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(v1.7.1.9019) Morganella MIC in EUCAST 2021

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dr. M.S. (Matthijs) Berends 2021-07-12 12:28:41 +02:00
parent 5ccb330b42
commit fc946564d1
30 changed files with 112 additions and 74 deletions
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4
DESCRIPTION
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@ -1,6 +1,6 @@
Package: AMR Package: AMR
Version: 1.7.1.9018 Version: 1.7.1.9019
Date: 2021-07-11 Date: 2021-07-12
Title: Antimicrobial Resistance Data Analysis Title: Antimicrobial Resistance Data Analysis
Authors@R: c( Authors@R: c(
person(role = c("aut", "cre"), person(role = c("aut", "cre"),

5
NEWS.md
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# `AMR` 1.7.1.9018 # `AMR` 1.7.1.9019
## <small>Last updated: 11 July 2021</small> ## <small>Last updated: 12 July 2021</small>
### Changed ### Changed
* Antibiotic class selectors (see `ab_class()`) * Antibiotic class selectors (see `ab_class()`)
@ -20,6 +20,7 @@
* `ab_name()` gained argument `snake_case`, which is useful for column renaming * `ab_name()` gained argument `snake_case`, which is useful for column renaming
* Fix for legends created with `scale_rsi_colours()` when using `ggplot2` v3.3.4 or higher (this is bug ggplot2#4511, soon to be fixed) * Fix for legends created with `scale_rsi_colours()` when using `ggplot2` v3.3.4 or higher (this is bug ggplot2#4511, soon to be fixed)
* Fix for minor translation errors * Fix for minor translation errors
* Fix for the MIC interpretation of *Morganellaceae* (such as *Morganella* and *Proteus*) when using the EUCAST 2021 guideline
# `AMR` 1.7.1 # `AMR` 1.7.1

3
R/aa_helper_functions.R
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@ -400,6 +400,9 @@ word_wrap <- function(...,
# format backticks # format backticks
msg <- gsub("(`.+?`)", font_grey_bg("\\1"), msg) msg <- gsub("(`.+?`)", font_grey_bg("\\1"), msg)
# clean introduced whitespace between fullstops
msg <- gsub("[.] +[.]", "..", msg)
msg msg
} }

3
R/plot.R
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@ -684,6 +684,7 @@ plot_prepare_table <- function(x, expand) {
if (is.mic(x)) { if (is.mic(x)) {
if (expand == TRUE) { if (expand == TRUE) {
# expand range for MIC by adding factors of 2 from lowest to highest so all MICs in between also print # expand range for MIC by adding factors of 2 from lowest to highest so all MICs in between also print
valid_lvls <- levels(x)
extra_range <- max(x) / 2 extra_range <- max(x) / 2
while (min(extra_range) / 2 > min(x)) { while (min(extra_range) / 2 > min(x)) {
extra_range <- c(min(extra_range) / 2, extra_range) extra_range <- c(min(extra_range) / 2, extra_range)
@ -692,7 +693,7 @@ plot_prepare_table <- function(x, expand) {
extra_range <- rep(0, length(extra_range)) extra_range <- rep(0, length(extra_range))
names(extra_range) <- nms names(extra_range) <- nms
x <- table(droplevels(x, as.mic = FALSE)) x <- table(droplevels(x, as.mic = FALSE))
extra_range <- extra_range[!names(extra_range) %in% names(x)] extra_range <- extra_range[!names(extra_range) %in% names(x) & names(extra_range) %in% valid_lvls]
x <- as.table(c(x, extra_range)) x <- as.table(c(x, extra_range))
} else { } else {
x <- table(droplevels(x, as.mic = FALSE)) x <- table(droplevels(x, as.mic = FALSE))

