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(v1.2.0.9033) speed improvement mdro(), filter_ab_class()
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parent
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.lintr
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.lintr
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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))
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@ -1,6 +1,6 @@
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Package: AMR
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Version: 1.2.0.9032
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Date: 2020-07-09
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Version: 1.2.0.9033
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Date: 2020-07-12
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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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5
NEWS.md
5
NEWS.md
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# AMR 1.2.0.9032
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## <small>Last updated: 09-Jul-2020</small>
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# AMR 1.2.0.9033
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## <small>Last updated: 12-Jul-2020</small>
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### New
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* 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
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@ -36,6 +36,7 @@
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* Changed the summary for class `<mo>`, to highlight the %SI vs. %R
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* Improved error handling, giving more useful info when functions return an error
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* Any progress bar will now only show in interactive mode (i.e. not in R Markdown)
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* Speed improvement for `mdro()` and `filter_ab_class()`
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### Other
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* 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.
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@ -27,7 +27,7 @@
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#' @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.
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#' @param result an antibiotic result: S, I or R (or a combination of more of them)
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#' @param scope the scope to check which variables to check, can be `"any"` (default) or `"all"`
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#' @param ... parameters passed on to `filter_at` from the `dplyr` package
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#' @param ... previously used when this package still depended on the `dplyr` package, now ignored
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#' @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.
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#' @rdname filter_ab_class
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#' @seealso [antibiotic_class_selectors()] for the `select()` equivalent.
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@ -85,13 +85,13 @@ filter_ab_class <- function(x,
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# make result = "SI" works too:
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result <- unlist(strsplit(result, ""))
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stop_ifnot(all(result %in% c("S", "I", "R")), "`result` must be one or more of: S, I, R")
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stop_ifnot(all(scope %in% c("any", "all")), "`scope` must be one of: any, all")
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stop_ifnot(all(result %in% c("S", "I", "R")), "`result` must be one or more of: 'S', 'I', 'R'")
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stop_ifnot(all(scope %in% c("any", "all")), "`scope` must be one of: 'any', 'all'")
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# get all columns in data with names that resemble antibiotics
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ab_in_data <- suppressMessages(get_column_abx(x))
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if (length(ab_in_data) == 0) {
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message(font_blue("NOTE: no antimicrobial agents found, data left unchanged."))
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message(font_blue("NOTE: no columns with class <rsi> found (see ?as.rsi), data left unchanged."))
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return(x.bak)
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}
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# get reference data
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@ -146,8 +146,8 @@ filter_ab_class <- function(x,
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"` (", ab_name(names(agents), tolower = TRUE, language = NULL), ")"),
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collapse = scope_txt),
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operator, toString(result))))
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filtered <- as.logical(by(x, seq_len(nrow(x)),
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function(row) scope_fn(unlist(row[, agents]) %in% result, na.rm = TRUE)))
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x_transposed <- as.list(as.data.frame(t(x[, agents, drop = FALSE])))
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filtered <- sapply(x_transposed, function(y) scope_fn(y %in% result, na.rm = TRUE))
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x <- x[which(filtered), , drop = FALSE]
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class(x) <- x_class
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x
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10
R/mdro.R
10
R/mdro.R
@ -468,9 +468,8 @@ mdro <- function(x,
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} else if (any_all == "all") {
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search_function <- all
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}
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row_filter <- as.logical(by(x,
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seq_len(nrow(x)),
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function(row) search_function(unlist(row[, cols]) %in% search_result, na.rm = TRUE)))
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x_transposed <- as.list(as.data.frame(t(x[, cols, drop = FALSE])))
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row_filter <- sapply(x_transposed, function(y) search_function(y %in% search_result, na.rm = TRUE))
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row_filter <- x[row_filter, "row_number", drop = TRUE]
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rows <- rows[rows %in% row_filter]
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x[rows, "MDRO"] <<- to
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@ -507,9 +506,8 @@ mdro <- function(x,
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na.rm = TRUE)
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})
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# for PDR; all agents are R (or I if combine_SI = FALSE)
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row_filter <- as.logical(by(x[rows, ],
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seq_len(nrow(x[rows, ])),
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function(row) all(unlist(row[, lst_vector]) %in% search_result, na.rm = TRUE)))
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x_transposed <- as.list(as.data.frame(t(x[rows, lst_vector, drop = FALSE])))
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row_filter <- sapply(x_transposed, function(y) all(y %in% search_result, na.rm = TRUE))
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x[row_filter, "classes_affected"] <<- 999
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}
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34
codecov.yml
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34
codecov.yml
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# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Analysis #
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# #
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# SOURCE #
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# https://github.com/msberends/AMR #
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# #
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# LICENCE #
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# (c) 2018-2020 Berends MS, Luz CF et al. #
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# #
