v0.7.0

R/age.R

@@ -24,7 +24,7 @@
 #' Calculates age in years based on a reference date, which is the sytem date at default.
 #' @param x date(s), will be coerced with \code{\link{as.POSIXlt}}
 #' @param reference reference date(s) (defaults to today), will be coerced with \code{\link{as.POSIXlt}} and cannot be lower than \code{x}
-#' @param exact a logical to indicate whether age calculation should be exact, i.e. with decimals
+#' @param exact a logical to indicate whether age calculation should be exact, i.e. with decimals. It divides the number of days of \href{https://en.wikipedia.org/wiki/Year-to-date}{year-to-date} (YTD) of \code{x} by the number of days in a year of \code{reference} (either 365 or 366).
 #' @return An integer (no decimals) if \code{exact = FALSE}, a double (with decimals) otherwise
 #' @seealso \code{\link{age_groups}} to split age into age groups
 #' @importFrom dplyr if_else

R/amr.R

@@ -46,7 +46,7 @@
 #' Matthijs S. Berends[1,2] Christian F. Luz[1], Erwin E.A. Hassing[2],  Corinna Glasner[1],  Alex W. Friedrich[1],  Bhanu N.M. Sinha[1] \cr
 #'
 #' [1] Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands - \url{https://www.rug.nl} \url{https://www.umcg.nl} \cr
-#' [2] Certe Medical Diagnostics & Advice, Groningen, the Netherlands - \url{certe.nl}
+#' [2] Certe Medical Diagnostics & Advice, Groningen, the Netherlands - \url{https://www.certe.nl}
 
 #' @section Read more on our website!:
 #' On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.

R/data.R

@@ -78,7 +78,7 @@
 #' Names of prokaryotes are defined as being validly published by the International Code of Nomenclature of Bacteria. Validly published are all names which are included in the Approved Lists of Bacterial Names and the names subsequently published in the International Journal of Systematic Bacteriology (IJSB) and, from January 2000, in the International Journal of Systematic and Evolutionary Microbiology (IJSEM) as original articles or in the validation lists.
 #'
 #' From: \url{https://www.dsmz.de/support/bacterial-nomenclature-up-to-date-downloads/readme.html}
-#' @source Catalogue of Life: Annual Checklist (public online taxonomic database), \url{www.catalogueoflife.org} (check included annual version with \code{\link{catalogue_of_life_version}()}).
+#' @source Catalogue of Life: Annual Checklist (public online taxonomic database), \url{http://www.catalogueoflife.org} (check included annual version with \code{\link{catalogue_of_life_version}()}).
 #'
 #' Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Germany, Prokaryotic Nomenclature Up-to-Date, \url{http://www.dsmz.de/bacterial-diversity/prokaryotic-nomenclature-up-to-date} (check included version with \code{\link{catalogue_of_life_version}()}).
 #' @inheritSection AMR Read more on our website!
@@ -104,7 +104,7 @@ catalogue_of_life <- list(
 #'   \item{\code{fullname}}{Old full taxonomic name of the microorganism}
 #'   \item{\code{ref}}{Author(s) and year of concerning scientific publication}
 #' }
-#' @source Catalogue of Life: Annual Checklist (public online taxonomic database), \url{www.catalogueoflife.org} (check included annual version with \code{\link{catalogue_of_life_version}()}).
+#' @source Catalogue of Life: Annual Checklist (public online taxonomic database), \url{http://www.catalogueoflife.org} (check included annual version with \code{\link{catalogue_of_life_version}()}).
 #' @inheritSection AMR Read more on our website!
 #' @seealso \code{\link{as.mo}} \code{\link{mo_property}} \code{\link{microorganisms}}
 "microorganisms.old"

R/mdro.R

@@ -69,6 +69,9 @@ mdro <- function(x,
   if (length(guideline) > 1) {
     stop("`guideline` must be a length one character string.", call. = FALSE)
   }
+  if (length(country) > 1) {
+    stop("`country` must be a length one character string.", call. = FALSE)
+  }
   if (!is.null(country)) {
     guideline <- country
   }

R/misc.R

@@ -154,6 +154,7 @@ search_type_in_df <- function(x, type) {
   found
 }
 
+#' @importFrom crayon blue bold
 get_column_abx <- function(x,
                            soft_dependencies = NULL,
                            hard_dependencies = NULL,
@@ -219,10 +220,8 @@ get_column_abx <- function(x,
     if (!all(soft_dependencies %in% names(x))) {
       # missing a soft dependency may lower the reliability
       missing <- soft_dependencies[!soft_dependencies %in% names(x)]
-      missing <- paste0(missing, " (", ab_name(missing, tolower = TRUE), ")")
-      warning('Reliability might be improved if these antimicrobial results would be available too: ', paste(missing, collapse = ", "),
-              immediate. = TRUE,
-              call. = FALSE)
+      missing <- paste0(bold(missing), " (", ab_name(missing, tolower = TRUE), ")")
+      message(blue('NOTE: Reliability might be improved if these antimicrobial results would be available too:', paste(missing, collapse = ", ")))
     }
   }
   x

R/mo.R

@@ -130,7 +130,7 @@
 #'
 #' [3] Lancefield RC \strong{A serological differentiation of human and other groups of hemolytic streptococci}. 1933. J Exp Med. 57(4): 571–95. \url{https://dx.doi.org/10.1084/jem.57.4.571}
 #'
-#' [4] Catalogue of Life: Annual Checklist (public online taxonomic database), \url{www.catalogueoflife.org} (check included annual version with \code{\link{catalogue_of_life_version}()}).
+#' [4] Catalogue of Life: Annual Checklist (public online taxonomic database), \url{http://www.catalogueoflife.org} (check included annual version with \code{\link{catalogue_of_life_version}()}).
 #' @export
 #' @return Character (vector) with class \code{"mo"}
 #' @seealso \code{\link{microorganisms}} for the \code{data.frame} that is being used to determine ID's. \cr

R/zzz.R

@@ -254,6 +254,7 @@ make_trans_tbl <- function() {
     F_CCCCS = "F_CRYPT",
     # renamings of old genus + species
     F_CANDD_GLB = "F_CANDD_GLA", F_CANDD_KRU = "F_ISSTC_ORI",
+    F_CANDD_GUI = "F_MYRZY_GUI",
     F_CANDD_LUS = "F_CLVSP_LUS", B_STRPT_TUS = "B_STRPT",
     B_PRVTL_OLA = "B_PRVTL_OULO", B_FSBCT_RUM = "B_FSBCT",
     B_CRYNB_EYI = "B_CRYNB_FRE", B_OLGLL_LIS = "B_OLGLL_URE")