26
R/rsi.R
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@ -411,13 +411,18 @@ as.rsi.mic <- function(x,
uti <- rep(uti, length(x)) uti <- rep(uti, length(x))
} }
message_("=> Interpreting MIC values of ", ifelse(isTRUE(list(...)$is_data.frame), "column ", ""), "'", font_bold(ab), "' (", agent_formatted <- paste0("'", font_bold(ab), "'")
ifelse(ab_coerced != ab, paste0(ab_coerced, ", "), ""), agent_name <- ab_name(ab_coerced, tolower = TRUE, language = NULL)
ab_name(ab_coerced, tolower = TRUE), ")", mo_var_found, if (generalise_antibiotic_name(ab) != generalise_antibiotic_name(agent_name)) {
agent_formatted <- paste0(agent_formatted, " (", ab_coerced, ", ", agent_name, ")")
}
message_("=> Interpreting MIC values of ", ifelse(isTRUE(list(...)$is_data.frame), "column ", ""),
agent_formatted,
mo_var_found,
" according to ", ifelse(identical(reference_data, AMR::rsi_translation), " according to ", ifelse(identical(reference_data, AMR::rsi_translation),
font_bold(guideline_coerced), font_bold(guideline_coerced),
"manually defined 'reference_data'"), "manually defined 'reference_data'"),
" ... ", "... ",
appendLF = FALSE, appendLF = FALSE,
as_note = FALSE) as_note = FALSE)
@ -500,13 +505,18 @@ as.rsi.disk <- function(x,
uti <- rep(uti, length(x)) uti <- rep(uti, length(x))
} }
message_("=> Interpreting disk zones of ", ifelse(isTRUE(list(...)$is_data.frame), "column ", ""), "'", font_bold(ab), "' (", agent_formatted <- paste0("'", font_bold(ab), "'")
ifelse(ab_coerced != ab, paste0(ab_coerced, ", "), ""), agent_name <- ab_name(ab_coerced, tolower = TRUE, language = NULL)
ab_name(ab_coerced, tolower = TRUE), ")", mo_var_found, if (generalise_antibiotic_name(ab) != generalise_antibiotic_name(agent_name)) {
agent_formatted <- paste0(agent_formatted, " (", ab_coerced, ", ", agent_name, ")")
}
message_("=> Interpreting disk zones of ", ifelse(isTRUE(list(...)$is_data.frame), "column ", ""),
agent_formatted,
mo_var_found,
" according to ", ifelse(identical(reference_data, AMR::rsi_translation), " according to ", ifelse(identical(reference_data, AMR::rsi_translation),
font_bold(guideline_coerced), font_bold(guideline_coerced),
"manually defined 'reference_data'"), "manually defined 'reference_data'"),
" ... ", "... ",
appendLF = FALSE, appendLF = FALSE,
as_note = FALSE) as_note = FALSE)

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data-raw/read_EUCAST.R
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@ -118,7 +118,7 @@ read_EUCAST <- function(sheet, file, guideline_name) {
seq(from = 41, to = 49, by = 1), seq(from = 41, to = 49, by = 1),
seq(from = 81, to = 89, by = 1)) seq(from = 81, to = 89, by = 1))
has_superscript <- function(x) { has_superscript <- function(x) {
# because due to floating point error 0.1252 is not in: # because due to floating point error, 0.1252 is not in:
# seq(from = 0.1251, to = 0.1259, by = 0.0001) # seq(from = 0.1251, to = 0.1259, by = 0.0001)
sapply(x, function(x) any(near(x, MICs_with_trailing_superscript))) sapply(x, function(x) any(near(x, MICs_with_trailing_superscript)))
} }
@ -242,3 +242,21 @@ for (i in 2:length(sheets_to_analyse)) {
guideline_name = guideline_name)) guideline_name = guideline_name))
, error = function(e) message(e$message)) , error = function(e) message(e$message))
} }
# 2021-07-12 fix for Morganellaceae (check other lines too next time)
morg <- rsi_translation %>%
as_tibble() %>%
filter(ab == "IPM",
guideline == "EUCAST 2021",
mo == as.mo("Enterobacterales")) %>%
mutate(mo = as.mo("Morganellaceae"))
morg[which(morg$method == "MIC"), "breakpoint_S"] <- 0.001
morg[which(morg$method == "MIC"), "breakpoint_R"] <- 4
morg[which(morg$method == "DISK"), "breakpoint_S"] <- 50
morg[which(morg$method == "DISK"), "breakpoint_R"] <- 19
rsi_translation <- rsi_translation %>%
bind_rows(morg) %>%
bind_rows(morg %>%
mutate(guideline = "EUCAST 2020")) %>%
arrange(desc(guideline), ab, mo, method)