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# This R package is free software; you can freely use and distribute #
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# it for both personal and commercial purposes under the terms of the #
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# GNU General Public License version 2.0 (GNU GPL-2), as published by #
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# the Free Software Foundation. #
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# #
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# We created this package for both routine data analysis and academic #
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# research and it was publicly released in the hope that it will be #
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# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
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# Visit our website for more info: https://msberends.github.io/AMR. #
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# ==================================================================== #
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codecov:
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require_ci_to_pass: no # allow fail
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comment: no
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coverage:
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precision: 1
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round: up
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range: "0...100"
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status:
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project: no
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patch: no
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changes: no
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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">1.2.0.9032</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9033</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">1.2.0.9032</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9033</span>
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</span>
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</div>
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@ -39,7 +39,7 @@
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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">1.2.0.9032</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9033</span>
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</span>
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</div>
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@ -186,7 +186,7 @@
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<h1 data-toc-skip>How to work with WHONET data</h1>
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<h4 class="author">Matthijs S. Berends</h4>
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<h4 class="date">09 July 2020</h4>
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<h4 class="date">12 July 2020</h4>
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<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/WHONET.Rmd"><code>vignettes/WHONET.Rmd</code></a></small>
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<div class="hidden name"><code>WHONET.Rmd</code></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">1.2.0.9032</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9033</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">1.2.0.9032</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9033</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">1.2.0.9032</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9033</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">1.2.0.9032</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9033</span>
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</span>
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</div>
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@ -229,13 +229,13 @@
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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-1209032" class="section level1">
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<h1 class="page-header" data-toc-text="1.2.0.9032">
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<a href="#amr-1209032" class="anchor"></a>AMR 1.2.0.9032<small> Unreleased </small>
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<div id="amr-1209033" class="section level1">
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<h1 class="page-header" data-toc-text="1.2.0.9033">
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<a href="#amr-1209033" class="anchor"></a>AMR 1.2.0.9033<small> Unreleased </small>
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</h1>
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<div id="last-updated-09-jul-2020" class="section level2">
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<div id="last-updated-12-jul-2020" class="section level2">
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<h2 class="hasAnchor">
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<a href="#last-updated-09-jul-2020" class="anchor"></a><small>Last updated: 09-Jul-2020</small>
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<a href="#last-updated-12-jul-2020" class="anchor"></a><small>Last updated: 12-Jul-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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@ -286,6 +286,8 @@
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<li>Changed the summary for class <code><mo></code>, to highlight the %SI vs. %R</li>
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<li>Improved error handling, giving more useful info when functions return an error</li>
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<li>Any progress bar will now only show in interactive mode (i.e. not in R Markdown)</li>
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<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>
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</li>
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</ul>
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</div>
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<div id="other" class="section level3">
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WHONET: WHONET.html
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benchmarks: benchmarks.html
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resistance_predict: resistance_predict.html
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last_built: 2020-07-09T18:06Z
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last_built: 2020-07-12T09:42Z
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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">1.2.0.9032</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9033</span>
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</span>
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</div>
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@ -284,7 +284,7 @@
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</tr>
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<tr>
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<th>...</th>
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<td><p>parameters passed on to <code>filter_at</code> from the <code>dplyr</code> package</p></td>
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<td><p>previously used when this package still depended on the <code>dplyr</code> package, now ignored</p></td>
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</tr>
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</table>
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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">1.2.0.9032</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.2.0.9033</span>
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</span>
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</div>
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@ -54,7 +54,7 @@ filter_tetracyclines(x, result = NULL, scope = "any", ...)
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\item{scope}{the scope to check which variables to check, can be \code{"any"} (default) or \code{"all"}}
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\item{...}{parameters passed on to \code{filter_at} from the \code{dplyr} package}
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\item{...}{previously used when this package still depended on the \code{dplyr} package, now ignored}
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}
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\description{
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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.
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