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(v1.4.0.9026) docu update

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dr. M.S. (Matthijs) Berends 2020-11-24 11:47:54 +01:00
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DESCRIPTION
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@ -1,6 +1,6 @@
Package: AMR
Version: 1.4.0.9025
Date: 2020-11-23
Version: 1.4.0.9026
Date: 2020-11-24
Title: Antimicrobial Resistance Analysis
Authors@R: c(
person(role = c("aut", "cre"),

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NEWS.md
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@ -1,5 +1,5 @@
# AMR 1.4.0.9025
## <small>Last updated: 23 November 2020</small>
# AMR 1.4.0.9026
## <small>Last updated: 24 November 2020</small>
### New
* Function `is_new_episode()` to determine patient episodes which are not necessarily based on microorganisms. It also supports grouped variables with e.g. `mutate()`, `filter()` and `summarise()` of the `dplyr` package:

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R/first_isolate.R
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@ -27,7 +27,7 @@
#'
#' Determine first (weighted) isolates of all microorganisms of every patient per episode and (if needed) per specimen type. To determine patient episodes not necessarily based on microorganisms, use [is_new_episode()] that also supports grouping with the `dplyr` package.
#' @inheritSection lifecycle Stable lifecycle
#' @param x,.data a [data.frame] containing isolates.
#' @param x a [data.frame] containing isolates.
#' @param col_date column name of the result date (or date that is was received on the lab), defaults to the first column with a date class
#' @param col_patient_id column name of the unique IDs of the patients, defaults to the first column that starts with 'patient' or 'patid' (case insensitive)
#' @param col_mo column name of the IDs of the microorganisms (see [as.mo()]), defaults to the first column of class [`mo`]. Values will be coerced using [as.mo()].
@ -44,7 +44,7 @@
#' @param points_threshold points until the comparison of key antibiotics will lead to inclusion of an isolate when `type = "points"`, see Details
#' @param info print progress
#' @param include_unknown logical to determine 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 ... parameters passed on to the [first_isolate()] function
#' @param ... parameters passed on to [first_isolate()] when using [filter_first_isolate()], or parameters passed on to [key_antibiotics()] when using [filter_first_weighted_isolate()]
#' @details The [first_isolate()] function is a wrapper around the [is_new_episode()] function, but more efficient for data sets containing microorganism codes or names.
#'
#' All isolates with a microbial ID of `NA` will be excluded as first isolate.

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R/ggplot_rsi.R
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@ -36,7 +36,7 @@
#' @param facet variable to split plots by, either `"interpretation"` (default) or `"antibiotic"` or a grouping variable
#' @inheritParams proportion
#' @param nrow (when using `facet`) number of rows
#' @param colours a named vector with colours for the bars. The names must be one or more of: S, SI, I, IR, R or be `FALSE` to use default [ggplot2][[ggplot2::ggplot()] colours.
#' @param colours a named vector with colours for the bars. The names must be one or more of: S, SI, I, IR, R or be `FALSE` to use default [ggplot2][ggplot2::ggplot()] colours.
#' @param datalabels show datalabels using [labels_rsi_count()]
#' @param datalabels.size size of the datalabels
#' @param datalabels.colour colour of the datalabels
@ -107,13 +107,12 @@
#' }
#'
#' \donttest{
#'
#' # resistance of ciprofloxacine per age group
#' example_isolates %>%
#' mutate(first_isolate = first_isolate(.)) %>%
#' filter(first_isolate == TRUE,
#' mo == as.mo("E. coli")) %>%
#' # `age_groups` is also a function of this AMR package:
#' # age_groups() is also a function in this AMR package:
#' group_by(age_group = age_groups(age)) %>%
#' select(age_group,
#' CIP) %>%

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R/globals.R
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@ -73,5 +73,6 @@ globalVariables(c(".rowid",
"value",
"varname",
"xvar",
"y",
"year",
"yvar"))

