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dr. M.S. (Matthijs) Berends 2019-11-29 19:43:23 +01:00
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4
DESCRIPTION
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@ -1,6 +1,6 @@
Package: AMR
Version: 0.8.0.9037
Date: 2019-11-28
Version: 0.9.0
Date: 2019-11-29
Title: Antimicrobial Resistance Analysis
Authors@R: c(
person(role = c("aut", "cre"),

3
NEWS.md
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@ -1,5 +1,4 @@
# AMR 0.8.0.9037
## <small>Last updated: 28-Nov-2019</small>
# AMR 0.9.0
### Breaking
* Adopted Adeolu *et al.* (2016), [PMID 27620848](https://www.ncbi.nlm.nih.gov/pubmed/27620848) for the `microorganisms` data set, which means that the new order Enterobacterales now consists of a part of the existing family Enterobacteriaceae, but that this family has been split into other families as well (like *Morganellaceae* and *Yersiniaceae*). Although published in 2016, this information is not yet in the Catalogue of Life version of 2019. All MDRO determinations with `mdro()` will now use the Enterobacterales order for all guidelines before 2016 that were dependent on the Enterobacteriaceae family.

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R/count.R
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@ -26,7 +26,7 @@
#' [count_resistant()] should be used to count resistant isolates, [count_susceptible()] should be used to count susceptible isolates.
#' @param ... one or more vectors (or columns) with antibiotic interpretations. They will be transformed internally with [as.rsi()] if needed.
#' @inheritParams proportion
#' @inheritSection as.rsi Interpretation of S, I and R
#' @inheritSection as.rsi Interpretation of R and S/I
#' @details These functions are meant to count isolates. Use the [resistance()]/[susceptibility()] functions to calculate microbial resistance/susceptibility.
#'
#' The function [count_resistant()] is equal to the function [count_R()]. The function [count_susceptible()] is equal to the function [count_SI()].

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R/freq.R
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@ -46,8 +46,8 @@ freq.mo <- function(x, ...) {
decimal.mark = "."),
" (", percentage(sum(grams == "Gram-positive", na.rm = TRUE) / length(grams), digits = digits),
")"),
`Nr of genera` = n_distinct(mo_genus(x_noNA, language = NULL)),
`Nr of species` = n_distinct(paste(mo_genus(x_noNA, language = NULL),
`No of genera` = n_distinct(mo_genus(x_noNA, language = NULL)),
`No of species` = n_distinct(paste(mo_genus(x_noNA, language = NULL),
mo_species(x_noNA, language = NULL)))))
}

12
R/like.R
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@ -22,7 +22,9 @@
#' Pattern Matching
#'
#' Convenient wrapper around [base::grep()] to match a pattern: `a %like% b`. It always returns a [`logical`] vector and is always case-insensitive (use `a %like_case% b` for case-sensitive matching). Also, `pattern` (*b*) can be as long as `x` (*a*) to compare items of each index in both vectors, or can both have the same length to iterate over all cases.
#' @inheritParams base::grepl
#' @param x a character vector where matches are sought, or an object which can be coerced by [as.character()] to a character vector.
#' @param pattern a character string containing a regular expression (or [`character`] string for `fixed = TRUE`) to be matched in the given character vector. Coerced by [as.character()] to a character string if possible. If a [`character`] vector of length 2 or more is supplied, the first element is used with a warning.
#' @param ignore.case if `FALSE`, the pattern matching is *case sensitive* and if `TRUE`, case is ignored during matching.
#' @return A [`logical`] vector
#' @name like
#' @rdname like
@ -83,10 +85,12 @@ like <- function(x, pattern, ignore.case = TRUE) {
as.integer(x) %in% base::grep(pattern, levels(x), ignore.case = ignore.case)
} else {
tryCatch(base::grepl(pattern, x, ignore.case = ignore.case),
error = function(e) ifelse(test = grepl("Invalid regexp", e$message),
error = function(e) ifelse(grepl("Invalid regexp", e$message),
# try with perl = TRUE:
yes = return(base::grepl(pattern, x, ignore.case = ignore.case, perl = TRUE)),
no = stop(e$message)))
return(base::grepl(pattern = pattern, x = x,
ignore.case = ignore.case, perl = TRUE)),
# stop otherwise
stop(e$message)))
}
}

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R/mdro.R
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@ -48,7 +48,7 @@
#' Please suggest your own (country-specific) guidelines by letting us know: <https://gitlab.com/msberends/AMR/issues/new>.
#'
#' **Note:** Every test that involves the Enterobacteriaceae family, will internally be performed using its newly named order Enterobacterales, since the Enterobacteriaceae family has been taxonomically reclassified by Adeolu *et al.* in 2016. Before that, Enterobacteriaceae was the only family under the Enterobacteriales (with an i) order. All species under the old Enterobacteriaceae family are still under the new Enterobacterales (without an i) order, but divided into multiple families. The way tests are performed now by this [mdro()] function makes sure that results from before 2016 and after 2016 are identical.
#' @inheritSection as.rsi Interpretation of S, I and R
#' @inheritSection as.rsi Interpretation of R and S/I
#' @return
#' - CMI 2012 paper - function [mdr_cmi2012()] or [mdro()]:\cr
#' Ordered [`factor`] with levels `Negative` < `Multi-drug-resistant (MDR)` < `Extensively drug-resistant (XDR)` < `Pandrug-resistant (PDR)`

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R/proportion.R
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@ -33,7 +33,7 @@
#' @inheritParams ab_property
#' @param combine_SI a logical to indicate whether all values of S and I must be merged into one, so the output only consists of S+I vs. R (susceptible vs. resistant). This used to be the parameter `combine_IR`, but this now follows the redefinition by EUCAST about the interpretion of I (increased exposure) in 2019, see section 'Interpretation of S, I and R' below. Default is `TRUE`.
#' @param combine_IR a logical to indicate whether all values of I and R must be merged into one, so the output only consists of S vs. I+R (susceptible vs. non-susceptible). This is outdated, see parameter `combine_SI`.
#' @inheritSection as.rsi Interpretation of S, I and R
#' @inheritSection as.rsi Interpretation of R and S/I
#' @details
#' The function [resistance()] is equal to the function [proportion_R()]. The function [susceptibility()] is equal to the function [proportion_SI()].
#'

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R/resistance_predict.R
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@ -35,7 +35,7 @@
#' @param main title of the plot
#' @param ribbon a logical to indicate whether a ribbon should be shown (default) or error bars
#' @param ... parameters passed on to functions
#' @inheritSection as.rsi Interpretation of S, I and R
#' @inheritSection as.rsi Interpretation of R and S/I
#' @inheritParams first_isolate
#' @inheritParams graphics::plot
#' @details Valid options for the statistical model (parameter `model`) are:

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R/rsi.R
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@ -21,7 +21,7 @@
#' Class 'rsi'
#'
#' Interpret MIC values and disk diffusion diameters according to EUCAST or CLSI, or clean up existing RSI values. This transforms the input to a new class [`rsi`], which is an ordered factor with levels `S < I < R`. Invalid antimicrobial interpretations will be translated as `NA` with a warning.
#' Interpret MIC values and disk diffusion diameters according to EUCAST or CLSI, or clean up existing R/SI values. This transforms the input to a new class [`rsi`], which is an ordered factor with levels `S < I < R`. Invalid antimicrobial interpretations will be translated as `NA` with a warning.
#' @rdname as.rsi
#' @param x vector of values (for class [`mic`]: an MIC value in mg/L, for class [`disk`]: a disk diffusion radius in millimeters)
#' @param mo a microorganism code, generated with [as.mo()]
@ -35,14 +35,15 @@
#' After using [as.rsi()], you can use [eucast_rules()] to (1) apply inferred susceptibility and resistance based on results of other antimicrobials and (2) apply intrinsic resistance based on taxonomic properties of a microorganism.
#'
#' The function [is.rsi.eligible()] returns `TRUE` when a columns contains at most 5% invalid antimicrobial interpretations (not S and/or I and/or R), and `FALSE` otherwise. The threshold of 5% can be set with the `threshold` parameter.
#' @section Interpretation of S, I and R:
#' In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I and R as shown below (<http://www.eucast.org/newsiandr/>). Results of several consultations on the new definitions are available on the EUCAST website under "Consultations".
#' @section Interpretation of R and S/I:
#' In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories R and S/I as shown below (<http://www.eucast.org/newsiandr/>). Results of several consultations on the new definitions are available on the EUCAST website under "Consultations".
#'
#' - **S** - Susceptible, standard dosing regimen: A microorganism is categorised as "Susceptible, standard dosing regimen", when there is a high likelihood of therapeutic success using a standard dosing regimen of the agent.
#' - **I** - Susceptible, increased exposure: A microorganism is categorised as "Susceptible, Increased exposure" when there is a high likelihood of therapeutic success because exposure to the agent is increased by adjusting the dosing regimen or by its concentration at the site of infection.
#' - **R** - Resistant: A microorganism is categorised as "Resistant" when there is a high likelihood of therapeutic failure even when there is increased exposure.
#'
#' Exposure is a function of how the mode of administration, dose, dosing interval, infusion time, as well as distribution and excretion of the antimicrobial agent will influence the infecting organism at the site of infection.
#' - **R = Resistant**\cr
#' A microorganism is categorised as *Resistant* when there is a high likelihood of therapeutic failure even when there is increased exposure. Exposure is a function of how the mode of administration, dose, dosing interval, infusion time, as well as distribution and excretion of the antimicrobial agent will influence the infecting organism at the site of infection.
#' - **S = Susceptible**\cr
#' A microorganism is categorised as *Susceptible, standard dosing regimen*, when there is a high likelihood of therapeutic success using a standard dosing regimen of the agent.
#' - **I = Increased exposure, but still susceptible**\cr
#' A microorganism is categorised as *Susceptible, Increased exposure* when there is a high likelihood of therapeutic success because exposure to the agent is increased by adjusting the dosing regimen or by its concentration at the site of infection.
#'
#' This AMR package honours this new insight. Use [susceptibility()] (equal to [proportion_SI()]) to determine antimicrobial susceptibility and [count_susceptible()] (equal to [count_SI()]) to count susceptible isolates.
#' @return Ordered factor with new class [`rsi`]