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data-raw/rsi.md5
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1a7fe52f8185c9bb2c470712863d1887 67a83b234f25a303c7944222bea47d73

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data-raw/rsi_translation.txt
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@ -754,6 +754,8 @@
"EUCAST 2021" "MIC" "Staphylococcus saccharolyticus" "Imipenem/relebactam" "Anaerobes, Grampositive" 2 2 FALSE "EUCAST 2021" "MIC" "Staphylococcus saccharolyticus" "Imipenem/relebactam" "Anaerobes, Grampositive" 2 2 FALSE
"EUCAST 2021" "MIC" "Viridans Group Streptococcus (VGS)" "Imipenem/relebactam" "Viridans group streptococci" 2 2 FALSE "EUCAST 2021" "MIC" "Viridans Group Streptococcus (VGS)" "Imipenem/relebactam" "Viridans group streptococci" 2 2 FALSE
"EUCAST 2021" "MIC" "(unknown name)" "Imipenem/relebactam" "PK PD breakpoints" 2 2 FALSE "EUCAST 2021" "MIC" "(unknown name)" "Imipenem/relebactam" "PK PD breakpoints" 2 2 FALSE
"EUCAST 2021" "DISK" "Morganellaceae" "Imipenem" "Enterobacterales" "10ug" 50 19 FALSE
"EUCAST 2021" "MIC" "Morganellaceae" "Imipenem" "Enterobacterales" 0.001 4 FALSE
"EUCAST 2021" "DISK" "Enterobacterales" "Imipenem" "Enterobacterales" "10ug" 22 19 FALSE "EUCAST 2021" "DISK" "Enterobacterales" "Imipenem" "Enterobacterales" "10ug" 22 19 FALSE
"EUCAST 2021" "MIC" "Enterobacterales" "Imipenem" "Enterobacterales" 2 4 FALSE "EUCAST 2021" "MIC" "Enterobacterales" "Imipenem" "Enterobacterales" 2 4 FALSE
"EUCAST 2021" "DISK" "Acinetobacter" "Imipenem" "Acinetobacter" "10ug" 24 21 FALSE "EUCAST 2021" "DISK" "Acinetobacter" "Imipenem" "Acinetobacter" "10ug" 24 21 FALSE
@ -2542,6 +2544,8 @@
"EUCAST 2020" "MIC" "Staphylococcus saccharolyticus" "Imipenem/relebactam" "Anaerobes, Grampositive" 2 2 FALSE "EUCAST 2020" "MIC" "Staphylococcus saccharolyticus" "Imipenem/relebactam" "Anaerobes, Grampositive" 2 2 FALSE
"EUCAST 2020" "MIC" "Viridans Group Streptococcus (VGS)" "Imipenem/relebactam" "Viridans group streptococci" 2 2 FALSE "EUCAST 2020" "MIC" "Viridans Group Streptococcus (VGS)" "Imipenem/relebactam" "Viridans group streptococci" 2 2 FALSE
"EUCAST 2020" "MIC" "(unknown name)" "Imipenem/relebactam" "PK PD breakpoints" 2 2 FALSE "EUCAST 2020" "MIC" "(unknown name)" "Imipenem/relebactam" "PK PD breakpoints" 2 2 FALSE
"EUCAST 2020" "DISK" "Morganellaceae" "Imipenem" "Enterobacterales" "10ug" 50 19 FALSE
"EUCAST 2020" "MIC" "Morganellaceae" "Imipenem" "Enterobacterales" 0.001 4 FALSE
"EUCAST 2020" "DISK" "Enterobacterales" "Imipenem" "Enterobacterales" "10ug" 22 17 FALSE "EUCAST 2020" "DISK" "Enterobacterales" "Imipenem" "Enterobacterales" "10ug" 22 17 FALSE
"EUCAST 2020" "MIC" "Enterobacterales" "Imipenem" "Enterobacterales" 2 4 FALSE "EUCAST 2020" "MIC" "Enterobacterales" "Imipenem" "Enterobacterales" 2 4 FALSE
"EUCAST 2020" "DISK" "Acinetobacter" "Imipenem" "Acinetobacter" "10ug" 24 21 FALSE "EUCAST 2020" "DISK" "Acinetobacter" "Imipenem" "Acinetobacter" "10ug" 24 21 FALSE

