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(v1.4.0.9051) ab class

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dr. M.S. (Matthijs) Berends 2020-12-27 23:19:41 +01:00
parent afc325c314
commit ccf13dd6c0
17 changed files with 58 additions and 32 deletions
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2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR
Version: 1.4.0.9050
Version: 1.4.0.9051
Date: 2020-12-27
Title: Antimicrobial Resistance Analysis
Authors@R: c(

2
NEWS.md
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@ -1,4 +1,4 @@
# AMR 1.4.0.9050
# AMR 1.4.0.9051
## <small>Last updated: 27 December 2020</small>
### New

41
R/ab_class_selectors.R
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@ -69,7 +69,12 @@
#' data.frame(some_column = "some_value",
#' J01CA01 = "S") %>% # ATC code of ampicillin
#' select(penicillins()) # only the 'J01CA01' column will be selected
#'
#'
#'
#' # with dplyr 1.0.0 and higher (that adds 'across()'), this is equal:
#' # (though the row names on the first are more correct)
#' example_isolates %>% filter_carbapenems("R", "all")
#' example_isolates %>% filter(across(carbapenems(), ~. == "R"))
#' }
ab_class <- function(ab_class) {
ab_selector(ab_class, function_name = "ab_class")
@ -156,14 +161,19 @@ tetracyclines <- function() {
ab_selector <- function(ab_class, function_name) {
meet_criteria(ab_class, allow_class = "character", has_length = 1, .call_depth = 1)
meet_criteria(function_name, allow_class = "character", has_length = 1, .call_depth = 1)
for (i in seq_len(length(sys.frames()))) {
vars_df <- sys.frames()[[i]]$x
vars_df <- tryCatch(sys.frames()[[i]]$x, error = function(e) NULL)
if (!is.null(vars_df) && is.data.frame(vars_df)) {
# when using e.g. example_isolates[, carbapenems()] or example_isolates %>% select(carbapenems())
break
} else if (!is.null(vars_df) && is.list(vars_df)) {
# when using e.g. example_isolates %>% filter(across(carbapenems(), ~. == "R"))
vars_df <- as.data.frame(vars_df, stringsAsFactors = FALSE)
break
}
}
stop_ifnot(is.data.frame(vars_df), "the ", function_name, "() function must be used inside dplyr verbs or a data.frame call.")
stop_ifnot(is.data.frame(vars_df), "this function must be used inside dplyr selection verbs or within a data.frame call.", call = -2)
ab_in_data <- get_column_abx(vars_df, info = FALSE)
if (length(ab_in_data) == 0) {
@ -184,15 +194,18 @@ ab_selector <- function(ab_class, function_name) {
}
# get the columns with a group names in the chosen ab class
agents <- ab_in_data[names(ab_in_data) %in% ab_reference$ab]
if (length(agents) == 0) {
message_("No antimicrobial agents of class ", ab_group, " found", examples, ".")
} else {
message_("Selecting ", ab_group, ": ",
paste(paste0("'", font_bold(agents, collapse = NULL),
"' (", ab_name(names(agents), tolower = TRUE, language = NULL), ")"),
collapse = ", "),
as_note = FALSE,
extra_indent = nchar(paste0("Selecting ", ab_group, ": ")))
}
if (message_not_thrown_before(function_name)) {
if (length(agents) == 0) {
message_("No antimicrobial agents of class ", ab_group, " found", examples, ".")
} else {
message_("Selecting ", ab_group, ": ",
paste(paste0("'", font_bold(agents, collapse = NULL),
"' (", ab_name(names(agents), tolower = TRUE, language = NULL), ")"),
collapse = ", "),
as_note = FALSE,
extra_indent = nchar(paste0("Selecting ", ab_group, ": ")))
}
remember_thrown_message(function_name)
}
unname(agents)
}

1
R/filter_ab_class.R
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@ -71,6 +71,7 @@
#' filter_fluoroquinolones("R", "all")
#'
#' # with dplyr 1.0.0 and higher (that adds 'across()'), this is equal:
#' # (though the row names on the first are more correct)
#' example_isolates %>% filter_carbapenems("R", "all")
#' example_isolates %>% filter(across(carbapenems(), ~. == "R"))
#' }

2
docs/404.html
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@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="https://msberends.github.io/AMR//index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9050</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9051</span>
</span>
</div>