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docs/404.html
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@ -84,7 +84,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="https://msberends.gitlab.io/AMR/index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9037</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</span>
</span>
</div>

2
docs/LICENSE-text.html
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@ -84,7 +84,7 @@
</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="Latest development version">0.8.0.9037</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</span>
</span>
</div>

520
docs/articles/AMR.html
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@ -41,7 +41,7 @@
</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="Latest development version">0.8.0.9033</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</span>
</span>
</div>
@ -187,7 +187,7 @@
<h1>How to conduct AMR analysis</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">23 November 2019</h4>
<h4 class="date">29 November 2019</h4>
<div class="hidden name"><code>AMR.Rmd</code></div>
@ -196,7 +196,7 @@
<p><strong>Note:</strong> values on this page will change with every website update since they are based on randomly created values and the page was written in <a href="https://rmarkdown.rstudio.com/">R Markdown</a>. However, the methodology remains unchanged. This page was generated on 23 November 2019.</p>
<p><strong>Note:</strong> values on this page will change with every website update since they are based on randomly created values and the page was written in <a href="https://rmarkdown.rstudio.com/">R Markdown</a>. However, the methodology remains unchanged. This page was generated on 29 November 2019.</p>
<div id="introduction" class="section level1">
<h1 class="hasAnchor">
<a href="#introduction" class="anchor"></a>Introduction</h1>
@ -212,21 +212,21 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2019-11-23</td>
<td align="center">2019-11-29</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
</tr>
<tr class="even">
<td align="center">2019-11-23</td>
<td align="center">2019-11-29</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">R</td>
</tr>
<tr class="odd">
<td align="center">2019-11-23</td>
<td align="center">2019-11-29</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -321,43 +321,43 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2016-08-29</td>
<td align="center">I4</td>
<td align="center">Hospital B</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2016-04-25</td>
<td align="center">U3</td>
<td align="center">Hospital A</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2013-06-29</td>
<td align="center">W2</td>
<td align="center">Hospital B</td>
<td align="center">2015-06-06</td>
<td align="center">I1</td>
<td align="center">Hospital D</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2016-06-07</td>
<td align="center">Z6</td>
<td align="center">Hospital D</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2013-01-19</td>
<td align="center">D3</td>
<td align="center">Hospital B</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2011-12-21</td>
<td align="center">D5</td>
<td align="center">Hospital C</td>
<td align="center">Escherichia coli</td>
<td align="center">2013-10-19</td>
<td align="center">M2</td>
<td align="center">Hospital B</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
@ -365,26 +365,26 @@
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2016-10-19</td>
<td align="center">G6</td>
<td align="center">2011-04-28</td>
<td align="center">F10</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2017-08-29</td>
<td align="center">Y5</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">2014-02-17</td>
<td align="center">I9</td>
<td align="center">Hospital D</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">M</td>
</tr>
</tbody>
</table>
@ -406,8 +406,8 @@
#
# Item Count Percent Cum. Count Cum. Percent
# --- ----- ------- -------- ----------- -------------
# 1 M 10,451 52.26% 10,451 52.26%
# 2 F 9,549 47.75% 20,000 100.00%</code></pre>
# 1 M 10,446 52.23% 10,446 52.23%
# 2 F 9,554 47.77% 20,000 100.00%</code></pre>
<p>So, we can draw at least two conclusions immediately. From a data scientists perspective, the data looks clean: only values <code>M</code> and <code>F</code>. From a researchers perspective: there are slightly more men. Nothing we didn’t already know.</p>
<p>The data is already quite clean, but we still need to transform some variables. The <code>bacteria</code> column now consists of text, and we want to add more variables based on microbial IDs later on. So, we will transform this column to valid IDs. The <code><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate()</a></code> function of the <code>dplyr</code> package makes this really easy:</p>
<div class="sourceCode" id="cb12"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb12-1" data-line-number="1">data &lt;-<span class="st"> </span>data <span class="op">%&gt;%</span></a>
@ -422,8 +422,8 @@
<a class="sourceLine" id="cb14-3" data-line-number="3"><span class="co"># Other rules by this AMR package</span></a>
<a class="sourceLine" id="cb14-4" data-line-number="4"><span class="co"># Non-EUCAST: inherit amoxicillin results for unavailable ampicillin (no changes)</span></a>
<a class="sourceLine" id="cb14-5" data-line-number="5"><span class="co"># Non-EUCAST: inherit ampicillin results for unavailable amoxicillin (no changes)</span></a>
<a class="sourceLine" id="cb14-6" data-line-number="6"><span class="co"># Non-EUCAST: set amoxicillin/clav acid = S where ampicillin = S (2,952 values changed)</span></a>
<a class="sourceLine" id="cb14-7" data-line-number="7"><span class="co"># Non-EUCAST: set ampicillin = R where amoxicillin/clav acid = R (155 values changed)</span></a>
<a class="sourceLine" id="cb14-6" data-line-number="6"><span class="co"># Non-EUCAST: set amoxicillin/clav acid = S where ampicillin = S (2,987 values changed)</span></a>
<a class="sourceLine" id="cb14-7" data-line-number="7"><span class="co"># Non-EUCAST: set ampicillin = R where amoxicillin/clav acid = R (122 values changed)</span></a>
<a class="sourceLine" id="cb14-8" data-line-number="8"><span class="co"># Non-EUCAST: set piperacillin = R where piperacillin/tazobactam = R (no changes)</span></a>
<a class="sourceLine" id="cb14-9" data-line-number="9"><span class="co"># Non-EUCAST: set piperacillin/tazobactam = S where piperacillin = S (no changes)</span></a>
<a class="sourceLine" id="cb14-10" data-line-number="10"><span class="co"># Non-EUCAST: set trimethoprim = R where trimethoprim/sulfa = R (no changes)</span></a>
@ -448,31 +448,31 @@
<a class="sourceLine" id="cb14-29" data-line-number="29"><span class="co"># Pasteurella multocida (no changes)</span></a>
<a class="sourceLine" id="cb14-30" data-line-number="30"><span class="co"># Staphylococcus (no changes)</span></a>
<a class="sourceLine" id="cb14-31" data-line-number="31"><span class="co"># Streptococcus groups A, B, C, G (no changes)</span></a>
<a class="sourceLine" id="cb14-32" data-line-number="32"><span class="co"># Streptococcus pneumoniae (984 values changed)</span></a>
<a class="sourceLine" id="cb14-32" data-line-number="32"><span class="co"># Streptococcus pneumoniae (1,064 values changed)</span></a>
<a class="sourceLine" id="cb14-33" data-line-number="33"><span class="co"># Viridans group streptococci (no changes)</span></a>
<a class="sourceLine" id="cb14-34" data-line-number="34"><span class="co"># </span></a>
<a class="sourceLine" id="cb14-35" data-line-number="35"><span class="co"># EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes (v3.1, 2016)</span></a>
<a class="sourceLine" id="cb14-36" data-line-number="36"><span class="co"># Table 01: Intrinsic resistance in Enterobacteriaceae (1,309 values changed)</span></a>
<a class="sourceLine" id="cb14-36" data-line-number="36"><span class="co"># Table 01: Intrinsic resistance in Enterobacteriaceae (1,300 values changed)</span></a>
<a class="sourceLine" id="cb14-37" data-line-number="37"><span class="co"># Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria (no changes)</span></a>
<a class="sourceLine" id="cb14-38" data-line-number="38"><span class="co"># Table 03: Intrinsic resistance in other Gram-negative bacteria (no changes)</span></a>
<a class="sourceLine" id="cb14-39" data-line-number="39"><span class="co"># Table 04: Intrinsic resistance in Gram-positive bacteria (2,719 values changed)</span></a>
<a class="sourceLine" id="cb14-39" data-line-number="39"><span class="co"># Table 04: Intrinsic resistance in Gram-positive bacteria (2,722 values changed)</span></a>
<a class="sourceLine" id="cb14-40" data-line-number="40"><span class="co"># Table 08: Interpretive rules for B-lactam agents and Gram-positive cocci (no changes)</span></a>
<a class="sourceLine" id="cb14-41" data-line-number="41"><span class="co"># Table 09: Interpretive rules for B-lactam agents and Gram-negative rods (no changes)</span></a>
<a class="sourceLine" id="cb14-42" data-line-number="42"><span class="co"># Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins (no changes)</span></a>
<a class="sourceLine" id="cb14-43" data-line-number="43"><span class="co"># Table 12: Interpretive rules for aminoglycosides (no changes)</span></a>
<a class="sourceLine" id="cb14-44" data-line-number="44"><span class="co"># Table 13: Interpretive rules for quinolones (no changes)</span></a>
<a class="sourceLine" id="cb14-45" data-line-number="45"><span class="co"># </span></a>
<a class="sourceLine" id="cb14-46" data-line-number="46"><span class="co"># --------------------------------------------------------------------------</span></a>
<a class="sourceLine" id="cb14-47" data-line-number="47"><span class="co"># EUCAST rules affected 6,464 out of 20,000 rows, making a total of 8,119 edits</span></a>
<a class="sourceLine" id="cb14-46" data-line-number="46"><span class="co"># -------------------------------------------------------------------------------</span></a>
<a class="sourceLine" id="cb14-47" data-line-number="47"><span class="co"># EUCAST rules affected 6,539 out of 20,000 rows, making a total of 8,195 edits</span></a>
<a class="sourceLine" id="cb14-48" data-line-number="48"><span class="co"># =&gt; added 0 test results</span></a>
<a class="sourceLine" id="cb14-49" data-line-number="49"><span class="co"># </span></a>
<a class="sourceLine" id="cb14-50" data-line-number="50"><span class="co"># =&gt; changed 8,119 test results</span></a>
<a class="sourceLine" id="cb14-51" data-line-number="51"><span class="co"># - 109 test results changed from S to I</span></a>
<a class="sourceLine" id="cb14-52" data-line-number="52"><span class="co"># - 4,710 test results changed from S to R</span></a>
<a class="sourceLine" id="cb14-53" data-line-number="53"><span class="co"># - 1,166 test results changed from I to S</span></a>
<a class="sourceLine" id="cb14-54" data-line-number="54"><span class="co"># - 348 test results changed from I to R</span></a>
