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(v1.6.0.9009) key_antibiotics update

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dr. M.S. (Matthijs) Berends 2021-04-23 16:13:26 +02:00
parent 70b803dbb6
commit 5f9e7bd3ee
20 changed files with 100 additions and 98 deletions
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2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR
Version: 1.6.0.9008
Version: 1.6.0.9009
Date: 2021-04-23
Title: Antimicrobial Resistance Data Analysis
Authors@R: c(

5
NEWS.md
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@ -1,4 +1,4 @@
# AMR 1.6.0.9008
# AMR 1.6.0.9009
## <small>Last updated: 23 April 2021</small>
### New
@ -25,6 +25,9 @@
* Fixed an installation error on R-3.0
* Added `info` argument to `as.mo()` to turn on/off the progress bar
* Fixed a bug that `col_mo` for some functions (esp. `eucast_rules()` and `mdro()`) could not be column names of the `microorganisms` data set as it would throw an error
* Using `first_isolate()` with key antibiotics:
* Fixed a bug in the algorithm when using `type == "points"`, that now leads to inclusion of slightly more isolates
* Big speed improvement for `key_antibiotics_equal()` when using `type == "points"`
# AMR 1.6.0

4
R/first_isolate.R
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@ -42,7 +42,7 @@
#' @param type type to determine weighed isolates; can be `"keyantibiotics"` or `"points"`, see *Details*
#' @param ignore_I logical to indicate whether antibiotic interpretations with `"I"` will be ignored when `type = "keyantibiotics"`, see *Details*
#' @param points_threshold points until the comparison of key antibiotics will lead to inclusion of an isolate when `type = "points"`, see *Details*
#' @param info a [logical] to indicate whether a progress bar should be printed, defaults to `TRUE` only in interactive mode
#' @param info a [logical] to indicate info should be printed, defaults to `TRUE` only in interactive mode
#' @param include_unknown logical to indicate whether 'unknown' microorganisms should be included too, i.e. microbial code `"UNKNOWN"`, which defaults to `FALSE`. For WHONET users, this means that all records with organism code `"con"` (*contamination*) will be excluded at default. Isolates with a microbial ID of `NA` will always be excluded as first isolate.
#' @param include_untested_rsi logical to indicate whether also rows without antibiotic results are still eligible for becoming a first isolate. Use `include_untested_rsi = FALSE` to always return `FALSE` for such rows. This checks the data set for columns of class `<rsi>` and consequently requires transforming columns with antibiotic results using [as.rsi()] first.
#' @param ... arguments passed on to [first_isolate()] when using [filter_first_isolate()], or arguments passed on to [key_antibiotics()] when using [filter_first_weighted_isolate()]
@ -402,7 +402,7 @@ first_isolate <- function(x = NULL,
type = type_param,
ignore_I = ignore_I,
points_threshold = points_threshold,
info = info)
na.rm = TRUE)
# with key antibiotics
x$newvar_first_isolate <- pm_if_else(x$newvar_row_index_sorted >= row.start &
x$newvar_row_index_sorted <= row.end &

