(v1.6.0.9061) age() update

v1.8.2
parent fa2f5214b9
commit 07939b1a14
  1. 17
      .github/workflows/check.yaml
  2. 8
      .github/workflows/codecovr.yaml
  3. 4
      DESCRIPTION
  4. 5
      NEWS.md
  5. 2
      R/ab_class_selectors.R
  6. 23
      R/age.R
  7. BIN
      data-raw/AMR_latest.tar.gz
  8. 2
      docs/404.html
  9. 2
      docs/LICENSE-text.html
  10. 4
      docs/articles/datasets.html
  11. 2
      docs/articles/index.html
  12. 2
      docs/authors.html
  13. 3
      docs/extra.css
  14. 2
      docs/index.html
  15. 15
      docs/news/index.html
  16. 2
      docs/pkgdown.yml
  17. 7
      docs/reference/age.html
  18. 4
      docs/reference/antibiotic_class_selectors.html
  19. 2
      docs/reference/index.html
  20. 2
      docs/survey.html
  21. 6
      man/age.Rd
  22. 2
      man/antibiotic_class_selectors.Rd
  23. 3
      pkgdown/extra.css

@ -50,17 +50,22 @@ jobs:
fail-fast: false
matrix:
config:
# these are the developmental version of R - we allow those tests to fail
- {os: macOS-latest, r: 'devel', allowfail: true}
- {os: macOS-latest, r: 'release', allowfail: false}
- {os: macOS-latest, r: 'oldrel', allowfail: false}
- {os: windows-latest, r: 'devel', allowfail: true}
- {os: windows-latest, r: 'release', allowfail: false}
- {os: windows-latest, r: 'oldrel', allowfail: false}
- {os: ubuntu-20.04, r: 'devel', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
# these are the current release of R
- {os: macOS-latest, r: 'release', allowfail: false}
- {os: windows-latest, r: 'release', allowfail: false}
- {os: ubuntu-20.04, r: 'release', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
# these are the previous release of R
- {os: macOS-latest, r: 'oldrel', allowfail: false}
- {os: windows-latest, r: 'oldrel', allowfail: false}
- {os: ubuntu-20.04, r: 'oldrel', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
# test against all released versions of R >= 3.0, we support them all!
- {os: ubuntu-20.04, r: '4.1', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
- {os: ubuntu-20.04, r: '4.0', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
- {os: ubuntu-20.04, r: '3.6', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}

@ -30,7 +30,6 @@ on:
- master
pull_request:
branches:
- premaster
- master
name: code-coverage
@ -76,10 +75,9 @@ jobs:
library(AMR)
library(tinytest)
library(covr)
source_files <- list.files("AMR/R", pattern = ".R$", full.names = TRUE)
test_files <- list.files("AMR/inst/tinytest", full.names = TRUE)
cov <- file_coverage(source_files = source_files, test_files = test_files, parent_env = asNamespace("AMR"), line_exclusions = list("AMR/R/atc_online.R", "AMR/R/mo_source.R", "AMR/R/translate.R", "AMR/R/resistance_predict.R", "AMR/R/aa_helper_functions.R", "AMR/R/aa_helper_pm_functions.R", "AMR/R/zzz.R"))
print(cov)
source_files <- list.files("R", pattern = ".R$", full.names = TRUE)
test_files <- list.files("inst/tinytest", full.names = TRUE)
cov <- file_coverage(source_files = source_files, test_files = test_files, parent_env = asNamespace("AMR"), line_exclusions = list("R/atc_online.R", "R/mo_source.R", "R/translate.R", "R/resistance_predict.R", "R/aa_helper_functions.R", "R/aa_helper_pm_functions.R", "R/zzz.R"))
attr(cov, which = "package") <- list(path = ".") # until https://github.com/r-lib/covr/issues/478 is solved
codecov(coverage = cov, quiet = FALSE)
shell: Rscript {0}

@ -1,6 +1,6 @@
Package: AMR
Version: 1.6.0.9060
Date: 2021-05-22
Version: 1.6.0.9061
Date: 2021-05-23
Title: Antimicrobial Resistance Data Analysis
Authors@R: c(
person(role = c("aut", "cre"),