<a class="sourceLine" id="cb14-55" data-line-number="55"><span class="co"># - 1,786 test results changed from R to S</span></a>
<a class="sourceLine" id="cb14-56" data-line-number="56"><span class="co"># --------------------------------------------------------------------------</span></a>
<a class="sourceLine" id="cb14-50" data-line-number="50"><span class="co"># =&gt; changed 8,195 test results</span></a>
<a class="sourceLine" id="cb14-51" data-line-number="51"><span class="co"># - 125 test results changed from S to I</span></a>
<a class="sourceLine" id="cb14-52" data-line-number="52"><span class="co"># - 4,759 test results changed from S to R</span></a>
<a class="sourceLine" id="cb14-53" data-line-number="53"><span class="co"># - 1,206 test results changed from I to S</span></a>
<a class="sourceLine" id="cb14-54" data-line-number="54"><span class="co"># - 324 test results changed from I to R</span></a>
<a class="sourceLine" id="cb14-55" data-line-number="55"><span class="co"># - 1,781 test results changed from R to S</span></a>
<a class="sourceLine" id="cb14-56" data-line-number="56"><span class="co"># -------------------------------------------------------------------------------</span></a>
<a class="sourceLine" id="cb14-57" data-line-number="57"><span class="co"># </span></a>
<a class="sourceLine" id="cb14-58" data-line-number="58"><span class="co"># Use eucast_rules(..., verbose = TRUE) (on your original data) to get a data.frame with all specified edits instead.</span></a></code></pre></div>
</div>
@ -499,8 +499,8 @@
<a class="sourceLine" id="cb16-3" data-line-number="3"><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `bacteria` as input for `col_mo`.</span></a>
<a class="sourceLine" id="cb16-4" data-line-number="4"><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `date` as input for `col_date`.</span></a>
<a class="sourceLine" id="cb16-5" data-line-number="5"><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `patient_id` as input for `col_patient_id`.</span></a>
<a class="sourceLine" id="cb16-6" data-line-number="6"><span class="co"># =&gt; Found 5,669 first isolates (28.3% of total)</span></a></code></pre></div>
<p>So only 28.3% is suitable for resistance analysis! We can now filter on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html">filter()</a></code> function, also from the <code>dplyr</code> package:</p>
<a class="sourceLine" id="cb16-6" data-line-number="6"><span class="co"># =&gt; Found 5,689 first isolates (28.4% of total)</span></a></code></pre></div>
<p>So only 28.4% is suitable for resistance analysis! We can now filter on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html">filter()</a></code> function, also from the <code>dplyr</code> package:</p>
<div class="sourceCode" id="cb17"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb17-1" data-line-number="1">data_1st &lt;-<span class="st"> </span>data <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb17-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span>(first <span class="op">==</span><span class="st"> </span><span class="ot">TRUE</span>)</a></code></pre></div>
<p>For future use, the above two syntaxes can be shortened with the <code><a href="../reference/first_isolate.html">filter_first_isolate()</a></code> function:</p>
@ -510,7 +510,7 @@
<div id="first-weighted-isolates" class="section level2">
<h2 class="hasAnchor">
<a href="#first-weighted-isolates" class="anchor"></a>First <em>weighted</em> isolates</h2>
<p>We made a slight twist to the CLSI algorithm, to take into account the antimicrobial susceptibility profile. Have a look at all isolates of patient T6, sorted on date:</p>
<p>We made a slight twist to the CLSI algorithm, to take into account the antimicrobial susceptibility profile. Have a look at all isolates of patient N6, sorted on date:</p>
<table class="table">
<thead><tr class="header">
<th align="center">isolate</th>
@ -526,19 +526,19 @@
<tbody>
<tr class="odd">
<td align="center">1</td>
<td align="center">2010-02-28</td>
<td align="center">T6</td>
<td align="center">2010-02-23</td>
<td align="center">N6</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2</td>
<td align="center">2010-03-01</td>
<td align="center">T6</td>
<td align="center">2010-04-09</td>
<td align="center">N6</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
@ -548,21 +548,21 @@
</tr>
<tr class="odd">
<td align="center">3</td>
<td align="center">2010-05-20</td>
<td align="center">T6</td>
<td align="center">2010-04-23</td>
<td align="center">N6</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">4</td>
<td align="center">2010-06-21</td>
<td align="center">T6</td>
<td align="center">2010-05-12</td>
<td align="center">N6</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
@ -570,10 +570,10 @@
</tr>
<tr class="odd">
<td align="center">5</td>
<td align="center">2010-09-24</td>
<td align="center">T6</td>
<td align="center">2010-06-27</td>
<td align="center">N6</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
@ -581,52 +581,52 @@
</tr>
<tr class="even">
<td align="center">6</td>
<td align="center">2010-11-18</td>
<td align="center">T6</td>
<td align="center">2010-08-09</td>
<td align="center">N6</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">7</td>
<td align="center">2011-02-07</td>
<td align="center">T6</td>
<td align="center">2010-09-01</td>
<td align="center">N6</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">8</td>
<td align="center">2011-03-09</td>
<td align="center">T6</td>
<td align="center">2010-10-18</td>
<td align="center">N6</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">9</td>
<td align="center">2011-03-23</td>
<td align="center">T6</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">9</td>
<td align="center">2011-01-18</td>
<td align="center">N6</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">10</td>
<td align="center">2011-04-01</td>
<td align="center">T6</td>
<td align="center">2011-02-15</td>
<td align="center">N6</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
@ -636,7 +636,7 @@
</tr>
</tbody>
</table>
<p>Only 2 isolates are marked as ‘first’ according to CLSI guideline. But when reviewing the antibiogram, it is obvious that some isolates are absolutely different strains and should be included too. This is why we weigh isolates, based on their antibiogram. The <code><a href="../reference/key_antibiotics.html">key_antibiotics()</a></code> function adds a vector with 18 key antibiotics: 6 broad spectrum ones, 6 small spectrum for Gram negatives and 6 small spectrum for Gram positives. These can be defined by the user.</p>
<p>Only 1 isolates are marked as ‘first’ according to CLSI guideline. But when reviewing the antibiogram, it is obvious that some isolates are absolutely different strains and should be included too. This is why we weigh isolates, based on their antibiogram. The <code><a href="../reference/key_antibiotics.html">key_antibiotics()</a></code> function adds a vector with 18 key antibiotics: 6 broad spectrum ones, 6 small spectrum for Gram negatives and 6 small spectrum for Gram positives. These can be defined by the user.</p>
<p>If a column exists with a name like ‘key(…)ab’ the <code><a href="../reference/first_isolate.html">first_isolate()</a></code> function will automatically use it and determine the first weighted isolates. Mind the NOTEs in below output:</p>
<div class="sourceCode" id="cb19"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb19-1" data-line-number="1">data &lt;-<span class="st"> </span>data <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb19-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span>(<span class="dt">keyab =</span> <span class="kw"><a href="../reference/key_antibiotics.html">key_antibiotics</a></span>(.)) <span class="op">%&gt;%</span><span class="st"> </span></a>
@ -647,7 +647,7 @@
<a class="sourceLine" id="cb19-7" data-line-number="7"><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `patient_id` as input for `col_patient_id`.</span></a>
<a class="sourceLine" id="cb19-8" data-line-number="8"><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `keyab` as input for `col_keyantibiotics`. Use col_keyantibiotics = FALSE to prevent this.</span></a>
<a class="sourceLine" id="cb19-9" data-line-number="9"><span class="co"># [Criterion] Inclusion based on key antibiotics, ignoring I</span></a>
<a class="sourceLine" id="cb19-10" data-line-number="10"><span class="co"># =&gt; Found 15,096 first weighted isolates (75.5% of total)</span></a></code></pre></div>
<a class="sourceLine" id="cb19-10" data-line-number="10"><span class="co"># =&gt; Found 15,038 first weighted isolates (75.2% of total)</span></a></code></pre></div>
<table class="table">
<thead><tr class="header">
<th align="center">isolate</th>
@ -664,20 +664,20 @@
<tbody>
<tr class="odd">
<td align="center">1</td>
<td align="center">2010-02-28</td>
<td align="center">T6</td>
<td align="center">2010-02-23</td>
<td align="center">N6</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">TRUE</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2</td>
<td align="center">2010-03-01</td>
<td align="center">T6</td>
<td align="center">2010-04-09</td>
<td align="center">N6</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
@ -688,22 +688,22 @@
</tr>
<tr class="odd">
<td align="center">3</td>
<td align="center">2010-05-20</td>
<td align="center">T6</td>
<td align="center">2010-04-23</td>
<td align="center">N6</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">4</td>
<td align="center">2010-06-21</td>
<td align="center">T6</td>
<td align="center">2010-05-12</td>
<td align="center">N6</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
@ -712,10 +712,10 @@
</tr>
<tr class="odd">
<td align="center">5</td>
<td align="center">2010-09-24</td>
<td align="center">T6</td>
<td align="center">2010-06-27</td>
<td align="center">N6</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
@ -724,56 +724,56 @@
</tr>
<tr class="even">
<td align="center">6</td>
<td align="center">2010-11-18</td>
<td align="center">T6</td>
<td align="center">2010-08-09</td>
<td align="center">N6</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">7</td>
<td align="center">2011-02-07</td>
<td align="center">T6</td>
<td align="center">2010-09-01</td>
<td align="center">N6</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">8</td>
<td align="center">2011-03-09</td>
<td align="center">T6</td>
<td align="center">2010-10-18</td>
<td align="center">N6</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">TRUE</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">9</td>
<td align="center">2011-03-23</td>
<td align="center">T6</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">9</td>
<td align="center">2011-01-18</td>
<td align="center">N6</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">10</td>
<td align="center">2011-04-01</td>
<td align="center">T6</td>
