P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2026-09-22 22:21:03 +02:00
Code Releases Activity

(v1.8.1.9005) as.rsi() fix for EUCAST

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2022-05-10 17:01:37 +02:00
parent d4e22069bc
commit 680e8e7a41
21 changed files with 7475 additions and 7454 deletions
Download Patch File Download Diff File Expand all files Collapse all files
DESCRIPTION
+2 -2
View File
@@ -1,6 +1,6 @@
Package: AMR Package: AMR
Version: 1.8.1.9004 Version: 1.8.1.9005
Date: 2022-05-09 Date: 2022-05-10
Title: Antimicrobial Resistance Data Analysis Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR) Description: Functions to simplify and standardise antimicrobial resistance (AMR)
data analysis and to work with microbial and antimicrobial properties by data analysis and to work with microbial and antimicrobial properties by
NEWS.md
+3 -2
View File
@@ -1,7 +1,8 @@
# `AMR` 1.8.1.9004 # `AMR` 1.8.1.9005
## <small>Last updated: 9 May 2022</small> ## <small>Last updated: 10 May 2022</small>
### Changed ### 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) * 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. * `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()` * Small fix for using `ab_from_text()`
R/rsi.R
+7 -5
View File
@@ -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))) { if (is.na(x[i]) | (is.na(get_record$breakpoint_S) & is.na(get_record$breakpoint_R))) {
new_rsi[i] <- NA_character_ new_rsi[i] <- NA_character_
} else if (method == "mic") { } else if (method == "mic") {
new_rsi[i] <- quick_case_when(isTRUE(conserve_capped_values) & x[i] %like% "^<[0-9]" ~ "S", new_rsi[i] <- quick_case_when(isTRUE(conserve_capped_values) & isTRUE(x[i] %like% "^<[0-9]") ~ "S",
isTRUE(conserve_capped_values) & x[i] %like% "^>[0-9]" ~ "R", isTRUE(conserve_capped_values) & isTRUE(x[i] %like% "^>[0-9]") ~ "R",
# these basically call `<=.mic()` and `>=.mic()`: # these basically call `<=.mic()` and `>=.mic()`:
x[i] <= get_record$breakpoint_S ~ "S", isTRUE(x[i] <= get_record$breakpoint_S) ~ "S",
x[i] >= get_record$breakpoint_R ~ "R", guideline_coerced %like% "EUCAST" & isTRUE(x[i] > get_record$breakpoint_R) ~ "R",
guideline_coerced %like% "CLSI" & isTRUE(x[i] >= get_record$breakpoint_R) ~ "R",
# return "I" when not match the bottom or top # return "I" when not match the bottom or top
!is.na(get_record$breakpoint_S) & !is.na(get_record$breakpoint_R) ~ "I", !is.na(get_record$breakpoint_S) & !is.na(get_record$breakpoint_R) ~ "I",
# and NA otherwise # and NA otherwise
TRUE ~ NA_character_) TRUE ~ NA_character_)
} else if (method == "disk") { } else if (method == "disk") {
new_rsi[i] <- quick_case_when(isTRUE(as.double(x[i]) >= as.double(get_record$breakpoint_S)) ~ "S", 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 # 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
data-raw/AMR_latest.tar.gz
BIN
View File
Binary file not shown.
data-raw/reproduction_of_rsi_translation.R
+14 -1
View File
@@ -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$breakpoint_R == 513), "breakpoint_R"] <- m[which(m == 512) + 1]
rsi_translation[which(rsi_translation$breakpoint_R == 1025), "breakpoint_R"] <- m[which(m == 1024) + 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$breakpoint_R != 0)
rsi_translation[eucast_disks, "breakpoint_R"] <- rsi_translation[eucast_disks, "breakpoint_R", drop = TRUE] + 1
# Greek symbols and EM dash symbols are not allowed by CRAN, so replace them with ASCII: # Greek symbols and EM dash symbols are not allowed by CRAN, so replace them with ASCII:
rsi_translation$disk_dose <- gsub("μ", "u", rsi_translation$disk_dose, fixed = TRUE) rsi_translation$disk_dose <- gsub("μ", "u", rsi_translation$disk_dose, fixed = TRUE)
rsi_translation$disk_dose <- gsub("–", "-", rsi_translation$disk_dose, fixed = TRUE) rsi_translation$disk_dose <- gsub("–", "-", rsi_translation$disk_dose, fixed = TRUE)
# save to package # save to package
usethis::use_data(rsi_translation, overwrite = TRUE) usethis::use_data(rsi_translation, overwrite = TRUE, compress = "xz")
rm(rsi_translation) rm(rsi_translation)
devtools::load_all(".") devtools::load_all(".")
