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(v1.2.0.9012) mo_domain(), improved error handling
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Package: AMR
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Version: 1.2.0.9011
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Version: 1.2.0.9012
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Date: 2020-06-22
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Title: Antimicrobial Resistance Analysis
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Authors@R: c(
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2
NEWS.md
2
NEWS.md
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# AMR 1.2.0.9011
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# AMR 1.2.0.9012
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## <small>Last updated: 22-Jun-2020</small>
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### New
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@ -163,11 +163,10 @@ rsi_calc_df <- function(type, # "proportion", "count" or "both"
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stop_ifnot(is.data.frame(data), "`data` must be a data.frame", call = -2)
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stop_if(any(dim(data) == 0), "`data` must contain rows and columns", call = -2)
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stop_ifnot(any(sapply(data, is.rsi), na.rm = TRUE), "no columns with class <rsi> found. See ?as.rsi.", call = -2)
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stop_if(isTRUE(combine_SI) & isTRUE(combine_IR), "either `combine_SI` or `combine_IR` can be TRUE, not both", call = -2)
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if (isTRUE(combine_IR) & isTRUE(combine_SI_missing)) {
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combine_SI <- FALSE
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}
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stop_if(isTRUE(combine_SI) & isTRUE(combine_IR), "either `combine_SI` or `combine_IR` can be TRUE, not both", call = -2)
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if (as.character(translate_ab) %in% c("TRUE", "official")) {
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translate_ab <- "name"
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@ -81,7 +81,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="https://msberends.gitlab.io/AMR/index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9011</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9012</span>
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</span>
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</div>
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@ -81,7 +81,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9011</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9012</span>
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</span>
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</div>
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@ -81,7 +81,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9011</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9012</span>
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</span>
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</div>
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@ -81,7 +81,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9011</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9012</span>
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</span>
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</div>
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@ -43,7 +43,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9011</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9012</span>
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</span>
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</div>
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@ -81,7 +81,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9011</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9012</span>
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</span>
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</div>
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@ -229,9 +229,9 @@
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<small>Source: <a href='https://gitlab.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
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</div>
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<div id="amr-1209011" class="section level1">
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<h1 class="page-header" data-toc-text="1.2.0.9011">
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<a href="#amr-1209011" class="anchor"></a>AMR 1.2.0.9011<small> Unreleased </small>
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<div id="amr-1209012" class="section level1">
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<h1 class="page-header" data-toc-text="1.2.0.9012">
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<a href="#amr-1209012" class="anchor"></a>AMR 1.2.0.9012<small> Unreleased </small>
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</h1>
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<div id="last-updated-22-jun-2020" class="section level2">
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<h2 class="hasAnchor">
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@ -10,7 +10,7 @@ articles:
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WHONET: WHONET.html
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benchmarks: benchmarks.html
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resistance_predict: resistance_predict.html
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last_built: 2020-06-22T09:16Z
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last_built: 2020-06-22T10:13Z
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urls:
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reference: https://msberends.gitlab.io/AMR/reference
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article: https://msberends.gitlab.io/AMR/articles
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@ -81,7 +81,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9011</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9012</span>
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</span>
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</div>
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@ -28,13 +28,13 @@ test_that("counts work", {
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expect_equal(count_all(example_isolates$AMX), n_rsi(example_isolates$AMX))
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# AMX resistance in `example_isolates`
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expect_equal(count_R(example_isolates$AMX), 683)
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expect_equal(count_I(example_isolates$AMX), 3)
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expect_equal(suppressWarnings(count_S(example_isolates$AMX)), 543)
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expect_equal(count_R(example_isolates$AMX) + count_I(example_isolates$AMX),
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suppressWarnings(count_IR(example_isolates$AMX)))
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expect_equal(suppressWarnings(count_S(example_isolates$AMX)) + count_I(example_isolates$AMX),
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count_SI(example_isolates$AMX))
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expect_equal(count_R(example_isolates$AMX), 683)
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expect_equal(count_I(example_isolates$AMX), 3)
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expect_equal(suppressWarnings(count_S(example_isolates$AMX)), 543)
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expect_equal(count_R(example_isolates$AMX) + count_I(example_isolates$AMX),
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suppressWarnings(count_IR(example_isolates$AMX)))
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expect_equal(suppressWarnings(count_S(example_isolates$AMX)) + count_I(example_isolates$AMX),
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count_SI(example_isolates$AMX))
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library(dplyr)
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expect_equal(example_isolates %>% count_susceptible(AMC), 1433)
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expect_identical(example_isolates %>% count_all(AMC, GEN, only_all_tested = TRUE),
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example_isolates %>% count_susceptible(AMC, GEN, only_all_tested = TRUE) +
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example_isolates %>% count_resistant(AMC, GEN, only_all_tested = TRUE))
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# count of cases
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expect_equal(example_isolates %>%
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group_by(hospital_id) %>%
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expect_error(count_resistant("test", as_percent = "test"))
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expect_error(count_susceptible("test", minimum = "test"))
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expect_error(count_susceptible("test", as_percent = "test"))
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expect_error(count_df(c("A", "B", "C")))
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expect_error(count_df(example_isolates[, "date"]))
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})
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