<td align="center">2011-02-15</td>
<td align="center">N6</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
@ -784,11 +784,11 @@
</tr>
</tbody>
</table>
<p>Instead of 2, now 10 isolates are flagged. In total, 75.5% of all isolates are marked ‘first weighted’ - 47.1% more than when using the CLSI guideline. In real life, this novel algorithm will yield 5-10% more isolates than the classic CLSI guideline.</p>
<p>Instead of 1, now 9 isolates are flagged. In total, 75.2% of all isolates are marked ‘first weighted’ - 46.7% more than when using the CLSI guideline. In real life, this novel algorithm will yield 5-10% more isolates than the classic CLSI guideline.</p>
<p>As with <code><a href="../reference/first_isolate.html">filter_first_isolate()</a></code>, there’s a shortcut for this new algorithm too:</p>
<div class="sourceCode" id="cb20"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb20-1" data-line-number="1">data_1st &lt;-<span class="st"> </span>data <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb20-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="../reference/first_isolate.html">filter_first_weighted_isolate</a></span>()</a></code></pre></div>
<p>So we end up with 15,096 isolates for analysis.</p>
<p>So we end up with 15,038 isolates for analysis.</p>
<p>We can remove unneeded columns:</p>
<div class="sourceCode" id="cb21"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb21-1" data-line-number="1">data_1st &lt;-<span class="st"> </span>data_1st <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb21-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(<span class="op">-</span><span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(first, keyab))</a></code></pre></div>
@ -813,44 +813,12 @@
</tr></thead>
<tbody>
<tr class="odd">
<td>1</td>
<td align="center">2016-08-29</td>
<td align="center">I4</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td>2</td>
<td align="center">2016-04-25</td>
<td align="center">U3</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td>3</td>
<td align="center">2013-06-29</td>
<td align="center">W2</td>
<td align="center">Hospital B</td>
<td align="center">2016-06-07</td>
<td align="center">Z6</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
@ -861,42 +829,10 @@
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td>5</td>
<td align="center">2016-10-19</td>
<td align="center">G6</td>
<td>3</td>
<td align="center">2013-01-19</td>
<td align="center">D3</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td>6</td>
<td align="center">2017-08-29</td>
<td align="center">Y5</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td>10</td>
<td align="center">2016-02-16</td>
<td align="center">L3</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
@ -908,6 +844,70 @@
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td>5</td>
<td align="center">2011-04-28</td>
<td align="center">F10</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td>6</td>
<td align="center">2014-02-17</td>
<td align="center">I9</td>
<td align="center">Hospital D</td>
<td align="center">B_KLBSL_PNMN</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Klebsiella</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td>7</td>
<td align="center">2016-03-10</td>
<td align="center">C8</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td>8</td>
<td align="center">2014-02-08</td>
<td align="center">M8</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
</tbody>
</table>
<p>Time for the analysis!</p>
@ -927,7 +927,7 @@
<div class="sourceCode" id="cb24"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb24-1" data-line-number="1">data_1st <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(genus, species)</a></code></pre></div>
<p><strong>Frequency table</strong></p>
<p>Class: character<br>
Length: 15,096 (of which NA: 0 = 0%)<br>
Length: 15,038 (of which NA: 0 = 0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -944,33 +944,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">7,646</td>
<td align="right">50.65%</td>
<td align="right">7,646</td>
<td align="right">50.65%</td>
<td align="right">7,487</td>
<td align="right">49.79%</td>
<td align="right">7,487</td>
<td align="right">49.79%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">3,610</td>
<td align="right">23.91%</td>
<td align="right">11,256</td>
<td align="right">74.56%</td>
<td align="right">3,697</td>
<td align="right">24.58%</td>
<td align="right">11,184</td>
<td align="right">74.37%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,315</td>
<td align="right">15.34%</td>
<td align="right">13,571</td>
<td align="right">89.90%</td>
<td align="right">2,303</td>
<td align="right">15.31%</td>
<td align="right">13,487</td>
<td align="right">89.69%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,525</td>
<td align="right">10.10%</td>
<td align="right">15,096</td>
<td align="right">1,551</td>
<td align="right">10.31%</td>
<td align="right">15,038</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -982,7 +982,7 @@ Longest: 24</p>
<p>The functions <code><a href="../reference/proportion.html">resistance()</a></code> and <code><a href="../reference/proportion.html">susceptibility()</a></code> can be used to calculate antimicrobial resistance or susceptibility. For more specific analyses, the functions <code><a href="../reference/proportion.html">proportion_S()</a></code>, <code><a href="../reference/proportion.html">proportion_SI()</a></code>, <code><a href="../reference/proportion.html">proportion_I()</a></code>, <code><a href="../reference/proportion.html">proportion_IR()</a></code> and <code><a href="../reference/proportion.html">proportion_R()</a></code> can be used to determine the proportion of a specific antimicrobial outcome.</p>
<p>As per the EUCAST guideline of 2019, we calculate resistance as the proportion of R (<code><a href="../reference/proportion.html">proportion_R()</a></code>, equal to <code><a href="../reference/proportion.html">resistance()</a></code>) and susceptibility as the proportion of S and I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equal to <code><a href="../reference/proportion.html">susceptibility()</a></code>). These functions can be used on their own:</p>
<div class="sourceCode" id="cb25"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb25-1" data-line-number="1">data_1st <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/proportion.html">resistance</a></span>(AMX)</a>
<a class="sourceLine" id="cb25-2" data-line-number="2"><span class="co"># [1] 0.4690647</span></a></code></pre></div>
<a class="sourceLine" id="cb25-2" data-line-number="2"><span class="co"># [1] 0.4674824</span></a></code></pre></div>
<p>Or can be used in conjuction with <code><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by()</a></code> and <code><a href="https://dplyr.tidyverse.org/reference/summarise.html">summarise()</a></code>, both from the <code>dplyr</code> package:</p>
<div class="sourceCode" id="cb26"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb26-1" data-line-number="1">data_1st <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb26-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(hospital) <span class="op">%&gt;%</span><span class="st"> </span></a>
@ -995,19 +995,19 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.4740061</td>
<td align="center">0.4688268</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.4707669</td>
<td align="center">0.4681135</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.4640934</td>
<td align="center">0.4541020</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.4622766</td>
<td align="center">0.4743044</td>
</tr>
</tbody>
</table>
@ -1025,23 +1025,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.4740061</td>
<td align="center">4578</td>
<td align="center">0.4688268</td>
<td align="center">4475</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.4707669</td>
<td align="center">5268</td>
<td align="center">0.4681135</td>
<td align="center">5253</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.4640934</td>
<td align="center">2228</td>
<td align="center">0.4541020</td>
<td align="center">2255</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.4622766</td>
<td align="center">3022</td>
<td align="center">0.4743044</td>
<td align="center">3055</td>
</tr>
</tbody>
</table>
@ -1061,27 +1061,27 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.9193042</td>
<td align="center">0.8966780</td>
<td align="center">0.9935914</td>
<td align="center">0.9244023</td>
<td align="center">0.8946173</td>
<td align="center">0.9929211</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.9285246</td>
<td align="center">0.8878689</td>
<td align="center">0.9940984</td>
<td align="center">0.9174726</td>
<td align="center">0.8891038</td>
<td align="center">0.9929078</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.9166205</td>
<td align="center">0.9171745</td>
<td align="center">0.9919668</td>
<td align="center">0.9193941</td>
<td align="center">0.9248039</td>
<td align="center">0.9940492</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.6241901</td>
<td align="center">0.6070343</td>
<td align="center">0.0000000</td>
<td align="center">0.6241901</td>
<td align="center">0.6070343</td>
</tr>
</tbody>
</table>
@ -1129,7 +1129,7 @@ Longest: 24</p>
<a class="sourceLine" id="cb32-6" data-line-number="6"><span class="st"> </span><span class="kw"><a href="../reference/ggplot_rsi.html">geom_rsi</a></span>(<span class="dt">x =</span> <span class="st">"genus"</span>) <span class="op">+</span><span class="st"> </span></a>
<a class="sourceLine" id="cb32-7" data-line-number="7"><span class="st"> </span><span class="co"># split plots on antibiotic</span></a>
<a class="sourceLine" id="cb32-8" data-line-number="8"><span class="st"> </span><span class="kw"><a href="../reference/ggplot_rsi.html">facet_rsi</a></span>(<span class="dt">facet =</span> <span class="st">"antibiotic"</span>) <span class="op">+</span></a>
<a class="sourceLine" id="cb32-9" data-line-number="9"><span class="st"> </span><span class="co"># make R red, I yellow and S green</span></a>
<a class="sourceLine" id="cb32-9" data-line-number="9"><span class="st"> </span><span class="co"># set colours to the R/SI interpretations</span></a>
<a class="sourceLine" id="cb32-10" data-line-number="10"><span class="st"> </span><span class="kw"><a href="../reference/ggplot_rsi.html">scale_rsi_colours</a></span>() <span class="op">+</span></a>
<a class="sourceLine" id="cb32-11" data-line-number="11"><span class="st"> </span><span class="co"># show percentages on y axis</span></a>
<a class="sourceLine" id="cb32-12" data-line-number="12"><span class="st"> </span><span class="kw"><a href="../reference/ggplot_rsi.html">scale_y_percent</a></span>(<span class="dt">breaks =</span> <span class="dv">0</span><span class="op">:</span><span class="dv">4</span> <span class="op">*</span><span class="st"> </span><span class="dv">25</span>) <span class="op">+</span></a>