@ -1,5 +1,5 @@
# `AMR` 1.6.0.9060
## <small>Last updated: 22 May 2021</small>
# `AMR` 1.6.0.9061
## <small>Last updated: 23 May 2021</small>
### Breaking change
* All antibiotic class selectors (such as `carbapenems()`, `aminoglycosides()`) can now be used for filtering as well, making all their accompanying `filter_*()` functions redundant (such as `filter_carbapenems()`, `filter_aminoglycosides()`). These functions are now deprecated and will be removed in a next release.
@ -64,6 +64,7 @@
* Updated join functions to always use `dplyr` join functions if the `dplyr` package is installed - now also preserving grouped variables
* Antibiotic class selectors (such as `cephalosporins()`) now maintain the column order from the original data
* Fix for selecting columns using `fluoroquinolones()`
* `age()` now vectorises over both `x` and `reference`
### Other
* All unit tests are now processed by the `tinytest` package, instead of the `testthat` package. The `testthat` package unfortunately requires tons of dependencies that are also heavy and only usable for recent R versions, disallowing developers to test a package under any R 3.* version. On the contrary, the `tinytest` package is very lightweight and dependency-free.

@ -27,7 +27,7 @@
#'
#' These functions help to filter and select columns with antibiotic test results that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations. \strong{\Sexpr{ifelse(as.double(R.Version()$major) + (as.double(R.Version()$minor) / 10) < 3.2, paste0("NOTE: THESE FUNCTIONS DO NOT WORK ON YOUR CURRENT R VERSION. These functions require R version 3.2 or later - you have ", R.version.string, "."), "")}}
#' @inheritSection lifecycle Stable Lifecycle
#' @param ab_class an antimicrobial class, like `"carbapenems"`. The columns `group`, `atc_group1` and `atc_group2` of the [antibiotics] data set will be searched (case-insensitive) for this value.
#' @param ab_class an antimicrobial class, such as `"carbapenems"`. The columns `group`, `atc_group1` and `atc_group2` of the [antibiotics] data set will be searched (case-insensitive) for this value.
#' @param only_rsi_columns a [logical] to indicate whether only columns of class `<rsi>` must be selected (defaults to `FALSE`), see [as.rsi()]
#' @details \strong{\Sexpr{ifelse(as.double(R.Version()$major) + (as.double(R.Version()$minor) / 10) < 3.2, paste0("NOTE: THESE FUNCTIONS DO NOT WORK ON YOUR CURRENT R VERSION. These functions require R version 3.2 or later - you have ", R.version.string, "."), "")}}
#'

@ -27,12 +27,14 @@
#'
#' Calculates age in years based on a reference date, which is the sytem date at default.
#' @inheritSection lifecycle Stable Lifecycle
#' @param x date(s), will be coerced with [as.POSIXlt()]
#' @param reference reference date(s) (defaults to today), will be coerced with [as.POSIXlt()]
#' @param x date(s), [character] (vectors) will be coerced with [as.POSIXlt()]
#' @param reference reference date(s) (defaults to today), [character] (vectors) will be coerced with [as.POSIXlt()]
#' @param exact a [logical] to indicate whether age calculation should be exact, i.e. with decimals. It divides the number of days of [year-to-date](https://en.wikipedia.org/wiki/Year-to-date) (YTD) of `x` by the number of days in the year of `reference` (either 365 or 366).
#' @param na.rm a [logical] to indicate whether missing values should be removed
#' @param ... arguments passed on to [as.POSIXlt()], such as `origin`
#' @details Ages below 0 will be returned as `NA` with a warning. Ages above 120 will only give a warning.
#'
#' This function vectorises over both `x` and `reference`, meaning that either can have a length of 1 while the other argument has a larger length.
#' @return An [integer] (no decimals) if `exact = FALSE`, a [double] (with decimals) otherwise
#' @seealso To split ages into groups, use the [age_groups()] function.
#' @inheritSection AMR Read more on Our Website!
@ -53,8 +55,13 @@ age <- function(x, reference = Sys.Date(), exact = FALSE, na.rm = FALSE, ...) {
meet_criteria(na.rm, allow_class = "logical", has_length = 1)
if (length(x) != length(reference)) {
stop_if(length(reference) != 1, "`x` and `reference` must be of same length, or `reference` must be of length 1.")
reference <- rep(reference, length(x))
if (length(x) == 1) {
x <- rep(x, length(reference))
} else if (length(reference) == 1) {
reference <- rep(reference, length(x))
} else {
stop_("`x` and `reference` must be of same length, or `reference` must be of length 1.")
}
}
x <- as.POSIXlt(x, ...)
reference <- as.POSIXlt(reference, ...)
@ -68,15 +75,15 @@ age <- function(x, reference = Sys.Date(), exact = FALSE, na.rm = FALSE, ...) {
# add decimals
if (exact == TRUE) {
# get dates of `x` when `x` would have the year of `reference`
x_in_reference_year <- as.POSIXlt(paste0(format(reference, "%Y"), format(x, "-%m-%d")))
x_in_reference_year <- as.POSIXlt(paste0(format(as.Date(reference), "%Y"), format(as.Date(x), "-%m-%d")))
# get differences in days
n_days_x_rest <- as.double(difftime(reference, x_in_reference_year, units = "days"))
n_days_x_rest <- as.double(difftime(as.Date(reference), as.Date(x_in_reference_year), units = "days"))
# get numbers of days the years of `reference` has for a reliable denominator
n_days_reference_year <- as.POSIXlt(paste0(format(reference, "%Y"), "-12-31"))$yday + 1
n_days_reference_year <- as.POSIXlt(paste0(format(as.Date(reference), "%Y"), "-12-31"))$yday + 1
# add decimal parts of year
mod <- n_days_x_rest / n_days_reference_year
# negative mods are cases where `x_in_reference_year` > `reference` - so 'add' a year
mod[mod < 0] <- 1 + mod[mod < 0]
mod[mod < 0] <- mod[mod < 0] + 1
# and finally add to ages
ages <- ages + mod
}

