}
 #'   \item{\code{oral_ddd}}{Daily Defined Dose (DDD) according to the WHO, oral treatment}
 #'   \item{\code{oral_units}}{Units of \code{ddd_units}}
 #'   \item{\code{iv_ddd}}{Daily Defined Dose (DDD) according to the WHO, parenteral treatment}

R/rsi_analysis.R

@@ -254,7 +254,8 @@ rsi <- function(ab1, ab2 = NA, interpretation = 'IR', minimum = 30, percent = FA
 #' @examples
 #' \dontrun{
 #' # use it directly:
-#' rsi_predict(tbl[which(first_isolate == TRUE & genus == "Haemophilus"),], col_ab = "amcl", coldate = "date")
+#' rsi_predict(tbl = tbl[which(first_isolate == TRUE & genus == "Haemophilus"),],
+#'             col_ab = "amcl", coldate = "date")
 #'   
 #' # or with dplyr so you can actually read it:
 #' library(dplyr)

man/EUCAST.Rd

@@ -13,22 +13,21 @@ EUCAST Expert Rules Version 2.0: \cr
   \url{http://www.eucast.org/expert_rules_and_intrinsic_resistance}
 }
 \usage{
-EUCAST_rules(tbl, col_bactcode = "bactid", info = TRUE, amcl = "amcl",
-  amik = "amik", amox = "amox", ampi = "ampi", azit = "azit",
-  aztr = "aztr", cefa = "cefa", cfra = "cfra", cfep = "cfep",
-  cfot = "cfot", cfox = "cfox", cfta = "cfta", cftr = "cftr",
-  cfur = "cfur", chlo = "chlo", cipr = "cipr", clar = "clar",
-  clin = "clin", clox = "clox", coli = "coli", czol = "czol",
-  dapt = "dapt", doxy = "doxy", erta = "erta", eryt = "eryt",
-  fosf = "fosf", fusi = "fusi", gent = "gent", imip = "imip",
-  kana = "kana", levo = "levo", linc = "linc", line = "line",
-  mero = "mero", mino = "mino", moxi = "moxi", nali = "nali",
-  neom = "neom", neti = "neti", nitr = "nitr", novo = "novo",
-  norf = "norf", oflo = "oflo", peni = "peni", pita = "pita",
-  poly = "poly", qida = "qida", rifa = "rifa", roxi = "roxi",
-  siso = "siso", teic = "teic", tetr = "tetr", tica = "tica",
-  tige = "tige", tobr = "tobr", trim = "trim", trsu = "trsu",
-  vanc = "vanc")
+EUCAST_rules(tbl, col_bactcode, info = TRUE, amcl = "amcl", amik = "amik",
+  amox = "amox", ampi = "ampi", azit = "azit", aztr = "aztr",
+  cefa = "cefa", cfra = "cfra", cfep = "cfep", cfot = "cfot",
+  cfox = "cfox", cfta = "cfta", cftr = "cftr", cfur = "cfur",
+  chlo = "chlo", cipr = "cipr", clar = "clar", clin = "clin",
+  clox = "clox", coli = "coli", czol = "czol", dapt = "dapt",
+  doxy = "doxy", erta = "erta", eryt = "eryt", fosf = "fosf",
+  fusi = "fusi", gent = "gent", imip = "imip", kana = "kana",
+  levo = "levo", linc = "linc", line = "line", mero = "mero",
+  mino = "mino", moxi = "moxi", nali = "nali", neom = "neom",
+  neti = "neti", nitr = "nitr", novo = "novo", norf = "norf",
+  oflo = "oflo", peni = "peni", pita = "pita", poly = "poly",
+  qida = "qida", rifa = "rifa", roxi = "roxi", siso = "siso",
+  teic = "teic", tetr = "tetr", tica = "tica", tige = "tige",
+  tobr = "tobr", trim = "trim", trsu = "trsu", vanc = "vanc")
 
 interpretive_reading(...)
 }
@@ -59,6 +58,6 @@ a <- data.frame(bactid = c("STAAUR", "ESCCOL", "KLEPNE", "PSEAER"),
                 stringsAsFactors = FALSE)
 a
 
-b <- EUCAST_rules(a)
+b <- EUCAST_rules(a, "bactid")
 b
 }

man/ablist.Rd

@@ -11,7 +11,7 @@
   \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}}{Trivial name in Dutch, like \code{"Amoxicilline/clavulaanzuur"}}
+  \item{\code{trivial_nl}}{Trivial name in Dutch, like \code{"Amoxicilline/clavulaanzuur"}}
   \item{\code{oral_ddd}}{Daily Defined Dose (DDD) according to the WHO, oral treatment}
   \item{\code{oral_units}}{Units of \code{ddd_units}}
   \item{\code{iv_ddd}}{Daily Defined Dose (DDD) according to the WHO, parenteral treatment}

man/abname.Rd

@@ -11,7 +11,7 @@ abname(abcode, from = "umcg", to = "official", textbetween = " + ",
   tolower = FALSE)
 }
 \arguments{
-\item{abcode}{a code or name, like \code{"amox"}, \code{"cftr"} or \code{"J01CA04"}}
+\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.}
 
@@ -32,7 +32,7 @@ abname("AMCL+GENT")
 abname(c("AMCL", "GENT"))
 # "amoxicillin and enzyme inhibitor" "gentamicin" 
 
-abname("AMCL", to = "trivial")
+abname("AMCL", to = "trivial_nl")
 # "Amoxicilline/clavulaanzuur"
 
 abname("AMCL", to = "atc")

man/rsi_predict.Rd

@@ -37,7 +37,8 @@ Create a prediction model to predict antimicrobial resistance for the next years
 \examples{
 \dontrun{
 # use it directly:
-rsi_predict(tbl[which(first_isolate == TRUE & genus == "Haemophilus"),], col_ab = "amcl", coldate = "date")
+rsi_predict(tbl = tbl[which(first_isolate == TRUE & genus == "Haemophilus"),],
+            col_ab = "amcl", coldate = "date")
   
 # or with dplyr so you can actually read it:
 library(dplyr)