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(v0.9.0.9015) Fix for as.rsi.disk()
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Package: AMR
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Version: 0.9.0.9014
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Version: 0.9.0.9015
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Date: 2020-01-27
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Title: Antimicrobial Resistance Analysis
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Authors@R: c(
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2
NEWS.md
2
NEWS.md
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# AMR 0.9.0.9014
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# AMR 0.9.0.9015
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## <small>Last updated: 27-Jan-2020</small>
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### New
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@ -7,6 +7,8 @@ DRGLST1 <- readxl::read_excel("data-raw/DRGLST1.xlsx")
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rsi_translation <- DRGLST1 %>%
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# only keep CLSI and EUCAST guidelines:
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filter(GUIDELINES %like% "^(CLSI|EUCST)") %>%
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mutate(DISK_S = ifelse(as.double(DISK_S) > 50, 50, DISK_S),
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MIC_R = ifelse(as.double(MIC_R) %in% c(1025, 129, 513), as.double(MIC_R) - 1, MIC_R)) %>%
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# set a nice layout:
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transmute(guideline = gsub("([0-9]+)$", " 20\\1", gsub("EUCST", "EUCAST", GUIDELINES)),
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method = TESTMETHOD,
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@ -15,10 +17,10 @@ rsi_translation <- DRGLST1 %>%
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ab = as.ab(WHON5_CODE),
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ref_tbl = REF_TABLE,
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dose_disk = POTENCY,
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S_disk = as.disk(min(DISK_S, 50, na.rm = TRUE)),
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S_disk = as.disk(DISK_S),
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R_disk = as.disk(DISK_R),
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S_mic = as.mic(MIC_S),
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R_mic = as.mic(ifelse(MIC_R %in% c(1025, 129, 513), as.double(MIC_R) - 1, MIC_R))) %>%
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R_mic = as.mic(MIC_R)) %>%
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filter(!is.na(mo) & !is.na(ab) & !mo %in% c("UNKNOWN", "B_GRAMN", "B_GRAMP", "F_FUNGUS", "F_YEAST")) %>%
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arrange(desc(guideline), mo, ab)
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@ -84,7 +84,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="https://msberends.gitlab.io/AMR/index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9014</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9015</span>
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</span>
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</div>
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@ -84,7 +84,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9014</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9015</span>
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</span>
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</div>
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@ -84,7 +84,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9014</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9015</span>
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</span>
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</div>
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@ -84,7 +84,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9014</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9015</span>
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</span>
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</div>
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@ -45,7 +45,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9014</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9015</span>
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</span>
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</div>
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@ -84,7 +84,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9014</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9015</span>
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</span>
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</div>
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@ -231,9 +231,9 @@
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</div>
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<div id="amr-0-9-0-9014" class="section level1">
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<div id="amr-0-9-0-9015" class="section level1">
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<h1 class="page-header">
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<a href="#amr-0-9-0-9014" class="anchor"></a>AMR 0.9.0.9014<small> Unreleased </small>
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<a href="#amr-0-9-0-9015" class="anchor"></a>AMR 0.9.0.9015<small> Unreleased </small>
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</h1>
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<div id="last-updated-27-jan-2020" class="section level2">
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<h2 class="hasAnchor">
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@ -1446,7 +1446,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
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<div id="tocnav">
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<h2>Contents</h2>
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<ul class="nav nav-pills nav-stacked">
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<li><a href="#amr-0-9-0-9014">0.9.0.9014</a></li>
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<li><a href="#amr-0-9-0-9015">0.9.0.9015</a></li>
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<li><a href="#amr-0-9-0">0.9.0</a></li>
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<li><a href="#amr-0-8-0">0.8.0</a></li>
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<li><a href="#amr-0-7-1">0.7.1</a></li>
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@ -84,7 +84,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9014</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0.9015</span>
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</span>
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</div>
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