fix documentation

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 2.0.0.9002
+Version: 2.0.0.9003
-Date: 2023-03-14
+Date: 2023-03-16
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)
   data analysis and to work with microbial and antimicrobial properties by

NEWS.md

@@ -1,4 +1,10 @@
-# AMR 2.0.0.9002
+# AMR 2.0.0.9003
+
+## Changed
+* formatting fix for `sir_interpretation_history()`
+
+
+# AMR 2.0.0
 
 This is a new major release of the AMR package, with great new additions but also some breaking changes for current users. These are all listed below.
 

R/aa_helper_functions.R

@@ -670,10 +670,15 @@ create_eucast_ab_documentation <- function() {
   atcs <- ab_atc(ab, only_first = TRUE)
   # only keep ABx with an ATC code:
   ab <- ab[!is.na(atcs)]
+  atcs <- atcs[!is.na(atcs)]
+
+  # sort all vectors on name:
   ab_names <- ab_name(ab, language = NULL, tolower = TRUE)
   ab <- ab[order(ab_names)]
+  atcs <- atcs[order(ab_names)]
   ab_names <- ab_names[order(ab_names)]
-  atc_txt <- paste0("[", atcs[!is.na(atcs)], "](", ab_url(ab), ")")
+  # create the text:
+  atc_txt <- paste0("[", atcs, "](", ab_url(ab), ")")
   out <- paste0(ab_names, " (`", ab, "`, ", atc_txt, ")", collapse = ", ")
   substr(out, 1, 1) <- toupper(substr(out, 1, 1))
   out

R/like.R

@@ -49,8 +49,8 @@
 #' @seealso [grepl()]
 
 #' @examples
-#' # data.table has a more limited version of %like%, so:
+#' # data.table has a more limited version of %like%, so unload it:
-#' detach("package:data.table", unload = TRUE)
+#' try(detach("package:data.table", unload = TRUE), silent = TRUE)
 #' 
 #' a <- "This is a test"
 #' b <- "TEST"

R/zzz.R

@@ -59,16 +59,15 @@ AMR_env$sir_interpretation_history <- data.frame(
   datetime = Sys.time()[0],
   index = integer(0),
   ab_input = character(0),
-  ab_considered = character(0),
+  ab_guideline = set_clean_class(character(0), c("ab", "character")),
   mo_input = character(0),
-  mo_considered = character(0),
+  mo_guideline = set_clean_class(character(0), c("mo", "character")),
   guideline = character(0),
   ref_table = character(0),
   method = character(0),
-  breakpoint_S = double(0),
-  breakpoint_R = double(0),
   input = double(0),
-  interpretation = character(0),
+  outcome = NA_sir_[0],
+  breakpoint_S_R = character(0),
   stringsAsFactors = FALSE
 )
 AMR_env$custom_ab_codes <- character(0)

data-raw/_pre_commit_hook.R

@@ -31,6 +31,7 @@
 # source("data-raw/_pre_commit_hook.R")
 
 library(dplyr, warn.conflicts = FALSE)
+try(detach("package:data.table", unload = TRUE), silent = TRUE)
 devtools::load_all(quiet = TRUE)
 
 suppressMessages(set_AMR_locale("English"))

man/AMR.Rd

@@ -32,7 +32,7 @@ The \code{AMR} package is a \href{https://msberends.github.io/AMR/#copyright}{fr
 
 This work was published in the Journal of Statistical Software (Volume 104(3); \doi{jss.v104.i03}) and formed the basis of two PhD theses (\doi{10.33612/diss.177417131} and \doi{10.33612/diss.192486375}).
 
-After installing this package, R knows \href{https://msberends.github.io/AMR/reference/microorganisms.html}{\strong{~52 000 microorganisms}} (updated december 2022) and all \href{https://msberends.github.io/AMR/reference/antibiotics.html}{\strong{~600 antibiotic, antimycotic and antiviral drugs}} by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral breakpoint guidelines from CLSI and EUCAST are included from the last 10 years. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). \strong{It was designed to work in any setting, including those with very limited resources}. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the \href{https://www.rug.nl}{University of Groningen}, in collaboration with non-profit organisations \href{https://www.certe.nl}{Certe Medical Diagnostics and Advice Foundation} and \href{https://www.umcg.nl}{University Medical Center Groningen}.
+After installing this package, R knows \href{https://msberends.github.io/AMR/reference/microorganisms.html}{\strong{~52 000 microorganisms}} (updated December 2022) and all \href{https://msberends.github.io/AMR/reference/antibiotics.html}{\strong{~600 antibiotic, antimycotic and antiviral drugs}} by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral breakpoint guidelines from CLSI and EUCAST are included from the last 10 years. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). \strong{It was designed to work in any setting, including those with very limited resources}. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the \href{https://www.rug.nl}{University of Groningen}, in collaboration with non-profit organisations \href{https://www.certe.nl}{Certe Medical Diagnostics and Advice Foundation} and \href{https://www.umcg.nl}{University Medical Center Groningen}.
 
 The \code{AMR} package is available in English, Chinese, Czech, Danish, Dutch, Finnish, French, German, Greek, Italian, Japanese, Norwegian, Polish, Portuguese, Romanian, Russian, Spanish, Swedish, Turkish, and Ukrainian. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages.
 }

man/like.Rd

@@ -46,8 +46,8 @@ These \code{\link[=like]{like()}} and \verb{\%like\%}/\verb{\%unlike\%} function
 Using RStudio? The \verb{\%like\%}/\verb{\%unlike\%} functions can also be directly inserted in your code from the Addins menu and can have its own keyboard shortcut like \code{Shift+Ctrl+L} or \code{Shift+Cmd+L} (see menu \code{Tools} > \verb{Modify Keyboard Shortcuts...}). If you keep pressing your shortcut, the inserted text will be iterated over \verb{\%like\%} -> \verb{\%unlike\%} -> \verb{\%like_case\%} -> \verb{\%unlike_case\%}.
 }
 \examples{
-# data.table has a more limited version of \%like\%, so:
+# data.table has a more limited version of \%like\%, so unload it:
-detach("package:data.table", unload = TRUE)
+try(detach("package:data.table", unload = TRUE), silent = TRUE)
 
 a <- "This is a test"
 b <- "TEST"