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(v1.2.0.9033) speed improvement mdro(), filter_ab_class()

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dr. M.S. (Matthijs) Berends 2020-07-12 11:43:31 +02:00
parent 1d66b5c43c
commit c0cf7ab02b
17 changed files with 69 additions and 35 deletions
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1
.lintr
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@ -1 +0,0 @@
linters: with_defaults(line_length_linter = NULL, trailing_whitespace_linter = NULL, object_name_linter = NULL, cyclocomp_linter = NULL, object_usage_linter = NULL, object_length_linter(length = 50L))

4
DESCRIPTION
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@ -1,6 +1,6 @@
Package: AMR Package: AMR
Version: 1.2.0.9032 Version: 1.2.0.9033
Date: 2020-07-09 Date: 2020-07-12
Title: Antimicrobial Resistance Analysis Title: Antimicrobial Resistance Analysis
Authors@R: c( Authors@R: c(
person(role = c("aut", "cre"), person(role = c("aut", "cre"),

5
NEWS.md
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@ -1,5 +1,5 @@
# AMR 1.2.0.9032 # AMR 1.2.0.9033
## <small>Last updated: 09-Jul-2020</small> ## <small>Last updated: 12-Jul-2020</small>
### New ### New
* Function `ab_from_text()` to retrieve antimicrobial drug names, doses and forms of administration from clinical texts in e.g. health care records, which also corrects for misspelling since it uses `as.ab()` internally * Function `ab_from_text()` to retrieve antimicrobial drug names, doses and forms of administration from clinical texts in e.g. health care records, which also corrects for misspelling since it uses `as.ab()` internally
@ -36,6 +36,7 @@
* Changed the summary for class `<mo>`, to highlight the %SI vs. %R * Changed the summary for class `<mo>`, to highlight the %SI vs. %R
* Improved error handling, giving more useful info when functions return an error * Improved error handling, giving more useful info when functions return an error
* Any progress bar will now only show in interactive mode (i.e. not in R Markdown) * Any progress bar will now only show in interactive mode (i.e. not in R Markdown)
* Speed improvement for `mdro()` and `filter_ab_class()`
### Other ### Other
* Moved primary location of this project from GitLab to [GitHub](https://github.com/msberends/AMR), giving us native support for automated syntax checking without being dependent on external services such as AppVeyor and Travis CI. * Moved primary location of this project from GitLab to [GitHub](https://github.com/msberends/AMR), giving us native support for automated syntax checking without being dependent on external services such as AppVeyor and Travis CI.

12
R/filter_ab_class.R
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@ -27,7 +27,7 @@
#' @param ab_class an antimicrobial class, like `"carbapenems"`. The columns `group`, `atc_group1` and `atc_group2` of the [antibiotics] data set will be searched (case-insensitive) for this value. #' @param ab_class an antimicrobial class, like `"carbapenems"`. The columns `group`, `atc_group1` and `atc_group2` of the [antibiotics] data set will be searched (case-insensitive) for this value.
#' @param result an antibiotic result: S, I or R (or a combination of more of them) #' @param result an antibiotic result: S, I or R (or a combination of more of them)
#' @param scope the scope to check which variables to check, can be `"any"` (default) or `"all"` #' @param scope the scope to check which variables to check, can be `"any"` (default) or `"all"`
#' @param ... parameters passed on to `filter_at` from the `dplyr` package #' @param ... previously used when this package still depended on the `dplyr` package, now ignored
#' @details All columns of `x` will be searched for known antibiotic names, abbreviations, brand names and codes (ATC, EARS-Net, WHO, etc.). This means that a filter function like e.g. [filter_aminoglycosides()] will include column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc. #' @details All columns of `x` will be searched for known antibiotic names, abbreviations, brand names and codes (ATC, EARS-Net, WHO, etc.). This means that a filter function like e.g. [filter_aminoglycosides()] will include column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc.
#' @rdname filter_ab_class #' @rdname filter_ab_class
#' @seealso [antibiotic_class_selectors()] for the `select()` equivalent. #' @seealso [antibiotic_class_selectors()] for the `select()` equivalent.
@ -85,13 +85,13 @@ filter_ab_class <- function(x,
# make result = "SI" works too: # make result = "SI" works too:
result <- unlist(strsplit(result, "")) result <- unlist(strsplit(result, ""))
stop_ifnot(all(result %in% c("S", "I", "R")), "`result` must be one or more of: S, I, R") stop_ifnot(all(result %in% c("S", "I", "R")), "`result` must be one or more of: 'S', 'I', 'R'")
stop_ifnot(all(scope %in% c("any", "all")), "`scope` must be one of: any, all") stop_ifnot(all(scope %in% c("any", "all")), "`scope` must be one of: 'any', 'all'")
# get all columns in data with names that resemble antibiotics # get all columns in data with names that resemble antibiotics
ab_in_data <- suppressMessages(get_column_abx(x)) ab_in_data <- suppressMessages(get_column_abx(x))
if (length(ab_in_data) == 0) { if (length(ab_in_data) == 0) {
message(font_blue("NOTE: no antimicrobial agents found, data left unchanged.")) message(font_blue("NOTE: no columns with class <rsi> found (see ?as.rsi), data left unchanged."))
return(x.bak) return(x.bak)
} }
# get reference data # get reference data
@ -146,8 +146,8 @@ filter_ab_class <- function(x,
"` (", ab_name(names(agents), tolower = TRUE, language = NULL), ")"), "` (", ab_name(names(agents), tolower = TRUE, language = NULL), ")"),
collapse = scope_txt), collapse = scope_txt),
operator, toString(result)))) operator, toString(result))))
filtered <- as.logical(by(x, seq_len(nrow(x)), x_transposed <- as.list(as.data.frame(t(x[, agents, drop = FALSE])))
function(row) scope_fn(unlist(row[, agents]) %in% result, na.rm = TRUE))) filtered <- sapply(x_transposed, function(y) scope_fn(y %in% result, na.rm = TRUE))
x <- x[which(filtered), , drop = FALSE] x <- x[which(filtered), , drop = FALSE]
class(x) <- x_class class(x) <- x_class
x x