Binary file not shown.

@ -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">1.6.0.9060</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9061</span>
</span>
</div>

@ -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">1.6.0.9060</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9061</span>
</span>
</div>

@ -39,7 +39,7 @@
</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">1.6.0.9060</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9061</span>
</span>
</div>
@ -192,7 +192,7 @@
<div class="page-header toc-ignore">
<h1 data-toc-skip>Data sets for download / own use</h1>
<h4 class="date">22 May 2021</h4>
<h4 class="date">23 May 2021</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/datasets.Rmd"><code>vignettes/datasets.Rmd</code></a></small>
<div class="hidden name"><code>datasets.Rmd</code></div>

@ -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">1.6.0.9060</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9061</span>
</span>
</div>

@ -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">1.6.0.9060</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9061</span>
</span>
</div>

@ -222,6 +222,9 @@ table a:not(.btn) {
table a:not(.btn):hover {
text-decoration: underline;
}
.template-article thead th {
text-align: inherit;
}
/* text below header in manual overview */
.template-reference-index h2 ~ p {

@ -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">1.6.0.9060</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9061</span>
</span>
</div>

@ -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">1.6.0.9060</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9061</span>
</span>
</div>
@ -236,12 +236,12 @@
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div>
<div id="amr-1609060" class="section level1">
<h1 class="page-header" data-toc-text="1.6.0.9060">
<a href="#amr-1609060" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.6.0.9060</h1>
<div id="last-updated-22-may-2021" class="section level2">
<div id="amr-1609061" class="section level1">
<h1 class="page-header" data-toc-text="1.6.0.9061">
<a href="#amr-1609061" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.6.0.9061</h1>
<div id="last-updated-23-may-2021" class="section level2">
<h2 class="hasAnchor">
<a href="#last-updated-22-may-2021" class="anchor"></a><small>Last updated: 22 May 2021</small>
<a href="#last-updated-23-may-2021" class="anchor"></a><small>Last updated: 23 May 2021</small>
</h2>
<div id="breaking-change" class="section level3">
<h3 class="hasAnchor">
@ -335,6 +335,9 @@
<li>Antibiotic class selectors (such as <code><a href="../reference/antibiotic_class_selectors.html">cephalosporins()</a></code>) now maintain the column order from the original data</li>
<li>Fix for selecting columns using <code><a href="../reference/antibiotic_class_selectors.html">fluoroquinolones()</a></code>
</li>
<li>
<code><a href="../reference/age.html">age()</a></code> now vectorises over both <code>x</code> and <code>reference</code>
</li>
</ul>
</div>
<div id="other" class="section level3">

@ -12,7 +12,7 @@ articles:
datasets: datasets.html
resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html
last_built: 2021-05-22T07:53Z
last_built: 2021-05-23T20:10Z
urls:
reference: https://msberends.github.io/AMR//reference
article: https://msberends.github.io/AMR//articles

