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(v1.5.0.9033) as.rsi fix

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dr. M.S. (Matthijs) Berends 2021-03-07 16:15:43 +01:00
parent 850c123de7
commit 1bbf409fe5
15 changed files with 22 additions and 26 deletions
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2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR Package: AMR
Version: 1.5.0.9032 Version: 1.5.0.9033
Date: 2021-03-07 Date: 2021-03-07
Title: Antimicrobial Resistance Data Analysis Title: Antimicrobial Resistance Data Analysis
Authors@R: c( Authors@R: c(

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NEWS.md
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@ -1,4 +1,4 @@
# AMR 1.5.0.9032 # AMR 1.5.0.9033
## <small>Last updated: 7 March 2021</small> ## <small>Last updated: 7 March 2021</small>
### New ### New

2
R/mic.R
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@ -341,7 +341,7 @@ get_skimmers.mic <- function(column) {
skim_type = "mic", skim_type = "mic",
min = ~min(., na.rm = TRUE), min = ~min(., na.rm = TRUE),
max = ~max(., na.rm = TRUE), max = ~max(., na.rm = TRUE),
median = ~median(., na.rm = TRUE), median = ~stats::median(., na.rm = TRUE),
n_unique = ~pm_n_distinct(., na.rm = TRUE), n_unique = ~pm_n_distinct(., na.rm = TRUE),
hist_log2 = ~skimr::inline_hist(log2(stats::na.omit(.))) hist_log2 = ~skimr::inline_hist(log2(stats::na.omit(.)))
) )

1
R/plot.R
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@ -527,7 +527,6 @@ plot_colours_subtitle_guideline <- function(x, mo, ab, guideline, colours_RSI, f
list(cols = cols, count = as.double(x), sub = sub, guideline = guideline) list(cols = cols, count = as.double(x), sub = sub, guideline = guideline)
} }
#' @method plot rsi #' @method plot rsi
#' @export #' @export
#' @importFrom graphics plot text axis #' @importFrom graphics plot text axis

13
R/rsi.R
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@ -814,17 +814,14 @@ exec_as.rsi <- function(method,
if (is.na(x[i])) { if (is.na(x[i])) {
new_rsi[i] <- NA_character_ new_rsi[i] <- NA_character_
} else if (method == "mic") { } else if (method == "mic") {
mic_input <- x[i] new_rsi[i] <- quick_case_when(isTRUE(conserve_capped_values) & x[i] %like% "^<[0-9]" ~ "S",
mic_S <- as.mic(get_record$breakpoint_S) isTRUE(conserve_capped_values) & x[i] %like% "^>[0-9]" ~ "R",
mic_R <- as.mic(get_record$breakpoint_R)
new_rsi[i] <- quick_case_when(isTRUE(conserve_capped_values) & mic_input %like% "^<[0-9]" ~ "S",
isTRUE(conserve_capped_values) & mic_input %like% "^>[0-9]" ~ "R",
# start interpreting: EUCAST uses <= S and > R, CLSI uses <=S and >= R # start interpreting: EUCAST uses <= S and > R, CLSI uses <=S and >= R
isTRUE(which(levels(mic_input) == mic_input) <= which(levels(mic_S) == mic_S)) ~ "S", isTRUE(x[i] <= get_record$breakpoint_S) ~ "S",
guideline_coerced %like% "EUCAST" & guideline_coerced %like% "EUCAST" &
isTRUE(which(levels(mic_input) == mic_input) > which(levels(mic_R) == mic_R)) ~ "R", isTRUE(x[i] > get_record$breakpoint_R) ~ "R",
guideline_coerced %like% "CLSI" & guideline_coerced %like% "CLSI" &
isTRUE(which(levels(mic_input) == mic_input) >= which(levels(mic_R) == mic_R)) ~ "R", isTRUE(x[i] >= get_record$breakpoint_R) ~ "R",
# return "I" when not match the bottom or top # return "I" when not match the bottom or top
!is.na(get_record$breakpoint_S) & !is.na(get_record$breakpoint_R) ~ "I", !is.na(get_record$breakpoint_S) & !is.na(get_record$breakpoint_R) ~ "I",
# and NA otherwise # and NA otherwise

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data-raw/AMR_latest.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">1.5.0.9032</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9033</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">1.5.0.9032</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9033</span>
</span> </span>
</div> </div>