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@ -41,7 +41,7 @@
</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="Latest development version">0.8.0.9032</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</span>
</span>
</div>
@ -187,7 +187,7 @@
<h1>How to apply EUCAST rules</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">18 November 2019</h4>
<h4 class="date">29 November 2019</h4>
<div class="hidden name"><code>EUCAST.Rmd</code></div>

71
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@ -41,7 +41,7 @@
</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="Latest development version">0.8.0.9033</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</span>
</span>
</div>
@ -187,7 +187,7 @@
<h1>How to determine multi-drug resistance (MDR)</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">23 November 2019</h4>
<h4 class="date">29 November 2019</h4>
<div class="hidden name"><code>MDR.Rmd</code></div>
@ -243,9 +243,8 @@ The German national guideline - Mueller et al. (2015) Antimicrobial Resistance a
<a class="sourceLine" id="cb2-9" data-line-number="9"><span class="co"># Table 3 - Enterobacteriaceae ... OK</span></a>
<a class="sourceLine" id="cb2-10" data-line-number="10"><span class="co"># Table 4 - Pseudomonas aeruginosa ... OK</span></a>
<a class="sourceLine" id="cb2-11" data-line-number="11"><span class="co"># Table 5 - Acinetobacter spp. ... OK</span></a>
<a class="sourceLine" id="cb2-12" data-line-number="12"><span class="co"># Warning in mdro(.): NA introduced for isolates where the available</span></a>
<a class="sourceLine" id="cb2-13" data-line-number="13"><span class="co"># percentage of antimicrobial classes was below 50% (set with</span></a>
<a class="sourceLine" id="cb2-14" data-line-number="14"><span class="co"># `pct_required_classes`)</span></a></code></pre></div>
<a class="sourceLine" id="cb2-12" data-line-number="12"><span class="co"># Warning in mdro(.): NA introduced for isolates where the available percentage of</span></a>
<a class="sourceLine" id="cb2-13" data-line-number="13"><span class="co"># antimicrobial classes was below 50% (set with `pct_required_classes`)</span></a></code></pre></div>
<p><strong>Frequency table</strong></p>
<p>Class: factor &gt; ordered (numeric)<br>
Length: 2,000 (of which NA: 289 = 14.45%)<br>
@ -307,19 +306,19 @@ Unique: 2</p>
<p>The data set now looks like this:</p>
<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" data-line-number="1"><span class="kw"><a href="https://rdrr.io/r/utils/head.html">head</a></span>(my_TB_data)</a>
<a class="sourceLine" id="cb5-2" data-line-number="2"><span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></a>
<a class="sourceLine" id="cb5-3" data-line-number="3"><span class="co"># 1 S R I S I S</span></a>
<a class="sourceLine" id="cb5-4" data-line-number="4"><span class="co"># 2 S I S S R R</span></a>
<a class="sourceLine" id="cb5-5" data-line-number="5"><span class="co"># 3 R I R R R I</span></a>
<a class="sourceLine" id="cb5-6" data-line-number="6"><span class="co"># 4 S S S R R R</span></a>
<a class="sourceLine" id="cb5-7" data-line-number="7"><span class="co"># 5 I S R S R I</span></a>
<a class="sourceLine" id="cb5-8" data-line-number="8"><span class="co"># 6 R S R R S R</span></a>
<a class="sourceLine" id="cb5-3" data-line-number="3"><span class="co"># 1 S S I R R S</span></a>
<a class="sourceLine" id="cb5-4" data-line-number="4"><span class="co"># 2 S S R R I S</span></a>
<a class="sourceLine" id="cb5-5" data-line-number="5"><span class="co"># 3 S S S I R I</span></a>
<a class="sourceLine" id="cb5-6" data-line-number="6"><span class="co"># 4 R R S R R S</span></a>
<a class="sourceLine" id="cb5-7" data-line-number="7"><span class="co"># 5 R R S R I S</span></a>
<a class="sourceLine" id="cb5-8" data-line-number="8"><span class="co"># 6 R R R R S R</span></a>
<a class="sourceLine" id="cb5-9" data-line-number="9"><span class="co"># kanamycin</span></a>
<a class="sourceLine" id="cb5-10" data-line-number="10"><span class="co"># 1 S</span></a>
<a class="sourceLine" id="cb5-11" data-line-number="11"><span class="co"># 2 S</span></a>
<a class="sourceLine" id="cb5-12" data-line-number="12"><span class="co"># 3 S</span></a>
<a class="sourceLine" id="cb5-11" data-line-number="11"><span class="co"># 2 I</span></a>
<a class="sourceLine" id="cb5-12" data-line-number="12"><span class="co"># 3 I</span></a>
<a class="sourceLine" id="cb5-13" data-line-number="13"><span class="co"># 4 R</span></a>
<a class="sourceLine" id="cb5-14" data-line-number="14"><span class="co"># 5 S</span></a>
<a class="sourceLine" id="cb5-15" data-line-number="15"><span class="co"># 6 R</span></a></code></pre></div>
<a class="sourceLine" id="cb5-14" data-line-number="14"><span class="co"># 5 R</span></a>
<a class="sourceLine" id="cb5-15" data-line-number="15"><span class="co"># 6 S</span></a></code></pre></div>
<p>We can now add the interpretation of MDR-TB to our data set. You can use:</p>
<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" data-line-number="1"><span class="kw"><a href="../reference/mdro.html">mdro</a></span>(my_TB_data, <span class="dt">guideline =</span> <span class="st">"TB"</span>)</a></code></pre></div>
<p>or its shortcut <code><a href="../reference/mdro.html">mdr_tb()</a></code>:</p>
@ -336,7 +335,7 @@ Unique: 2</p>
<a class="sourceLine" id="cb7-11" data-line-number="11"><span class="co"># Author: WHO (World Health Organization)</span></a>
<a class="sourceLine" id="cb7-12" data-line-number="12"><span class="co"># Source: https://www.who.int/tb/publications/pmdt_companionhandbook/en/</span></a>
<a class="sourceLine" id="cb7-13" data-line-number="13"><span class="co"># </span></a>
<a class="sourceLine" id="cb7-14" data-line-number="14"><span class="co"># =&gt; Found 4367 MDROs out of 5000 tested isolates (87.3%)</span></a></code></pre></div>
<a class="sourceLine" id="cb7-14" data-line-number="14"><span class="co"># =&gt; Found 4377 MDROs out of 5000 tested isolates (87.5%)</span></a></code></pre></div>
<p>Create a frequency table of the results:</p>
<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb8-1" data-line-number="1"><span class="kw"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(my_TB_data<span class="op">$</span>mdr)</a></code></pre></div>
<p><strong>Frequency table</strong></p>
@ -357,40 +356,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3272</td>
<td align="right">65.44%</td>
<td align="right">3272</td>
<td align="right">65.44%</td>
<td align="right">3240</td>
<td align="right">64.80%</td>
<td align="right">3240</td>
<td align="right">64.80%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">633</td>
<td align="right">12.66%</td>
<td align="right">3905</td>
<td align="right">78.10%</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">647</td>
<td align="right">12.94%</td>
<td align="right">3887</td>
<td align="right">77.74%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">584</td>
<td align="right">11.68%</td>
<td align="right">4489</td>
<td align="right">89.78%</td>
<td align="left">Negative</td>
<td align="right">623</td>
<td align="right">12.46%</td>
<td align="right">4510</td>
<td align="right">90.20%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">293</td>
<td align="right">5.86%</td>
<td align="right">4782</td>
<td align="right">95.64%</td>
<td align="right">304</td>
<td align="right">6.08%</td>
<td align="right">4814</td>
<td align="right">96.28%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">218</td>
<td align="right">4.36%</td>
<td align="right">186</td>
<td align="right">3.72%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>