10
R/mdro.R
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@ -468,9 +468,8 @@ mdro <- function(x,
} else if (any_all == "all") { } else if (any_all == "all") {
search_function <- all search_function <- all
} }
row_filter <- as.logical(by(x, x_transposed <- as.list(as.data.frame(t(x[, cols, drop = FALSE])))
seq_len(nrow(x)), row_filter <- sapply(x_transposed, function(y) search_function(y %in% search_result, na.rm = TRUE))
function(row) search_function(unlist(row[, cols]) %in% search_result, na.rm = TRUE)))
row_filter <- x[row_filter, "row_number", drop = TRUE] row_filter <- x[row_filter, "row_number", drop = TRUE]
rows <- rows[rows %in% row_filter] rows <- rows[rows %in% row_filter]
x[rows, "MDRO"] <<- to x[rows, "MDRO"] <<- to
@ -507,9 +506,8 @@ mdro <- function(x,
na.rm = TRUE) na.rm = TRUE)
}) })
# for PDR; all agents are R (or I if combine_SI = FALSE) # for PDR; all agents are R (or I if combine_SI = FALSE)
row_filter <- as.logical(by(x[rows, ], x_transposed <- as.list(as.data.frame(t(x[rows, lst_vector, drop = FALSE])))
seq_len(nrow(x[rows, ])), row_filter <- sapply(x_transposed, function(y) all(y %in% search_result, na.rm = TRUE))
function(row) all(unlist(row[, lst_vector]) %in% search_result, na.rm = TRUE)))
x[row_filter, "classes_affected"] <<- 999 x[row_filter, "classes_affected"] <<- 999
} }

34
codecov.yml Normal file
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@ -0,0 +1,34 @@
# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2020 Berends MS, Luz CF et al. #
# #
# This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the #
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
# the Free Software Foundation. #
# #
# We created this package for both routine data analysis and academic #
# research and it was publicly released in the hope that it will be #
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.github.io/AMR. #
# ==================================================================== #
codecov:
require_ci_to_pass: no # allow fail
comment: no
coverage:
precision: 1
round: up
range: "0...100"
status:
project: no
patch: no
changes: no

2
docs/404.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a> <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">1.2.0.9032</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9033</span>
</span> </span>
</div> </div>

2
docs/LICENSE-text.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <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">1.2.0.9032</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9033</span>
</span> </span>
</div> </div>

4
docs/articles/WHONET.html
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@ -39,7 +39,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <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">1.2.0.9032</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9033</span>
</span> </span>
</div> </div>
@ -186,7 +186,7 @@
<h1 data-toc-skip>How to work with WHONET data</h1> <h1 data-toc-skip>How to work with WHONET data</h1>
<h4 class="author">Matthijs S. Berends</h4> <h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">09 July 2020</h4> <h4 class="date">12 July 2020</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/WHONET.Rmd"><code>vignettes/WHONET.Rmd</code></a></small> <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/WHONET.Rmd"><code>vignettes/WHONET.Rmd</code></a></small>
<div class="hidden name"><code>WHONET.Rmd</code></div> <div class="hidden name"><code>WHONET.Rmd</code></div>