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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">1.5.0.9032</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9033</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">1.5.0.9032</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9033</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">1.5.0.9032</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9033</span>
</span> </span>
</div> </div>

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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">1.5.0.9032</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9033</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-1509032" class="section level1"> <div id="amr-1509033" class="section level1">
<h1 class="page-header" data-toc-text="1.5.0.9032"> <h1 class="page-header" data-toc-text="1.5.0.9033">
<a href="#amr-1509032" class="anchor"></a>AMR 1.5.0.9032<small> Unreleased </small> <a href="#amr-1509033" class="anchor"></a>AMR 1.5.0.9033<small> Unreleased </small>
</h1> </h1>
<div id="last-updated-7-march-2021" class="section level2"> <div id="last-updated-7-march-2021" class="section level2">
<h2 class="hasAnchor"> <h2 class="hasAnchor">
@ -280,7 +280,7 @@
</li> </li>
<li><p>Support for custom MDRO guidelines, using the new <code><a href="../reference/mdro.html">custom_mdro_guideline()</a></code> function, please see <code><a href="../reference/mdro.html">mdro()</a></code> for additional info</p></li> <li><p>Support for custom MDRO guidelines, using the new <code><a href="../reference/mdro.html">custom_mdro_guideline()</a></code> function, please see <code><a href="../reference/mdro.html">mdro()</a></code> for additional info</p></li>
<li><p>Function <code><a href="../reference/isolate_identifier.html">isolate_identifier()</a></code>, which will paste a microorganism code with all antimicrobial results of a data set into one string for each row. This is useful to compare isolates, e.g. between institutions or regions, when there is no genotyping available.</p></li> <li><p>Function <code><a href="../reference/isolate_identifier.html">isolate_identifier()</a></code>, which will paste a microorganism code with all antimicrobial results of a data set into one string for each row. This is useful to compare isolates, e.g. between institutions or regions, when there is no genotyping available.</p></li>
<li><p><code><a href="https://ggplot2.tidyverse.org/reference/ggplot.html">ggplot()</a></code> generics for classes <code>&lt;mic&gt;</code> and <code>&lt;disk&gt;</code></p></li> <li><p><code>ggplot()</code> generics for classes <code>&lt;mic&gt;</code> and <code>&lt;disk&gt;</code></p></li>
<li> <li>
<p>Function <code><a href="../reference/mo_property.html">mo_is_yeast()</a></code>, which determines whether a microorganism is a member of the taxonomic class Saccharomycetes or the taxonomic order Saccharomycetales:</p> <p>Function <code><a href="../reference/mo_property.html">mo_is_yeast()</a></code>, which determines whether a microorganism is a member of the taxonomic class Saccharomycetes or the taxonomic order Saccharomycetales:</p>
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r"> <div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
@ -321,7 +321,7 @@
<li>Plotting of MIC and disk diffusion values now support interpretation colouring if you supply the microorganism and antimicrobial agent</li> <li>Plotting of MIC and disk diffusion values now support interpretation colouring if you supply the microorganism and antimicrobial agent</li>
<li>All colours were updated to colour-blind friendly versions for values R, S and I for all plot methods (also applies to tibble printing)</li> <li>All colours were updated to colour-blind friendly versions for values R, S and I for all plot methods (also applies to tibble printing)</li>
<li>Interpretation of MIC and disk diffusion values to R/SI will now be translated if the system language is German, Dutch or Spanish (see <code>translate</code>)</li> <li>Interpretation of MIC and disk diffusion values to R/SI will now be translated if the system language is German, Dutch or Spanish (see <code>translate</code>)</li>
<li>Plotting is now possible with base R using <code><a href="../reference/plot.html">plot()</a></code> and with ggplot2 using <code><a href="https://ggplot2.tidyverse.org/reference/ggplot.html">ggplot()</a></code> on any vector of MIC and disk diffusion values</li> <li>Plotting is now possible with base R using <code><a href="../reference/plot.html">plot()</a></code> and with ggplot2 using <code>ggplot()</code> on any vector of MIC and disk diffusion values</li>
</ul> </ul>
</li> </li>
<li> <li>

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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: 2021-03-07T12:50Z last_built: 2021-03-07T15:15Z
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">1.5.0.9032</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9033</span>
</span> </span>
</div> </div>

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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">1.5.0.9032</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9033</span>
</span> </span>
</div> </div>