(v1.3.0.9008) also tibble printing for ab

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 1.3.0.9007
+Version: 1.3.0.9008
 Date: 2020-08-26
 Title: Antimicrobial Resistance Analysis
 Authors@R: c(

NAMESPACE

@@ -40,6 +40,7 @@ S3method(format,bug_drug_combinations)
 S3method(kurtosis,data.frame)
 S3method(kurtosis,default)
 S3method(kurtosis,matrix)
+S3method(pillar_shaft,ab)
 S3method(pillar_shaft,disk)
 S3method(pillar_shaft,mic)
 S3method(pillar_shaft,mo)
@@ -62,6 +63,7 @@ S3method(skewness,matrix)
 S3method(summary,mic)
 S3method(summary,mo)
 S3method(summary,rsi)
+S3method(type_sum,ab)
 S3method(type_sum,disk)
 S3method(type_sum,mic)
 S3method(type_sum,mo)

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 1.3.0.9007
+# AMR 1.3.0.9008
 ## <small>Last updated: 26 August 2020</small>
 
 ### New

R/aa_helper_functions.R

@@ -575,9 +575,9 @@ isFALSE <- function(x) {
 deparse1 <- function(expr, collapse = " ", width.cutoff = 500L, ...) {
   paste(deparse(expr, width.cutoff, ...), collapse = collapse)
 }
-file.size <- function (...) {
+file.size <- function(...) {
   base::file.info(...)$size
 }
-file.mtime <- function (...) {
+file.mtime <- function(...) {
   base::file.info(...)$mtime
 }

R/ab.R

@@ -467,6 +467,26 @@ is.ab <- function(x) {
   inherits(x, "ab")
 }
 
+
+#' @method pillar_shaft ab
+#' @export
+pillar_shaft.ab <- function(x, ...) {
+  # import from the pillar package, without being dependent on it!
+  style_na <- import_fn("style_na", "pillar", error_on_fail = FALSE)
+  new_pillar_shaft_simple <- import_fn("new_pillar_shaft_simple", "pillar", error_on_fail = FALSE)
+  out <- format(x)
+  out[is.na(x)] <- style_na(NA)
+  new_pillar_shaft_simple(out,
+                          align = "left", 
+                          min_width = 4)
+}
+
+#' @method type_sum ab
+#' @export
+type_sum.ab <- function(x, ...) {
+  "ab"
+}
+
 #' @method print ab
 #' @export
 #' @noRd

R/eucast_rules.R

@@ -40,17 +40,12 @@ EUCAST_VERSION_EXPERT_RULES <- "3.1, 2016"
 #' **Note:** This function does not translate MIC values to RSI values. Use [as.rsi()] for that. \cr
 #' **Note:** When ampicillin (AMP, J01CA01) is not available but amoxicillin (AMX, J01CA04) is, the latter will be used for all rules where there is a dependency on ampicillin. These drugs are interchangeable when it comes to expression of antimicrobial resistance.
 #'
-#' Before further processing, some non-EUCAST rules can be applied to improve the efficacy of the EUCAST rules. These non-EUCAST rules, that are then applied to all isolates, are:
-#' - Inherit amoxicillin (AMX) from ampicillin (AMP), where amoxicillin (AMX) is unavailable;
-#' - Inherit ampicillin (AMP) from amoxicillin (AMX), where ampicillin (AMP) is unavailable;
-#' - Set amoxicillin (AMX) = R where amoxicillin/clavulanic acid (AMC) = R;
-#' - Set piperacillin (PIP) = R where piperacillin/tazobactam (TZP) = R;
-#' - Set trimethoprim (TMP) = R where trimethoprim/sulfamethoxazole (SXT) = R;
-#' - Set amoxicillin/clavulanic acid (AMC) = S where amoxicillin (AMX) = S;
-#' - Set piperacillin/tazobactam (TZP) = S where piperacillin (PIP) = S;
-#' - Set trimethoprim/sulfamethoxazole (SXT) = S where trimethoprim (TMP) = S.
+#' Before further processing, two non-EUCAST rules about drug combinations can be applied to improve the efficacy of the EUCAST rules. These rules are:
 #' 
-#' These rules are not applied at default, since they are not approved by EUCAST. To use these rules, please use `eucast_rules(..., rules = "all")`, or set the default behaviour of the `[eucast_rules()]` function with `options(AMR.eucast_rules = "all")` (or any other valid input value(s) to the `rules` parameter).
+#' 1. A drug **with** enzyme inhibitor will be set to S if the drug **without** enzyme inhibitor is S
+#' 2. A drug **without** enzyme inhibitor will be set to R if the drug **with** enzyme inhibitor is R
+#' 
+#' These rules are not applied at default, since they are not approved by EUCAST. To use these rules, use `eucast_rules(..., rules = "all")`, or set the default behaviour of the `[eucast_rules()]` function with `options(AMR.eucast_rules = "all")` (or any other valid input value(s) to the `rules` parameter).
 #'
 #' The file containing all EUCAST rules is located here: <https://github.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv>.
 #'

