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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$ ^data-raw$
R/aa_test.R$ R/aa_test.R$
^\.lintr$ ^\.lintr$
^vignettes/benchmark.*
^vignettes/SPSS.*

8
DESCRIPTION
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@ -1,6 +1,6 @@
Package: AMR Package: AMR
Version: 0.7.1.9106 Version: 0.7.1.9107
Date: 2019-10-13 Date: 2019-10-15
Title: Antimicrobial Resistance Analysis Title: Antimicrobial Resistance Analysis
Authors@R: c( Authors@R: c(
person(role = c("aut", "cre"), person(role = c("aut", "cre"),
@ -29,7 +29,9 @@ Authors@R: c(
family = "Souverein", given = "Dennis", email = "d.souvereing@streeklabhaarlem.nl")) family = "Souverein", given = "Dennis", email = "d.souvereing@streeklabhaarlem.nl"))
Description: Functions to simplify the analysis and prediction of Antimicrobial Description: Functions to simplify the analysis and prediction of Antimicrobial
Resistance (AMR) and to work with microbial and antimicrobial properties by 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: Depends:
R (>= 3.1.0) R (>= 3.1.0)
Imports: Imports:

5
NEWS.md
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@ -1,6 +1,5 @@
# AMR 0.7.1.9106 # AMR 0.7.1.9107
<small>Last updated: 13-Oct-2019</small> <small>Last updated: 15-Oct-2019</small>
### Breaking ### 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`: * 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 ```r

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

2
docs/404.html
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@ -84,7 +84,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="https://msberends.gitlab.io/AMR/index.html">AMR (for R)</a> <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> </span>
</div> </div>

2
docs/LICENSE-text.html
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@ -84,7 +84,7 @@
</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">0.7.1.9106</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9107</span>
</span> </span>
</div> </div>

2
docs/articles/index.html
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@ -84,7 +84,7 @@
</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">0.7.1.9106</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9107</span>
</span> </span>
</div> </div>

2
docs/authors.html
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@ -84,7 +84,7 @@
</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">0.7.1.9106</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9107</span>
</span> </span>
</div> </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"> <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 <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 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 property="og:image" content="https://msberends.gitlab.io/AMR/logo.png">
<meta name="twitter:card" content="summary"> <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]> <!-- 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> </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">0.7.1.9106</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9107</span>
</span> </span>
</div> </div>

10
docs/news/index.html
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@ -84,7 +84,7 @@
</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">0.7.1.9106</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9107</span>
</span> </span>
</div> </div>
@ -231,11 +231,11 @@
</div> </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"> <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> </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"> <div id="breaking" class="section level3">
<h3 class="hasAnchor"> <h3 class="hasAnchor">
<a href="#breaking" class="anchor"></a>Breaking</h3> <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"> <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-0-7-1-9106">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-0-7-1">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>

2
docs/reference/index.html
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@ -84,7 +84,7 @@
</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">0.7.1.9106</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9107</span>
</span> </span>
</div> </div>

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

2
tests/testthat/test-eucast_rules.R
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@ -23,6 +23,8 @@ context("eucast_rules.R")
test_that("EUCAST rules work", { test_that("EUCAST rules work", {
skip_on_cran()
# thoroughly check input table # thoroughly check input table
expect_equal(colnames(eucast_rules_file), expect_equal(colnames(eucast_rules_file),
c("if_mo_property", "like.is.one_of", "this_value", c("if_mo_property", "like.is.one_of", "this_value",

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

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

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

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