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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">1.7.1.9018</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9019</span>
</span> </span>
</div> </div>

2
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">1.7.1.9018</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9019</span>
</span> </span>
</div> </div>

8
docs/articles/datasets.html
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@ -39,7 +39,7 @@
</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">1.7.1.9018</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9019</span>
</span> </span>
</div> </div>
@ -192,7 +192,7 @@
<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 class="date">11 July 2021</h4> <h4 class="date">12 July 2021</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/datasets.Rmd"><code>vignettes/datasets.Rmd</code></a></small> <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/datasets.Rmd"><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>
@ -1005,9 +1005,9 @@ If you are reading this page from within R, please <a href="https://msberends.gi
<div id="interpretation-from-mic-values-disk-diameters-to-rsi" class="section level2"> <div id="interpretation-from-mic-values-disk-diameters-to-rsi" class="section level2">
<h2 class="hasAnchor"> <h2 class="hasAnchor">
<a href="#interpretation-from-mic-values-disk-diameters-to-rsi" class="anchor"></a>Interpretation from MIC values / disk diameters to R/SI</h2> <a href="#interpretation-from-mic-values-disk-diameters-to-rsi" class="anchor"></a>Interpretation from MIC values / disk diameters to R/SI</h2>
<p>A data set with 21,996 rows and 10 columns, containing the following column names:<br><em>guideline</em>, <em>method</em>, <em>site</em>, <em>mo</em>, <em>ab</em>, <em>ref_tbl</em>, <em>disk_dose</em>, <em>breakpoint_S</em>, <em>breakpoint_R</em> and <em>uti</em>.</p> <p>A data set with 22,000 rows and 10 columns, containing the following column names:<br><em>guideline</em>, <em>method</em>, <em>site</em>, <em>mo</em>, <em>ab</em>, <em>ref_tbl</em>, <em>disk_dose</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>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 1 June 2021 14:47:11 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 12 July 2021 10:10:26 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> <p><strong>Direct download links:</strong></p>
<ul> <ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.rds">R file</a> (37 kB)<br> <li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.rds">R file</a> (37 kB)<br>

2
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">1.7.1.9018</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9019</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">1.7.1.9018</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9019</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="Latest development version">1.7.1.9018</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9019</span>
</span> </span>
</div> </div>

