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(v0.7.0.9003) scale fix

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dr. M.S. (Matthijs) Berends 2019-06-08 23:50:06 +02:00
parent f50d3a5ba1
commit ec48f1d83b
16 changed files with 403 additions and 32 deletions
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2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR Package: AMR
Version: 0.7.0.9002 Version: 0.7.0.9003
Date: 2019-06-08 Date: 2019-06-08
Title: Antimicrobial Resistance Analysis Title: Antimicrobial Resistance Analysis
Authors@R: c( Authors@R: c(

2
NAMESPACE
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@ -173,6 +173,8 @@ export(resistance_predict)
export(right_join_microorganisms) export(right_join_microorganisms)
export(rsi_predict) export(rsi_predict)
export(scale_rsi_colours) export(scale_rsi_colours)
export(scale_type.ab)
export(scale_type.mo)
export(scale_y_percent) export(scale_y_percent)
export(semi_join_microorganisms) export(semi_join_microorganisms)
export(set_mo_source) export(set_mo_source)

4
NEWS.md
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@ -1,4 +1,4 @@
# AMR 0.7.0.9002 # AMR 0.7.0.9003
#### New #### New
* Support for all scientifically published pathotypes of *E. coli* to date. Supported are: AIEC (Adherent-Invasive *E. coli*), ATEC (Atypical Entero-pathogenic *E. coli*), DAEC (Diffusely Adhering *E. coli*), EAEC (Entero-Aggresive *E. coli*), EHEC (Entero-Haemorrhagic *E. coli*), EIEC (Entero-Invasive *E. coli*), EPEC (Entero-Pathogenic *E. coli*), ETEC (Entero-Toxigenic *E. coli*), NMEC (Neonatal Meningitis‐causing *E. coli*), STEC (Shiga-toxin producing *E. coli*) and UPEC (Uropathogenic *E. coli*). All these lead to the microbial ID of *E. coli*: * Support for all scientifically published pathotypes of *E. coli* to date. Supported are: AIEC (Adherent-Invasive *E. coli*), ATEC (Atypical Entero-pathogenic *E. coli*), DAEC (Diffusely Adhering *E. coli*), EAEC (Entero-Aggresive *E. coli*), EHEC (Entero-Haemorrhagic *E. coli*), EIEC (Entero-Invasive *E. coli*), EPEC (Entero-Pathogenic *E. coli*), ETEC (Entero-Toxigenic *E. coli*), NMEC (Neonatal Meningitis‐causing *E. coli*), STEC (Shiga-toxin producing *E. coli*) and UPEC (Uropathogenic *E. coli*). All these lead to the microbial ID of *E. coli*:
@ -12,7 +12,7 @@
#### Changed #### Changed
* Fixed bug in translation of microorganism names * Fixed bug in translation of microorganism names
* Fixed bug in determining taxonomic kingdoms * Fixed bug in determining taxonomic kingdoms
* Algorithm improvements for `as.ab()` and `as.mo()` to understand even more severe misspelled input * Algorithm improvements for `as.ab()` and `as.mo()` to understand even more severely misspelled input
* Added `ggplot2` methods for automatically determining the scale type of classes `mo` and `ab` * Added `ggplot2` methods for automatically determining the scale type of classes `mo` and `ab`
* Added names of object in the header in frequency tables, even when using pipes * Added names of object in the header in frequency tables, even when using pipes
* Prevented `"bacteria"` from getting coerced by `as.ab()` because Bacterial is a brand name of trimethoprim (TMP) * Prevented `"bacteria"` from getting coerced by `as.ab()` because Bacterial is a brand name of trimethoprim (TMP)

9
R/ab.R
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@ -258,12 +258,3 @@ as.data.frame.ab <- function (x, ...) {
pull.ab <- function(.data, ...) { pull.ab <- function(.data, ...) {
pull(as.data.frame(.data), ...) pull(as.data.frame(.data), ...)
} }
#' @exportMethod scale_type.ab
#' @noRd
scale_type.ab <- function(x) {
# fix for:
# "Don't know how to automatically pick scale for object of type ab. Defaulting to continuous."
# "Error: Discrete value supplied to continuous scale"
"discrete"
}

48
R/extended.R Normal file
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@ -0,0 +1,48 @@
# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# #
# This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the #
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
# the Free Software Foundation. #
# #
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
#' Extended functions
#'
#' These functions are extensions of functions in other packages.
#' @inheritSection AMR Read more on our website!
#' @export
#' @keywords internal
#' @name extended-functions
#' @rdname extended-functions
#' @exportMethod scale_type.mo
#' @export
scale_type.mo <- function(x) {
# fix for:
# "Don't know how to automatically pick scale for object of type mo. Defaulting to continuous."
# "Error: Discrete value supplied to continuous scale"
"discrete"
}
#' @rdname extended-functions
#' @exportMethod scale_type.ab
#' @export
scale_type.ab <- function(x) {
# fix for:
# "Don't know how to automatically pick scale for object of type mo. Defaulting to continuous."
# "Error: Discrete value supplied to continuous scale"
"discrete"
}

