From f7dd890b79d765ec68b921c36ae9ad2c51952f67 Mon Sep 17 00:00:00 2001
From: "Matthijs S. Berends" <m.s.berends@umcg.nl>
Date: Mon, 6 Feb 2023 12:38:52 +0100
Subject: [PATCH] fixes

---
 DESCRIPTION        |  2 +-
 NEWS.md            |  2 +-
 R/aa_globals.R     | 14 ++++++++++----
 R/ab_property.R    |  2 +-
 R/antibiogram.R    | 14 +++++++++-----
 man/antibiogram.Rd |  4 ++++
 6 files changed, 26 insertions(+), 12 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 6fe7c1ea..0a30c9b8 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: AMR
-Version: 1.8.2.9106
+Version: 1.8.2.9107
 Date: 2023-02-06
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)
diff --git a/NEWS.md b/NEWS.md
index d66e8e7e..acc5b44b 100755
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,4 +1,4 @@
-# AMR 1.8.2.9106
+# AMR 1.8.2.9107
 
 *(this beta version will eventually become v2.0! We're happy to reach a new major milestone soon!)*
 
diff --git a/R/aa_globals.R b/R/aa_globals.R
index e87f094f..ee47c959 100755
--- a/R/aa_globals.R
+++ b/R/aa_globals.R
@@ -94,7 +94,9 @@ TAXONOMY_VERSION <- list(
 )
 
 globalVariables(c(
+  ".mo",
   ".rowid",
+  ".syndromic_group",
   "ab",
   "ab_txt",
   "affect_ab_name",
@@ -105,8 +107,9 @@ globalVariables(c(
   "atc_group1",
   "atc_group2",
   "base_ab",
-  "ci_min",
   "ci_max",
+  "ci_min",
+  "clinical_breakpoints",
   "code",
   "cols",
   "count",
@@ -130,14 +133,15 @@ globalVariables(c(
   "language",
   "lookup",
   "method",
-  "mic",
   "mic ",
+  "mic",
   "microorganism",
   "microorganisms",
   "microorganisms.codes",
   "mo",
   "name",
   "new",
+  "numerator",
   "observations",
   "old",
   "old_name",
@@ -149,13 +153,15 @@ globalVariables(c(
   "reference.rule_group",
   "reference.version",
   "rowid",
-  "sir",
-  "clinical_breakpoints",
   "rule_group",
   "rule_name",
+  "S",
   "se_max",
   "se_min",
+  "SI",
+  "sir",
   "species",
+  "syndromic_group",
   "total",
   "txt",
   "type",
diff --git a/R/ab_property.R b/R/ab_property.R
index 52eb469e..16e9784d 100755
--- a/R/ab_property.R
+++ b/R/ab_property.R
@@ -363,7 +363,7 @@ set_ab_names <- function(data, ..., property = "name", language = get_AMR_locale
 
   if (is.data.frame(data)) {
     if (tryCatch(length(list(...)) > 0, error = function(e) TRUE)) {
-      out <- tryCatch(suppressWarnings(c(...)), error = function(e) NULL)
+      out <- tryCatch(suppressWarnings(unlist(list(...))), error = function(e) NULL)
       if (!is.null(out)) {
         df <- data[, out, drop = FALSE]
       } else {
diff --git a/R/antibiogram.R b/R/antibiogram.R
index dbec5b7d..4aa951a0 100755
--- a/R/antibiogram.R
+++ b/R/antibiogram.R
@@ -43,6 +43,8 @@
 #' @param minimum the minimum allowed number of available (tested) isolates. Any isolate count lower than `minimum` will return `NA` with a warning. The default number of `30` isolates is advised by the Clinical and Laboratory Standards Institute (CLSI) as best practice, see *Source*.
 #' @param combine_SI a [logical] to indicate whether all susceptibility should be determined by results of either S or I, instead of only S (defaults to `TRUE`)
 #' @param sep a separating character for antibiotic columns in combination antibiograms
+#' @param object an [antibiogram()] object
+#' @param ... method extensions
 #' @details This function returns a table with values between 0 and 100 for *susceptibility*, not resistance.
 #' 
 #' **Remember that you should filter your data to let it contain only first isolates!** This is needed to exclude duplicates and to reduce selection bias. Use [first_isolate()] to determine them in your data set with one of the four available algorithms.
@@ -314,7 +316,7 @@ antibiogram <- function(x,
     if (identical(select, import_fn("select", "dplyr", error_on_fail = FALSE))) {
       antibiotics <- suppressWarnings(x %>% select({{ antibiotics }}) %>% colnames())
     } else {
-      antibiotics <- x %>% select(antibiotics) %>% colnames()
+      antibiotics <- colnames(x[, antibiotics, drop = FALSE])
     }
   }
   
@@ -447,9 +449,9 @@ plot.antibiogram <- function(x, ...) {
     df <- df[order(df$mo), , drop = FALSE]
   }
   mo_levels = unique(df$mo)
-  mfrow_old <- par()$mfrow
+  mfrow_old <- graphics::par()$mfrow
   sqrt_levels <- sqrt(length(mo_levels))
-  par(mfrow = c(ceiling(sqrt_levels), floor(sqrt_levels)))
+  graphics::par(mfrow = c(ceiling(sqrt_levels), floor(sqrt_levels)))
   for (i in seq_along(mo_levels)) {
     mo <- mo_levels[i]
     df_sub <- df[df$mo == mo, , drop = FALSE]
@@ -463,12 +465,14 @@ plot.antibiogram <- function(x, ...) {
             main = mo,
             legend = NULL)
   }
-  par(mfrow = mfrow_old)
+  graphics::par(mfrow = mfrow_old)
 }
 
 #' @export
 #' @noRd
-barplot.antibiogram <- plot.antibiogram
+barplot.antibiogram <- function(height, ...) {
+  plot(height, ...)
+}
 
 #' @method autoplot antibiogram
 #' @rdname antibiogram
diff --git a/man/antibiogram.Rd b/man/antibiogram.Rd
index efaabee3..36f122e9 100644
--- a/man/antibiogram.Rd
+++ b/man/antibiogram.Rd
@@ -63,6 +63,10 @@ antibiogram(
 
 \item{sep}{a separating character for antibiotic columns in combination antibiograms}
 
+\item{...}{method extensions}
+
+\item{object}{an \code{\link[=antibiogram]{antibiogram()}} object}
+
 \item{as_kable}{a \link{logical} to indicate whether the printing should be done using \code{\link[knitr:kable]{knitr::kable()}} (which is the default in non-interactive sessions)}
 }
 \description{