15
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">1.7.1.9018</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9019</span>
</span> </span>
</div> </div>
@ -236,12 +236,12 @@
<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-1719018" class="section level1"> <div id="amr-1719019" class="section level1">
<h1 class="page-header" data-toc-text="1.7.1.9018"> <h1 class="page-header" data-toc-text="1.7.1.9019">
<a href="#amr-1719018" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9018</h1> <a href="#amr-1719019" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9019</h1>
<div id="last-updated-11-july-2021" class="section level2"> <div id="last-updated-12-july-2021" class="section level2">
<h2 class="hasAnchor"> <h2 class="hasAnchor">
<a href="#last-updated-11-july-2021" class="anchor"></a><small>Last updated: 11 July 2021</small> <a href="#last-updated-12-july-2021" class="anchor"></a><small>Last updated: 12 July 2021</small>
</h2> </h2>
<div id="changed" class="section level3"> <div id="changed" class="section level3">
<h3 class="hasAnchor"> <h3 class="hasAnchor">
@ -275,6 +275,7 @@
<code><a href="../reference/ab_property.html">ab_name()</a></code> gained argument <code>snake_case</code>, which is useful for column renaming</li> <code><a href="../reference/ab_property.html">ab_name()</a></code> gained argument <code>snake_case</code>, which is useful for column renaming</li>
<li>Fix for legends created with <code><a href="../reference/ggplot_rsi.html">scale_rsi_colours()</a></code> when using <code>ggplot2</code> v3.3.4 or higher (this is bug ggplot2<a href='https://github.com/msberends/AMR/issues/4511'>#4511</a>, soon to be fixed)</li> <li>Fix for legends created with <code><a href="../reference/ggplot_rsi.html">scale_rsi_colours()</a></code> when using <code>ggplot2</code> v3.3.4 or higher (this is bug ggplot2<a href='https://github.com/msberends/AMR/issues/4511'>#4511</a>, soon to be fixed)</li>
<li>Fix for minor translation errors</li> <li>Fix for minor translation errors</li>
<li>Fix for the MIC interpretation of <em>Morganellaceae</em> (such as <em>Morganella</em> and <em>Proteus</em>) when using the EUCAST 2021 guideline</li>
</ul> </ul>
</div> </div>
</div> </div>
@ -503,7 +504,7 @@
<code><a href="../reference/as.rsi.html">is.rsi.eligible()</a></code> now detects if the column name resembles an antibiotic name or code and now returns <code>TRUE</code> immediately if the input contains any of the values “R”, “S” or “I”. This drastically improves speed, also for a lot of other functions that rely on automatic determination of antibiotic columns.</li> <code><a href="../reference/as.rsi.html">is.rsi.eligible()</a></code> now detects if the column name resembles an antibiotic name or code and now returns <code>TRUE</code> immediately if the input contains any of the values “R”, “S” or “I”. This drastically improves speed, also for a lot of other functions that rely on automatic determination of antibiotic columns.</li>
<li>Functions <code><a href="../reference/get_episode.html">get_episode()</a></code> and <code><a href="../reference/get_episode.html">is_new_episode()</a></code> now support less than a day as value for argument <code>episode_days</code> (e.g., to include one patient/test per hour)</li> <li>Functions <code><a href="../reference/get_episode.html">get_episode()</a></code> and <code><a href="../reference/get_episode.html">is_new_episode()</a></code> now support less than a day as value for argument <code>episode_days</code> (e.g., to include one patient/test per hour)</li>
<li>Argument <code>ampc_cephalosporin_resistance</code> in <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> now also applies to value “I” (not only “S”)</li> <li>Argument <code>ampc_cephalosporin_resistance</code> in <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> now also applies to value “I” (not only “S”)</li>
<li>Functions <code><a href="https://rdrr.io/r/base/print.html">print()</a></code> and <code><a href="https://rdrr.io/r/base/summary.html">summary()</a></code> on a Principal Components Analysis object (<code><a href="../reference/pca.html">pca()</a></code>) now print additional group info if the original data was grouped using <code><a href="https://dplyr.tidyverse.org/reference/group_by.html">dplyr::group_by()</a></code> <li>Functions <code><a href="https://docs.ropensci.org/skimr/reference/print.html">print()</a></code> and <code><a href="https://rdrr.io/r/base/summary.html">summary()</a></code> on a Principal Components Analysis object (<code><a href="../reference/pca.html">pca()</a></code>) now print additional group info if the original data was grouped using <code><a href="https://dplyr.tidyverse.org/reference/group_by.html">dplyr::group_by()</a></code>
</li> </li>
<li>Improved speed and reliability of <code><a href="../reference/guess_ab_col.html">guess_ab_col()</a></code>. As this also internally improves the reliability of <code><a href="../reference/first_isolate.html">first_isolate()</a></code> and <code><a href="../reference/mdro.html">mdro()</a></code>, this might have a slight impact on the results of those functions.</li> <li>Improved speed and reliability of <code><a href="../reference/guess_ab_col.html">guess_ab_col()</a></code>. As this also internally improves the reliability of <code><a href="../reference/first_isolate.html">first_isolate()</a></code> and <code><a href="../reference/mdro.html">mdro()</a></code>, this might have a slight impact on the results of those functions.</li>
<li>Fix for <code><a href="../reference/mo_property.html">mo_name()</a></code> when used in other languages than English</li> <li>Fix for <code><a href="../reference/mo_property.html">mo_name()</a></code> when used in other languages than English</li>

2
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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: 2021-07-11T11:19Z last_built: 2021-07-12T10:28Z
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

2
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@ -82,7 +82,7 @@
</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">1.7.1.9016</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9019</span>
</span> </span>
</div> </div>