4
docs/articles/SPSS.html
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@ -41,7 +41,7 @@
</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="Latest development version">0.8.0.9032</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</span>
</span>
</div>
@ -187,7 +187,7 @@
<h1>How to import data from SPSS / SAS / Stata</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">18 November 2019</h4>
<h4 class="date">29 November 2019</h4>
<div class="hidden name"><code>SPSS.Rmd</code></div>

52
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@ -41,7 +41,7 @@
</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="Latest development version">0.8.0.9032</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</span>
</span>
</div>
@ -187,7 +187,7 @@
<h1>How to work with WHONET data</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">18 November 2019</h4>
<h4 class="date">29 November 2019</h4>
<div class="hidden name"><code>WHONET.Rmd</code></div>
@ -226,16 +226,14 @@
<p>No errors or warnings, so all values are transformed succesfully.</p>
<p>We also created a package dedicated to data cleaning and checking, called the <code>cleaner</code> package. It gets automatically installed with the <code>AMR</code> package. For its <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code> function to create frequency tables, you don’t even need to load it yourself as it is available through the <code>AMR</code> package as well.</p>
<p>So let’s check our data, with a couple of frequency tables:</p>
<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" data-line-number="1"><span class="co"># our newly created `mo` variable</span></a>
<a class="sourceLine" id="cb4-2" data-line-number="2">data <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(mo, <span class="dt">nmax =</span> <span class="dv">10</span>)</a></code></pre></div>
<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" data-line-number="1"><span class="co"># our newly created `mo` variable, put in the mo_name() function</span></a>
<a class="sourceLine" id="cb4-2" data-line-number="2">data <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(<span class="kw"><a href="../reference/mo_property.html">mo_name</a></span>(mo), <span class="dt">nmax =</span> <span class="dv">10</span>)</a></code></pre></div>
<p><strong>Frequency table</strong></p>
<p>Class: mo (character)<br>
<p>Class: character<br>
Length: 500 (of which NA: 0 = 0%)<br>
Unique: 39</p>
<p>Gram-negative: 280 (56.00%)<br>
Gram-positive: 220 (44.00%)<br>
Nr of genera: 17<br>
Nr of species: 39</p>
<p>Shortest: 11<br>
Longest: 40</p>
<table class="table">
<thead><tr class="header">
<th align="left"></th>
@ -248,7 +246,7 @@ Nr of species: 39</p>
<tbody>
<tr class="odd">
<td align="left">1</td>
<td align="left">B_ESCHR_COLI</td>
<td align="left">Escherichia coli</td>
<td align="right">245</td>
<td align="right">49.0%</td>
<td align="right">245</td>
@ -256,7 +254,7 @@ Nr of species: 39</p>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">B_STPHY_CONS</td>
<td align="left">Coagulase-negative Staphylococcus (CoNS)</td>
<td align="right">74</td>
<td align="right">14.8%</td>
<td align="right">319</td>
@ -264,7 +262,7 @@ Nr of species: 39</p>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">B_STPHY_EPDR</td>
<td align="left">Staphylococcus epidermidis</td>
<td align="right">38</td>
<td align="right">7.6%</td>
<td align="right">357</td>
@ -272,7 +270,7 @@ Nr of species: 39</p>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">B_STRPT_PNMN</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">31</td>
<td align="right">6.2%</td>
<td align="right">388</td>
@ -280,7 +278,7 @@ Nr of species: 39</p>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">B_STPHY_HMNS</td>
<td align="left">Staphylococcus hominis</td>
<td align="right">21</td>
<td align="right">4.2%</td>
<td align="right">409</td>
@ -288,7 +286,7 @@ Nr of species: 39</p>
</tr>
<tr class="even">
<td align="left">6</td>
<td align="left">B_PROTS_MRBL</td>
<td align="left">Proteus mirabilis</td>
<td align="right">9</td>
<td align="right">1.8%</td>
<td align="right">418</td>
@ -296,7 +294,7 @@ Nr of species: 39</p>
</tr>
<tr class="odd">
<td align="left">7</td>
<td align="left">B_ENTRC_FACM</td>
<td align="left">Enterococcus faecium</td>
<td align="right">8</td>
<td align="right">1.6%</td>
<td align="right">426</td>
@ -304,7 +302,7 @@ Nr of species: 39</p>
</tr>
<tr class="even">
<td align="left">8</td>
<td align="left">B_STPHY_CPTS</td>
<td align="left">Staphylococcus capitis</td>
<td align="right">8</td>
<td align="right">1.6%</td>
<td align="right">434</td>
@ -312,7 +310,7 @@ Nr of species: 39</p>
</tr>
<tr class="odd">
<td align="left">9</td>
<td align="left">B_ENTRB_CLOC</td>
<td align="left">Enterobacter cloacae</td>
<td align="right">5</td>
<td align="right">1.0%</td>
<td align="right">439</td>
@ -320,7 +318,7 @@ Nr of species: 39</p>
</tr>
<tr class="even">
<td align="left">10</td>
<td align="left">B_ENTRC_CLMB</td>
<td align="left">Enterococcus columbae</td>
<td align="right">4</td>
<td align="right">0.8%</td>
<td align="right">443</td>
@ -329,10 +327,9 @@ Nr of species: 39</p>
</tbody>
</table>
<p>(omitted 29 entries, n = 57 [11.40%])</p>
<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" data-line-number="1"></a>
<a class="sourceLine" id="cb5-2" data-line-number="2"><span class="co"># our transformed antibiotic columns</span></a>
<a class="sourceLine" id="cb5-3" data-line-number="3"><span class="co"># amoxicillin/clavulanic acid (J01CR02) as an example</span></a>
<a class="sourceLine" id="cb5-4" data-line-number="4">data <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(AMC_ND2)</a></code></pre></div>
<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" data-line-number="1"><span class="co"># our transformed antibiotic columns</span></a>
<a class="sourceLine" id="cb5-2" data-line-number="2"><span class="co"># amoxicillin/clavulanic acid (J01CR02) as an example</span></a>
<a class="sourceLine" id="cb5-3" data-line-number="3">data <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span>(AMC_ND2)</a></code></pre></div>
<p><strong>Frequency table</strong></p>
<p>Class: factor &gt; ordered &gt; rsi (numeric)<br>
Length: 500 (of which NA: 19 = 3.8%)<br>
@ -379,9 +376,12 @@ Unique: 3</p>
<div id="a-first-glimpse-at-results" class="section level3">
<h3 class="hasAnchor">
<a href="#a-first-glimpse-at-results" class="anchor"></a>A first glimpse at results</h3>
<p>An easy ggplot will already give a lot of information, using the included <code><a href="../reference/ggplot_rsi.html">ggplot_rsi()</a></code> function:</p>
<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" data-line-number="1"><span class="kw"><a href="../reference/ggplot_rsi.html">ggplot_rsi</a></span>(data, <span class="dt">translate_ab =</span> <span class="st">'ab'</span>)</a></code></pre></div>
<p><img src="WHONET_files/figure-html/unnamed-chunk-5-1.png" width="720"></p>
<p>An easy <code>ggplot</code> will already give a lot of information, using the included <code><a href="../reference/ggplot_rsi.html">ggplot_rsi()</a></code> function:</p>
<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" data-line-number="1">data <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb6-2" data-line-number="2"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(Country) <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb6-3" data-line-number="3"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(Country, AMP_ND2, AMC_ED20, CAZ_ED10, CIP_ED5) <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb6-4" data-line-number="4"><span class="st"> </span><span class="kw"><a href="../reference/ggplot_rsi.html">ggplot_rsi</a></span>(<span class="dt">translate_ab =</span> <span class="st">'ab'</span>, <span class="dt">facet =</span> <span class="st">"Country"</span>, <span class="dt">datalabels =</span> <span class="ot">FALSE</span>)</a></code></pre></div>
<p><img src="WHONET_files/figure-html/unnamed-chunk-7-1.png" width="720"></p>
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@ -41,7 +41,7 @@
</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="Latest development version">0.8.0.9032</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</span>
</span>
</div>
@ -187,7 +187,7 @@
<h1>Benchmarks</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">18 November 2019</h4>
<h4 class="date">29 November 2019</h4>
<div class="hidden name"><code>benchmarks.Rmd</code></div>
@ -222,20 +222,20 @@
<a class="sourceLine" id="cb2-17" data-line-number="17"><span class="kw"><a href="https://rdrr.io/r/base/print.html">print</a></span>(S.aureus, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">2</span>)</a>
