(v1.3.0.9024) optimalisation

2020-09-19 12:57:51 +02:00 · 2020-09-19 12:57:51 +02:00 · 2f0186ace2
parent d049cce69b
commit 2f0186ace2
17 changed files with 24 additions and 20 deletions
--- a/2
+++ b/2
@ -1,5 +1,5 @@
 Package: AMR
-Version: 1.3.0.9023
+Version: 1.3.0.9024
 Date: 2020-09-19
 Title: Antimicrobial Resistance Analysis
 Authors@R: c(
--- a/NEWS.md
+++ b/NEWS.md
@ -1,4 +1,4 @@
-# AMR 1.3.0.9023
+# AMR 1.3.0.9024
 ## <small>Last updated: 19 September 2020</small>

 Note: some changes in this version were suggested by anonymous reviewers from the journal we submitted our manuscipt to. We are those reviewers very grateful for going through our code so thoroughly!
--- a/R/mo_matching_score.R
+++ b/R/mo_matching_score.R
@ -68,5 +68,5 @@ mo_matching_score <- function(x, fullname, uncertainty = 1) {
  var_U <- uncertainty
  
  # matching score:
-  (var_F - 0.5 * L) / (var_F * var_P * var_K * var_U)
+  (var_F - 0.5 * var_L) / (var_F * var_P * var_K * var_U)
 }
--- a/R/rsi_calc.R
+++ b/R/rsi_calc.R
@ -263,7 +263,6 @@ rsi_calc_df <- function(type, # "proportion", "count" or "both"
  
  # based on pm_apply_grouped_function
  apply_group <- function(.data, fn, groups, drop = FALSE, ...) {
-    #groups <- get_groups(.data)
    grouped <- pm_split_into_groups(.data, groups, drop)
    res <- do.call(rbind, unname(lapply(grouped, fn, ...)))
    if (any(groups %in% colnames(res))) {
--- a/R/sysdata.rda
+++ b/R/sysdata.rda
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@ -172,7 +172,7 @@ reference:
    - "`ggplot_pca`"
    - "`join`"
    - "`like`"
-    - "`mo_matching_score"
+    - "`mo_matching_score`"
    - "`pca`"
  
  - title: "Other: statistical tests"
--- a/data-raw/eucast_rules.tsv
+++ b/data-raw/eucast_rules.tsv
@ -1,5 +1,5 @@
 # -------------------------------------------------------------------------------------------------------------------------------
-# For editing this EUCAST reference file, these values can all be used for target antibiotics:
+# For editing this EUCAST reference file, these values can all be used for targeting antibiotics:
 # 'all_betalactams', 'aminoglycosides', 'aminopenicillins', 'carbapenems', 'cephalosporins', 'cephalosporins_except_CAZ',
 # 'fluoroquinolones', 'glycopeptides', 'macrolides', 'polymyxins', 'streptogramins', 'tetracyclines', 'ureidopenicillins'
 # and all separate EARS-Net letter codes like 'AMC'. They can be separated by comma: 'AMC, fluoroquinolones'.
@ -8,7 +8,7 @@
 # The EUCAST guideline contains references to the 'Burkholderia cepacia complex'. All species in this group are noted on the 'B.cepacia' sheet of the EUCAST Clinical Breakpoint v.10.0 Excel file of 2020 (v_10.0_Breakpoint_Tables.xlsx).
 # >>>>> IF YOU WANT TO IMPORT THIS FILE INTO YOUR OWN SOFTWARE, HAVE THE FIRST 10 LINES SKIPPED <<<<<
 # -------------------------------------------------------------------------------------------------------------------------------
-if_mo_property	like.is.one_of	this_value	and_these_antibiotics	have_these_values	then_change_these_antibiotics	to_value	reference.rule	reference.rule_group
+if_mo_property	like.is.one_of	this_value	and_these_antibiotics	have_these_values	then_change_these_antibiotics	to_value	reference.rule	reference.rule_group	reference.version
 order	is	Enterobacterales	AMP	S	AMX	S	Enterobacterales (Order)	Breakpoints
 order	is	Enterobacterales	AMP	I	AMX	I	Enterobacterales (Order)	Breakpoints
 order	is	Enterobacterales	AMP	R	AMX	R	Enterobacterales (Order)	Breakpoints
--- a/docs/404.html
+++ b/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">1.3.0.9023</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9024</span>
      </span>
    </div>

--- a/docs/LICENSE-text.html
+++ b/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">1.3.0.9023</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9024</span>
      </span>
    </div>

--- a/docs/articles/index.html
+++ b/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">1.3.0.9023</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9024</span>
      </span>
    </div>

--- a/docs/authors.html
+++ b/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">1.3.0.9023</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9024</span>
      </span>
    </div>

--- a/docs/index.html
+++ b/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">1.3.0.9023</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9024</span>
      </span>
    </div>

--- a/docs/news/index.html
+++ b/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">1.3.0.9023</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9024</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-1309023" class="section level1">
-<h1 class="page-header" data-toc-text="1.3.0.9023">
-<a href="#amr-1309023" class="anchor"></a>AMR 1.3.0.9023<small> Unreleased </small>
+    <div id="amr-1309024" class="section level1">
+<h1 class="page-header" data-toc-text="1.3.0.9024">
+<a href="#amr-1309024" class="anchor"></a>AMR 1.3.0.9024<small> Unreleased </small>
 </h1>
 <div id="last-updated-19-september-2020" class="section level2">
 <h2 class="hasAnchor">
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@ -2,7 +2,7 @@ pandoc: 2.7.3
 pkgdown: 1.5.1.9000
 pkgdown_sha: eae56f08694abebf93cdfc0dd8e9ede06d8c815f
 articles: []
-last_built: 2020-09-19T09:53Z
+last_built: 2020-09-19T10:17Z
 urls:
  reference: https://msberends.github.io/AMR/reference
  article: https://msberends.github.io/AMR/articles
--- a/docs/reference/index.html
+++ b/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">1.3.0.9023</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9024</span>
      </span>
    </div>

@ -586,6 +586,12 @@
        <td><p>Pattern Matching</p></td>
      </tr><tr>
        
+        <td>
+          <p><code><a href="mo_matching_score.html">mo_matching_score()</a></code> </p>
+        </td>
+        <td><p>Calculate the matching score for microorganisms</p></td>
+      </tr><tr>
+        
        <td>
          <p><code><a href="pca.html">pca()</a></code> </p>
        </td>
--- a/docs/survey.html
+++ b/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">1.3.0.9023</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9024</span>
      </span>
    </div>

--- a/tests/testthat/test-_all_examples.R
+++ b/tests/testthat/test-_all_examples.R
@ -18,4 +18,3 @@
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
 # Visit our website for more info: https://msberends.github.io/AMR.    #
 # ==================================================================== #
-