P281424
/
AMR
mirror of https://github.com/msberends/AMR.git
1
0
Fork 0
Code Releases Activity

(v1.3.0.9027) unit tests

This commit is contained in:
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
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
DESCRIPTION
View File

@ -1,5 +1,5 @@
Package: AMR
Version: 1.3.0.9026
Version: 1.3.0.9027
Date: 2020-09-24
Title: Antimicrobial Resistance Analysis
Authors@R: c(

2
NEWS.md
View File

@ -1,4 +1,4 @@
# AMR 1.3.0.9026
# AMR 1.3.0.9027
## <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!

2
R/eucast_rules.R
View File

@ -157,7 +157,7 @@ eucast_rules <- function(x,
"\n\nThis may overwrite your existing data if you use e.g.:",
"\ndata <- eucast_rules(data, verbose = TRUE)\n\nDo you want to continue?")
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)
} else {
q_continue <- utils::menu(choices = c("OK", "Cancel"), graphics = FALSE, title = txt)

3
R/globals.R
View File

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

2
docs/404.html
View File

@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<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>
</div>

2
docs/LICENSE-text.html
View File

@ -81,7 +81,7 @@
</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">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>
</div>

2
docs/articles/index.html
View File

@ -81,7 +81,7 @@
</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">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>
</div>

2
docs/authors.html
View File

@ -81,7 +81,7 @@
</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">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>
</div>

2
docs/index.html
View File

@ -43,7 +43,7 @@
</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">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>
</div>

8
docs/news/index.html
View File

@ -81,7 +81,7 @@
</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">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>
</div>
@ -236,9 +236,9 @@
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div>
<div id="amr-1309026" class="section level1">
<h1 class="page-header" data-toc-text="1.3.0.9026">
<a href="#amr-1309026" class="anchor"></a>AMR 1.3.0.9026<small> Unreleased </small>
<div id="amr-1309027" class="section level1">
<h1 class="page-header" data-toc-text="1.3.0.9027">
<a href="#amr-1309027" class="anchor"></a>AMR 1.3.0.9027<small> Unreleased </small>
</h1>
<div id="last-updated-24-september-2020" class="section level2">
<h2 class="hasAnchor">

2
docs/pkgdown.yml
View File

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

2
docs/reference/index.html
View File

@ -81,7 +81,7 @@
</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">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>
</div>

2
docs/survey.html
View File

@ -81,7 +81,7 @@
</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">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>
</div>

2
tests/testthat/test-ab_property.R
View File

@ -43,7 +43,7 @@ test_that("ab_property works", {
expect_identical(ab_ddd("AMX", "oral"), 1.5)
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_name(x = c("AMC", "PLB"), language = NULL), c("Amoxicillin/clavulanic acid", "Polymyxin B"))

2
tests/testthat/test-count.R
View File

@ -29,7 +29,7 @@ test_that("counts work", {
expect_equal(count_all(example_isolates$AMX), n_rsi(example_isolates$AMX))
# 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$AMX), 3)
expect_equal(suppressWarnings(count_S(example_isolates$AMX)), 543)
expect_equal(count_R(example_isolates$AMX) + count_I(example_isolates$AMX),

2
tests/testthat/test-first_isolate.R
View File

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

4
tests/testthat/test-proportion.R
View File

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