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AMR
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(v0.9.0.9015) Fix for as.rsi.disk()

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dr. M.S. (Matthijs) Berends 2020-01-27 11:37:00 +01:00
parent 9a3891efe4
commit 42b079cdb7
12 changed files with 4438 additions and 4436 deletions
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2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR
Version: 0.9.0.9014
Version: 0.9.0.9015
Date: 2020-01-27
Title: Antimicrobial Resistance Analysis
Authors@R: c(

2
NEWS.md
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@ -1,4 +1,4 @@
# AMR 0.9.0.9014
# AMR 0.9.0.9015
## <small>Last updated: 27-Jan-2020</small>
### New

6
data-raw/reproduction_of_rsi_translation.R
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@ -7,6 +7,8 @@ DRGLST1 <- readxl::read_excel("data-raw/DRGLST1.xlsx")
rsi_translation <- DRGLST1 %>%
# only keep CLSI and EUCAST guidelines:
filter(GUIDELINES %like% "^(CLSI|EUCST)") %>%
mutate(DISK_S = ifelse(as.double(DISK_S) > 50, 50, DISK_S),
MIC_R = ifelse(as.double(MIC_R) %in% c(1025, 129, 513), as.double(MIC_R) - 1, MIC_R)) %>%
# set a nice layout:
transmute(guideline = gsub("([0-9]+)$", " 20\\1", gsub("EUCST", "EUCAST", GUIDELINES)),
method = TESTMETHOD,
@ -15,10 +17,10 @@ rsi_translation <- DRGLST1 %>%
ab = as.ab(WHON5_CODE),
ref_tbl = REF_TABLE,
dose_disk = POTENCY,
S_disk = as.disk(min(DISK_S, 50, na.rm = TRUE)),
S_disk = as.disk(DISK_S),
R_disk = as.disk(DISK_R),
S_mic = as.mic(MIC_S),
R_mic = as.mic(ifelse(MIC_R %in% c(1025, 129, 513), as.double(MIC_R) - 1, MIC_R))) %>%
R_mic = as.mic(MIC_R)) %>%
filter(!is.na(mo) & !is.na(ab) & !mo %in% c("UNKNOWN", "B_GRAMN", "B_GRAMP", "F_FUNGUS", "F_YEAST")) %>%
arrange(desc(guideline), mo, ab)

8844
data-raw/rsi_translation.txt
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data/rsi_translation.rda
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docs/404.html
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@ -84,7 +84,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="https://msberends.gitlab.io/AMR/index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9014</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9015</span>
</span>
</div>

2
docs/LICENSE-text.html
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@ -84,7 +84,7 @@
</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">0.9.0.9014</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9015</span>
</span>
</div>

2
docs/articles/index.html
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@ -84,7 +84,7 @@
</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">0.9.0.9014</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9015</span>
</span>
</div>

2
docs/authors.html
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@ -84,7 +84,7 @@
</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">0.9.0.9014</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9015</span>
</span>
</div>

2
docs/index.html
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@ -45,7 +45,7 @@
</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">0.9.0.9014</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9015</span>
</span>
</div>

8
docs/news/index.html
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@ -84,7 +84,7 @@
</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">0.9.0.9014</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9015</span>
</span>
</div>
@ -231,9 +231,9 @@
</div>
<div id="amr-0-9-0-9014" class="section level1">
<div id="amr-0-9-0-9015" class="section level1">
<h1 class="page-header">
<a href="#amr-0-9-0-9014" class="anchor"></a>AMR 0.9.0.9014<small> Unreleased </small>
<a href="#amr-0-9-0-9015" class="anchor"></a>AMR 0.9.0.9015<small> Unreleased </small>
</h1>
<div id="last-updated-27-jan-2020" class="section level2">
<h2 class="hasAnchor">
@ -1446,7 +1446,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
<div id="tocnav">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#amr-0-9-0-9014">0.9.0.9014</a></li>
<li><a href="#amr-0-9-0-9015">0.9.0.9015</a></li>
<li><a href="#amr-0-9-0">0.9.0</a></li>
<li><a href="#amr-0-8-0">0.8.0</a></li>
<li><a href="#amr-0-7-1">0.7.1</a></li>

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docs/reference/index.html
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@ -84,7 +84,7 @@
</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">0.9.0.9014</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9015</span>
</span>
</div>