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(v1.3.0.9027) unit tests

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dr. M.S. (Matthijs) Berends 2020-09-24 00:50:23 +02:00
parent c19095a3d5
commit 027215ed94
17 changed files with 23 additions and 20 deletions
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2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR Package: AMR
Version: 1.3.0.9026 Version: 1.3.0.9027
Date: 2020-09-24 Date: 2020-09-24
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 1.3.0.9026 # AMR 1.3.0.9027
## <small>Last updated: 24 September 2020</small> ## <small>Last updated: 24 September 2020</small>
Note: some changes in this version were suggested by anonymous reviewers from the journal we submitted our manuscipt to. We are those reviewers very grateful for going through our code so thoroughly! Note: some changes in this version were suggested by anonymous reviewers from the journal we submitted our manuscipt to. We are those reviewers very grateful for going through our code so thoroughly!

2
R/eucast_rules.R
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@ -157,7 +157,7 @@ eucast_rules <- function(x,
"\n\nThis may overwrite your existing data if you use e.g.:", "\n\nThis may overwrite your existing data if you use e.g.:",
"\ndata <- eucast_rules(data, verbose = TRUE)\n\nDo you want to continue?") "\ndata <- eucast_rules(data, verbose = TRUE)\n\nDo you want to continue?")
showQuestion <- import_fn("showQuestion", "rstudioapi", error_on_fail = FALSE) showQuestion <- import_fn("showQuestion", "rstudioapi", error_on_fail = FALSE)
if (!is.null(showQuestion)) { if (!is.null(showQuestion) & interactive()) {
q_continue <- showQuestion("Using verbose = TRUE with eucast_rules()", txt) q_continue <- showQuestion("Using verbose = TRUE with eucast_rules()", txt)
} else { } else {
q_continue <- utils::menu(choices = c("OK", "Cancel"), graphics = FALSE, title = txt) q_continue <- utils::menu(choices = c("OK", "Cancel"), graphics = FALSE, title = txt)

3
R/globals.R
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@ -54,7 +54,10 @@ globalVariables(c(".rowid",
"old_name", "old_name",
"pattern", "pattern",
"R", "R",
"reference.rule_group",
"reference.version",
"rsi_translation", "rsi_translation",
"rowid",
"rule_group", "rule_group",
"rule_name", "rule_name",
"se_max", "se_max",

2
docs/404.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a> <a class="navbar-link" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9026</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9027</span>
</span> </span>
</div> </div>

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docs/LICENSE-text.html
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@ -81,7 +81,7 @@
</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">1.3.0.9026</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9027</span>
</span> </span>
</div> </div>

2
docs/articles/index.html
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@ -81,7 +81,7 @@
</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">1.3.0.9026</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9027</span>
</span> </span>
</div> </div>

2
docs/authors.html
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@ -81,7 +81,7 @@
</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">1.3.0.9026</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9027</span>
</span> </span>
</div> </div>

2
docs/index.html
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@ -43,7 +43,7 @@
</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">1.3.0.9026</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9027</span>
</span> </span>
</div> </div>

8
docs/news/index.html
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@ -81,7 +81,7 @@
</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">1.3.0.9026</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9027</span>
</span> </span>
</div> </div>
@ -236,9 +236,9 @@
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small> <small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div> </div>
<div id="amr-1309026" class="section level1"> <div id="amr-1309027" class="section level1">
<h1 class="page-header" data-toc-text="1.3.0.9026"> <h1 class="page-header" data-toc-text="1.3.0.9027">
<a href="#amr-1309026" class="anchor"></a>AMR 1.3.0.9026<small> Unreleased </small> <a href="#amr-1309027" class="anchor"></a>AMR 1.3.0.9027<small> Unreleased </small>
</h1> </h1>
<div id="last-updated-24-september-2020" class="section level2"> <div id="last-updated-24-september-2020" class="section level2">
<h2 class="hasAnchor"> <h2 class="hasAnchor">

