1
0
mirror of https://github.com/msberends/AMR.git synced 2024-12-25 19:26:13 +01:00

(v1.7.1.9033) dplyr grouping fix on windows?

This commit is contained in:
dr. M.S. (Matthijs) Berends 2021-08-30 15:01:32 +02:00
parent 6ca6a3f6df
commit 1daa117e9f
17 changed files with 44 additions and 26 deletions

View File

@ -1,5 +1,5 @@
Package: AMR Package: AMR
Version: 1.7.1.9032 Version: 1.7.1.9033
Date: 2021-08-30 Date: 2021-08-30
Title: Antimicrobial Resistance Data Analysis Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR) Description: Functions to simplify and standardise antimicrobial resistance (AMR)

View File

@ -1,4 +1,4 @@
# `AMR` 1.7.1.9032 # `AMR` 1.7.1.9033
## <small>Last updated: 30 August 2021</small> ## <small>Last updated: 30 August 2021</small>
### Breaking changes ### Breaking changes

View File

@ -25,7 +25,7 @@
#' Determine First Isolates #' Determine First Isolates
#' #'
#' Determine first isolates of all microorganisms of every patient per episode and (if needed) per specimen type. These functions support all four methods as summarised by Hindler *et al.* in 2007 (\doi{10.1086/511864}). To determine patient episodes not necessarily based on microorganisms, use [is_new_episode()] that also supports [grouping with the `dplyr` package][dplyr::group_by()] . #' Determine first isolates of all microorganisms of every patient per episode and (if needed) per specimen type. These functions support all four methods as summarised by Hindler *et al.* in 2007 (\doi{10.1086/511864}). 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 #' @inheritSection lifecycle Stable Lifecycle
#' @param x a [data.frame] containing isolates. Can be left blank for automatic determination, see *Examples*. #' @param x a [data.frame] containing isolates. Can be left blank for automatic determination, see *Examples*.
#' @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_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

Binary file not shown.

View File

@ -24,13 +24,13 @@
# ==================================================================== # # ==================================================================== #
# some old R instances have trouble installing tinytest, so we ship it too # some old R instances have trouble installing tinytest, so we ship it too
install.packages("data-raw/tinytest_1.2.4.10.tar.gz", dependencies = c("Depends", "Imports")) install.packages("data-raw/tinytest_1.3.1.tar.gz", dependencies = c("Depends", "Imports"))
install.packages("data-raw/AMR_latest.tar.gz", dependencies = FALSE) install.packages("data-raw/AMR_latest.tar.gz", dependencies = FALSE)
pkg_suggests <- gsub("[^a-zA-Z0-9]+", "", pkg_suggests <- gsub("[^a-zA-Z0-9]+", "",
unlist(strsplit(unlist(packageDescription("AMR", unlist(strsplit(unlist(packageDescription("AMR",
fields = c("Suggests", "Enhances"))), fields = c("Suggests", "Enhances"))),
", ?"))) split = ", ?")))
cat("Packages listed in Suggests/Enhances:", paste(pkg_suggests, collapse = ", "), "\n") cat("Packages listed in Suggests/Enhances:", paste(pkg_suggests, collapse = ", "), "\n")
to_install <- pkg_suggests[!pkg_suggests %in% rownames(utils::installed.packages())] to_install <- pkg_suggests[!pkg_suggests %in% rownames(utils::installed.packages())]

Binary file not shown.

View File

@ -92,7 +92,7 @@
</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">1.7.1.9030</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9033</span>
</span> </span>
</div> </div>

View File

@ -44,7 +44,7 @@
</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">1.7.1.9032</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9033</span>
</span> </span>
</div> </div>

