mirror of https://github.com/msberends/AMR.git
(v1.4.0.9051) ab class
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Package: AMR
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Version: 1.4.0.9050
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Version: 1.4.0.9051
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Date: 2020-12-27
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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 1.4.0.9050
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# AMR 1.4.0.9051
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## <small>Last updated: 27 December 2020</small>
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### New
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@ -70,6 +70,11 @@
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#' J01CA01 = "S") %>% # ATC code of ampicillin
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#' select(penicillins()) # only the 'J01CA01' column will be selected
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#'
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#'
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#' # with dplyr 1.0.0 and higher (that adds 'across()'), this is equal:
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#' # (though the row names on the first are more correct)
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#' example_isolates %>% filter_carbapenems("R", "all")
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#' example_isolates %>% filter(across(carbapenems(), ~. == "R"))
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#' }
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ab_class <- function(ab_class) {
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ab_selector(ab_class, function_name = "ab_class")
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@ -158,12 +163,17 @@ ab_selector <- function(ab_class, function_name) {
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meet_criteria(function_name, allow_class = "character", has_length = 1, .call_depth = 1)
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for (i in seq_len(length(sys.frames()))) {
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vars_df <- sys.frames()[[i]]$x
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vars_df <- tryCatch(sys.frames()[[i]]$x, error = function(e) NULL)
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if (!is.null(vars_df) && is.data.frame(vars_df)) {
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# when using e.g. example_isolates[, carbapenems()] or example_isolates %>% select(carbapenems())
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break
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} else if (!is.null(vars_df) && is.list(vars_df)) {
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# when using e.g. example_isolates %>% filter(across(carbapenems(), ~. == "R"))
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vars_df <- as.data.frame(vars_df, stringsAsFactors = FALSE)
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break
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}
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}
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stop_ifnot(is.data.frame(vars_df), "the ", function_name, "() function must be used inside dplyr verbs or a data.frame call.")
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stop_ifnot(is.data.frame(vars_df), "this function must be used inside dplyr selection verbs or within a data.frame call.", call = -2)
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ab_in_data <- get_column_abx(vars_df, info = FALSE)
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if (length(ab_in_data) == 0) {
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@ -184,6 +194,7 @@ ab_selector <- function(ab_class, function_name) {
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}
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# get the columns with a group names in the chosen ab class
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agents <- ab_in_data[names(ab_in_data) %in% ab_reference$ab]
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if (message_not_thrown_before(function_name)) {
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if (length(agents) == 0) {
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message_("No antimicrobial agents of class ", ab_group, " found", examples, ".")
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} else {
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@ -194,5 +205,7 @@ ab_selector <- function(ab_class, function_name) {
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as_note = FALSE,
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extra_indent = nchar(paste0("Selecting ", ab_group, ": ")))
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}
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remember_thrown_message(function_name)
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}
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unname(agents)
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}
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@ -71,6 +71,7 @@
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#' filter_fluoroquinolones("R", "all")
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#'
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#' # with dplyr 1.0.0 and higher (that adds 'across()'), this is equal:
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#' # (though the row names on the first are more correct)
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#' example_isolates %>% filter_carbapenems("R", "all")
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#' example_isolates %>% filter(across(carbapenems(), ~. == "R"))
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#' }
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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.github.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">1.4.0.9050</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9051</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">1.4.0.9050</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9051</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">1.4.0.9050</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9051</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">1.4.0.9050</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9051</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">1.4.0.9050</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9051</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">1.4.0.9050</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9051</span>
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</span>
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</div>
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@ -236,9 +236,9 @@
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<small>Source: <a href='https://github.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-1409050" class="section level1">
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<h1 class="page-header" data-toc-text="1.4.0.9050">
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<a href="#amr-1409050" class="anchor"></a>AMR 1.4.0.9050<small> Unreleased </small>
