mirror of https://github.com/msberends/AMR.git
(v1.8.1.9005) as.rsi() fix for EUCAST
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Package: AMR
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Version: 1.8.1.9004
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Date: 2022-05-09
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Version: 1.8.1.9005
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Date: 2022-05-10
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Title: Antimicrobial Resistance Data Analysis
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Description: Functions to simplify and standardise antimicrobial resistance (AMR)
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data analysis and to work with microbial and antimicrobial properties by
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5
NEWS.md
5
NEWS.md
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@ -1,7 +1,8 @@
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# `AMR` 1.8.1.9004
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## <small>Last updated: 9 May 2022</small>
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# `AMR` 1.8.1.9005
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## <small>Last updated: 10 May 2022</small>
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### Changed
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* Fix for `as.rsi()` on certain EUCAST breakpoints for MIC values
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* 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)
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* `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.
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* Small fix for using `ab_from_text()`
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12
R/rsi.R
12
R/rsi.R
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@ -818,18 +818,20 @@ exec_as.rsi <- function(method,
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if (is.na(x[i]) | (is.na(get_record$breakpoint_S) & is.na(get_record$breakpoint_R))) {
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new_rsi[i] <- NA_character_
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} else if (method == "mic") {
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new_rsi[i] <- quick_case_when(isTRUE(conserve_capped_values) & x[i] %like% "^<[0-9]" ~ "S",
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isTRUE(conserve_capped_values) & x[i] %like% "^>[0-9]" ~ "R",
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new_rsi[i] <- quick_case_when(isTRUE(conserve_capped_values) & isTRUE(x[i] %like% "^<[0-9]") ~ "S",
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isTRUE(conserve_capped_values) & isTRUE(x[i] %like% "^>[0-9]") ~ "R",
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# these basically call `<=.mic()` and `>=.mic()`:
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x[i] <= get_record$breakpoint_S ~ "S",
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x[i] >= get_record$breakpoint_R ~ "R",
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isTRUE(x[i] <= get_record$breakpoint_S) ~ "S",
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guideline_coerced %like% "EUCAST" & isTRUE(x[i] > get_record$breakpoint_R) ~ "R",
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guideline_coerced %like% "CLSI" & isTRUE(x[i] >= get_record$breakpoint_R) ~ "R",
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# return "I" when not match the bottom or top
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!is.na(get_record$breakpoint_S) & !is.na(get_record$breakpoint_R) ~ "I",
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# and NA otherwise
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TRUE ~ NA_character_)
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} else if (method == "disk") {
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new_rsi[i] <- quick_case_when(isTRUE(as.double(x[i]) >= as.double(get_record$breakpoint_S)) ~ "S",
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isTRUE(as.double(x[i]) <= as.double(get_record$breakpoint_R)) ~ "R",
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guideline_coerced %like% "EUCAST" & isTRUE(as.double(x[i]) < as.double(get_record$breakpoint_R)) ~ "R",
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guideline_coerced %like% "CLSI" & isTRUE(as.double(x[i]) <= as.double(get_record$breakpoint_R)) ~ "R",
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# return "I" when not match the bottom or top
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!is.na(get_record$breakpoint_S) & !is.na(get_record$breakpoint_R) ~ "I",
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# and NA otherwise
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@ -128,11 +128,24 @@ rsi_translation[which(rsi_translation$breakpoint_R == 257), "breakpoint_R"] <- m
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rsi_translation[which(rsi_translation$breakpoint_R == 513), "breakpoint_R"] <- m[which(m == 512) + 1]
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rsi_translation[which(rsi_translation$breakpoint_R == 1025), "breakpoint_R"] <- m[which(m == 1024) + 1]
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# WHONET adds one log2 level to the R breakpoint for their software, e.g. in AMC in Enterobacterales:
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# EUCAST 2021 guideline: S <= 8 and R > 8
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# WHONET file: S <= 8 and R >= 16
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# this will make an MIC of 12 I, which should be R, so:
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eucast_mics <- which(rsi_translation$guideline %like% "EUCAST" &
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rsi_translation$method == "MIC" &
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log2(as.double(rsi_translation$breakpoint_R)) - log2(as.double(rsi_translation$breakpoint_S)) != 0)
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rsi_translation[eucast_mics, "breakpoint_R"] <- 2 ^ (log2(as.double(rsi_translation[eucast_mics, "breakpoint_R", drop = TRUE])) - 1)
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eucast_disks <- which(rsi_translation$guideline %like% "EUCAST" &
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rsi_translation$method == "DISK" &
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rsi_translation$breakpoint_S - rsi_translation$breakpoint_R != 0)
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rsi_translation[eucast_disks, "breakpoint_R"] <- rsi_translation[eucast_disks, "breakpoint_R", drop = TRUE] + 1
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# Greek symbols and EM dash symbols are not allowed by CRAN, so replace them with ASCII:
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rsi_translation$disk_dose <- gsub("μ", "u", rsi_translation$disk_dose, fixed = TRUE)
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rsi_translation$disk_dose <- gsub("–", "-", rsi_translation$disk_dose, fixed = TRUE)
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# save to package
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usethis::use_data(rsi_translation, overwrite = TRUE)
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usethis::use_data(rsi_translation, overwrite = TRUE, compress = "xz")
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rm(rsi_translation)
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devtools::load_all(".")