2
docs/LICENSE-text.html
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@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<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">1.4.0.9050</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9051</span>
</span>
</div>

2
docs/articles/index.html
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@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<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">1.4.0.9050</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9051</span>
</span>
</div>

2
docs/authors.html
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@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<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">1.4.0.9050</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9051</span>
</span>
</div>

2
docs/index.html
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@ -43,7 +43,7 @@
</button>
<span class="navbar-brand">
<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">1.4.0.9050</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9051</span>
</span>
</div>

8
docs/news/index.html
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@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<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">1.4.0.9050</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9051</span>
</span>
</div>
@ -236,9 +236,9 @@
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div>
<div id="amr-1409050" class="section level1">
<h1 class="page-header" data-toc-text="1.4.0.9050">
<a href="#amr-1409050" class="anchor"></a>AMR 1.4.0.9050<small> Unreleased </small>
<div id="amr-1409051" class="section level1">
<h1 class="page-header" data-toc-text="1.4.0.9051">
<a href="#amr-1409051" class="anchor"></a>AMR 1.4.0.9051<small> Unreleased </small>
</h1>
<div id="last-updated-27-december-2020" class="section level2">
<h2 class="hasAnchor">

2
docs/pkgdown.yml
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@ -12,7 +12,7 @@ articles:
datasets: datasets.html
resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html
last_built: 2020-12-27T19:32Z
last_built: 2020-12-27T22:17Z
urls:
reference: https://msberends.github.io/AMR//reference
article: https://msberends.github.io/AMR//articles

9
docs/reference/antibiotic_class_selectors.html
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@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<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">1.4.0.9050</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9051</span>
</span>
</div>
@ -331,7 +331,12 @@
<span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span><span class='op'>(</span>some_column <span class='op'>=</span> <span class='st'>"some_value"</span>,
J01CA01 <span class='op'>=</span> <span class='st'>"S"</span><span class='op'>)</span> <span class='op'>%&gt;%</span> <span class='co'># ATC code of ampicillin</span>
<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>
<span class='co'># with dplyr 1.0.0 and higher (that adds 'across()'), this is equal:</span>
<span class='co'># (though the row names on the first are more correct)</span>
<span class='va'>example_isolates</span> <span class='op'>%&gt;%</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>
<span class='va'>example_isolates</span> <span class='op'>%&gt;%</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>
<span class='op'>}</span>
</pre>
</div>

3
docs/reference/filter_ab_class.html
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@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<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">1.4.0.9046</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9051</span>
</span>
</div>
@ -344,6 +344,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='fu'>filter_fluoroquinolones</span><span class='op'>(</span><span class='st'>"R"</span>, <span class='st'>"all"</span><span class='op'>)</span>
<span class='co'># with dplyr 1.0.0 and higher (that adds 'across()'), this is equal:</span>
<span class='co'># (though the row names on the first are more correct)</span>
<span class='va'>example_isolates</span> <span class='op'>%&gt;%</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>
<span class='va'>example_isolates</span> <span class='op'>%&gt;%</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>
<span class='op'>}</span>

2
docs/reference/index.html
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@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<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">1.4.0.9050</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9051</span>
</span>
</div>

2
docs/survey.html
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@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<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">1.4.0.9050</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9051</span>
</span>
</div>

7
man/antibiotic_class_selectors.Rd
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@ -100,7 +100,12 @@ if (require("dplyr")) {
data.frame(some_column = "some_value",
J01CA01 = "S") \%>\% # ATC code of ampicillin
select(penicillins()) # only the 'J01CA01' column will be selected
# with dplyr 1.0.0 and higher (that adds 'across()'), this is equal:
# (though the row names on the first are more correct)
example_isolates \%>\% filter_carbapenems("R", "all")
example_isolates \%>\% filter(across(carbapenems(), ~. == "R"))
}
}
\seealso{

1
man/filter_ab_class.Rd
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@ -105,6 +105,7 @@ if (require("dplyr")) {
filter_fluoroquinolones("R", "all")
# with dplyr 1.0.0 and higher (that adds 'across()'), this is equal:
# (though the row names on the first are more correct)
example_isolates \%>\% filter_carbapenems("R", "all")
example_isolates \%>\% filter(across(carbapenems(), ~. == "R"))
}