@ -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">1.6.0.9055</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9061</span>
</span>
</div>
@ -249,11 +249,11 @@
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>x</th>
<td><p>date(s), will be coerced with <code><a href='https://rdrr.io/r/base/as.POSIXlt.html'>as.POSIXlt()</a></code></p></td>
<td><p>date(s), <a href='https://rdrr.io/r/base/character.html'>character</a> (vectors) will be coerced with <code><a href='https://rdrr.io/r/base/as.POSIXlt.html'>as.POSIXlt()</a></code></p></td>
</tr>
<tr>
<th>reference</th>
<td><p>reference date(s) (defaults to today), will be coerced with <code><a href='https://rdrr.io/r/base/as.POSIXlt.html'>as.POSIXlt()</a></code></p></td>
<td><p>reference date(s) (defaults to today), <a href='https://rdrr.io/r/base/character.html'>character</a> (vectors) will be coerced with <code><a href='https://rdrr.io/r/base/as.POSIXlt.html'>as.POSIXlt()</a></code></p></td>
</tr>
<tr>
<th>exact</th>
@ -275,6 +275,7 @@
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>Ages below 0 will be returned as <code>NA</code> with a warning. Ages above 120 will only give a warning.</p>
<p>This function vectorises over both <code>x</code> and <code>reference</code>, meaning that either can have a length of 1 while the other argument has a larger length.</p>
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable Lifecycle</h2>

@ -83,7 +83,7 @@
</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">1.6.0.9055</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9061</span>
</span>
</div>
@ -281,7 +281,7 @@
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>ab_class</th>
<td><p>an antimicrobial class, like <code>"carbapenems"</code>. The columns <code>group</code>, <code>atc_group1</code> and <code>atc_group2</code> of the <a href='antibiotics.html'>antibiotics</a> data set will be searched (case-insensitive) for this value.</p></td>
<td><p>an antimicrobial class, such as <code>"carbapenems"</code>. The columns <code>group</code>, <code>atc_group1</code> and <code>atc_group2</code> of the <a href='antibiotics.html'>antibiotics</a> data set will be searched (case-insensitive) for this value.</p></td>
</tr>
<tr>
<th>only_rsi_columns</th>

@ -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">1.6.0.9060</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9061</span>
</span>
</div>

@ -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">1.6.0.9060</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9061</span>
</span>
</div>

@ -7,9 +7,9 @@
age(x, reference = Sys.Date(), exact = FALSE, na.rm = FALSE, ...)
}
\arguments{
\item{x}{date(s), will be coerced with \code{\link[=as.POSIXlt]{as.POSIXlt()}}}
\item{x}{date(s), \link{character} (vectors) will be coerced with \code{\link[=as.POSIXlt]{as.POSIXlt()}}}
\item{reference}{reference date(s) (defaults to today), will be coerced with \code{\link[=as.POSIXlt]{as.POSIXlt()}}}
\item{reference}{reference date(s) (defaults to today), \link{character} (vectors) will be coerced with \code{\link[=as.POSIXlt]{as.POSIXlt()}}}
\item{exact}{a \link{logical} to indicate whether age calculation should be exact, i.e. with decimals. It divides the number of days of \href{https://en.wikipedia.org/wiki/Year-to-date}{year-to-date} (YTD) of \code{x} by the number of days in the year of \code{reference} (either 365 or 366).}
@ -25,6 +25,8 @@ Calculates age in years based on a reference date, which is the sytem date at de
}
\details{
Ages below 0 will be returned as \code{NA} with a warning. Ages above 120 will only give a warning.
This function vectorises over both \code{x} and \code{reference}, meaning that either can have a length of 1 while the other argument has a larger length.
}
\section{Stable Lifecycle}{

@ -53,7 +53,7 @@ penicillins(only_rsi_columns = FALSE)
tetracyclines(only_rsi_columns = FALSE)
}
\arguments{
\item{ab_class}{an antimicrobial class, like \code{"carbapenems"}. The columns \code{group}, \code{atc_group1} and \code{atc_group2} of the \link{antibiotics} data set will be searched (case-insensitive) for this value.}
\item{ab_class}{an antimicrobial class, such as \code{"carbapenems"}. The columns \code{group}, \code{atc_group1} and \code{atc_group2} of the \link{antibiotics} data set will be searched (case-insensitive) for this value.}
\item{only_rsi_columns}{a \link{logical} to indicate whether only columns of class \verb{<rsi>} must be selected (defaults to \code{FALSE}), see \code{\link[=as.rsi]{as.rsi()}}}
}

@ -222,6 +222,9 @@ table a:not(.btn) {
table a:not(.btn):hover {
text-decoration: underline;
}
.template-article thead th {
text-align: inherit;
}
/* text below header in manual overview */
.template-reference-index h2 ~ p {

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