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<div id="amr-1409051" class="section level1">
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<h1 class="page-header" data-toc-text="1.4.0.9051">
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<a href="#amr-1409051" class="anchor"></a>AMR 1.4.0.9051<small> Unreleased </small>
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</h1>
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<div id="last-updated-27-december-2020" class="section level2">
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<h2 class="hasAnchor">
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@ -12,7 +12,7 @@ articles:
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datasets: datasets.html
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resistance_predict: resistance_predict.html
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welcome_to_AMR: welcome_to_AMR.html
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last_built: 2020-12-27T19:32Z
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last_built: 2020-12-27T22:17Z
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urls:
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reference: https://msberends.github.io/AMR//reference
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article: https://msberends.github.io/AMR//articles
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@ -82,7 +82,7 @@
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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">1.4.0.9050</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9051</span>
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</span>
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</div>
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J01CA01 <span class='op'>=</span> <span class='st'>"S"</span><span class='op'>)</span> <span class='op'>%>%</span> <span class='co'># ATC code of ampicillin</span>
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<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span><span class='op'>(</span><span class='fu'>penicillins</span><span class='op'>(</span><span class='op'>)</span><span class='op'>)</span> <span class='co'># only the 'J01CA01' column will be selected</span>
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<span class='co'># with dplyr 1.0.0 and higher (that adds 'across()'), this is equal:</span>
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<span class='co'># (though the row names on the first are more correct)</span>
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<span class='va'>example_isolates</span> <span class='op'>%>%</span> <span class='fu'><a href='filter_ab_class.html'>filter_carbapenems</a></span><span class='op'>(</span><span class='st'>"R"</span>, <span class='st'>"all"</span><span class='op'>)</span>
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<span class='va'>example_isolates</span> <span class='op'>%>%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span><span class='op'>(</span><span class='fu'><a href='https://dplyr.tidyverse.org/reference/across.html'>across</a></span><span class='op'>(</span><span class='fu'>carbapenems</span><span class='op'>(</span><span class='op'>)</span>, <span class='op'>~</span><span class='va'>.</span> <span class='op'>==</span> <span class='st'>"R"</span><span class='op'>)</span><span class='op'>)</span>
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<span class='op'>}</span>
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</pre>
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</div>
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@ -82,7 +82,7 @@
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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">1.4.0.9046</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9051</span>
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</span>
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</div>
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<span class='fu'>filter_fluoroquinolones</span><span class='op'>(</span><span class='st'>"R"</span>, <span class='st'>"all"</span><span class='op'>)</span>
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<span class='co'># with dplyr 1.0.0 and higher (that adds 'across()'), this is equal:</span>
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<span class='co'># (though the row names on the first are more correct)</span>
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<span class='va'>example_isolates</span> <span class='op'>%>%</span> <span class='fu'>filter_carbapenems</span><span class='op'>(</span><span class='st'>"R"</span>, <span class='st'>"all"</span><span class='op'>)</span>
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<span class='va'>example_isolates</span> <span class='op'>%>%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span><span class='op'>(</span><span class='fu'><a href='https://dplyr.tidyverse.org/reference/across.html'>across</a></span><span class='op'>(</span><span class='fu'><a href='antibiotic_class_selectors.html'>carbapenems</a></span><span class='op'>(</span><span class='op'>)</span>, <span class='op'>~</span><span class='va'>.</span> <span class='op'>==</span> <span class='st'>"R"</span><span class='op'>)</span><span class='op'>)</span>
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<span class='op'>}</span>
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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">1.4.0.9050</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9051</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">1.4.0.9050</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9051</span>
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</span>
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</div>
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@ -101,6 +101,11 @@ if (require("dplyr")) {
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J01CA01 = "S") \%>\% # ATC code of ampicillin
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select(penicillins()) # only the 'J01CA01' column will be selected
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# with dplyr 1.0.0 and higher (that adds 'across()'), this is equal:
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# (though the row names on the first are more correct)
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example_isolates \%>\% filter_carbapenems("R", "all")
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example_isolates \%>\% filter(across(carbapenems(), ~. == "R"))
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}
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}
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\seealso{
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filter_fluoroquinolones("R", "all")
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# with dplyr 1.0.0 and higher (that adds 'across()'), this is equal:
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# (though the row names on the first are more correct)
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example_isolates \%>\% filter_carbapenems("R", "all")
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example_isolates \%>\% filter(across(carbapenems(), ~. == "R"))
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}
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