View File

@ -92,7 +92,7 @@
</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">1.7.1.9030</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9033</span>
</span> </span>
</div> </div>
@ -241,7 +241,7 @@
</div> </div>
<p>Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C (2021). AMR - An R Package for Working with <p>Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C (2021). AMR - An R Package for Working with
Antimicrobial Resistance Data. Journal of Statistical Software (accepted for publication), https://www.biorxiv.org/content/10.1101/810622v4</p> Antimicrobial Resistance Data. Journal of Statistical Software (accepted for publication), https://www.biorxiv.org/content/10.1101/810622v4.</p>
<pre>@Article{, <pre>@Article{,
title = {AMR - An R Package for Working with Antimicrobial Resistance Data}, title = {AMR - An R Package for Working with Antimicrobial Resistance Data},
author = {M S Berends and C F Luz and A W Friedrich and B N M Sinha and C J Albers and C Glasner}, author = {M S Berends and C F Luz and A W Friedrich and B N M Sinha and C J Albers and C Glasner},
@ -251,6 +251,16 @@ Antimicrobial Resistance Data. Journal of Statistical Software (accepted for pub
year = {2021}, year = {2021},
url = {https://www.biorxiv.org/content/10.1101/810622v4}, url = {https://www.biorxiv.org/content/10.1101/810622v4},
}</pre> }</pre>
<p>Berends, MS (2021). A New Instrument for Microbial Epidemiology: Empowering Antimicrobial Resistance Data Analysis (PhD thesis). University of Groningen, doi: 10.33612/diss.177417131.</p>
<pre>@PhdThesis{,
title = {A New Instrument for Microbial Epidemiology: Empowering Antimicrobial Resistance Data Analysis},
author = {M S Berends},
publisher = {University of Groningen},
school = {University of Groningen},
doi = {10.33612/diss.177417131},
pages = {288},
year = {2021},
}</pre>
<div class="page-header"> <div class="page-header">
<h1>Authors</h1> <h1>Authors</h1>

View File

@ -47,7 +47,7 @@
</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">1.7.1.9030</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9033</span>
</span> </span>
</div> </div>

View File

@ -92,7 +92,7 @@
</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">1.7.1.9032</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9033</span>
</span> </span>
</div> </div>
@ -240,9 +240,9 @@
<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-1719032" class="section level1"> <div id="amr-1719033" class="section level1">
<h1 class="page-header" data-toc-text="1.7.1.9032"> <h1 class="page-header" data-toc-text="1.7.1.9033">
<a href="#amr-1719032" class="anchor" aria-hidden="true"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9032</h1> <a href="#amr-1719033" class="anchor" aria-hidden="true"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9033</h1>
<div id="last-updated-30-august-2021" class="section level2"> <div id="last-updated-30-august-2021" class="section level2">
<h2 class="hasAnchor"> <h2 class="hasAnchor">
<a href="#last-updated-30-august-2021" class="anchor" aria-hidden="true"></a><small>Last updated: 30 August 2021</small> <a href="#last-updated-30-august-2021" class="anchor" aria-hidden="true"></a><small>Last updated: 30 August 2021</small>

View File

@ -50,7 +50,7 @@
<meta property="og:title" content="Determine First Isolates — first_isolate" /> <meta property="og:title" content="Determine First Isolates — first_isolate" />
<meta property="og:description" content="Determine first isolates of all microorganisms of every patient per episode and (if needed) per specimen type. These functions support all four methods as summarised by Hindler et al. in 2007 (doi: 10.1086/511864 <meta property="og:description" content="Determine first isolates of all microorganisms of every patient per episode and (if needed) per specimen type. These functions support all four methods as summarised by Hindler et al. in 2007 (doi: 10.1086/511864
). To determine patient episodes not necessarily based on microorganisms, use is_new_episode() that also supports grouping with the dplyr package ." /> ). To determine patient episodes not necessarily based on microorganisms, use is_new_episode() that also supports grouping with the dplyr package." />
<meta property="og:image" content="https://msberends.github.io/AMR/logo.png" /> <meta property="og:image" content="https://msberends.github.io/AMR/logo.png" />
<meta name="twitter:card" content="summary_large_image" /> <meta name="twitter:card" content="summary_large_image" />
<meta name="twitter:creator" content="@msberends" /> <meta name="twitter:creator" content="@msberends" />
@ -94,7 +94,7 @@
</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">1.7.1.9031</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9033</span>
</span> </span>
</div> </div>
@ -245,7 +245,7 @@
<div class="ref-description"> <div class="ref-description">
<p>Determine first isolates of all microorganisms of every patient per episode and (if needed) per specimen type. These functions support all four methods as summarised by Hindler <em>et al.</em> in 2007 (doi: <a href='https://doi.org/10.1086/511864'>10.1086/511864</a> <p>Determine first isolates of all microorganisms of every patient per episode and (if needed) per specimen type. These functions support all four methods as summarised by Hindler <em>et al.</em> in 2007 (doi: <a href='https://doi.org/10.1086/511864'>10.1086/511864</a>
). To determine patient episodes not necessarily based on microorganisms, use <code><a href='get_episode.html'>is_new_episode()</a></code> that also supports <a href='https://dplyr.tidyverse.org/reference/group_by.html'>grouping with the <code>dplyr</code> package</a> .</p> ). To determine patient episodes not necessarily based on microorganisms, use <code><a href='get_episode.html'>is_new_episode()</a></code> that also supports grouping with the <code>dplyr</code> package.</p>
</div> </div>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='fu'>first_isolate</span><span class='op'>(</span> <div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='fu'>first_isolate</span><span class='op'>(</span>