36
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@ -82,7 +82,7 @@
</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">1.7.1</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9019</span>
</span> </span>
</div> </div>
@ -90,14 +90,14 @@
<ul class="nav navbar-nav"> <ul class="nav navbar-nav">
<li> <li>
<a href="../index.html"> <a href="../index.html">
<span class="fas fa-home"></span> <span class="fa fa-home"></span>
Home Home
</a> </a>
</li> </li>
<li class="dropdown"> <li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-question-circle"></span> <span class="fa fa-question-circle"></span>
How to How to
@ -106,77 +106,77 @@
<ul class="dropdown-menu" role="menu"> <ul class="dropdown-menu" role="menu">
<li> <li>
<a href="../articles/AMR.html"> <a href="../articles/AMR.html">
<span class="fas fa-directions"></span> <span class="fa fa-directions"></span>
Conduct AMR analysis Conduct AMR analysis
</a> </a>
</li> </li>
<li> <li>
<a href="../articles/resistance_predict.html"> <a href="../articles/resistance_predict.html">
<span class="fas fa-dice"></span> <span class="fa fa-dice"></span>
Predict antimicrobial resistance Predict antimicrobial resistance
</a> </a>
</li> </li>
<li> <li>
<a href="../articles/datasets.html"> <a href="../articles/datasets.html">
<span class="fas fa-database"></span> <span class="fa fa-database"></span>
Data sets for download / own use Data sets for download / own use
</a> </a>
</li> </li>
<li> <li>
<a href="../articles/PCA.html"> <a href="../articles/PCA.html">
<span class="fas fa-compress"></span> <span class="fa fa-compress"></span>
Conduct principal component analysis for AMR Conduct principal component analysis for AMR
</a> </a>
</li> </li>
<li> <li>
<a href="../articles/MDR.html"> <a href="../articles/MDR.html">
<span class="fas fa-skull-crossbones"></span> <span class="fa fa-skull-crossbones"></span>
Determine multi-drug resistance (MDR) Determine multi-drug resistance (MDR)
</a> </a>
</li> </li>
<li> <li>
<a href="../articles/WHONET.html"> <a href="../articles/WHONET.html">
<span class="fas fa-globe-americas"></span> <span class="fa fa-globe-americas"></span>
Work with WHONET data Work with WHONET data
</a> </a>
</li> </li>
<li> <li>
<a href="../articles/SPSS.html"> <a href="../articles/SPSS.html">
<span class="fas fa-file-upload"></span> <span class="fa fa-file-upload"></span>
Import data from SPSS/SAS/Stata Import data from SPSS/SAS/Stata
</a> </a>
</li> </li>
<li> <li>
<a href="../articles/EUCAST.html"> <a href="../articles/EUCAST.html">
<span class="fas fa-exchange-alt"></span> <span class="fa fa-exchange-alt"></span>
Apply EUCAST rules Apply EUCAST rules
</a> </a>
</li> </li>
<li> <li>
<a href="../reference/mo_property.html"> <a href="../reference/mo_property.html">
<span class="fas fa-bug"></span> <span class="fa fa-bug"></span>
Get properties of a microorganism Get properties of a microorganism
</a> </a>
</li> </li>
<li> <li>
<a href="../reference/ab_property.html"> <a href="../reference/ab_property.html">
<span class="fas fa-capsules"></span> <span class="fa fa-capsules"></span>
Get properties of an antibiotic Get properties of an antibiotic
</a> </a>
</li> </li>
<li> <li>
<a href="../articles/benchmarks.html"> <a href="../articles/benchmarks.html">
<span class="fas fa-shipping-fast"></span> <span class="fa fa-shipping-fast"></span>
Other: benchmarks Other: benchmarks
</a> </a>
@ -185,14 +185,14 @@
</li> </li>
<li> <li>
<a href="../reference/index.html"> <a href="../reference/index.html">
<span class="fas fa-book-open"></span> <span class="fa fa-book-open"></span>
Manual Manual
</a> </a>
</li> </li>
<li> <li>
<a href="../authors.html"> <a href="../authors.html">
<span class="fas fa-users"></span> <span class="fa fa-users"></span>
Authors Authors
</a> </a>
@ -215,7 +215,7 @@
</li> </li>
<li> <li>
<a href="../survey.html"> <a href="../survey.html">
<span class="fas fa-clipboard-list"></span> <span class="fa fa-clipboard-list"></span>
Survey Survey
</a> </a>
@ -374,7 +374,7 @@
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Machine-Readable Interpretation Guidelines</h3> <h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Machine-Readable Interpretation Guidelines</h3>
<p>The repository of this package <a href='https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt'>contains a machine-readable version</a> of all guidelines. This is a CSV file consisting of 21,996 rows and 10 columns. This file is machine-readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial agent and the microorganism. <strong>This allows for easy implementation of these rules in laboratory information systems (LIS)</strong>. Note that it only contains interpretation guidelines for humans - interpretation guidelines from CLSI for animals were removed.</p> <p>The repository of this package <a href='https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt'>contains a machine-readable version</a> of all guidelines. This is a CSV file consisting of 22,000 rows and 10 columns. This file is machine-readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial agent and the microorganism. <strong>This allows for easy implementation of these rules in laboratory information systems (LIS)</strong>. Note that it only contains interpretation guidelines for humans - interpretation guidelines from CLSI for animals were removed.</p>
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Other</h3> <h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Other</h3>

