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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 Package: AMR
Version: 1.6.0.9008 Version: 1.6.0.9009
Date: 2021-04-23 Date: 2021-04-23
Title: Antimicrobial Resistance Data Analysis Title: Antimicrobial Resistance Data Analysis
Authors@R: c( 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> ## <small>Last updated: 23 April 2021</small>
### New ### New
@ -25,6 +25,9 @@
* Fixed an installation error on R-3.0 * Fixed an installation error on R-3.0
* Added `info` argument to `as.mo()` to turn on/off the progress bar * 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 * 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 # 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 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 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 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_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 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()] #' @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, type = type_param,
ignore_I = ignore_I, ignore_I = ignore_I,
points_threshold = points_threshold, points_threshold = points_threshold,
info = info) na.rm = TRUE)
# with key antibiotics # with key antibiotics
x$newvar_first_isolate <- pm_if_else(x$newvar_row_index_sorted >= row.start & x$newvar_first_isolate <- pm_if_else(x$newvar_row_index_sorted >= row.start &
x$newvar_row_index_sorted <= row.end & x$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 #' @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 #' @export
key_antibiotics_equal <- function(y, key_antibiotics_equal <- function(y,
z, z,
type = c("keyantibiotics", "points"), type = c("keyantibiotics", "points"),
ignore_I = TRUE, ignore_I = TRUE,
points_threshold = 2, points_threshold = 2,
info = FALSE) { info = FALSE,
na.rm = TRUE,
...) {
meet_criteria(y, allow_class = "character") meet_criteria(y, allow_class = "character")
meet_criteria(z, 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(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(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(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") stop_ifnot(length(y) == length(z), "length of `y` and `z` must be equal")
# y is active row, z is lag
x <- y key2rsi <- function(val) {
y <- z as.double(as.rsi(gsub(".", NA_character_, unlist(strsplit(val, "")), fixed = TRUE)))
}
y <- lapply(y, key2rsi)
z <- lapply(z, key2rsi)
type <- type[1] determine_equality <- function(a, b, type, points_threshold, ignore_I) {
if (length(a) != length(b)) {
# only show progress bar on points or when at least 5000 isolates # incomparable, so not equal
info_needed <- info == TRUE & (type == "points" | length(x) > 5000) return(FALSE)
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()
} }
# 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])) { if (type == "points") {
x[i] <- "" # count points for every single character:
} # - no change is 0 points
if (is.na(y[i])) { # - I <-> S|R is 0.5 point
y[i] <- "" # - 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
if (x[i] == y[i]) {
result[i] <- TRUE
} else if (nchar(x[i]) != nchar(y[i])) {
result[i] <- FALSE
} else { } else {
if (ignore_I == TRUE) {
x_split <- strsplit(x[i], "")[[1]] ind <- which(a == 2 | b == 2) # since as.double(as.rsi("I")) == 2
y_split <- strsplit(y[i], "")[[1]] a[ind] <- NA_real_
b[ind] <- NA_real_
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')
} }
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) out
result
} }

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R/rsi.R
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@ -263,8 +263,8 @@ as.rsi.default <- function(x, ...) {
x[x == 2] <- "I" x[x == 2] <- "I"
x[x == 3] <- "R" 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)) { if (all(x %unlike% "(R|S|I)", na.rm = TRUE)) {
# check if they are actually MICs or disks # check if they are actually MICs or disks
if (all_valid_mics(x)) { if (all_valid_mics(x)) {

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

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

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

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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">1.6.0.9008</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9009</span>
</span> </span>
</div> </div>
@ -236,9 +236,9 @@
<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-1609008" class="section level1"> <div id="amr-1609009" class="section level1">
<h1 class="page-header" data-toc-text="1.6.0.9008"> <h1 class="page-header" data-toc-text="1.6.0.9009">
<a href="#amr-1609008" class="anchor"></a>AMR 1.6.0.9008<small> Unreleased </small> <a href="#amr-1609009" class="anchor"></a>AMR 1.6.0.9009<small> Unreleased </small>
</h1> </h1>
<div id="last-updated-23-april-2021" class="section level2"> <div id="last-updated-23-april-2021" class="section level2">
<h2 class="hasAnchor"> <h2 class="hasAnchor">
@ -287,6 +287,13 @@
<li>Fixed an installation error on R-3.0</li> <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>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>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> </ul>
</div> </div>
</div> </div>

2
docs/pkgdown.yml
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@ -12,7 +12,7 @@ articles:
datasets: datasets.html datasets: datasets.html
resistance_predict: resistance_predict.html resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html welcome_to_AMR: welcome_to_AMR.html
last_built: 2021-04-23T07:52Z last_built: 2021-04-23T14:13Z
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/first_isolate.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">1.6.0.9007</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9009</span>
</span> </span>
</div> </div>
@ -346,7 +346,7 @@
</tr> </tr>
<tr> <tr>
<th>info</th> <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>
<tr> <tr>
<th>include_unknown</th> <th>include_unknown</th>

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

12
docs/reference/key_antibiotics.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">1.6.0.9007</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9009</span>
</span> </span>
</div> </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>, 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>, ignore_I <span class='op'>=</span> <span class='cn'>TRUE</span>,
points_threshold <span class='op'>=</span> <span class='fl'>2</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> <span class='op'>)</span></pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
@ -325,7 +327,11 @@
</tr> </tr>
<tr> <tr>
<th>info</th> <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> </tr>
</table> </table>

2
docs/survey.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">1.6.0.9008</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9009</span>
</span> </span>
</div> </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{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.} \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"), type = c("keyantibiotics", "points"),
ignore_I = TRUE, ignore_I = TRUE,
points_threshold = 2, points_threshold = 2,
info = FALSE info = FALSE,
na.rm = TRUE,
...
) )
} }
\arguments{ \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{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{ \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. 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
View File

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