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R/is_new_episode.R
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@ -33,7 +33,7 @@
#' @details
#' Dates are first sorted from old to new. The oldest date will mark the start of the first episode. After this date, the next date will be marked that is at least `episode_days` days later than the start of the first episode. From that second marked date on, the next date will be marked that is at least `episode_days` days later than the start of the second episode which will be the start of the third episode, and so on. Before the vector is being returned, the original order will be restored.
#'
#' The `dplyr` package is not required for this function to work, but this function works conveniently inside `dplyr` verbs such as [filter()], [mutate()] and [summarise()].
#' The `dplyr` package is not required for this function to work, but this function works conveniently inside `dplyr` verbs such as [`filter()`][dplyr::filter()], [`mutate()`][dplyr::mutate()] and [`summarise()`][dplyr::summarise()].
#' @return a [logical] vector
#' @export
#' @inheritSection AMR Read more on our website!
@ -86,23 +86,17 @@ is_new_episode <- function(x, episode_days = 365, ...) {
x <- as.double(as.Date(x, ...)) # as.Date() for POSIX classes
if (length(x) == 1) {
return(TRUE)
}
if (length(x) == 2 && max(x) - min(x) >= episode_days) {
return(rep(TRUE, 2))
} else if (length(x) == 2) {
if (max(x) - min(x) >= episode_days) {
return(c(TRUE, TRUE))
} else {
return(c(TRUE, FALSE))
}
}
# I asked on StackOverflow:
# https://stackoverflow.com/questions/42122245/filter-one-row-every-year
exec <- function(x, episode_days) {
if (length(x) == 1) {
return(TRUE)
} else if (length(x) == 2) {
if (max(x) - min(x) >= episode_days) {
return(c(TRUE, TRUE))
} else {
return(c(TRUE, FALSE))
}
}
indices <- integer()
start <- x[1]
ind <- 1

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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">1.4.0.9025</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9026</span>
</span>
</div>

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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">1.4.0.9025</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9026</span>
</span>
</div>

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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">1.4.0.9025</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9026</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">1.4.0.9025</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9026</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">1.4.0.9025</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9026</span>
</span>
</div>

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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">1.4.0.9025</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9026</span>
</span>
</div>
@ -236,13 +236,13 @@
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div>
<div id="amr-1409025" class="section level1">
<h1 class="page-header" data-toc-text="1.4.0.9025">
<a href="#amr-1409025" class="anchor"></a>AMR 1.4.0.9025<small> Unreleased </small>
<div id="amr-1409026" class="section level1">
<h1 class="page-header" data-toc-text="1.4.0.9026">
<a href="#amr-1409026" class="anchor"></a>AMR 1.4.0.9026<small> Unreleased </small>
</h1>
<div id="last-updated-23-november-2020" class="section level2">
<div id="last-updated-24-november-2020" class="section level2">
<h2 class="hasAnchor">
<a href="#last-updated-23-november-2020" class="anchor"></a><small>Last updated: 23 November 2020</small>
<a href="#last-updated-24-november-2020" class="anchor"></a><small>Last updated: 24 November 2020</small>
</h2>
<div id="new" class="section level3">
<h3 class="hasAnchor">

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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: 2020-11-23T20:45Z
last_built: 2020-11-24T10:47Z
urls:
reference: https://msberends.github.io/AMR//reference
article: https://msberends.github.io/AMR//articles

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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">1.4.0.9025</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9026</span>
</span>
</div>
@ -284,7 +284,7 @@
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>x, .data</th>
<th>x</th>
<td><p>a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> containing isolates.</p></td>
</tr>
<tr>
@ -353,7 +353,7 @@
</tr>
<tr>
<th>...</th>
<td><p>parameters passed on to the <code>first_isolate()</code> function</p></td>
<td><p>parameters passed on to <code>first_isolate()</code> when using <code>filter_first_isolate()</code>, or parameters passed on to <code><a href='key_antibiotics.html'>key_antibiotics()</a></code> when using <code>filter_first_weighted_isolate()</code></p></td>
</tr>
</table>

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docs/reference/ggplot_rsi.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">1.4.0.9008</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9026</span>
</span>
</div>
@ -361,7 +361,7 @@
</tr>
<tr>
<th>colours</th>
<td><p>a named vector with colours for the bars. The names must be one or more of: S, SI, I, IR, R or be <code>FALSE</code> to use default [ggplot2][<code><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot2::ggplot()</a></code> colours.</p></td>
<td><p>a named vector with colours for the bars. The names must be one or more of: S, SI, I, IR, R or be <code>FALSE</code> to use default <a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot2</a> colours.</p></td>
</tr>
<tr>
<th>datalabels</th>
@ -468,13 +468,12 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
<span class='op'>}</span>
<span class='co'># \donttest{</span>
<span class='co'># resistance of ciprofloxacine per age group</span>
<span class='va'>example_isolates</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span><span class='op'>(</span>first_isolate <span class='op'>=</span> <span class='fu'><a href='first_isolate.html'>first_isolate</a></span><span class='op'>(</span><span class='va'>.</span><span class='op'>)</span><span class='op'>)</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='va'>first_isolate</span> <span class='op'>==</span> <span class='cn'>TRUE</span>,
<span class='va'>mo</span> <span class='op'>==</span> <span class='fu'><a href='as.mo.html'>as.mo</a></span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>%&gt;%</span>
<span class='co'># `age_groups` is also a function of this AMR package:</span>
<span class='co'># age_groups() is also a function in this AMR package:</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span><span class='op'>(</span>age_group <span class='op'>=</span> <span class='fu'><a href='age_groups.html'>age_groups</a></span><span class='op'>(</span><span class='va'>age</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span><span class='op'>(</span><span class='va'>age_group</span>,
<span class='va'>CIP</span><span class='op'>)</span> <span class='op'>%&gt;%</span>