data-raw/rsi.md5
+1 -1
View File
@@ -1 +1 @@
d8083b68d4e492ea8e87c1eae4da4196 657a743283954b40bb68fd3b965462a2
data-raw/rsi_translation.dta
BIN
View File
Binary file not shown.
data-raw/rsi_translation.rds
BIN
View File
Binary file not shown.
data-raw/rsi_translation.sas
BIN
View File
Binary file not shown.
data-raw/rsi_translation.sav
BIN
View File
Binary file not shown.
data-raw/rsi_translation.txt
+7428 -7428
View File
File diff suppressed because it is too large Load Diff
data-raw/rsi_translation.xlsx
BIN
View File
Binary file not shown.
data/rsi_translation.rda
BIN
View File
Binary file not shown.
docs/404.html
+1 -1
View File
@@ -43,7 +43,7 @@
</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="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> </span>
</div> </div>
docs/LICENSE-text.html
+1 -1
View File
@@ -17,7 +17,7 @@
</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">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> </span>
</div> </div>
docs/articles/datasets.html
+4 -4
View File
@@ -44,7 +44,7 @@
</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">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> </span>
</div> </div>
@@ -190,7 +190,7 @@
<div class="page-header toc-ignore"> <div class="page-header toc-ignore">
<h1 data-toc-skip>Data sets for download / own use</h1> <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> <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> <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> <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>, <p>This data set is in R available as <code>rsi_translation</code>,
after you load the <code>AMR</code> package.</p> 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 <p>It was last updated on 10 May 2022 13:51:53 UTC. Find more info about
about the structure of this data set <a href="https://msberends.github.io/AMR/reference/rsi_translation.html">here</a>.</p> 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> <p><strong>Direct download links:</strong></p>
<ul> <ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.rds" class="external-link">R <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.rds" class="external-link">R
docs/authors.html
+1 -1
View File
@@ -17,7 +17,7 @@
</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">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> </span>
</div> </div>
docs/index.html
+1 -1
View File
@@ -47,7 +47,7 @@
</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">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> </span>
</div> </div>
docs/news/index.html
+7 -6
View File
@@ -17,7 +17,7 @@
</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">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> </span>
</div> </div>
@@ -157,13 +157,14 @@
</div> </div>
<div class="section level2"> <div class="section level2">
<h2 class="page-header" data-toc-text="1.8.1.9004" id="amr-1819004"> <h2 class="page-header" data-toc-text="1.8.1.9005" id="amr-1819005">
<code>AMR</code> 1.8.1.9004<a class="anchor" aria-label="anchor" href="#amr-1819004"></a></h2> <code>AMR</code> 1.8.1.9005<a class="anchor" aria-label="anchor" href="#amr-1819005"></a></h2>
<div class="section level3"> <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"> <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> <h4 id="changed-1-8-1-9005">Changed<a class="anchor" aria-label="anchor" href="#changed-1-8-1-9005"></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> <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> <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>&lt;mic&gt;</code> class. Use <code>droplevels(..., as.mic = TRUE)</code> to keep the <code>&lt;mic&gt;</code> class.</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>&lt;mic&gt;</code> class. Use <code>droplevels(..., as.mic = TRUE)</code> to keep the <code>&lt;mic&gt;</code> class.</li>
<li>Small fix for using <code><a href="../reference/ab_from_text.html">ab_from_text()</a></code> <li>Small fix for using <code><a href="../reference/ab_from_text.html">ab_from_text()</a></code>
docs/survey.html
+1 -1
View File
@@ -17,7 +17,7 @@
</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">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> </span>
</div> </div>
inst/tinytest/test-rsi.R
+4
View File
@@ -23,6 +23,10 @@
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ # # 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("S") < as.rsi("I"))
expect_true(as.rsi("I") < as.rsi("R")) expect_true(as.rsi("I") < as.rsi("R"))
expect_true(is.rsi(as.rsi("S"))) expect_true(is.rsi(as.rsi("S")))