120
R/key_antibiotics.R
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@ -286,93 +286,75 @@ key_antibiotics <- function(x = NULL,
}
#' @rdname key_antibiotics
#' @param info unused - previously used to indicate whether a progress bar should print
#' @param na.rm a [logical] to indicate whether comparison with `NA` should return `FALSE` (defaults to `TRUE` for backwards compatibility)
#' @export
key_antibiotics_equal <- function(y,
z,
type = c("keyantibiotics", "points"),
ignore_I = TRUE,
points_threshold = 2,
info = FALSE) {
info = FALSE,
na.rm = TRUE,
...) {
meet_criteria(y, allow_class = "character")
meet_criteria(z, allow_class = "character")
meet_criteria(type, allow_class = "character", has_length = c(1, 2))
if (length(type) == 2) {
type <- type[1L]
}
meet_criteria(type, allow_class = "character", has_length = 1, is_in = c("keyantibiotics", "points"))
meet_criteria(ignore_I, allow_class = "logical", has_length = 1)
meet_criteria(points_threshold, allow_class = c("numeric", "integer"), has_length = 1, is_positive = TRUE, is_finite = TRUE)
meet_criteria(info, allow_class = "logical", has_length = 1)
meet_criteria(na.rm, allow_class = "logical", has_length = 1)
stop_ifnot(length(y) == length(z), "length of `y` and `z` must be equal")
# y is active row, z is lag
x <- y
y <- z
key2rsi <- function(val) {
as.double(as.rsi(gsub(".", NA_character_, unlist(strsplit(val, "")), fixed = TRUE)))
}
y <- lapply(y, key2rsi)
z <- lapply(z, key2rsi)
type <- type[1]
# only show progress bar on points or when at least 5000 isolates
info_needed <- info == TRUE & (type == "points" | length(x) > 5000)
result <- logical(length(x))
p <- progress_ticker(length(x), print = info_needed)
on.exit(close(p))
for (i in seq_len(length(x))) {
if (info_needed == TRUE) {
p$tick()
determine_equality <- function(a, b, type, points_threshold, ignore_I) {
if (length(a) != length(b)) {
# incomparable, so not equal
return(FALSE)
}
# ignore NAs on both sides
NA_ind <- which(is.na(a) | is.na(b))
a[NA_ind] <- NA_real_
b[NA_ind] <- NA_real_
if (is.na(x[i])) {
x[i] <- ""
}
if (is.na(y[i])) {
y[i] <- ""
}
if (x[i] == y[i]) {
result[i] <- TRUE
} else if (nchar(x[i]) != nchar(y[i])) {
result[i] <- FALSE
if (type == "points") {
# count points for every single character:
# - no change is 0 points
# - I <-> S|R is 0.5 point
# - S|R <-> R|S is 1 point
# use the levels of as.rsi (S = 1, I = 2, R = 3)
(sum(abs(a - b), na.rm = TRUE) / 2) < points_threshold
} else {
x_split <- strsplit(x[i], "")[[1]]
y_split <- strsplit(y[i], "")[[1]]
if (type == "keyantibiotics") {
if (ignore_I == TRUE) {
x_split[x_split == "I"] <- "."
y_split[y_split == "I"] <- "."
}
y_split[x_split == "."] <- "."
x_split[y_split == "."] <- "."
result[i] <- all(x_split == y_split)
} else if (type == "points") {
# count points for every single character:
# - no change is 0 points
# - I <-> S|R is 0.5 point
# - S|R <-> R|S is 1 point
# use the levels of as.rsi (S = 1, I = 2, R = 3)
suppressWarnings(x_split <- x_split %pm>% as.rsi() %pm>% as.double())
suppressWarnings(y_split <- y_split %pm>% as.rsi() %pm>% as.double())
points <- (x_split - y_split) %pm>% abs() %pm>% sum(na.rm = TRUE) / 2
result[i] <- points >= points_threshold
} else {
stop("`", type, '` is not a valid value for type, must be "points" or "keyantibiotics". See ?key_antibiotics')
if (ignore_I == TRUE) {
ind <- which(a == 2 | b == 2) # since as.double(as.rsi("I")) == 2
a[ind] <- NA_real_
b[ind] <- NA_real_
}
all(a == b, na.rm = TRUE)
}
}
out <- unlist(mapply(FUN = determine_equality,
y,
z,
MoreArgs = list(type = type,
points_threshold = points_threshold,
ignore_I = ignore_I),
SIMPLIFY = FALSE,
USE.NAMES = FALSE))
if (na.rm == FALSE) {
out[is.na(y) | is.na(z)] <- NA
} else {
# NA means not equal if `na.rm == TRUE`, as per the manual
out[is.na(y) | is.na(z)] <- FALSE
}
close(p)
result
out
}

4
R/rsi.R
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@ -263,8 +263,8 @@ as.rsi.default <- function(x, ...) {
x[x == 2] <- "I"
x[x == 3] <- "R"
} else if (!all(is.na(x)) && !identical(levels(x), c("S", "I", "R"))) {
} else if (!all(is.na(x)) && !identical(levels(x), c("S", "I", "R")) && !all(x %in% c("R", "S", "I", NA))) {
if (all(x %unlike% "(R|S|I)", na.rm = TRUE)) {
# check if they are actually MICs or disks
if (all_valid_mics(x)) {

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data-raw/AMR_latest.tar.gz
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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">1.6.0.9008</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9009</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">1.6.0.9008</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9009</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">1.6.0.9008</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9009</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">1.6.0.9008</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9009</span>
</span>
</div>

2
docs/index.html
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@ -42,7 +42,7 @@
</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">1.6.0.9008</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9009</span>
</span>
</div>

15
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">1.6.0.9008</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9009</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-1609008" class="section level1">
<h1 class="page-header" data-toc-text="1.6.0.9008">
<a href="#amr-1609008" class="anchor"></a>AMR 1.6.0.9008<small> Unreleased </small>
<div id="amr-1609009" class="section level1">
<h1 class="page-header" data-toc-text="1.6.0.9009">
<a href="#amr-1609009" class="anchor"></a>AMR 1.6.0.9009<small> Unreleased </small>
</h1>
<div id="last-updated-23-april-2021" class="section level2">
<h2 class="hasAnchor">
@ -287,6 +287,13 @@
<li>Fixed an installation error on R-3.0</li>
<li>Added <code>info</code> argument to <code><a href="../reference/as.mo.html">as.mo()</a></code> to turn on/off the progress bar</li>
<li>Fixed a bug that <code>col_mo</code> for some functions (esp. <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> and <code><a href="../reference/mdro.html">mdro()</a></code>) could not be column names of the <code>microorganisms</code> data set as it would throw an error</li>
<li>Using <code><a href="../reference/first_isolate.html">first_isolate()</a></code> with key antibiotics:
<ul>
<li>Fixed a bug in the algorithm when using <code>type == "points"</code>, that now leads to inclusion of slightly more isolates</li>
<li>Big speed improvement for <code><a href="../reference/key_antibiotics.html">key_antibiotics_equal()</a></code> when using <code>type == "points"</code>
</li>
</ul>
</li>
</ul>
</div>
</div>