2
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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">1.7.1.9018</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9019</span>
</span> </span>
</div> </div>

2
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@ -82,7 +82,7 @@
</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">1.7.1.9015</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9019</span>
</span> </span>
</div> </div>

36
docs/reference/rsi_translation.html
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@ -82,7 +82,7 @@
</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">1.7.1</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9019</span>
</span> </span>
</div> </div>
@ -90,14 +90,14 @@
<ul class="nav navbar-nav"> <ul class="nav navbar-nav">
<li> <li>
<a href="../index.html"> <a href="../index.html">
<span class="fas fa-home"></span> <span class="fa fa-home"></span>
Home Home
</a> </a>
</li> </li>
<li class="dropdown"> <li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fas fa-question-circle"></span> <span class="fa fa-question-circle"></span>
How to How to
@ -106,77 +106,77 @@
<ul class="dropdown-menu" role="menu"> <ul class="dropdown-menu" role="menu">
<li> <li>
<a href="../articles/AMR.html"> <a href="../articles/AMR.html">
<span class="fas fa-directions"></span> <span class="fa fa-directions"></span>
Conduct AMR analysis Conduct AMR analysis
</a> </a>
</li> </li>
<li> <li>
<a href="../articles/resistance_predict.html"> <a href="../articles/resistance_predict.html">
<span class="fas fa-dice"></span> <span class="fa fa-dice"></span>
Predict antimicrobial resistance Predict antimicrobial resistance
</a> </a>
</li> </li>
<li> <li>
<a href="../articles/datasets.html"> <a href="../articles/datasets.html">
<span class="fas fa-database"></span> <span class="fa fa-database"></span>
Data sets for download / own use Data sets for download / own use
</a> </a>
</li> </li>
<li> <li>
<a href="../articles/PCA.html"> <a href="../articles/PCA.html">
<span class="fas fa-compress"></span> <span class="fa fa-compress"></span>
Conduct principal component analysis for AMR Conduct principal component analysis for AMR
</a> </a>
</li> </li>
<li> <li>
<a href="../articles/MDR.html"> <a href="../articles/MDR.html">
<span class="fas fa-skull-crossbones"></span> <span class="fa fa-skull-crossbones"></span>
Determine multi-drug resistance (MDR) Determine multi-drug resistance (MDR)
</a> </a>
</li> </li>
<li> <li>
<a href="../articles/WHONET.html"> <a href="../articles/WHONET.html">
<span class="fas fa-globe-americas"></span> <span class="fa fa-globe-americas"></span>
Work with WHONET data Work with WHONET data
</a> </a>
</li> </li>
<li> <li>
<a href="../articles/SPSS.html"> <a href="../articles/SPSS.html">
<span class="fas fa-file-upload"></span> <span class="fa fa-file-upload"></span>
Import data from SPSS/SAS/Stata Import data from SPSS/SAS/Stata
</a> </a>
</li> </li>
<li> <li>
<a href="../articles/EUCAST.html"> <a href="../articles/EUCAST.html">
<span class="fas fa-exchange-alt"></span> <span class="fa fa-exchange-alt"></span>
Apply EUCAST rules Apply EUCAST rules
</a> </a>
</li> </li>
<li> <li>
<a href="../reference/mo_property.html"> <a href="../reference/mo_property.html">
<span class="fas fa-bug"></span> <span class="fa fa-bug"></span>
Get properties of a microorganism Get properties of a microorganism
</a> </a>
</li> </li>
<li> <li>
<a href="../reference/ab_property.html"> <a href="../reference/ab_property.html">
<span class="fas fa-capsules"></span> <span class="fa fa-capsules"></span>
Get properties of an antibiotic Get properties of an antibiotic
</a> </a>
</li> </li>
<li> <li>
<a href="../articles/benchmarks.html"> <a href="../articles/benchmarks.html">
<span class="fas fa-shipping-fast"></span> <span class="fa fa-shipping-fast"></span>
Other: benchmarks Other: benchmarks
</a> </a>
@ -185,14 +185,14 @@
</li> </li>
<li> <li>
<a href="../reference/index.html"> <a href="../reference/index.html">
<span class="fas fa-book-open"></span> <span class="fa fa-book-open"></span>
Manual Manual
</a> </a>
</li> </li>
<li> <li>
<a href="../authors.html"> <a href="../authors.html">
<span class="fas fa-users"></span> <span class="fa fa-users"></span>
Authors Authors
</a> </a>
@ -215,7 +215,7 @@
</li> </li>
<li> <li>
<a href="../survey.html"> <a href="../survey.html">
<span class="fas fa-clipboard-list"></span> <span class="fa fa-clipboard-list"></span>
Survey Survey
</a> </a>
@ -247,7 +247,7 @@
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
<p>A <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 21,996 observations and 10 variables:</p><ul> <p>A <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 22,000 observations and 10 variables:</p><ul>
<li><p><code>guideline</code><br /> Name of the guideline</p></li> <li><p><code>guideline</code><br /> Name of the guideline</p></li>
<li><p><code>method</code><br /> Either "DISK" or "MIC"</p></li> <li><p><code>method</code><br /> Either "DISK" or "MIC"</p></li>
<li><p><code>site</code><br /> Body site, e.g. "Oral" or "Respiratory"</p></li> <li><p><code>site</code><br /> Body site, e.g. "Oral" or "Respiratory"</p></li>