2
docs/pkgdown.yml
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@ -2,7 +2,7 @@ pandoc: 2.7.3
pkgdown: 1.5.1.9000 pkgdown: 1.5.1.9000
pkgdown_sha: eae56f08694abebf93cdfc0dd8e9ede06d8c815f pkgdown_sha: eae56f08694abebf93cdfc0dd8e9ede06d8c815f
articles: [] articles: []
last_built: 2020-09-23T22:29Z last_built: 2020-09-23T22:50Z
urls: urls:
reference: https://msberends.github.io/AMR/reference reference: https://msberends.github.io/AMR/reference
article: https://msberends.github.io/AMR/articles article: https://msberends.github.io/AMR/articles

2
docs/reference/index.html
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@ -81,7 +81,7 @@
</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">1.3.0.9026</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9027</span>
</span> </span>
</div> </div>

2
docs/survey.html
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@ -81,7 +81,7 @@
</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">1.3.0.9026</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9027</span>
</span> </span>
</div> </div>

2
tests/testthat/test-ab_property.R
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@ -43,7 +43,7 @@ test_that("ab_property works", {
expect_identical(ab_ddd("AMX", "oral"), 1.5) expect_identical(ab_ddd("AMX", "oral"), 1.5)
expect_identical(ab_ddd("AMX", "oral", units = TRUE), "g") expect_identical(ab_ddd("AMX", "oral", units = TRUE), "g")
expect_identical(ab_ddd("AMX", "iv"), 1) expect_identical(ab_ddd("AMX", "iv"), 3)
expect_identical(ab_ddd("AMX", "iv", units = TRUE), "g") expect_identical(ab_ddd("AMX", "iv", units = TRUE), "g")
expect_identical(ab_name(x = c("AMC", "PLB"), language = NULL), c("Amoxicillin/clavulanic acid", "Polymyxin B")) expect_identical(ab_name(x = c("AMC", "PLB"), language = NULL), c("Amoxicillin/clavulanic acid", "Polymyxin B"))

2
tests/testthat/test-count.R
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@ -29,7 +29,7 @@ test_that("counts work", {
expect_equal(count_all(example_isolates$AMX), n_rsi(example_isolates$AMX)) expect_equal(count_all(example_isolates$AMX), n_rsi(example_isolates$AMX))
# AMX resistance in `example_isolates` # AMX resistance in `example_isolates`
expect_equal(count_R(example_isolates$AMX), 683) expect_equal(count_R(example_isolates$AMX), 804)
expect_equal(count_I(example_isolates$AMX), 3) expect_equal(count_I(example_isolates$AMX), 3)
expect_equal(suppressWarnings(count_S(example_isolates$AMX)), 543) expect_equal(suppressWarnings(count_S(example_isolates$AMX)), 543)
expect_equal(count_R(example_isolates$AMX) + count_I(example_isolates$AMX), expect_equal(count_R(example_isolates$AMX) + count_I(example_isolates$AMX),

2
tests/testthat/test-first_isolate.R
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@ -74,7 +74,7 @@ test_that("first isolates work", {
type = "points", type = "points",
info = TRUE), info = TRUE),
na.rm = TRUE)), na.rm = TRUE)),
1400) 1399)
# first non-ICU isolates # first non-ICU isolates
expect_equal( expect_equal(

4
tests/testthat/test-proportion.R
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@ -29,8 +29,8 @@ test_that("proportions works", {
expect_equal(proportion_SI(example_isolates$AMX), susceptibility(example_isolates$AMX)) expect_equal(proportion_SI(example_isolates$AMX), susceptibility(example_isolates$AMX))
# AMX resistance in `example_isolates` # AMX resistance in `example_isolates`
expect_equal(proportion_R(example_isolates$AMX), 0.5557364, tolerance = 0.0001) expect_equal(proportion_R(example_isolates$AMX), 0.5955556, tolerance = 0.0001)
expect_equal(proportion_I(example_isolates$AMX), 0.002441009, tolerance = 0.0001) expect_equal(proportion_I(example_isolates$AMX), 0.002222222, tolerance = 0.0001)
expect_equal(1 - proportion_R(example_isolates$AMX) - proportion_I(example_isolates$AMX), expect_equal(1 - proportion_R(example_isolates$AMX) - proportion_I(example_isolates$AMX),
proportion_S(example_isolates$AMX)) proportion_S(example_isolates$AMX))
expect_equal(proportion_R(example_isolates$AMX) + proportion_I(example_isolates$AMX), expect_equal(proportion_R(example_isolates$AMX) + proportion_I(example_isolates$AMX),