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(v1.4.0.9004) bugfix
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Package: AMR
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Version: 1.4.0.9003
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Date: 2020-10-20
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Version: 1.4.0.9004
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Date: 2020-10-21
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Title: Antimicrobial Resistance Analysis
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Authors@R: c(
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person(role = c("aut", "cre"),
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4
NEWS.md
4
NEWS.md
@ -1,5 +1,5 @@
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# AMR 1.4.0.9003
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## <small>Last updated: 20 October 2020</small>
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# AMR 1.4.0.9004
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## <small>Last updated: 21 October 2020</small>
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### New
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* Functions `is_gram_negative()` and `is_gram_positive()` as wrappers around `mo_gramstain()`. They always return `TRUE` or `FALSE`, thus always return `FALSE` for species outside the taxonomic kingdom of Bacteria.
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@ -273,7 +273,7 @@ geom_rsi <- function(position = NULL,
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combine_SI = TRUE,
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combine_IR = FALSE,
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...) {
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x <- x[1]
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stop_ifnot_installed("ggplot2")
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stop_if(is.data.frame(position), "`position` is invalid. Did you accidentally use '%>%' instead of '+'?")
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meet_criteria(position, allow_class = "character", has_length = 1, is_in = c("fill", "stack", "dodge"), allow_NULL = TRUE)
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@ -294,8 +294,6 @@ geom_rsi <- function(position = NULL,
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position <- ggplot2::position_fill(vjust = 0.5, reverse = TRUE)
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}
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x <- x[1]
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# we work with aes_string later on
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x_deparse <- deparse(substitute(x))
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if (x_deparse != "x") {
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10
R/rsi.R
10
R/rsi.R
@ -100,14 +100,14 @@
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#' summary(example_isolates) # see all R/SI results at a glance
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#'
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#' if (require("skimr")) {
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#' # support for skim() too:
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#' # class <rsi> supported in skim() too:
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#' skim(example_isolates)
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#' }
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#'
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#' # For INTERPRETING disk diffusion and MIC values -----------------------
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#'
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#' # a whole data set, even with combined MIC values and disk zones
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#' df <- data.frame(microorganism = "E. coli",
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#' df <- data.frame(microorganism = "Escherichia coli",
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#' AMP = as.mic(8),
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#' CIP = as.mic(0.256),
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#' GEN = as.disk(18),
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@ -136,7 +136,7 @@
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#' df %>% mutate(across(AMP:TOB, as.rsi))
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#'
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#' df %>%
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#' mutate_at(vars(AMP:TOB), as.rsi, mo = "E. coli")
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#' mutate_at(vars(AMP:TOB), as.rsi, mo = .$microorganism)
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#'
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#' # to include information about urinary tract infections (UTI)
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#' data.frame(mo = "E. coli",
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@ -457,7 +457,7 @@ as.rsi.data.frame <- function(x,
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meet_criteria(x, allow_class = "data.frame") # will also check for dimensions > 0
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meet_criteria(col_mo, allow_class = "character", is_in = colnames(x), allow_NULL = TRUE)
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meet_criteria(guideline, allow_class = "character", has_length = 1)
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meet_criteria(uti, allow_class = "logical", has_length = c(1, nrow(x)), allow_NULL = TRUE)
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meet_criteria(uti, allow_class = c("logical", "character"), allow_NULL = TRUE)
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meet_criteria(conserve_capped_values, allow_class = "logical", has_length = 1)
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meet_criteria(add_intrinsic_resistance, allow_class = "logical", has_length = 1)
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@ -482,6 +482,8 @@ as.rsi.data.frame <- function(x,
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}
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} else {
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# column found, transform to logical
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stop_if(length(col_uti) != 1 | !col_uti %in% colnames(x),
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"argument `uti` must be a logical vector, of must be a single column name of `x`")
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uti <- as.logical(x[, col_uti, drop = TRUE])
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}
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} else {
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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">1.4.0.9003</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9004</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">1.4.0.9003</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9004</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">1.4.0.9003</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9004</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">1.4.0.9003</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9004</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">1.4.0.9003</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9004</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">1.4.0.9003</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9004</span>
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</span>
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</div>
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@ -236,13 +236,13 @@
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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-1409003" class="section level1">
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<h1 class="page-header" data-toc-text="1.4.0.9003">
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<a href="#amr-1409003" class="anchor"></a>AMR 1.4.0.9003<small> Unreleased </small>
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<div id="amr-1409004" class="section level1">
