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(v0.7.1.9107) v0.8.0

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dr. M.S. (Matthijs) Berends 2019-10-15 14:35:23 +02:00
parent 2c0f3534bf
commit 10e6b225e7
18 changed files with 49 additions and 19 deletions
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2
.Rbuildignore
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@ -23,3 +23,5 @@
^data-raw$
R/aa_test.R$
^\.lintr$
^vignettes/benchmark.*
^vignettes/SPSS.*

8
DESCRIPTION
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@ -1,6 +1,6 @@
Package: AMR
Version: 0.7.1.9106
Date: 2019-10-13
Version: 0.7.1.9107
Date: 2019-10-15
Title: Antimicrobial Resistance Analysis
Authors@R: c(
person(role = c("aut", "cre"),
@ -29,7 +29,9 @@ Authors@R: c(
family = "Souverein", given = "Dennis", email = "d.souvereing@streeklabhaarlem.nl"))
Description: Functions to simplify the analysis and prediction of Antimicrobial
Resistance (AMR) and to work with microbial and antimicrobial properties by
using evidence-based methods.
using evidence-based methods, like those defined by Leclercq et al. (2013)
<doi:10.1111/j.1469-0691.2011.03703.x> and the Clinical and Laboratory
Standards Institute (2014) <isbn: 1-56238-899-1>.
Depends:
R (>= 3.1.0)
Imports:

5
NEWS.md
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@ -1,6 +1,5 @@
# AMR 0.7.1.9106
<small>Last updated: 13-Oct-2019</small>
# AMR 0.7.1.9107
<small>Last updated: 15-Oct-2019</small>
### Breaking
* Determination of first isolates now **excludes** all 'unknown' microorganisms at default, i.e. microbial code `"UNKNOWN"`. They can be included with the new parameter `include_unknown`:
```r

2
R/atc_online.R
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@ -167,7 +167,7 @@ atc_online_property <- function(atc_code,
returnvalue[i] <- NA
next
} else {
for (j in seq_len(length(tbl))) {
for (j in seq_len(nrow(tbl))) {
if (tbl[j, "adm.r"] == administration) {
returnvalue[i] <- tbl[j, property]
}

2
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">0.7.1.9106</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9107</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">0.7.1.9106</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9107</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">0.7.1.9106</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9107</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">0.7.1.9106</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9107</span>
</span>
</div>

6
docs/index.html
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@ -22,7 +22,9 @@
<script src="extra.js"></script><meta property="og:title" content="Antimicrobial Resistance Analysis">
<meta property="og:description" content="Functions to simplify the analysis and prediction of Antimicrobial
Resistance (AMR) and to work with microbial and antimicrobial properties by
using evidence-based methods.">
using evidence-based methods, like those defined by Leclercq et al. (2013)
&lt;doi:10.1111/j.1469-0691.2011.03703.x&gt; and the Clinical and Laboratory
Standards Institute (2014) &lt;isbn: 1-56238-899-1&gt;.">
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png">
<meta name="twitter:card" content="summary">
<!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
@ -43,7 +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">0.7.1.9106</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9107</span>
</span>
</div>

10
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">0.7.1.9106</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9107</span>
</span>
</div>
@ -231,11 +231,11 @@
</div>
<div id="amr-0-7-1-9106" class="section level1">
<div id="amr-0-7-1-9107" class="section level1">
<h1 class="page-header">
<a href="#amr-0-7-1-9106" class="anchor"></a>AMR 0.7.1.9106<small> Unreleased </small>
<a href="#amr-0-7-1-9107" class="anchor"></a>AMR 0.7.1.9107<small> Unreleased </small>
</h1>
<p><small>Last updated: 13-Oct-2019</small></p>
<p><small>Last updated: 15-Oct-2019</small></p>
<div id="breaking" class="section level3">
<h3 class="hasAnchor">
<a href="#breaking" class="anchor"></a>Breaking</h3>
@ -1292,7 +1292,7 @@ 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-0-7-1-9106">0.7.1.9106</a></li>
<li><a href="#amr-0-7-1-9107">0.7.1.9107</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-0-6-1">0.6.1</a></li>

2
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">0.7.1.9106</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9107</span>
</span>
</div>

3
tests/testthat/test-bug_drug_combinations.R
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@ -22,6 +22,9 @@
context("bug_drug_combinations.R")
test_that("bug_drug_combinations works", {
skip_on_cran()
b <- suppressWarnings(bug_drug_combinations(example_isolates))
expect_s3_class(b, "bug_drug_combinations")
expect_output(print(b))

2
tests/testthat/test-eucast_rules.R
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@ -22,6 +22,8 @@
context("eucast_rules.R")
test_that("EUCAST rules work", {
skip_on_cran()
# thoroughly check input table
expect_equal(colnames(eucast_rules_file),

3
tests/testthat/test-first_isolate.R
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@ -22,6 +22,9 @@
context("first_isolate.R")
test_that("first isolates work", {
skip_on_cran()
# first isolates
expect_equal(
sum(

3
tests/testthat/test-mdro.R
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@ -22,6 +22,9 @@
context("mdro.R")
test_that("mdro works", {
skip_on_cran()
library(dplyr)
expect_error(suppressWarnings(mdro(example_isolates, country = "invalid", col_mo = "mo", info = TRUE)))

2
tests/testthat/test-mo.R
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@ -23,6 +23,8 @@ context("mo.R")
test_that("as.mo works", {
skip_on_cran()
clear_mo_history(force = TRUE)
library(dplyr)

3
tests/testthat/test-mo_property.R
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@ -22,6 +22,9 @@
context("mo_property.R")
test_that("mo_property works", {
skip_on_cran()
expect_equal(mo_kingdom("Escherichia coli"), "Bacteria")
expect_equal(mo_phylum("Escherichia coli"), "Proteobacteria")
expect_equal(mo_class("Escherichia coli"), "Gammaproteobacteria")

9
tests/testthat/test-rsi.R
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@ -22,6 +22,9 @@
context("rsi.R")
test_that("rsi works", {
skip_on_cran()
expect_true(as.rsi("S") < as.rsi("I"))
expect_true(as.rsi("I") < as.rsi("R"))
expect_true(as.rsi("R") > as.rsi("S"))
@ -56,6 +59,9 @@ test_that("rsi works", {
})
test_that("mic2rsi works", {
skip_on_cran()
expect_equal(as.character(
as.rsi(x = as.mic(0.125),
mo = "B_STRPT_PNMN",
@ -78,6 +84,9 @@ test_that("mic2rsi works", {
})
test_that("disk2rsi works", {
skip_on_cran()
expect_equal(as.character(
as.rsi(x = as.disk(22),
mo = "B_STRPT_PNMN",