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(v1.2.0.9012) mo_domain(), improved error handling

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dr. M.S. (Matthijs) Berends 2020-06-22 12:18:53 +02:00
parent 93a158aebd
commit 779a4e8348
12 changed files with 24 additions and 25 deletions
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2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR Package: AMR
Version: 1.2.0.9011 Version: 1.2.0.9012
Date: 2020-06-22 Date: 2020-06-22
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 1.2.0.9011 # AMR 1.2.0.9012
## <small>Last updated: 22-Jun-2020</small> ## <small>Last updated: 22-Jun-2020</small>
### New ### New

3
R/rsi_calc.R
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@ -163,11 +163,10 @@ rsi_calc_df <- function(type, # "proportion", "count" or "both"
stop_ifnot(is.data.frame(data), "`data` must be a data.frame", call = -2) stop_ifnot(is.data.frame(data), "`data` must be a data.frame", call = -2)
stop_if(any(dim(data) == 0), "`data` must contain rows and columns", call = -2) stop_if(any(dim(data) == 0), "`data` must contain rows and columns", call = -2)
stop_ifnot(any(sapply(data, is.rsi), na.rm = TRUE), "no columns with class <rsi> found. See ?as.rsi.", call = -2) stop_ifnot(any(sapply(data, is.rsi), na.rm = TRUE), "no columns with class <rsi> found. See ?as.rsi.", call = -2)
stop_if(isTRUE(combine_SI) & isTRUE(combine_IR), "either `combine_SI` or `combine_IR` can be TRUE, not both", call = -2)
if (isTRUE(combine_IR) & isTRUE(combine_SI_missing)) { if (isTRUE(combine_IR) & isTRUE(combine_SI_missing)) {
combine_SI <- FALSE combine_SI <- FALSE
} }
stop_if(isTRUE(combine_SI) & isTRUE(combine_IR), "either `combine_SI` or `combine_IR` can be TRUE, not both", call = -2)
if (as.character(translate_ab) %in% c("TRUE", "official")) { if (as.character(translate_ab) %in% c("TRUE", "official")) {
translate_ab <- "name" translate_ab <- "name"

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.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">1.2.0.9011</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9012</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">1.2.0.9011</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9012</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">1.2.0.9011</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9012</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">1.2.0.9011</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9012</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">1.2.0.9011</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9012</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">1.2.0.9011</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9012</span>
</span> </span>
</div> </div>
@ -229,9 +229,9 @@
<small>Source: <a href='https://gitlab.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small> <small>Source: <a href='https://gitlab.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div> </div>
<div id="amr-1209011" class="section level1"> <div id="amr-1209012" class="section level1">
<h1 class="page-header" data-toc-text="1.2.0.9011"> <h1 class="page-header" data-toc-text="1.2.0.9012">
<a href="#amr-1209011" class="anchor"></a>AMR 1.2.0.9011<small> Unreleased </small> <a href="#amr-1209012" class="anchor"></a>AMR 1.2.0.9012<small> Unreleased </small>
</h1> </h1>
<div id="last-updated-22-jun-2020" class="section level2"> <div id="last-updated-22-jun-2020" class="section level2">
<h2 class="hasAnchor"> <h2 class="hasAnchor">

2
docs/pkgdown.yml
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@ -10,7 +10,7 @@ articles:
WHONET: WHONET.html WHONET: WHONET.html
benchmarks: benchmarks.html benchmarks: benchmarks.html
resistance_predict: resistance_predict.html resistance_predict: resistance_predict.html
last_built: 2020-06-22T09:16Z last_built: 2020-06-22T10:13Z
urls: urls:
reference: https://msberends.gitlab.io/AMR/reference reference: https://msberends.gitlab.io/AMR/reference
article: https://msberends.gitlab.io/AMR/articles article: https://msberends.gitlab.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">1.2.0.9011</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9012</span>
</span> </span>
</div> </div>

20
tests/testthat/test-count.R
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@ -28,13 +28,13 @@ 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), 683)
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),
suppressWarnings(count_IR(example_isolates$AMX))) suppressWarnings(count_IR(example_isolates$AMX)))
expect_equal(suppressWarnings(count_S(example_isolates$AMX)) + count_I(example_isolates$AMX), expect_equal(suppressWarnings(count_S(example_isolates$AMX)) + count_I(example_isolates$AMX),
count_SI(example_isolates$AMX)) count_SI(example_isolates$AMX))
library(dplyr) library(dplyr)
expect_equal(example_isolates %>% count_susceptible(AMC), 1433) expect_equal(example_isolates %>% count_susceptible(AMC), 1433)
@ -45,7 +45,7 @@ test_that("counts work", {
expect_identical(example_isolates %>% count_all(AMC, GEN, only_all_tested = TRUE), expect_identical(example_isolates %>% count_all(AMC, GEN, only_all_tested = TRUE),
example_isolates %>% count_susceptible(AMC, GEN, only_all_tested = TRUE) + example_isolates %>% count_susceptible(AMC, GEN, only_all_tested = TRUE) +
example_isolates %>% count_resistant(AMC, GEN, only_all_tested = TRUE)) example_isolates %>% count_resistant(AMC, GEN, only_all_tested = TRUE))
# count of cases # count of cases
expect_equal(example_isolates %>% expect_equal(example_isolates %>%
group_by(hospital_id) %>% group_by(hospital_id) %>%
@ -83,8 +83,8 @@ test_that("counts work", {
expect_error(count_resistant("test", as_percent = "test")) expect_error(count_resistant("test", as_percent = "test"))
expect_error(count_susceptible("test", minimum = "test")) expect_error(count_susceptible("test", minimum = "test"))
expect_error(count_susceptible("test", as_percent = "test")) expect_error(count_susceptible("test", as_percent = "test"))
expect_error(count_df(c("A", "B", "C"))) expect_error(count_df(c("A", "B", "C")))
expect_error(count_df(example_isolates[, "date"])) expect_error(count_df(example_isolates[, "date"]))
}) })