<a class="sourceLine" id="cb2-18" data-line-number="18"><span class="co"># Unit: milliseconds</span></a>
<a class="sourceLine" id="cb2-19" data-line-number="19"><span class="co"># expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb2-20" data-line-number="20"><span class="co"># as.mo("sau") 10 10 16 11 13 58 10</span></a>
<a class="sourceLine" id="cb2-21" data-line-number="21"><span class="co"># as.mo("stau") 33 34 50 45 67 80 10</span></a>
<a class="sourceLine" id="cb2-22" data-line-number="22"><span class="co"># as.mo("STAU") 34 38 44 39 43 72 10</span></a>
<a class="sourceLine" id="cb2-23" data-line-number="23"><span class="co"># as.mo("staaur") 10 11 16 12 15 44 10</span></a>
<a class="sourceLine" id="cb2-24" data-line-number="24"><span class="co"># as.mo("STAAUR") 11 11 17 12 14 59 10</span></a>
<a class="sourceLine" id="cb2-25" data-line-number="25"><span class="co"># as.mo("S. aureus") 26 30 37 33 48 54 10</span></a>
<a class="sourceLine" id="cb2-26" data-line-number="26"><span class="co"># as.mo("S aureus") 26 27 31 28 32 48 10</span></a>
<a class="sourceLine" id="cb2-27" data-line-number="27"><span class="co"># as.mo("Staphylococcus aureus") 31 35 37 37 40 44 10</span></a>
<a class="sourceLine" id="cb2-28" data-line-number="28"><span class="co"># as.mo("Staphylococcus aureus (MRSA)") 650 690 750 710 840 900 10</span></a>
<a class="sourceLine" id="cb2-29" data-line-number="29"><span class="co"># as.mo("Sthafilokkockus aaureuz") 380 410 430 430 440 500 10</span></a>
<a class="sourceLine" id="cb2-30" data-line-number="30"><span class="co"># as.mo("MRSA") 10 11 20 11 37 44 10</span></a>
<a class="sourceLine" id="cb2-31" data-line-number="31"><span class="co"># as.mo("VISA") 20 22 51 29 47 220 10</span></a>
<a class="sourceLine" id="cb2-32" data-line-number="32"><span class="co"># as.mo("VRSA") 21 23 32 25 41 57 10</span></a>
<a class="sourceLine" id="cb2-33" data-line-number="33"><span class="co"># as.mo(22242419) 20 21 23 22 23 27 10</span></a></code></pre></div>
<a class="sourceLine" id="cb2-20" data-line-number="20"><span class="co"># as.mo("sau") 11 11 15 12 14 39 10</span></a>
<a class="sourceLine" id="cb2-21" data-line-number="21"><span class="co"># as.mo("stau") 36 38 49 48 60 65 10</span></a>
<a class="sourceLine" id="cb2-22" data-line-number="22"><span class="co"># as.mo("STAU") 36 38 46 40 59 71 10</span></a>
<a class="sourceLine" id="cb2-23" data-line-number="23"><span class="co"># as.mo("staaur") 11 11 21 11 37 37 10</span></a>
<a class="sourceLine" id="cb2-24" data-line-number="24"><span class="co"># as.mo("STAAUR") 11 11 12 12 12 17 10</span></a>
<a class="sourceLine" id="cb2-25" data-line-number="25"><span class="co"># as.mo("S. aureus") 26 29 36 32 48 53 10</span></a>
<a class="sourceLine" id="cb2-26" data-line-number="26"><span class="co"># as.mo("S aureus") 25 27 37 29 52 64 10</span></a>
<a class="sourceLine" id="cb2-27" data-line-number="27"><span class="co"># as.mo("Staphylococcus aureus") 33 34 39 36 45 53 10</span></a>
<a class="sourceLine" id="cb2-28" data-line-number="28"><span class="co"># as.mo("Staphylococcus aureus (MRSA)") 660 720 740 740 760 800 10</span></a>
<a class="sourceLine" id="cb2-29" data-line-number="29"><span class="co"># as.mo("Sthafilokkockus aaureuz") 350 360 410 380 400 660 10</span></a>
<a class="sourceLine" id="cb2-30" data-line-number="30"><span class="co"># as.mo("MRSA") 11 11 14 12 12 36 10</span></a>
<a class="sourceLine" id="cb2-31" data-line-number="31"><span class="co"># as.mo("VISA") 21 23 27 26 28 47 10</span></a>
<a class="sourceLine" id="cb2-32" data-line-number="32"><span class="co"># as.mo("VRSA") 21 22 30 23 44 52 10</span></a>
<a class="sourceLine" id="cb2-33" data-line-number="33"><span class="co"># as.mo(22242419) 20 20 24 21 21 52 10</span></a></code></pre></div>
<p><img src="benchmarks_files/figure-html/unnamed-chunk-5-1.png" width="562.5"></p>
<p>In the table above, all measurements are shown in milliseconds (thousands of seconds). A value of 5 milliseconds means it can determine 200 input values per second. It case of 100 milliseconds, this is only 10 input values per second. The second input is the only one that has to be looked up thoroughly. All the others are known codes (the first one is a WHONET code) or common laboratory codes, or common full organism names like the last one. Full organism names are always preferred.</p>
<p>To achieve this speed, the <code>as.mo</code> function also takes into account the prevalence of human pathogenic microorganisms. The downside is of course that less prevalent microorganisms will be determined less fast. See this example for the ID of <em>Methanosarcina semesiae</em> (<code>B_MTHNSR_SEMS</code>), a bug probably never found before in humans:</p>
@ -247,19 +247,19 @@
<a class="sourceLine" id="cb3-6" data-line-number="6"> <span class="dt">times =</span> <span class="dv">10</span>)</a>
<a class="sourceLine" id="cb3-7" data-line-number="7"><span class="kw"><a href="https://rdrr.io/r/base/print.html">print</a></span>(M.semesiae, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">4</span>)</a>
<a class="sourceLine" id="cb3-8" data-line-number="8"><span class="co"># Unit: milliseconds</span></a>
<a class="sourceLine" id="cb3-9" data-line-number="9"><span class="co"># expr min lq mean median uq</span></a>
<a class="sourceLine" id="cb3-10" data-line-number="10"><span class="co"># as.mo("metsem") 1415.00 1467.00 1505.00 1493.00 1537.00</span></a>
<a class="sourceLine" id="cb3-11" data-line-number="11"><span class="co"># as.mo("METSEM") 1447.00 1488.00 1530.00 1521.00 1555.00</span></a>
<a class="sourceLine" id="cb3-12" data-line-number="12"><span class="co"># as.mo("M. semesiae") 2216.00 2239.00 2293.00 2284.00 2351.00</span></a>
<a class="sourceLine" id="cb3-13" data-line-number="13"><span class="co"># as.mo("M. semesiae") 2143.00 2212.00 2304.00 2307.00 2332.00</span></a>
<a class="sourceLine" id="cb3-14" data-line-number="14"><span class="co"># as.mo("Methanosarcina semesiae") 32.44 35.59 43.59 38.19 45.88</span></a>
<a class="sourceLine" id="cb3-15" data-line-number="15"><span class="co"># max neval</span></a>
<a class="sourceLine" id="cb3-16" data-line-number="16"><span class="co"># 1627.00 10</span></a>
<a class="sourceLine" id="cb3-17" data-line-number="17"><span class="co"># 1628.00 10</span></a>
<a class="sourceLine" id="cb3-18" data-line-number="18"><span class="co"># 2395.00 10</span></a>
<a class="sourceLine" id="cb3-19" data-line-number="19"><span class="co"># 2535.00 10</span></a>
<a class="sourceLine" id="cb3-20" data-line-number="20"><span class="co"># 69.48 10</span></a></code></pre></div>
<p>That takes 13.8 times as much time on average. A value of 100 milliseconds means it can only determine ~10 different input values per second. We can conclude that looking up arbitrary codes of less prevalent microorganisms is the worst way to go, in terms of calculation performance. Full names (like <em>Methanosarcina semesiae</em>) are almost fast - these are the most probable input from most data sets.</p>
<a class="sourceLine" id="cb3-9" data-line-number="9"><span class="co"># expr min lq mean median uq max</span></a>
<a class="sourceLine" id="cb3-10" data-line-number="10"><span class="co"># as.mo("metsem") 1501.0 1506.00 1665.0 1569.00 1788.00 2141.00</span></a>
<a class="sourceLine" id="cb3-11" data-line-number="11"><span class="co"># as.mo("METSEM") 1586.0 1610.00 1727.0 1675.00 1793.00 2002.00</span></a>
<a class="sourceLine" id="cb3-12" data-line-number="12"><span class="co"># as.mo("M. semesiae") 2266.0 2335.00 2587.0 2418.00 2524.00 3676.00</span></a>
<a class="sourceLine" id="cb3-13" data-line-number="13"><span class="co"># as.mo("M. semesiae") 2143.0 2252.00 2334.0 2331.00 2396.00 2540.00</span></a>
<a class="sourceLine" id="cb3-14" data-line-number="14"><span class="co"># as.mo("Methanosarcina semesiae") 34.8 35.74 46.3 39.64 62.28 65.83</span></a>
<a class="sourceLine" id="cb3-15" data-line-number="15"><span class="co"># neval</span></a>
<a class="sourceLine" id="cb3-16" data-line-number="16"><span class="co"># 10</span></a>
<a class="sourceLine" id="cb3-17" data-line-number="17"><span class="co"># 10</span></a>
<a class="sourceLine" id="cb3-18" data-line-number="18"><span class="co"># 10</span></a>
<a class="sourceLine" id="cb3-19" data-line-number="19"><span class="co"># 10</span></a>
<a class="sourceLine" id="cb3-20" data-line-number="20"><span class="co"># 10</span></a></code></pre></div>
