mirror of
https://github.com/msberends/AMR.git
synced 2024-12-25 19:26:13 +01:00
(v1.8.1.9005) as.rsi() fix for EUCAST
This commit is contained in:
parent
d4e22069bc
commit
680e8e7a41
@ -1,6 +1,6 @@
|
||||
Package: AMR
|
||||
Version: 1.8.1.9004
|
||||
Date: 2022-05-09
|
||||
Version: 1.8.1.9005
|
||||
Date: 2022-05-10
|
||||
Title: Antimicrobial Resistance Data Analysis
|
||||
Description: Functions to simplify and standardise antimicrobial resistance (AMR)
|
||||
data analysis and to work with microbial and antimicrobial properties by
|
||||
|
5
NEWS.md
5
NEWS.md
@ -1,7 +1,8 @@
|
||||
# `AMR` 1.8.1.9004
|
||||
## <small>Last updated: 9 May 2022</small>
|
||||
# `AMR` 1.8.1.9005
|
||||
## <small>Last updated: 10 May 2022</small>
|
||||
|
||||
### Changed
|
||||
* Fix for `as.rsi()` on certain EUCAST breakpoints for MIC values
|
||||
* Removed `as.integer()` for MIC values, since MIC are not integer values and running `table()` on MIC values consequently failed for not being able to retrieve the level position (as that's how normally `as.integer()` on `factor`s work)
|
||||
* `droplevels()` on MIC will now return a common `factor` at default and will lose the `<mic>` class. Use `droplevels(..., as.mic = TRUE)` to keep the `<mic>` class.
|
||||
* Small fix for using `ab_from_text()`
|
||||
|
12
R/rsi.R
12
R/rsi.R
@ -818,18 +818,20 @@ exec_as.rsi <- function(method,
|
||||
if (is.na(x[i]) | (is.na(get_record$breakpoint_S) & is.na(get_record$breakpoint_R))) {
|
||||
new_rsi[i] <- NA_character_
|
||||
} else if (method == "mic") {
|
||||
new_rsi[i] <- quick_case_when(isTRUE(conserve_capped_values) & x[i] %like% "^<[0-9]" ~ "S",
|
||||
isTRUE(conserve_capped_values) & x[i] %like% "^>[0-9]" ~ "R",
|
||||
new_rsi[i] <- quick_case_when(isTRUE(conserve_capped_values) & isTRUE(x[i] %like% "^<[0-9]") ~ "S",
|
||||
isTRUE(conserve_capped_values) & isTRUE(x[i] %like% "^>[0-9]") ~ "R",
|
||||
# these basically call `<=.mic()` and `>=.mic()`:
|
||||
x[i] <= get_record$breakpoint_S ~ "S",
|
||||
x[i] >= get_record$breakpoint_R ~ "R",
|
||||
isTRUE(x[i] <= get_record$breakpoint_S) ~ "S",
|
||||
guideline_coerced %like% "EUCAST" & isTRUE(x[i] > get_record$breakpoint_R) ~ "R",
|
||||
guideline_coerced %like% "CLSI" & isTRUE(x[i] >= get_record$breakpoint_R) ~ "R",
|
||||
# return "I" when not match the bottom or top
|
||||
!is.na(get_record$breakpoint_S) & !is.na(get_record$breakpoint_R) ~ "I",
|
||||
# and NA otherwise
|
||||
TRUE ~ NA_character_)
|
||||
} else if (method == "disk") {
|
||||
new_rsi[i] <- quick_case_when(isTRUE(as.double(x[i]) >= as.double(get_record$breakpoint_S)) ~ "S",
|
||||
isTRUE(as.double(x[i]) <= as.double(get_record$breakpoint_R)) ~ "R",
|
||||
guideline_coerced %like% "EUCAST" & isTRUE(as.double(x[i]) < as.double(get_record$breakpoint_R)) ~ "R",
|
||||
guideline_coerced %like% "CLSI" & isTRUE(as.double(x[i]) <= as.double(get_record$breakpoint_R)) ~ "R",
|
||||
# return "I" when not match the bottom or top
|
||||
!is.na(get_record$breakpoint_S) & !is.na(get_record$breakpoint_R) ~ "I",
|
||||
# and NA otherwise
|
||||
|
Binary file not shown.