2
docs/articles/index.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <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">1.2.0.9032</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9033</span>
</span> </span>
</div> </div>

2
docs/authors.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <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">1.2.0.9032</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9033</span>
</span> </span>
</div> </div>

2
docs/index.html
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@ -43,7 +43,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <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">1.2.0.9032</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9033</span>
</span> </span>
</div> </div>

14
docs/news/index.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <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">1.2.0.9032</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9033</span>
</span> </span>
</div> </div>
@ -229,13 +229,13 @@
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small> <small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div> </div>
<div id="amr-1209032" class="section level1"> <div id="amr-1209033" class="section level1">
<h1 class="page-header" data-toc-text="1.2.0.9032"> <h1 class="page-header" data-toc-text="1.2.0.9033">
<a href="#amr-1209032" class="anchor"></a>AMR 1.2.0.9032<small> Unreleased </small> <a href="#amr-1209033" class="anchor"></a>AMR 1.2.0.9033<small> Unreleased </small>
</h1> </h1>
<div id="last-updated-09-jul-2020" class="section level2"> <div id="last-updated-12-jul-2020" class="section level2">
<h2 class="hasAnchor"> <h2 class="hasAnchor">
<a href="#last-updated-09-jul-2020" class="anchor"></a><small>Last updated: 09-Jul-2020</small> <a href="#last-updated-12-jul-2020" class="anchor"></a><small>Last updated: 12-Jul-2020</small>
</h2> </h2>
<div id="new" class="section level3"> <div id="new" class="section level3">
<h3 class="hasAnchor"> <h3 class="hasAnchor">
@ -286,6 +286,8 @@
<li>Changed the summary for class <code>&lt;mo&gt;</code>, to highlight the %SI vs. %R</li> <li>Changed the summary for class <code>&lt;mo&gt;</code>, to highlight the %SI vs. %R</li>
<li>Improved error handling, giving more useful info when functions return an error</li> <li>Improved error handling, giving more useful info when functions return an error</li>
<li>Any progress bar will now only show in interactive mode (i.e. not in R Markdown)</li> <li>Any progress bar will now only show in interactive mode (i.e. not in R Markdown)</li>
<li>Speed improvement for <code><a href="../reference/mdro.html">mdro()</a></code> and <code><a href="../reference/filter_ab_class.html">filter_ab_class()</a></code>
</li>
</ul> </ul>
</div> </div>
<div id="other" class="section level3"> <div id="other" class="section level3">

2
docs/pkgdown.yml
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@ -10,7 +10,7 @@ articles:
WHONET: WHONET.html WHONET: WHONET.html
benchmarks: benchmarks.html benchmarks: benchmarks.html
resistance_predict: resistance_predict.html resistance_predict: resistance_predict.html
last_built: 2020-07-09T18:06Z last_built: 2020-07-12T09:42Z
urls: urls:
reference: https://msberends.github.io/AMR/reference reference: https://msberends.github.io/AMR/reference
article: https://msberends.github.io/AMR/articles article: https://msberends.github.io/AMR/articles

4
docs/reference/filter_ab_class.html
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@ -82,7 +82,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <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">1.2.0.9032</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9033</span>
</span> </span>
</div> </div>
@ -284,7 +284,7 @@
</tr> </tr>
<tr> <tr>
<th>...</th> <th>...</th>
<td><p>parameters passed on to <code>filter_at</code> from the <code>dplyr</code> package</p></td> <td><p>previously used when this package still depended on the <code>dplyr</code> package, now ignored</p></td>
</tr> </tr>
</table> </table>

2
docs/reference/index.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <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">1.2.0.9032</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9033</span>
</span> </span>
</div> </div>

2
man/filter_ab_class.Rd
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@ -54,7 +54,7 @@ filter_tetracyclines(x, result = NULL, scope = "any", ...)
\item{scope}{the scope to check which variables to check, can be \code{"any"} (default) or \code{"all"}} \item{scope}{the scope to check which variables to check, can be \code{"any"} (default) or \code{"all"}}
\item{...}{parameters passed on to \code{filter_at} from the \code{dplyr} package} \item{...}{previously used when this package still depended on the \code{dplyr} package, now ignored}
} }
\description{ \description{
Filter isolates on results in specific antimicrobial classes. This makes it easy to filter on isolates that were tested for e.g. any aminoglycoside, or to filter on carbapenem-resistant isolates without the need to specify the drugs. Filter isolates on results in specific antimicrobial classes. This makes it easy to filter on isolates that were tested for e.g. any aminoglycoside, or to filter on carbapenem-resistant isolates without the need to specify the drugs.