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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">1.4.0.9025</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9026</span>
</span>
</div>

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docs/reference/is_new_episode.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">1.4.0.9025</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9026</span>
</span>
</div>
@ -274,6 +274,11 @@
<p><img src='figures/lifecycle_experimental.svg' style=margin-bottom:5px /> <br />
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>experimental</strong>. An experimental function is in early stages of development. The unlying code might be changing frequently. Experimental functions might be removed without deprecation, so you are generally best off waiting until a function is more mature before you use it in production code. Experimental functions are only available in development versions of this <code>AMR</code> package and will thus not be included in releases that are submitted to CRAN, since such functions have not yet matured enough.</p>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># `example_isolates` is a dataset available in the AMR package.</span>

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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">1.4.0.9025</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9026</span>
</span>
</div>

4
man/first_isolate.Rd
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@ -50,7 +50,7 @@ filter_first_weighted_isolate(
)
}
\arguments{
\item{x, .data}{a \link{data.frame} containing isolates.}
\item{x}{a \link{data.frame} containing isolates.}
\item{col_date}{column name of the result date (or date that is was received on the lab), defaults to the first column with a date class}
@ -84,7 +84,7 @@ filter_first_weighted_isolate(
\item{include_unknown}{logical to determine 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{...}{parameters passed on to the \code{\link[=first_isolate]{first_isolate()}} function}
\item{...}{parameters passed on to \code{\link[=first_isolate]{first_isolate()}} when using \code{\link[=filter_first_isolate]{filter_first_isolate()}}, or parameters passed on to \code{\link[=key_antibiotics]{key_antibiotics()}} when using \code{\link[=filter_first_weighted_isolate]{filter_first_weighted_isolate()}}}
}
\value{
A \code{\link{logical}} vector

5
man/ggplot_rsi.Rd
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@ -99,7 +99,7 @@ labels_rsi_count(
\item{nrow}{(when using \code{facet}) number of rows}
\item{colours}{a named vector with colours for the bars. The names must be one or more of: S, SI, I, IR, R or be \code{FALSE} to use default [ggplot2][\code{\link[ggplot2:ggplot]{ggplot2::ggplot()}} colours.}
\item{colours}{a named vector with colours for the bars. The names must be one or more of: S, SI, I, IR, R or be \code{FALSE} to use default \link[ggplot2:ggplot]{ggplot2} colours.}
\item{datalabels}{show datalabels using \code{\link[=labels_rsi_count]{labels_rsi_count()}}}
@ -194,13 +194,12 @@ if (require("ggplot2") & require("dplyr")) {
}
\donttest{
# resistance of ciprofloxacine per age group
example_isolates \%>\%
mutate(first_isolate = first_isolate(.)) \%>\%
filter(first_isolate == TRUE,
mo == as.mo("E. coli")) \%>\%
# `age_groups` is also a function of this AMR package:
# age_groups() is also a function in this AMR package:
group_by(age_group = age_groups(age)) \%>\%
select(age_group,
CIP) \%>\%

2
man/is_new_episode.Rd
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@ -22,7 +22,7 @@ This function determines which items in a vector can be considered (the start of
\details{
Dates are first sorted from old to new. The oldest date will mark the start of the first episode. After this date, the next date will be marked that is at least \code{episode_days} days later than the start of the first episode. From that second marked date on, the next date will be marked that is at least \code{episode_days} days later than the start of the second episode which will be the start of the third episode, and so on. Before the vector is being returned, the original order will be restored.
The \code{dplyr} package is not required for this function to work, but this function works conveniently inside \code{dplyr} verbs such as \code{\link[=filter]{filter()}}, \code{\link[=mutate]{mutate()}} and \code{\link[=summarise]{summarise()}}.
The \code{dplyr} package is not required for this function to work, but this function works conveniently inside \code{dplyr} verbs such as \code{\link[dplyr:filter]{filter()}}, \code{\link[dplyr:mutate]{mutate()}} and \code{\link[dplyr:summarise]{summarise()}}.
}
\section{Experimental lifecycle}{