CRAN fixes for release 0.4.0

https://cran.r-project.org/web/checks/check_results_AMR.html

R/eucast.R

@@ -20,7 +20,7 @@
 #'
 #' Apply expert rules (like intrinsic resistance), as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, \url{http://eucast.org}), see \emph{Source}.
 #' @param tbl table with antibiotic columns, like e.g. \code{amox} and \code{amcl}
-#' @param col_mo column name of the bacteria ID in \code{tbl} - values of this column should be present in \code{microorganisms$mo}, see \code{\link{microorganisms}}
+#' @param col_mo column name of the microbial ID in \code{tbl} - values in this column should be present in \code{microorganisms$mo}, see \code{\link{microorganisms}}
 #' @param info print progress
 #' @param amcl,amik,amox,ampi,azit,azlo,aztr,cefa,cfep,cfot,cfox,cfra,cfta,cftr,cfur,chlo,cipr,clar,clin,clox,coli,czol,dapt,doxy,erta,eryt,fosf,fusi,gent,imip,kana,levo,linc,line,mero,mezl,mino,moxi,nali,neom,neti,nitr,norf,novo,oflo,peni,pita,poly,pris,qida,rifa,roxi,siso,teic,tetr,tica,tige,tobr,trim,trsu,vanc column name of an antibiotic. Use \code{NA} to skip a column, like \code{tica = NA}. Non-existing columns will anyway be skipped. See the Antibiotics section for an explanation of the abbreviations.
 #' @param col_bactid Deprecated. Use \code{col_mo} instead.
@@ -103,11 +103,12 @@
 #'   \url{http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf}
 #' @examples
 #' a <- EUCAST_rules(septic_patients)
-#' a <- data.frame(mo = c("STAAUR",  # Staphylococcus aureus
-#'                        "ENCFAE",  # Enterococcus faecalis
-#'                        "ESCCOL",  # Escherichia coli
-#'                        "KLEPNE",  # Klebsiella pneumoniae
-#'                        "PSEAER"), # Pseudomonas aeruginosa
+#'
+#' a <- data.frame(mo = c("Staphylococcus aureus",
+#'                        "Enterococcus faecalis",
+#'                        "Escherichia coli",
+#'                        "Klebsiella pneumoniae",
+#'                        "Pseudomonas aeruginosa"),
 #'                 vanc = "-",       # Vancomycin
 #'                 amox = "-",       # Amoxicillin
 #'                 coli = "-",       # Colistin
@@ -116,7 +117,7 @@
 #'                 stringsAsFactors = FALSE)
 #' a
 #'
-#' b <- EUCAST_rules(a)
+#' b <- EUCAST_rules(a) # 11 results will be forced as R due to intrinsic resistance
 #' b
 EUCAST_rules <- function(tbl,
                          col_mo = 'mo',

R/freq.R

@@ -58,6 +58,7 @@
 #' @importFrom grDevices boxplot.stats
 #' @importFrom dplyr %>% select pull n_distinct group_by arrange desc mutate summarise n_distinct tibble
 #' @importFrom utils browseVignettes installed.packages
+#' @importFrom hms is.hms
 #' @keywords summary summarise frequency freq
 #' @rdname freq
 #' @name freq
@@ -366,7 +367,7 @@ frequency_tbl <- function(x,
   }
 
   formatdates <- "%e %B %Y" # = d mmmm yyyy
-  if (any(class(x) == 'hms')) {
+  if (is.hms(x)) {
     x <- x %>% as.POSIXlt()
     formatdates <- "%H:%M:%S"
   }

R/mo.R

@@ -63,7 +63,7 @@
 #' \if{html}{\figure{itis_logo.jpg}{options: height=60px style=margin-bottom:5px} \cr}
 #' This package contains the \strong{complete microbial taxonomic data} (with all  seven taxonomic ranks - from subkingdom to subspecies) from the publicly available Integrated Taxonomic Information System (ITIS, \url{https://www.itis.gov}).
 #'
-#' The complete taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package, as well as all previously accepted names known to ITIS. Furthermore, the responsible authors and year of publication are available too. This allows users to use authoritative taxonomic information for their data analyses on any microorganisms, not only human pathogens.
+#' All (sub)species from the taxonomic kingdoms Bacteria, Fungi and Protozoa are included in this package, as well as all previously accepted names known to ITIS. Furthermore, the responsible authors and year of publication are available. This allows users to use authoritative taxonomic information for their data analysis on any microorganism, not only human pathogens.
 #'
 #' ITIS is a partnership of U.S., Canadian, and Mexican agencies and taxonomic specialists [3].
 #  (source as a section, so it can be inherited by other man pages:)

R/mo_property.R

@@ -22,7 +22,7 @@
 #' @param x any (vector of) text that can be coerced to a valid microorganism code with \code{\link{as.mo}}
 #' @param property one of the column names of one of the \code{\link{microorganisms}} data set or \code{"shortname"}
 #' @param language language of the returned text, defaults to English (\code{"en"}) and can also be set with \code{\link{getOption}("AMR_locale")}. Either one of \code{"en"} (English), \code{"de"} (German), \code{"nl"} (Dutch), \code{"es"} (Spanish) or \code{"pt"} (Portuguese).
-#' @param ... other parameters passed on to \code{/link{as.mo}}
+#' @param ... other parameters passed on to \code{\link{as.mo}}
 #' @inheritSection as.mo ITIS
 #' @inheritSection as.mo Source
 #' @rdname mo_property