R/globals.R

@@ -19,9 +19,11 @@
 # Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
 
-globalVariables(c("ab",
+globalVariables(c(".rowid",
+                  "ab",
                   "ab_txt",
                   "angle",
+                  "antibiotic",
                   "antibiotics",
                   "atc_group1",
                   "atc_group2",
@@ -35,9 +37,11 @@ globalVariables(c("ab",
                   "group",
                   "hjust",
                   "input",
+                  "intrinsic_resistant",
                   "isolates",
                   "lang",
                   "lookup",
+                  "microorganism",
                   "microorganisms",
                   "microorganisms.codes",
                   "microorganisms.old",

R/zzz.R

@@ -29,6 +29,8 @@
          envir = asNamespace("AMR"))
   
   # support for tibble headers (type_sum) and tibble columns content (pillar_shaft)
+  s3_register("pillar::pillar_shaft", "ab")
+  s3_register("tibble::type_sum", "ab")
   s3_register("pillar::pillar_shaft", "mo")
   s3_register("tibble::type_sum", "mo")
   s3_register("pillar::pillar_shaft", "rsi")
@@ -87,7 +89,7 @@ create_MO.old_lookup <- function() {
 }
 
 # copied from vctrs::s3_register
-s3_register <- function (generic, class, method = NULL) {
+s3_register <- function(generic, class, method = NULL) {
   stopifnot(is.character(generic), length(generic) == 1)
   stopifnot(is.character(class), length(class) == 1)
   pieces <- strsplit(generic, "::")[[1]]

docs/404.html

@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9007</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9008</span>
       </span>
     </div>
 

docs/LICENSE-text.html

@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9007</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9008</span>
       </span>
     </div>
 

docs/articles/index.html

@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9007</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9008</span>
       </span>
     </div>
 

docs/authors.html

@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9007</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9008</span>
       </span>
     </div>
 

docs/index.html

@@ -43,7 +43,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9007</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9008</span>
       </span>
     </div>
 

docs/news/index.html

@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9007</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9008</span>
       </span>
     </div>
 
@@ -236,9 +236,9 @@
       <small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
     </div>
 
-    <div id="amr-1309007" class="section level1">
-<h1 class="page-header" data-toc-text="1.3.0.9007">
-<a href="#amr-1309007" class="anchor"></a>AMR 1.3.0.9007<small> Unreleased </small>
+    <div id="amr-1309008" class="section level1">
+<h1 class="page-header" data-toc-text="1.3.0.9008">
+<a href="#amr-1309008" class="anchor"></a>AMR 1.3.0.9008<small> Unreleased </small>
 </h1>
 <div id="last-updated-26-august-2020" class="section level2">
 <h2 class="hasAnchor">

docs/pkgdown.yml

@@ -2,7 +2,7 @@ pandoc: 2.7.3
 pkgdown: 1.5.1.9000
 pkgdown_sha: eae56f08694abebf93cdfc0dd8e9ede06d8c815f
 articles: []
-last_built: 2020-08-26T09:09Z
+last_built: 2020-08-26T13:33Z
 urls:
   reference: https://msberends.github.io/AMR/reference
   article: https://msberends.github.io/AMR/articles

docs/reference/eucast_rules.html

@@ -83,7 +83,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9007</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9008</span>
       </span>
     </div>
 
@@ -302,18 +302,12 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
 
     <p><strong>Note:</strong> This function does not translate MIC values to RSI values. Use <code><a href='as.rsi.html'>as.rsi()</a></code> for that. <br />
 <strong>Note:</strong> When ampicillin (AMP, J01CA01) is not available but amoxicillin (AMX, J01CA04) is, the latter will be used for all rules where there is a dependency on ampicillin. These drugs are interchangeable when it comes to expression of antimicrobial resistance.</p>
-<p>Before further processing, some non-EUCAST rules can be applied to improve the efficacy of the EUCAST rules. These non-EUCAST rules, that are then applied to all isolates, are:</p><ul>
-<li><p>Inherit amoxicillin (AMX) from ampicillin (AMP), where amoxicillin (AMX) is unavailable;</p></li>
-<li><p>Inherit ampicillin (AMP) from amoxicillin (AMX), where ampicillin (AMP) is unavailable;</p></li>
-<li><p>Set amoxicillin (AMX) = R where amoxicillin/clavulanic acid (AMC) = R;</p></li>
-<li><p>Set piperacillin (PIP) = R where piperacillin/tazobactam (TZP) = R;</p></li>
-<li><p>Set trimethoprim (TMP) = R where trimethoprim/sulfamethoxazole (SXT) = R;</p></li>
-<li><p>Set amoxicillin/clavulanic acid (AMC) = S where amoxicillin (AMX) = S;</p></li>
-<li><p>Set piperacillin/tazobactam (TZP) = S where piperacillin (PIP) = S;</p></li>
-<li><p>Set trimethoprim/sulfamethoxazole (SXT) = S where trimethoprim (TMP) = S.</p></li>
-</ul>
+<p>Before further processing, two non-EUCAST rules about drug combinations can be applied to improve the efficacy of the EUCAST rules. These rules are:</p><ol>
+<li><p>A drug <strong>with</strong> enzyme inhibitor will be set to S if the drug <strong>without</strong> enzyme inhibitor is S</p></li>
+<li><p>A drug <strong>without</strong> enzyme inhibitor will be set to R if the drug <strong>with</strong> enzyme inhibitor is R</p></li>
+</ol>
 