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@ -1 +1 @@
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d8083b68d4e492ea8e87c1eae4da4196
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657a743283954b40bb68fd3b965462a2
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@ -43,7 +43,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9004</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9005</span>
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</span>
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</div>
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@ -17,7 +17,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9004</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9005</span>
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</span>
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</div>
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@ -44,7 +44,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9004</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9005</span>
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</span>
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</div>
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@ -190,7 +190,7 @@
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<div class="page-header toc-ignore">
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<h1 data-toc-skip>Data sets for download / own use</h1>
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<h4 data-toc-skip class="date">09 May 2022</h4>
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<h4 data-toc-skip class="date">10 May 2022</h4>
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<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>
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<div class="hidden name"><code>datasets.Rmd</code></div>
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@ -1168,8 +1168,8 @@ column names:<br><em>guideline</em>, <em>method</em>, <em>site</em>, <em>mo</em>
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<em>breakpoint_S</em>, <em>breakpoint_R</em> and <em>uti</em>.</p>
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<p>This data set is in R available as <code>rsi_translation</code>,
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after you load the <code>AMR</code> package.</p>
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<p>It was last updated on 14 December 2021 21:59:33 UTC. Find more info
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about the structure of this data set <a href="https://msberends.github.io/AMR/reference/rsi_translation.html">here</a>.</p>
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<p>It was last updated on 10 May 2022 13:51:53 UTC. Find more info about
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the structure of this data set <a href="https://msberends.github.io/AMR/reference/rsi_translation.html">here</a>.</p>
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<p><strong>Direct download links:</strong></p>
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<ul>
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<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.rds" class="external-link">R
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@ -17,7 +17,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9004</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9005</span>
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</span>
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</div>
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@ -47,7 +47,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9004</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9005</span>
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</span>
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</div>
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@ -17,7 +17,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9004</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9005</span>
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</span>
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</div>
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@ -157,13 +157,14 @@
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</div>
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<div class="section level2">
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<h2 class="page-header" data-toc-text="1.8.1.9004" id="amr-1819004">
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<code>AMR</code> 1.8.1.9004<a class="anchor" aria-label="anchor" href="#amr-1819004"></a></h2>
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<h2 class="page-header" data-toc-text="1.8.1.9005" id="amr-1819005">
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<code>AMR</code> 1.8.1.9005<a class="anchor" aria-label="anchor" href="#amr-1819005"></a></h2>
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<div class="section level3">
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<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>
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<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>
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<div class="section level4">
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<h4 id="changed-1-8-1-9004">Changed<a class="anchor" aria-label="anchor" href="#changed-1-8-1-9004"></a></h4>
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<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>
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<h4 id="changed-1-8-1-9005">Changed<a class="anchor" aria-label="anchor" href="#changed-1-8-1-9005"></a></h4>
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<ul><li>Fix for <code><a href="../reference/as.rsi.html">as.rsi()</a></code> on certain EUCAST breakpoints for MIC values</li>
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<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>
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<li>
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<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>
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<li>Small fix for using <code><a href="../reference/ab_from_text.html">ab_from_text()</a></code>
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@ -17,7 +17,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9004</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9005</span>
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</span>
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</div>
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@ -23,6 +23,10 @@
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# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
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# ==================================================================== #
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# we must only have EUCAST and CLSI, because otherwise the rules in as.rsi() will fail
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expect_identical(unique(gsub("[^A-Z]", "", AMR::rsi_translation$guideline)),
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c("EUCAST", "CLSI"))
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expect_true(as.rsi("S") < as.rsi("I"))
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expect_true(as.rsi("I") < as.rsi("R"))
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expect_true(is.rsi(as.rsi("S")))
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