@ -128,11 +128,24 @@ rsi_translation[which(rsi_translation$breakpoint_R == 257), "breakpoint_R"] <- m
|
||||
rsi_translation[which(rsi_translation$breakpoint_R == 513), "breakpoint_R"] <- m[which(m == 512) + 1]
|
||||
rsi_translation[which(rsi_translation$breakpoint_R == 1025), "breakpoint_R"] <- m[which(m == 1024) + 1]
|
||||
|
||||
# WHONET adds one log2 level to the R breakpoint for their software, e.g. in AMC in Enterobacterales:
|
||||
# EUCAST 2021 guideline: S <= 8 and R > 8
|
||||
# WHONET file: S <= 8 and R >= 16
|
||||
# this will make an MIC of 12 I, which should be R, so:
|
||||
eucast_mics <- which(rsi_translation$guideline %like% "EUCAST" &
|
||||
rsi_translation$method == "MIC" &
|
||||
log2(as.double(rsi_translation$breakpoint_R)) - log2(as.double(rsi_translation$breakpoint_S)) != 0)
|
||||
rsi_translation[eucast_mics, "breakpoint_R"] <- 2 ^ (log2(as.double(rsi_translation[eucast_mics, "breakpoint_R", drop = TRUE])) - 1)
|
||||
eucast_disks <- which(rsi_translation$guideline %like% "EUCAST" &
|
||||
rsi_translation$method == "DISK" &
|
||||
rsi_translation$breakpoint_S - rsi_translation$breakpoint_R != 0)
|
||||
rsi_translation[eucast_disks, "breakpoint_R"] <- rsi_translation[eucast_disks, "breakpoint_R", drop = TRUE] + 1
|
||||
|
||||
# Greek symbols and EM dash symbols are not allowed by CRAN, so replace them with ASCII:
|
||||
rsi_translation$disk_dose <- gsub("μ", "u", rsi_translation$disk_dose, fixed = TRUE)
|
||||
rsi_translation$disk_dose <- gsub("–", "-", rsi_translation$disk_dose, fixed = TRUE)
|
||||
|
||||
# save to package
|
||||
usethis::use_data(rsi_translation, overwrite = TRUE)
|
||||
usethis::use_data(rsi_translation, overwrite = TRUE, compress = "xz")
|
||||
rm(rsi_translation)
|
||||
devtools::load_all(".")
|
||||
|
@ -1 +1 @@
|
||||
d8083b68d4e492ea8e87c1eae4da4196
|
||||
657a743283954b40bb68fd3b965462a2
|
||||
|
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
File diff suppressed because it is too large
Load Diff
Binary file not shown.
Binary file not shown.
@ -43,7 +43,7 @@
|
||||
</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="Released version">1.8.1.9004</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9005</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -17,7 +17,7 @@
|
||||
</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="Released version">1.8.1.9004</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9005</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -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="Released version">1.8.1.9004</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9005</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -190,7 +190,7 @@
|
||||
<div class="page-header toc-ignore">
|
||||
<h1 data-toc-skip>Data sets for download / own use</h1>
|
||||
|
||||
<h4 data-toc-skip class="date">09 May 2022</h4>
|
||||
<h4 data-toc-skip class="date">10 May 2022</h4>
|
||||
|
||||
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
|
||||
<div class="hidden name"><code>datasets.Rmd</code></div>
|
||||
@ -1168,8 +1168,8 @@ column names:<br><em>guideline</em>, <em>method</em>, <em>site</em>, <em>mo</em>
|
||||
<em>breakpoint_S</em>, <em>breakpoint_R</em> and <em>uti</em>.</p>
|
||||
<p>This data set is in R available as <code>rsi_translation</code>,
|
||||
after you load the <code>AMR</code> package.</p>
|
||||
<p>It was last updated on 14 December 2021 21:59:33 UTC. Find more info
|
||||
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/rsi_translation.html">here</a>.</p>
|
||||
<p>It was last updated on 10 May 2022 13:51:53 UTC. Find more info about
|
||||
the structure of this data set <a href="https://msberends.github.io/AMR/reference/rsi_translation.html">here</a>.</p>
|
||||
<p><strong>Direct download links:</strong></p>
|
||||
<ul>
|
||||
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.rds" class="external-link">R
|
||||
|
@ -17,7 +17,7 @@
|
||||
