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(v1.6.0.9020) fix for skimr in dplyr 1.0.6
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Package: AMR
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Version: 1.6.0.9019
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Date: 2021-05-05
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Version: 1.6.0.9020
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Date: 2021-05-06
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Title: Antimicrobial Resistance Data Analysis
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Authors@R: c(
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person(role = c("aut", "cre"),
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5
NEWS.md
5
NEWS.md
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# `AMR` 1.6.0.9019
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## <small>Last updated: 5 May 2021</small>
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# `AMR` 1.6.0.9020
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## <small>Last updated: 6 May 2021</small>
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### New
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* Function `custom_eucast_rules()` that brings support for custom AMR rules in `eucast_rules()`
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@ -36,6 +36,7 @@
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* Colour fix for using `barplot()` on an RSI class
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* Added 25 common system codes for bacteria to the `microorganisms.codes` data set
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* Added 16 common system codes for antimicrobial agents to the `antibiotics` data set
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* Fix for using `skimr::skim()` on classes `mo`, `mic` and `disk` when using the just released `dplyr` v1.0.6
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# `AMR` 1.6.0
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2
R/disk.R
2
R/disk.R
@ -202,7 +202,7 @@ get_skimmers.disk <- function(column) {
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min = ~min(as.double(.), na.rm = TRUE),
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max = ~max(as.double(.), na.rm = TRUE),
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median = ~stats::median(as.double(.), na.rm = TRUE),
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n_unique = ~pm_n_distinct(., na.rm = TRUE),
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n_unique = ~length(unique(stats::na.omit(.))),
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hist = ~skimr::inline_hist(stats::na.omit(as.double(.)))
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)
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}
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2
R/mic.R
2
R/mic.R
@ -348,7 +348,7 @@ get_skimmers.mic <- function(column) {
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min = ~min(., na.rm = TRUE),
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max = ~max(., na.rm = TRUE),
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median = ~stats::median(., na.rm = TRUE),
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n_unique = ~pm_n_distinct(., na.rm = TRUE),
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n_unique = ~length(unique(stats::na.omit(.))),
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hist_log2 = ~skimr::inline_hist(log2(stats::na.omit(.)))
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)
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}
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6
R/mo.R
6
R/mo.R
@ -1732,9 +1732,9 @@ freq.mo <- function(x, ...) {
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get_skimmers.mo <- function(column) {
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skimr::sfl(
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skim_type = "mo",
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unique_total = ~pm_n_distinct(., na.rm = TRUE),
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gram_negative = ~sum(mo_is_gram_negative(stats::na.omit(.))),
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gram_positive = ~sum(mo_is_gram_positive(stats::na.omit(.))),
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unique_total = ~length(unique(stats::na.omit(.))),
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gram_negative = ~sum(mo_is_gram_negative(.), na.rm = TRUE),
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gram_positive = ~sum(mo_is_gram_positive(.), na.rm = TRUE),
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top_genus = ~names(sort(-table(mo_genus(stats::na.omit(.), language = NULL))))[1L],
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top_species = ~names(sort(-table(mo_name(stats::na.omit(.), language = NULL))))[1L]
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)
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20
R/rsi.R
20
R/rsi.R
@ -934,28 +934,16 @@ get_skimmers.rsi <- function(column) {
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# get the variable name 'skim_variable'
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name_call <- function(.data) {
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calls <- sys.calls()
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frms <- sys.frames()
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calls_txt <- vapply(calls, function(x) paste(deparse(x), collapse = ""), FUN.VALUE = character(1))
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if (any(calls_txt %like% "skim_variable", na.rm = TRUE)) {
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ind <- which(calls_txt %like% "skim_variable")[1L]
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vars <- tryCatch(eval(parse(text = ".data$skim_variable"), envir = sys.frame(ind)),
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vars <- tryCatch(eval(parse(text = ".data$skim_variable$rsi"), envir = frms[[ind]]),
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error = function(e) NULL)
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tryCatch(ab_name(as.character(calls[[length(calls)]][[2]]), language = NULL),
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error = function(e) NA_character_)
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} else {
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vars <- NULL
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}
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i <- tryCatch(attributes(calls[[length(calls)]])$position,
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error = function(e) NULL)
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if (is.null(vars) | is.null(i)) {
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NA_character_
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} else {
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lengths <- vapply(FUN.VALUE = double(1), vars, length)
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when_starts_rsi <- which(names(vapply(FUN.VALUE = double(1), vars, length)) == "rsi")
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offset <- sum(lengths[c(1:when_starts_rsi - 1)])
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var <- vars$rsi[i - offset]
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if (!isFALSE(var == "data")) {
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NA_character_
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} else{
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ab_name(var)
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}
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}
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}
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BIN
R/sysdata.rda
BIN
R/sysdata.rda
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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">1.6.0.9019</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9020</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">1.6.0.9019</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9020</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">1.6.0.9019</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9020</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">1.6.0.9019</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9020</span>
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</span>
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</div>
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@ -42,7 +42,7 @@
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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">1.6.0.9019</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9020</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">1.6.0.9019</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9020</span>
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</span>
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</div>
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@ -236,12 +236,12 @@
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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-1609019" class="section level1">
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<h1 class="page-header" data-toc-text="1.6.0.9019">
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<a href="#amr-1609019" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.6.0.9019</h1>
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<div id="last-updated-5-may-2021" class="section level2">
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<div id="amr-1609020" class="section level1">
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<h1 class="page-header" data-toc-text="1.6.0.9020">
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<a href="#amr-1609020" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.6.0.9020</h1>
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<div id="last-updated-6-may-2021" class="section level2">
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<h2 class="hasAnchor">
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<a href="#last-updated-5-may-2021" class="anchor"></a><small>Last updated: 5 May 2021</small>
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<a href="#last-updated-6-may-2021" class="anchor"></a><small>Last updated: 6 May 2021</small>
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</h2>
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<div id="new" class="section level3">
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<h3 class="hasAnchor">
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@ -300,6 +300,7 @@
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<li>Colour fix for using <code><a href="https://rdrr.io/r/graphics/barplot.html">barplot()</a></code> on an RSI class</li>
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<li>Added 25 common system codes for bacteria to the <code>microorganisms.codes</code> data set</li>
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<li>Added 16 common system codes for antimicrobial agents to the <code>antibiotics</code> data set</li>
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<li>Fix for using <code><a href="https://docs.ropensci.org/skimr/reference/skim.html">skimr::skim()</a></code> on classes <code>mo</code>, <code>mic</code> and <code>disk</code> when using the just released <code>dplyr</code> v1.0.6</li>
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</ul>
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</div>
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</div>
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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: 2021-05-05T13:26Z
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last_built: 2021-05-06T13:16Z
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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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@ -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">1.6.0.9019</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9020</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">1.6.0.9019</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9020</span>
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</span>
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</div>
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