-<p>These rules are not applied at default, since they are not approved by EUCAST. To use these rules, please use <code>eucast_rules(..., rules = "all")</code>, or set the default behaviour of the <code>[eucast_rules()]</code> function with <code><a href='https://rdrr.io/r/base/options.html'>options(AMR.eucast_rules = "all")</a></code> (or any other valid input value(s) to the <code>rules</code> parameter).</p>
+<p>These rules are not applied at default, since they are not approved by EUCAST. To use these rules, use <code>eucast_rules(..., rules = "all")</code>, or set the default behaviour of the <code>[eucast_rules()]</code> function with <code><a href='https://rdrr.io/r/base/options.html'>options(AMR.eucast_rules = "all")</a></code> (or any other valid input value(s) to the <code>rules</code> parameter).</p>
 <p>The file containing all EUCAST rules is located here: <a href='https://github.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv'>https://github.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv</a>.</p>
     <h2 class="hasAnchor" id="antibiotics"><a class="anchor" href="#antibiotics"></a>Antibiotics</h2>
 

docs/reference/index.html

@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9007</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9008</span>
       </span>
     </div>
 

docs/survey.html

@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9007</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9008</span>
       </span>
     </div>
 

man/eucast_rules.Rd

@@ -50,19 +50,13 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
 \strong{Note:} This function does not translate MIC values to RSI values. Use \code{\link[=as.rsi]{as.rsi()}} for that. \cr
 \strong{Note:} When ampicillin (AMP, J01CA01) is not available but amoxicillin (AMX, J01CA04) is, the latter will be used for all rules where there is a dependency on ampicillin. These drugs are interchangeable when it comes to expression of antimicrobial resistance.
 
-Before further processing, some non-EUCAST rules can be applied to improve the efficacy of the EUCAST rules. These non-EUCAST rules, that are then applied to all isolates, are:
-\itemize{
-\item Inherit amoxicillin (AMX) from ampicillin (AMP), where amoxicillin (AMX) is unavailable;
-\item Inherit ampicillin (AMP) from amoxicillin (AMX), where ampicillin (AMP) is unavailable;
-\item Set amoxicillin (AMX) = R where amoxicillin/clavulanic acid (AMC) = R;
-\item Set piperacillin (PIP) = R where piperacillin/tazobactam (TZP) = R;
-\item Set trimethoprim (TMP) = R where trimethoprim/sulfamethoxazole (SXT) = R;
-\item Set amoxicillin/clavulanic acid (AMC) = S where amoxicillin (AMX) = S;
-\item Set piperacillin/tazobactam (TZP) = S where piperacillin (PIP) = S;
-\item Set trimethoprim/sulfamethoxazole (SXT) = S where trimethoprim (TMP) = S.
+Before further processing, two non-EUCAST rules about drug combinations can be applied to improve the efficacy of the EUCAST rules. These rules are:
+\enumerate{
+\item A drug \strong{with} enzyme inhibitor will be set to S if the drug \strong{without} enzyme inhibitor is S
+\item A drug \strong{without} enzyme inhibitor will be set to R if the drug \strong{with} enzyme inhibitor is R
 }
 
-These rules are not applied at default, since they are not approved by EUCAST. To use these rules, please use \code{eucast_rules(..., rules = "all")}, or set the default behaviour of the \verb{[eucast_rules()]} function with \code{options(AMR.eucast_rules = "all")} (or any other valid input value(s) to the \code{rules} parameter).
+These rules are not applied at default, since they are not approved by EUCAST. To use these rules, use \code{eucast_rules(..., rules = "all")}, or set the default behaviour of the \verb{[eucast_rules()]} function with \code{options(AMR.eucast_rules = "all")} (or any other valid input value(s) to the \code{rules} parameter).
 
 The file containing all EUCAST rules is located here: \url{https://github.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv}.
 }

tests/testthat/test-mo_property.R

@@ -54,7 +54,7 @@ test_that("mo_property works", {
   expect_equal(mo_year("Escherichia coli"), 1919)
 
   expect_equal(mo_shortname("Escherichia coli"), "E. coli")
-  expect_equal(mo_shortname("Escherichia"), "E. spp.")
+  expect_equal(mo_shortname("Escherichia"), "Escherichia")
   expect_equal(mo_shortname("Staphylococcus aureus"), "S. aureus")
   expect_equal(mo_shortname("Staphylococcus aureus", Becker = TRUE), "S. aureus")
   expect_equal(mo_shortname("Staphylococcus aureus", Becker = "all", language = "en"), "CoPS")