10
R/mo.R
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@ -1484,13 +1484,3 @@ translate_allow_uncertain <- function(allow_uncertain) {
} }
allow_uncertain allow_uncertain
} }
#' @exportMethod scale_type.mo
# @export
#' @noRd
scale_type.mo <- function(x) {
# fix for:
# "Don't know how to automatically pick scale for object of type mo. Defaulting to continuous."
# "Error: Discrete value supplied to continuous scale"
"discrete"
}

2
docs/LICENSE-text.html
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@ -78,7 +78,7 @@
</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="Released version">0.7.0.9002</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0.9003</span>
</span> </span>
</div> </div>

2
docs/articles/index.html
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@ -78,7 +78,7 @@
</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="Released version">0.7.0.9002</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0.9003</span>
</span> </span>
</div> </div>

2
docs/authors.html
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@ -78,7 +78,7 @@
</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="Released version">0.7.0.9002</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0.9003</span>
</span> </span>
</div> </div>

2
docs/index.html
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@ -42,7 +42,7 @@
</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="Released version">0.7.0.9002</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0.9003</span>
</span> </span>
</div> </div>

10
docs/news/index.html
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@ -78,7 +78,7 @@
</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="Released version">0.7.0.9002</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0.9003</span>
</span> </span>
</div> </div>
@ -239,9 +239,9 @@
</div> </div>
<div id="amr-0709002" class="section level1"> <div id="amr-0709003" class="section level1">
<h1 class="page-header"> <h1 class="page-header">
<a href="#amr-0709002" class="anchor"></a>AMR 0.7.0.9002<small> Unreleased </small> <a href="#amr-0709003" class="anchor"></a>AMR 0.7.0.9003<small> Unreleased </small>
</h1> </h1>
<div id="new" class="section level4"> <div id="new" class="section level4">
<h4 class="hasAnchor"> <h4 class="hasAnchor">
@ -262,7 +262,7 @@
<ul> <ul>
<li>Fixed bug in translation of microorganism names</li> <li>Fixed bug in translation of microorganism names</li>
<li>Fixed bug in determining taxonomic kingdoms</li> <li>Fixed bug in determining taxonomic kingdoms</li>
<li>Algorithm improvements for <code><a href="../reference/as.ab.html">as.ab()</a></code> and <code><a href="../reference/as.mo.html">as.mo()</a></code> to understand even more severe misspelled input</li> <li>Algorithm improvements for <code><a href="../reference/as.ab.html">as.ab()</a></code> and <code><a href="../reference/as.mo.html">as.mo()</a></code> to understand even more severely misspelled input</li>
<li>Added <code>ggplot2</code> methods for automatically determining the scale type of classes <code>mo</code> and <code>ab</code> <li>Added <code>ggplot2</code> methods for automatically determining the scale type of classes <code>mo</code> and <code>ab</code>
</li> </li>
<li>Added names of object in the header in frequency tables, even when using pipes</li> <li>Added names of object in the header in frequency tables, even when using pipes</li>
@ -1108,7 +1108,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
<div id="tocnav"> <div id="tocnav">
<h2>Contents</h2> <h2>Contents</h2>
<ul class="nav nav-pills nav-stacked"> <ul class="nav nav-pills nav-stacked">
<li><a href="#amr-0709002">0.7.0.9002</a></li> <li><a href="#amr-0709003">0.7.0.9003</a></li>
<li><a href="#amr-070">0.7.0</a></li> <li><a href="#amr-070">0.7.0</a></li>
<li><a href="#amr-061">0.6.1</a></li> <li><a href="#amr-061">0.6.1</a></li>
<li><a href="#amr-060">0.6.0</a></li> <li><a href="#amr-060">0.6.0</a></li>

304
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@ -0,0 +1,304 @@
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<h1>Extended functions</h1>
<div class="hidden name"><code>extended-functions.Rd</code></div>
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<p>These functions are extensions of functions in other packages.</p>
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<pre class="usage"><span class='fu'>scale_type.mo</span>(<span class='no'>x</span>)
<span class='fu'>scale_type.ab</span>(<span class='no'>x</span>)</pre>
<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.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0.9002</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.0.9003</span>
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@ -63,6 +63,9 @@
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21
man/extended-functions.Rd Normal file
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@ -0,0 +1,21 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/extended.R
\name{extended-functions}
\alias{extended-functions}
\alias{scale_type.mo}
\alias{scale_type.ab}
\title{Extended functions}
\usage{
scale_type.mo(x)
scale_type.ab(x)
}
\description{
These functions are extensions of functions in other packages.
}
\section{Read more on our website!}{
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
}
\keyword{internal}

12
tests/testthat/test-ggplot_rsi.R
View File

@ -62,4 +62,16 @@ test_that("ggplot_rsi works", {
expect_error(ggplot_rsi(septic_patients, fun = "invalid")) expect_error(ggplot_rsi(septic_patients, fun = "invalid"))
expect_error(geom_rsi(septic_patients, fun = "invalid")) expect_error(geom_rsi(septic_patients, fun = "invalid"))
# support for scale_type ab and mo
expect_equal(class((data.frame(mo = as.mo(c("e. coli", "s aureus")),
n = c(40, 100)) %>%
ggplot(aes(x = mo, y = n)) +
geom_col())$data),
"data.frame")
expect_equal(class((data.frame(ab = as.ab(c("amx", "amc")),
n = c(40, 100)) %>%
ggplot(aes(x = ab, y = n)) +
geom_col())$data),
"data.frame")
}) })