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(v0.7.1.9078) unit tests

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dr. M.S. (Matthijs) Berends 2019-09-20 14:50:02 +02:00
parent 40e6b3e8f6
commit 46b61e9a70
10 changed files with 14 additions and 20 deletions
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2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR Package: AMR
Version: 0.7.1.9077 Version: 0.7.1.9078
Date: 2019-09-20 Date: 2019-09-20
Title: Antimicrobial Resistance Analysis Title: Antimicrobial Resistance Analysis
Authors@R: c( Authors@R: c(

2
NEWS.md
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@ -1,4 +1,4 @@
# AMR 0.7.1.9077 # AMR 0.7.1.9078
<small>Last updated: 20-Sep-2019</small> <small>Last updated: 20-Sep-2019</small>
### Breaking ### Breaking

5
R/mo.R
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@ -1539,7 +1539,8 @@ exec_as.mo <- function(x,
# THEN TRY PREVALENT IN HUMAN INFECTIONS ---- # THEN TRY PREVALENT IN HUMAN INFECTIONS ----
x[i] <- check_per_prevalence(data_to_check = reference_data_to_use[prevalence == 2], x[i] <- check_per_prevalence(data_to_check = reference_data_to_use[prevalence == 2],
data.old_to_check = microorganisms.oldDT[prevalence == 2], data.old_to_check = microorganisms.oldDT[prevalence %in% c(2, 3)], # run all other old MOs the second time,
# otherwise e.g. mo_ref("Chlamydia psittaci") doesn't work correctly
a.x_backup = x_backup[i], a.x_backup = x_backup[i],
b.x_trimmed = x_trimmed[i], b.x_trimmed = x_trimmed[i],
c.x_trimmed_without_group = x_trimmed_without_group[i], c.x_trimmed_without_group = x_trimmed_without_group[i],
@ -1558,7 +1559,7 @@ exec_as.mo <- function(x,
# THEN UNPREVALENT IN HUMAN INFECTIONS ---- # THEN UNPREVALENT IN HUMAN INFECTIONS ----
x[i] <- check_per_prevalence(data_to_check = reference_data_to_use[prevalence == 3], x[i] <- check_per_prevalence(data_to_check = reference_data_to_use[prevalence == 3],
data.old_to_check = microorganisms.oldDT[prevalence == 3], data.old_to_check = microorganisms.oldDT[prevalence == 999],
a.x_backup = x_backup[i], a.x_backup = x_backup[i],
b.x_trimmed = x_trimmed[i], b.x_trimmed = x_trimmed[i],
c.x_trimmed_without_group = x_trimmed_without_group[i], c.x_trimmed_without_group = x_trimmed_without_group[i],

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docs/LICENSE-text.html
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@ -78,7 +78,7 @@
</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">0.7.1.9077</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9078</span>
</span> </span>
</div> </div>

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docs/articles/index.html
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@ -78,7 +78,7 @@
</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">0.7.1.9077</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9078</span>
</span> </span>
</div> </div>

2
docs/authors.html
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@ -78,7 +78,7 @@
</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">0.7.1.9077</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9078</span>
</span> </span>
</div> </div>

2
docs/index.html
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@ -42,7 +42,7 @@
</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">0.7.1.9077</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9078</span>
</span> </span>
</div> </div>

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docs/news/index.html
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@ -78,7 +78,7 @@
</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">0.7.1.9077</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9078</span>
</span> </span>
</div> </div>
@ -225,9 +225,9 @@
</div> </div>
<div id="amr-0-7-1-9077" class="section level1"> <div id="amr-0-7-1-9078" class="section level1">
<h1 class="page-header"> <h1 class="page-header">
<a href="#amr-0-7-1-9077" class="anchor"></a>AMR 0.7.1.9077<small> Unreleased </small> <a href="#amr-0-7-1-9078" class="anchor"></a>AMR 0.7.1.9078<small> Unreleased </small>
</h1> </h1>
<p><small>Last updated: 20-Sep-2019</small></p> <p><small>Last updated: 20-Sep-2019</small></p>
<div id="breaking" class="section level3"> <div id="breaking" class="section level3">
@ -1267,7 +1267,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
<div id="tocnav"> <div id="tocnav">
<h2>Contents</h2> <h2>Contents</h2>
<ul class="nav nav-pills nav-stacked"> <ul class="nav nav-pills nav-stacked">
<li><a href="#amr-0-7-1-9077">0.7.1.9077</a></li> <li><a href="#amr-0-7-1-9078">0.7.1.9078</a></li>
<li><a href="#amr-0-7-1">0.7.1</a></li> <li><a href="#amr-0-7-1">0.7.1</a></li>
<li><a href="#amr-0-7-0">0.7.0</a></li> <li><a href="#amr-0-7-0">0.7.0</a></li>
<li><a href="#amr-0-6-1">0.6.1</a></li> <li><a href="#amr-0-6-1">0.6.1</a></li>

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docs/reference/index.html
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@ -78,7 +78,7 @@
</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">0.7.1.9077</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9078</span>
</span> </span>
</div> </div>

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inst/mo_history/mo_history.csv
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"x","mo","uncertainty_level","package_version" "x","mo","uncertainty_level","package_version"
"M. SEMESIAE","B_MTHNSR_SEMS",0,"0.7.1.9077"
"METSEM","B_MTHNSR_SEMS",0,"0.7.1.9077"
"METHANOSARCINA SEMESIAE","B_MTHNSR_SEMS",0,"0.7.1.9077"
"PREVOTELLA BREVIS","B_PRVTL_BRVS",0,"0.7.1.9077"
"P. BREVIS","B_PRVTL_BRVS",0,"0.7.1.9077"
"E. COLI","B_ESCHR_COLI",0,"0.7.1.9077"
"ESCHERICHIA COLI","B_ESCHR_COLI",0,"0.7.1.9077"

1 x mo uncertainty_level package_version
M. SEMESIAE B_MTHNSR_SEMS 0 0.7.1.9077
METSEM B_MTHNSR_SEMS 0 0.7.1.9077
METHANOSARCINA SEMESIAE B_MTHNSR_SEMS 0 0.7.1.9077
PREVOTELLA BREVIS B_PRVTL_BRVS 0 0.7.1.9077
P. BREVIS B_PRVTL_BRVS 0 0.7.1.9077
E. COLI B_ESCHR_COLI 0 0.7.1.9077
ESCHERICHIA COLI B_ESCHR_COLI 0 0.7.1.9077