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(v1.7.1.9033) dplyr grouping fix on windows?

new-mo-algorithm
parent
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1daa117e9f
  1. 2
      DESCRIPTION
  2. 2
      NEWS.md
  3. 2
      R/first_isolate.R
  4. BIN
      data-raw/AMR_latest.tar.gz
  5. 4
      data-raw/_install_deps.R
  6. BIN
      data-raw/tinytest_1.3.1.tar.gz
  7. 2
      docs/LICENSE-text.html
  8. 2
      docs/articles/datasets.html
  9. 14
      docs/authors.html
  10. 2
      docs/index.html
  11. 8
      docs/news/index.html
  12. 6
      docs/reference/first_isolate.html
  13. 2
      docs/reference/index.html
  14. 2
      docs/survey.html
  15. 3
      index.md
  16. 17
      inst/CITATION
  17. 2
      man/first_isolate.Rd

2
DESCRIPTION

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

2
NEWS.md

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

2
R/first_isolate.R

@ -25,7 +25,7 @@ @@ -25,7 +25,7 @@
#' 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
#' @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

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data-raw/AMR_latest.tar.gz

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data-raw/_install_deps.R

@ -24,13 +24,13 @@ @@ -24,13 +24,13 @@
# ==================================================================== #
# 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)
pkg_suggests <- gsub("[^a-zA-Z0-9]+", "",
unlist(strsplit(unlist(packageDescription("AMR",
fields = c("Suggests", "Enhances"))),
", ?")))
split = ", ?")))
cat("Packages listed in Suggests/Enhances:", paste(pkg_suggests, collapse = ", "), "\n")
to_install <- pkg_suggests[!pkg_suggests %in% rownames(utils::installed.packages())]

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data-raw/tinytest_1.3.1.tar.gz

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docs/LICENSE-text.html

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

2
docs/articles/datasets.html

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

14
docs/authors.html

@ -92,7 +92,7 @@ @@ -92,7 +92,7 @@
</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">1.7.1.9030</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9033</span>
</span>
</div>
@ -241,7 +241,7 @@ @@ -241,7 +241,7 @@
</div>
<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{,
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},
@ -251,6 +251,16 @@ Antimicrobial Resistance Data. Journal of Statistical Software (accepted for pub @@ -251,6 +251,16 @@ Antimicrobial Resistance Data. Journal of Statistical Software (accepted for pub
year = {2021},
url = {https://www.biorxiv.org/content/10.1101/810622v4},
}</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">
<h1>Authors</h1>

2
docs/index.html

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

8
docs/news/index.html

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

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docs/reference/first_isolate.html

@ -50,7 +50,7 @@ @@ -50,7 +50,7 @@
<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
). 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 name="twitter:card" content="summary_large_image" />
<meta name="twitter:creator" content="@msberends" />
@ -94,7 +94,7 @@ @@ -94,7 +94,7 @@
</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">1.7.1.9031</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9033</span>
</span>
</div>
@ -245,7 +245,7 @@ @@ -245,7 +245,7 @@
<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>
). 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 class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='fu'>first_isolate</span><span class='op'>(</span>

2
docs/reference/index.html

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

2
docs/survey.html

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

3
index.md

@ -1,7 +1,6 @@ @@ -1,7 +1,6 @@
# `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.
> Click here to read it: [DOI 10.33612/diss.177417131](https://doi.org/10.33612/diss.177417131).
> 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).
### What is `AMR` (for R)?

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inst/CITATION

@ -1,4 +1,4 @@ @@ -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(
entry = "Article",
@ -10,7 +10,16 @@ citEntry( @@ -10,7 +10,16 @@ citEntry(
year = 2021,
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
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."
)

2
man/first_isolate.Rd

@ -90,7 +90,7 @@ filter_first_isolate( @@ -90,7 +90,7 @@ filter_first_isolate(
A \code{\link{logical}} vector
}
\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{
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.

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