2
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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">1.7.1.9018</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9019</span>
</span> </span>
</div> </div>

2
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@ -116,7 +116,7 @@ After using \code{\link[=as.rsi]{as.rsi()}}, you can use the \code{\link[=eucast
\subsection{Machine-Readable Interpretation Guidelines}{ \subsection{Machine-Readable Interpretation Guidelines}{
The repository of this package \href{https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt}{contains a machine-readable version} of all guidelines. This is a CSV file consisting of 21,996 rows and 10 columns. This file is machine-readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial agent and the microorganism. \strong{This allows for easy implementation of these rules in laboratory information systems (LIS)}. Note that it only contains interpretation guidelines for humans - interpretation guidelines from CLSI for animals were removed. The repository of this package \href{https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt}{contains a machine-readable version} of all guidelines. This is a CSV file consisting of 22,000 rows and 10 columns. This file is machine-readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial agent and the microorganism. \strong{This allows for easy implementation of these rules in laboratory information systems (LIS)}. Note that it only contains interpretation guidelines for humans - interpretation guidelines from CLSI for animals were removed.
} }
\subsection{Other}{ \subsection{Other}{

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@ -5,7 +5,7 @@
\alias{rsi_translation} \alias{rsi_translation}
\title{Data Set for R/SI Interpretation} \title{Data Set for R/SI Interpretation}
\format{ \format{
A \link{data.frame} with 21,996 observations and 10 variables: A \link{data.frame} with 22,000 observations and 10 variables:
\itemize{ \itemize{
\item \code{guideline}\cr Name of the guideline \item \code{guideline}\cr Name of the guideline
\item \code{method}\cr Either "DISK" or "MIC" \item \code{method}\cr Either "DISK" or "MIC"