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(v1.3.0.9024) optimalisation

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dr. M.S. (Matthijs) Berends 2020-09-19 12:57:51 +02:00
parent d049cce69b
commit 2f0186ace2
17 changed files with 24 additions and 20 deletions
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DESCRIPTION
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Package: AMR Package: AMR
Version: 1.3.0.9023 Version: 1.3.0.9024
Date: 2020-09-19 Date: 2020-09-19
Title: Antimicrobial Resistance Analysis Title: Antimicrobial Resistance Analysis
Authors@R: c( Authors@R: c(

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NEWS.md
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# AMR 1.3.0.9023 # AMR 1.3.0.9024
## <small>Last updated: 19 September 2020</small> ## <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! 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!

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R/mo_matching_score.R
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@ -68,5 +68,5 @@ mo_matching_score <- function(x, fullname, uncertainty = 1) {
var_U <- uncertainty var_U <- uncertainty
# matching score: # 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)
} }

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R/rsi_calc.R
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@ -263,7 +263,6 @@ rsi_calc_df <- function(type, # "proportion", "count" or "both"
# based on pm_apply_grouped_function # based on pm_apply_grouped_function
apply_group <- function(.data, fn, groups, drop = FALSE, ...) { apply_group <- function(.data, fn, groups, drop = FALSE, ...) {
#groups <- get_groups(.data)
grouped <- pm_split_into_groups(.data, groups, drop) grouped <- pm_split_into_groups(.data, groups, drop)
res <- do.call(rbind, unname(lapply(grouped, fn, ...))) res <- do.call(rbind, unname(lapply(grouped, fn, ...)))
if (any(groups %in% colnames(res))) { if (any(groups %in% colnames(res))) {

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R/sysdata.rda
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_pkgdown.yml
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@ -172,7 +172,7 @@ reference:
- "`ggplot_pca`" - "`ggplot_pca`"
- "`join`" - "`join`"
- "`like`" - "`like`"
- "`mo_matching_score" - "`mo_matching_score`"
- "`pca`" - "`pca`"
- title: "Other: statistical tests" - title: "Other: statistical tests"

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data-raw/eucast_rules.tsv
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# ------------------------------------------------------------------------------------------------------------------------------- # -------------------------------------------------------------------------------------------------------------------------------
# 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', # 'all_betalactams', 'aminoglycosides', 'aminopenicillins', 'carbapenems', 'cephalosporins', 'cephalosporins_except_CAZ',
# 'fluoroquinolones', 'glycopeptides', 'macrolides', 'polymyxins', 'streptogramins', 'tetracyclines', 'ureidopenicillins' # 'fluoroquinolones', 'glycopeptides', 'macrolides', 'polymyxins', 'streptogramins', 'tetracyclines', 'ureidopenicillins'
# and all separate EARS-Net letter codes like 'AMC'. They can be separated by comma: 'AMC, fluoroquinolones'. # 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). # 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 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 S AMX S Enterobacterales (Order) Breakpoints
order is Enterobacterales AMP I AMX I Enterobacterales (Order) Breakpoints order is Enterobacterales AMP I AMX I Enterobacterales (Order) Breakpoints
order is Enterobacterales AMP R AMX R Enterobacterales (Order) Breakpoints order is Enterobacterales AMP R AMX R Enterobacterales (Order) Breakpoints

Can't render this file because it contains an unexpected character in line 6 and column 96.

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docs/404.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a> <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> </span>
</div> </div>

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docs/LICENSE-text.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <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> </span>
</div> </div>

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docs/articles/index.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <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> </span>
</div> </div>

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docs/authors.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <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> </span>
</div> </div>

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docs/index.html
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@ -43,7 +43,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <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> </span>
</div> </div>

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docs/news/index.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <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> </span>
</div> </div>
@ -236,9 +236,9 @@
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small> <small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div> </div>
<div id="amr-1309023" class="section level1"> <div id="amr-1309024" class="section level1">
<h1 class="page-header" data-toc-text="1.3.0.9023"> <h1 class="page-header" data-toc-text="1.3.0.9024">
<a href="#amr-1309023" class="anchor"></a>AMR 1.3.0.9023<small> Unreleased </small> <a href="#amr-1309024" class="anchor"></a>AMR 1.3.0.9024<small> Unreleased </small>
</h1> </h1>
<div id="last-updated-19-september-2020" class="section level2"> <div id="last-updated-19-september-2020" class="section level2">
<h2 class="hasAnchor"> <h2 class="hasAnchor">

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docs/pkgdown.yml
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@ -2,7 +2,7 @@ pandoc: 2.7.3
pkgdown: 1.5.1.9000 pkgdown: 1.5.1.9000
pkgdown_sha: eae56f08694abebf93cdfc0dd8e9ede06d8c815f pkgdown_sha: eae56f08694abebf93cdfc0dd8e9ede06d8c815f
articles: [] articles: []
last_built: 2020-09-19T09:53Z last_built: 2020-09-19T10:17Z
urls: urls:
reference: https://msberends.github.io/AMR/reference reference: https://msberends.github.io/AMR/reference
article: https://msberends.github.io/AMR/articles article: https://msberends.github.io/AMR/articles

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docs/reference/index.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <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> </span>
</div> </div>
@ -586,6 +586,12 @@
<td><p>Pattern Matching</p></td> <td><p>Pattern Matching</p></td>
</tr><tr> </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> <td>
<p><code><a href="pca.html">pca()</a></code> </p> <p><code><a href="pca.html">pca()</a></code> </p>
</td> </td>

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docs/survey.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <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> </span>
</div> </div>

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