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: 2021-04-23T07:52Z
last_built: 2021-04-23T14:13Z
urls:
reference: https://msberends.github.io/AMR//reference
article: https://msberends.github.io/AMR//articles

4
docs/reference/first_isolate.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">1.6.0.9007</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9009</span>
</span>
</div>
@ -346,7 +346,7 @@
</tr>
<tr>
<th>info</th>
<td><p>a <a href='https://rdrr.io/r/base/logical.html'>logical</a> to indicate whether a progress bar should be printed, defaults to <code>TRUE</code> only in interactive mode</p></td>
<td><p>a <a href='https://rdrr.io/r/base/logical.html'>logical</a> to indicate info should be printed, defaults to <code>TRUE</code> only in interactive mode</p></td>
</tr>
<tr>
<th>include_unknown</th>

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">1.6.0.9008</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9009</span>
</span>
</div>

12
docs/reference/key_antibiotics.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">1.6.0.9007</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9009</span>
</span>
</div>
@ -273,7 +273,9 @@
type <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"keyantibiotics"</span>, <span class='st'>"points"</span><span class='op'>)</span>,
ignore_I <span class='op'>=</span> <span class='cn'>TRUE</span>,
points_threshold <span class='op'>=</span> <span class='fl'>2</span>,
info <span class='op'>=</span> <span class='cn'>FALSE</span>
info <span class='op'>=</span> <span class='cn'>FALSE</span>,
na.rm <span class='op'>=</span> <span class='cn'>TRUE</span>,
<span class='va'>...</span>
<span class='op'>)</span></pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
@ -325,7 +327,11 @@
</tr>
<tr>
<th>info</th>
<td><p>a <a href='https://rdrr.io/r/base/logical.html'>logical</a> to indicate whether a progress bar should be printed, defaults to <code>TRUE</code> only in interactive mode</p></td>
<td><p>unused - previously used to indicate whether a progress bar should print</p></td>
</tr>
<tr>
<th>na.rm</th>
<td><p>a <a href='https://rdrr.io/r/base/logical.html'>logical</a> to indicate whether comparison with <code>NA</code> should return <code>FALSE</code> (defaults to <code>TRUE</code> for backwards compatibility)</p></td>
</tr>
</table>

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">1.6.0.9008</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9009</span>
</span>
</div>

2
man/first_isolate.Rd
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@ -81,7 +81,7 @@ filter_first_weighted_isolate(
\item{points_threshold}{points until the comparison of key antibiotics will lead to inclusion of an isolate when \code{type = "points"}, see \emph{Details}}
\item{info}{a \link{logical} to indicate whether a progress bar should be printed, defaults to \code{TRUE} only in interactive mode}
\item{info}{a \link{logical} to indicate info should be printed, defaults to \code{TRUE} only in interactive mode}
\item{include_unknown}{logical to indicate whether 'unknown' microorganisms should be included too, i.e. microbial code \code{"UNKNOWN"}, which defaults to \code{FALSE}. For WHONET users, this means that all records with organism code \code{"con"} (\emph{contamination}) will be excluded at default. Isolates with a microbial ID of \code{NA} will always be excluded as first isolate.}

8
man/key_antibiotics.Rd
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@ -36,7 +36,9 @@ key_antibiotics_equal(
type = c("keyantibiotics", "points"),
ignore_I = TRUE,
points_threshold = 2,
info = FALSE
info = FALSE,
na.rm = TRUE,
...
)
}
\arguments{
@ -62,7 +64,9 @@ key_antibiotics_equal(
\item{points_threshold}{points until the comparison of key antibiotics will lead to inclusion of an isolate when \code{type = "points"}, see \emph{Details}}
\item{info}{a \link{logical} to indicate whether a progress bar should be printed, defaults to \code{TRUE} only in interactive mode}
\item{info}{unused - previously used to indicate whether a progress bar should print}
\item{na.rm}{a \link{logical} to indicate whether comparison with \code{NA} should return \code{FALSE} (defaults to \code{TRUE} for backwards compatibility)}
}
\description{
These function can be used to determine first isolates (see \code{\link[=first_isolate]{first_isolate()}}). Using key antibiotics to determine first isolates is more reliable than without key antibiotics. These selected isolates can then be called first 'weighted' isolates.

6
tests/testthat/test-first_isolate.R
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@ -50,7 +50,7 @@ test_that("first isolates work", {
type = "keyantibiotics",
info = TRUE),
na.rm = TRUE)),
1395)
1398)
# when not ignoring I
expect_equal(
@ -65,7 +65,7 @@ test_that("first isolates work", {
type = "keyantibiotics",
info = TRUE),
na.rm = TRUE)),
1418)
1421)
# when using points
expect_equal(
suppressWarnings(
@ -78,7 +78,7 @@ test_that("first isolates work", {
type = "points",
info = TRUE),
na.rm = TRUE)),
1398)
1348)
# first non-ICU isolates
expect_equal(