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<h1 class="page-header" data-toc-text="1.4.0.9004">
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<a href="#amr-1409004" class="anchor"></a>AMR 1.4.0.9004<small> Unreleased </small>
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</h1>
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<div id="last-updated-20-october-2020" class="section level2">
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<div id="last-updated-21-october-2020" class="section level2">
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<h2 class="hasAnchor">
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<a href="#last-updated-20-october-2020" class="anchor"></a><small>Last updated: 20 October 2020</small>
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<a href="#last-updated-21-october-2020" class="anchor"></a><small>Last updated: 21 October 2020</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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@ -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: 2020-10-20T18:59Z
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last_built: 2020-10-21T09:40Z
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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">1.4.0.9001</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9004</span>
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</span>
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</div>
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@ -414,14 +414,14 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
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<pre class="examples"><span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>)</span> <span class='co'># see all R/SI results at a glance</span>
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<span class='kw'>if</span> <span class='op'>(</span><span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='st'><a href='https://docs.ropensci.org/skimr'>"skimr"</a></span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
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<span class='co'># support for skim() too:</span>
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<span class='co'># class <rsi> supported in skim() too:</span>
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<span class='fu'><a href='https://docs.ropensci.org/skimr/reference/skim.html'>skim</a></span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>)</span>
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<span class='op'>}</span>
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<span class='co'># For INTERPRETING disk diffusion and MIC values -----------------------</span>
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<span class='co'># a whole data set, even with combined MIC values and disk zones</span>
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<span class='va'>df</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span><span class='op'>(</span>microorganism <span class='op'>=</span> <span class='st'>"E. coli"</span>,
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<span class='va'>df</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span><span class='op'>(</span>microorganism <span class='op'>=</span> <span class='st'>"Escherichia coli"</span>,
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AMP <span class='op'>=</span> <span class='fu'><a href='as.mic.html'>as.mic</a></span><span class='op'>(</span><span class='fl'>8</span><span class='op'>)</span>,
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CIP <span class='op'>=</span> <span class='fu'><a href='as.mic.html'>as.mic</a></span><span class='op'>(</span><span class='fl'>0.256</span><span class='op'>)</span>,
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GEN <span class='op'>=</span> <span class='fu'><a href='as.disk.html'>as.disk</a></span><span class='op'>(</span><span class='fl'>18</span><span class='op'>)</span>,
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@ -450,7 +450,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
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<span class='va'>df</span> <span class='op'>%>%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</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='va'>AMP</span><span class='op'>:</span><span class='va'>TOB</span>, <span class='va'>as.rsi</span><span class='op'>)</span><span class='op'>)</span>
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<span class='va'>df</span> <span class='op'>%>%</span>
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<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_at</a></span><span class='op'>(</span><span class='fu'><a href='https://dplyr.tidyverse.org/reference/vars.html'>vars</a></span><span class='op'>(</span><span class='va'>AMP</span><span class='op'>:</span><span class='va'>TOB</span><span class='op'>)</span>, <span class='va'>as.rsi</span>, mo <span class='op'>=</span> <span class='st'>"E. coli"</span><span class='op'>)</span>
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<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_at</a></span><span class='op'>(</span><span class='fu'><a href='https://dplyr.tidyverse.org/reference/vars.html'>vars</a></span><span class='op'>(</span><span class='va'>AMP</span><span class='op'>:</span><span class='va'>TOB</span><span class='op'>)</span>, <span class='va'>as.rsi</span>, mo <span class='op'>=</span> <span class='va'>.</span><span class='op'>$</span><span class='va'>microorganism</span><span class='op'>)</span>
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<span class='co'># to include information about urinary tract infections (UTI)</span>
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<span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span><span class='op'>(</span>mo <span class='op'>=</span> <span class='st'>"E. coli"</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">1.4.0.9003</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9004</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">1.4.0.9003</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9004</span>
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</span>
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</div>
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@ -157,14 +157,14 @@ On our website \url{https://msberends.github.io/AMR/} you can find \href{https:/
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summary(example_isolates) # see all R/SI results at a glance
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if (require("skimr")) {
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# support for skim() too:
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# class <rsi> supported in skim() too:
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skim(example_isolates)
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}
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# For INTERPRETING disk diffusion and MIC values -----------------------
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# a whole data set, even with combined MIC values and disk zones
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df <- data.frame(microorganism = "E. coli",
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df <- data.frame(microorganism = "Escherichia coli",
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AMP = as.mic(8),
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CIP = as.mic(0.256),
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GEN = as.disk(18),
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@ -193,7 +193,7 @@ if (require("dplyr")) {
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df \%>\% mutate(across(AMP:TOB, as.rsi))
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df \%>\%
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mutate_at(vars(AMP:TOB), as.rsi, mo = "E. coli")
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mutate_at(vars(AMP:TOB), as.rsi, mo = .$microorganism)
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# to include information about urinary tract infections (UTI)
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data.frame(mo = "E. coli",
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