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(v1.4.0.9060) ab class selector fix

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dr. M.S. (Matthijs) Berends 2021-01-04 13:39:06 +01:00
parent c9de74c81a
commit 8d117820b8
15 changed files with 20 additions and 19 deletions
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2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR Package: AMR
Version: 1.4.0.9059 Version: 1.4.0.9060
Date: 2021-01-04 Date: 2021-01-04
Title: Antimicrobial Resistance Analysis Title: Antimicrobial Resistance Analysis
Authors@R: c( Authors@R: c(

2
NEWS.md
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@ -1,4 +1,4 @@
# AMR 1.4.0.9059 # AMR 1.4.0.9060
## <small>Last updated: 4 January 2021</small> ## <small>Last updated: 4 January 2021</small>
### New ### New
* Functions `get_episode()` and `is_new_episode()` to determine (patient) episodes which are not necessarily based on microorganisms. The `get_episode()` function returns the index number of the episode per group, while the `is_new_episode()` function returns values `TRUE`/`FALSE` to indicate whether an item in a vector is the start of a new episode. They also support `dplyr`s grouping (i.e. using `group_by()`): * Functions `get_episode()` and `is_new_episode()` to determine (patient) episodes which are not necessarily based on microorganisms. The `get_episode()` function returns the index number of the episode per group, while the `is_new_episode()` function returns values `TRUE`/`FALSE` to indicate whether an item in a vector is the start of a new episode. They also support `dplyr`s grouping (i.e. using `group_by()`):

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R/aa_helper_functions.R
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@ -527,7 +527,7 @@ meet_criteria <- function(object,
} }
get_current_data <- function(arg_name, call) { get_current_data <- function(arg_name, call) {
if (as.double(R.Version()$major) + (as.double(R.Version()$minor) / 100) < 3.2) { if (as.double(R.Version()$major) + (as.double(R.Version()$minor) / 10) < 3.2) {
if (is.na(arg_name)) { if (is.na(arg_name)) {
warning_("this function can only be used in R >= 3.2", call = call) warning_("this function can only be used in R >= 3.2", call = call)
return(data.frame()) return(data.frame())

2
R/ab_class_selectors.R
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@ -164,7 +164,7 @@ ab_selector <- function(ab_class, function_name) {
meet_criteria(ab_class, allow_class = "character", has_length = 1, .call_depth = 1) meet_criteria(ab_class, allow_class = "character", has_length = 1, .call_depth = 1)
meet_criteria(function_name, allow_class = "character", has_length = 1, .call_depth = 1) meet_criteria(function_name, allow_class = "character", has_length = 1, .call_depth = 1)
if (as.double(R.Version()$major) + (as.double(R.Version()$minor) / 100) < 3.2) { if (as.double(R.Version()$major) + (as.double(R.Version()$minor) / 10) < 3.2) {
warning_(function_name, "() can only be used in R >= 3.2", call = FALSE) warning_(function_name, "() can only be used in R >= 3.2", call = FALSE)
return(NULL) return(NULL)
} }

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data-raw/AMR_1.4.0.9059.tar.gz → data-raw/AMR_1.4.0.9060.tar.gz
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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">1.4.0.9059</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9060</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">1.4.0.9059</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9060</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">1.4.0.9059</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9060</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">1.4.0.9059</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9060</span>
</span> </span>
</div> </div>

2
docs/index.html
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@ -43,7 +43,7 @@
</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">1.4.0.9059</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9060</span>
</span> </span>
</div> </div>

8
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">1.4.0.9059</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9060</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-1409059" class="section level1"> <div id="amr-1409060" class="section level1">
<h1 class="page-header" data-toc-text="1.4.0.9059"> <h1 class="page-header" data-toc-text="1.4.0.9060">
<a href="#amr-1409059" class="anchor"></a>AMR 1.4.0.9059<small> Unreleased </small> <a href="#amr-1409060" class="anchor"></a>AMR 1.4.0.9060<small> Unreleased </small>
</h1> </h1>
<div id="last-updated-4-january-2021" class="section level2"> <div id="last-updated-4-january-2021" class="section level2">
<h2 class="hasAnchor"> <h2 class="hasAnchor">

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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: 2021-01-04T11:28Z last_built: 2021-01-04T12:36Z
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

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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">1.4.0.9059</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9060</span>
</span> </span>
</div> </div>

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">1.4.0.9059</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9060</span>
</span> </span>
</div> </div>

7
tests/testthat/test-zzz.R
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@ -105,12 +105,13 @@ test_that("imports work", {
import_functions <- c(import_functions, call_functions) import_functions <- c(import_functions, call_functions)
# check if all are in Suggests field
expect_true(all(unique(import_functions) %in% strsplit(packageDescription("AMR")$Suggests, ",\n")[[1]]))
for (i in seq_len(length(import_functions))) { for (i in seq_len(length(import_functions))) {
fn <- names(import_functions)[i] fn <- names(import_functions)[i]
pkg <- unname(import_functions[i]) pkg <- unname(import_functions[i])
# package should be in Suggests field of DESCRIPTION
expect(pkg %in% strsplit(packageDescription("AMR")$Suggests, ",\n")[[1]],
failure_message = paste0("Package ", pkg, " is not in Suggests field"))
# function should exist in foreign pkg namespace
expect(!is.null(import_fn(name = fn, pkg = pkg, error_on_fail = FALSE)), expect(!is.null(import_fn(name = fn, pkg = pkg, error_on_fail = FALSE)),
failure_message = paste0("Function ", pkg, "::", fn, "() does not exist anymore")) failure_message = paste0("Function ", pkg, "::", fn, "() does not exist anymore"))
} }