View File

@ -92,7 +92,7 @@
</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">1.7.1.9031</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9033</span>
</span> </span>
</div> </div>

View File

@ -92,7 +92,7 @@
</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">1.7.1.9030</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9033</span>
</span> </span>
</div> </div>

View File

@ -1,7 +1,6 @@
# `AMR` (for R) <img src="./logo.png" align="right" height="120px" /> # `AMR` (for R) <img src="./logo.png" align="right" height="120px" />
> This package formed the basis of two PhD theses, of which the first was published and defended on 25 August 2021. > This package formed the basis of two PhD theses, of which the first was published and defended on 25 August 2021. Click here to read it: [DOI 10.33612/diss.177417131](https://doi.org/10.33612/diss.177417131).
> Click here to read it: [DOI 10.33612/diss.177417131](https://doi.org/10.33612/diss.177417131).
### What is `AMR` (for R)? ### What is `AMR` (for R)?

View File

@ -1,4 +1,4 @@
citHeader("To cite our AMR package in publications, please use (for now):") citHeader("To cite our AMR package in publications, please use below preprint. This preprint was accepted for publication in the Journal of Statistical Software, but we are awaiting the actual publication. Many thanks for using our open-source method to work with microbial and antimicrobial data!")
citEntry( citEntry(
entry = "Article", entry = "Article",
@ -10,7 +10,16 @@ citEntry(
year = 2021, year = 2021,
url = "https://www.biorxiv.org/content/10.1101/810622v4", url = "https://www.biorxiv.org/content/10.1101/810622v4",
textVersion = "Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C (2021). AMR - An R Package for Working with textVersion = "Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C (2021). AMR - An R Package for Working with
Antimicrobial Resistance Data. Journal of Statistical Software (accepted for publication), https://www.biorxiv.org/content/10.1101/810622v4" Antimicrobial Resistance Data. Journal of Statistical Software (accepted for publication), https://www.biorxiv.org/content/10.1101/810622v4.")
)
citFooter("This preprint was accepted for publication in the Journal of Statistical Software, but we are awaiting the actual publication. Many thanks for using our open-source method to work with microbial and antimicrobial data!") citEntry(
entry = "PhdThesis",
title = "A New Instrument for Microbial Epidemiology: Empowering Antimicrobial Resistance Data Analysis",
author = "M S Berends",
publisher = "University of Groningen",
school = "University of Groningen",
doi = "10.33612/diss.177417131",
pages = 288,
year = 2021,
textVersion = "Berends, MS (2021). A New Instrument for Microbial Epidemiology: Empowering Antimicrobial Resistance Data Analysis (PhD thesis). University of Groningen, doi: 10.33612/diss.177417131."
)

View File

@ -90,7 +90,7 @@ filter_first_isolate(
A \code{\link{logical}} vector A \code{\link{logical}} vector
} }
\description{ \description{
Determine first isolates of all microorganisms of every patient per episode and (if needed) per specimen type. These functions support all four methods as summarised by Hindler \emph{et al.} in 2007 (\doi{10.1086/511864}). To determine patient episodes not necessarily based on microorganisms, use \code{\link[=is_new_episode]{is_new_episode()}} that also supports \link[dplyr:group_by]{grouping with the \code{dplyr} package} . Determine first isolates of all microorganisms of every patient per episode and (if needed) per specimen type. These functions support all four methods as summarised by Hindler \emph{et al.} in 2007 (\doi{10.1086/511864}). To determine patient episodes not necessarily based on microorganisms, use \code{\link[=is_new_episode]{is_new_episode()}} that also supports grouping with the \code{dplyr} package.
} }
\details{ \details{
To conduct epidemiological analyses on antimicrobial resistance data, only so-called first isolates should be included to prevent overestimation and underestimation of antimicrobial resistance. Different methods can be used to do so, see below. To conduct epidemiological analyses on antimicrobial resistance data, only so-called first isolates should be included to prevent overestimation and underestimation of antimicrobial resistance. Different methods can be used to do so, see below.