</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="Released version">1.8.1.9004</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9005</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -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="Released version">1.8.1.9004</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9005</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -17,7 +17,7 @@
|
||||
</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="Released version">1.8.1.9004</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9005</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -157,13 +157,14 @@
|
||||
</div>
|
||||
|
||||
<div class="section level2">
|
||||
<h2 class="page-header" data-toc-text="1.8.1.9004" id="amr-1819004">
|
||||
<code>AMR</code> 1.8.1.9004<a class="anchor" aria-label="anchor" href="#amr-1819004"></a></h2>
|
||||
<h2 class="page-header" data-toc-text="1.8.1.9005" id="amr-1819005">
|
||||
<code>AMR</code> 1.8.1.9005<a class="anchor" aria-label="anchor" href="#amr-1819005"></a></h2>
|
||||
<div class="section level3">
|
||||
<h3 id="last-updated-may-1-8-1-9004"><small>Last updated: 9 May 2022</small><a class="anchor" aria-label="anchor" href="#last-updated-may-1-8-1-9004"></a></h3>
|
||||
<h3 id="last-updated-may-1-8-1-9005"><small>Last updated: 10 May 2022</small><a class="anchor" aria-label="anchor" href="#last-updated-may-1-8-1-9005"></a></h3>
|
||||
<div class="section level4">
|
||||
<h4 id="changed-1-8-1-9004">Changed<a class="anchor" aria-label="anchor" href="#changed-1-8-1-9004"></a></h4>
|
||||
<ul><li>Removed <code><a href="https://rdrr.io/r/base/integer.html" class="external-link">as.integer()</a></code> for MIC values, since MIC are not integer values and running <code><a href="https://rdrr.io/r/base/table.html" class="external-link">table()</a></code> on MIC values consequently failed for not being able to retrieve the level position (as that’s how normally <code><a href="https://rdrr.io/r/base/integer.html" class="external-link">as.integer()</a></code> on <code>factor</code>s work)</li>
|
||||
<h4 id="changed-1-8-1-9005">Changed<a class="anchor" aria-label="anchor" href="#changed-1-8-1-9005"></a></h4>
|
||||
<ul><li>Fix for <code><a href="../reference/as.rsi.html">as.rsi()</a></code> on certain EUCAST breakpoints for MIC values</li>
|
||||
<li>Removed <code><a href="https://rdrr.io/r/base/integer.html" class="external-link">as.integer()</a></code> for MIC values, since MIC are not integer values and running <code><a href="https://rdrr.io/r/base/table.html" class="external-link">table()</a></code> on MIC values consequently failed for not being able to retrieve the level position (as that’s how normally <code><a href="https://rdrr.io/r/base/integer.html" class="external-link">as.integer()</a></code> on <code>factor</code>s work)</li>
|
||||
<li>
|
||||
<code><a href="https://rdrr.io/r/base/droplevels.html" class="external-link">droplevels()</a></code> on MIC will now return a common <code>factor</code> at default and will lose the <code><mic></code> class. Use <code>droplevels(..., as.mic = TRUE)</code> to keep the <code><mic></code> class.</li>
|
||||
<li>Small fix for using <code><a href="../reference/ab_from_text.html">ab_from_text()</a></code>
|
||||
|
@ -17,7 +17,7 @@
|
||||
</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="Released version">1.8.1.9004</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9005</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -23,6 +23,10 @@
|
||||
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
|
||||
# ==================================================================== #
|
||||
|
||||
# we must only have EUCAST and CLSI, because otherwise the rules in as.rsi() will fail
|
||||
expect_identical(unique(gsub("[^A-Z]", "", AMR::rsi_translation$guideline)),
|
||||
c("EUCAST", "CLSI"))
|
||||
|
||||
expect_true(as.rsi("S") < as.rsi("I"))
|
||||
expect_true(as.rsi("I") < as.rsi("R"))
|
||||
expect_true(is.rsi(as.rsi("S")))
|
||||
|
Loading…
Reference in New Issue
Block a user