<p>That takes 15.6 times as much time on average. A value of 100 milliseconds means it can only determine ~10 different input values per second. We can conclude that looking up arbitrary codes of less prevalent microorganisms is the worst way to go, in terms of calculation performance. Full names (like <em>Methanosarcina semesiae</em>) are almost fast - these are the most probable input from most data sets.</p>
<p>In the figure below, we compare <em>Escherichia coli</em> (which is very common) with <em>Prevotella brevis</em> (which is moderately common) and with <em>Methanosarcina semesiae</em> (which is uncommon):</p>
<p><img src="benchmarks_files/figure-html/unnamed-chunk-9-1.png" width="562.5"></p>
<p>In reality, the <code><a href="../reference/as.mo.html">as.mo()</a></code> functions <strong>learns from its own output to speed up determinations for next times</strong>. In above figure, this effect was disabled to show the difference with the boxplot below - when you would use <code><a href="../reference/as.mo.html">as.mo()</a></code> yourself:</p>
@ -296,8 +296,8 @@
<a class="sourceLine" id="cb4-24" data-line-number="24"><span class="kw"><a href="https://rdrr.io/r/base/print.html">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">3</span>)</a>
<a class="sourceLine" id="cb4-25" data-line-number="25"><span class="co"># Unit: milliseconds</span></a>
<a class="sourceLine" id="cb4-26" data-line-number="26"><span class="co"># expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb4-27" data-line-number="27"><span class="co"># mo_name(x) 642 674 702 687 713 843 10</span></a></code></pre></div>
<p>So transforming 500,000 values (!!) of 50 unique values only takes 0.69 seconds (686 ms). You only lose time on your unique input values.</p>
<a class="sourceLine" id="cb4-27" data-line-number="27"><span class="co"># mo_name(x) 655 668 715 717 751 797 10</span></a></code></pre></div>
<p>So transforming 500,000 values (!!) of 50 unique values only takes 0.72 seconds (717 ms). You only lose time on your unique input values.</p>
</div>
<div id="precalculated-results" class="section level3">
<h3 class="hasAnchor">
@ -309,10 +309,10 @@
<a class="sourceLine" id="cb5-4" data-line-number="4"> <span class="dt">times =</span> <span class="dv">10</span>)</a>
<a class="sourceLine" id="cb5-5" data-line-number="5"><span class="kw"><a href="https://rdrr.io/r/base/print.html">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">3</span>)</a>
<a class="sourceLine" id="cb5-6" data-line-number="6"><span class="co"># Unit: milliseconds</span></a>
<a class="sourceLine" id="cb5-7" data-line-number="7"><span class="co"># expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb5-8" data-line-number="8"><span class="co"># A 6.350 6.420 6.880 6.530 7.180 8.56 10</span></a>
<a class="sourceLine" id="cb5-9" data-line-number="9"><span class="co"># B 24.600 25.100 31.300 25.700 27.900 62.80 10</span></a>
<a class="sourceLine" id="cb5-10" data-line-number="10"><span class="co"># C 0.798 0.867 0.914 0.892 0.931 1.14 10</span></a></code></pre></div>
<a class="sourceLine" id="cb5-7" data-line-number="7"><span class="co"># expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb5-8" data-line-number="8"><span class="co"># A 6.70 6.710 9.690 7.18 7.850 31.90 10</span></a>
<a class="sourceLine" id="cb5-9" data-line-number="9"><span class="co"># B 26.20 27.100 32.400 28.80 32.100 58.80 10</span></a>
<a class="sourceLine" id="cb5-10" data-line-number="10"><span class="co"># C 0.78 0.837 0.924 0.88 0.965 1.24 10</span></a></code></pre></div>
<p>So going from <code><a href="../reference/mo_property.html">mo_name("Staphylococcus aureus")</a></code> to <code>"Staphylococcus aureus"</code> takes 0.0009 seconds - it doesn’t even start calculating <em>if the result would be the same as the expected resulting value</em>. That goes for all helper functions:</p>
<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" data-line-number="1">run_it &lt;-<span class="st"> </span><span class="kw"><a href="https://rdrr.io/pkg/microbenchmark/man/microbenchmark.html">microbenchmark</a></span>(<span class="dt">A =</span> <span class="kw"><a href="../reference/mo_property.html">mo_species</a></span>(<span class="st">"aureus"</span>),</a>
<a class="sourceLine" id="cb6-2" data-line-number="2"> <span class="dt">B =</span> <span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="st">"Staphylococcus"</span>),</a>
@ -326,14 +326,14 @@
<a class="sourceLine" id="cb6-10" data-line-number="10"><span class="kw"><a href="https://rdrr.io/r/base/print.html">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">3</span>)</a>
<a class="sourceLine" id="cb6-11" data-line-number="11"><span class="co"># Unit: milliseconds</span></a>
<a class="sourceLine" id="cb6-12" data-line-number="12"><span class="co"># expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb6-13" data-line-number="13"><span class="co"># A 0.446 0.459 0.471 0.475 0.481 0.485 10</span></a>
<a class="sourceLine" id="cb6-14" data-line-number="14"><span class="co"># B 0.502 0.506 0.518 0.513 0.521 0.568 10</span></a>
<a class="sourceLine" id="cb6-15" data-line-number="15"><span class="co"># C 0.774 0.802 0.811 0.815 0.823 0.838 10</span></a>
<a class="sourceLine" id="cb6-16" data-line-number="16"><span class="co"># D 0.505 0.511 0.532 0.515 0.534 0.627 10</span></a>
<a class="sourceLine" id="cb6-17" data-line-number="17"><span class="co"># E 0.467 0.469 0.495 0.478 0.481 0.676 10</span></a>
<a class="sourceLine" id="cb6-18" data-line-number="18"><span class="co"># F 0.457 0.467 0.478 0.479 0.484 0.509 10</span></a>
<a class="sourceLine" id="cb6-19" data-line-number="19"><span class="co"># G 0.452 0.460 0.467 0.471 0.472 0.478 10</span></a>
<a class="sourceLine" id="cb6-20" data-line-number="20"><span class="co"># H 0.460 0.469 0.473 0.473 0.480 0.486 10</span></a></code></pre></div>
<a class="sourceLine" id="cb6-13" data-line-number="13"><span class="co"># A 0.444 0.449 0.473 0.460 0.466 0.630 10</span></a>
<a class="sourceLine" id="cb6-14" data-line-number="14"><span class="co"># B 0.483 0.496 0.511 0.505 0.535 0.539 10</span></a>
<a class="sourceLine" id="cb6-15" data-line-number="15"><span class="co"># C 0.709 0.839 0.850 0.846 0.886 0.921 10</span></a>
<a class="sourceLine" id="cb6-16" data-line-number="16"><span class="co"># D 0.463 0.483 0.521 0.499 0.548 0.694 10</span></a>
<a class="sourceLine" id="cb6-17" data-line-number="17"><span class="co"># E 0.433 0.451 0.493 0.484 0.513 0.611 10</span></a>
<a class="sourceLine" id="cb6-18" data-line-number="18"><span class="co"># F 0.434 0.450 0.481 0.458 0.484 0.582 10</span></a>
<a class="sourceLine" id="cb6-19" data-line-number="19"><span class="co"># G 0.434 0.443 0.471 0.455 0.489 0.577 10</span></a>
<a class="sourceLine" id="cb6-20" data-line-number="20"><span class="co"># H 0.434 0.436 0.471 0.451 0.480 0.614 10</span></a></code></pre></div>
<p>Of course, when running <code><a href="../reference/mo_property.html">mo_phylum("Firmicutes")</a></code> the function has zero knowledge about the actual microorganism, namely <em>S. aureus</em>. But since the result would be <code>"Firmicutes"</code> too, there is no point in calculating the result. And because this package ‘knows’ all phyla of all known bacteria (according to the Catalogue of Life), it can just return the initial value immediately.</p>
</div>
<div id="results-in-other-languages" class="section level3">
@ -360,13 +360,13 @@
<a class="sourceLine" id="cb7-18" data-line-number="18"><span class="kw"><a href="https://rdrr.io/r/base/print.html">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">4</span>)</a>
<a class="sourceLine" id="cb7-19" data-line-number="19"><span class="co"># Unit: milliseconds</span></a>
<a class="sourceLine" id="cb7-20" data-line-number="20"><span class="co"># expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb7-21" data-line-number="21"><span class="co"># en 20.49 21.64 27.36 23.44 27.96 53.91 10</span></a>
<a class="sourceLine" id="cb7-22" data-line-number="22"><span class="co"># de 23.26 23.37 28.22 24.42 26.13 60.60 10</span></a>
<a class="sourceLine" id="cb7-23" data-line-number="23"><span class="co"># nl 28.62 29.74 36.90 30.18 33.12 72.41 10</span></a>
<a class="sourceLine" id="cb7-24" data-line-number="24"><span class="co"># es 21.77 23.08 27.71 24.75 26.98 55.14 10</span></a>
<a class="sourceLine" id="cb7-25" data-line-number="25"><span class="co"># it 22.54 23.37 25.19 25.25 26.41 29.08 10</span></a>
<a class="sourceLine" id="cb7-26" data-line-number="26"><span class="co"># fr 23.04 23.99 30.97 26.14 30.78 52.61 10</span></a>
<a class="sourceLine" id="cb7-27" data-line-number="27"><span class="co"># pt 22.40 23.07 24.26 23.14 24.44 31.60 10</span></a></code></pre></div>
<a class="sourceLine" id="cb7-21" data-line-number="21"><span class="co"># en 22.05 22.65 29.93 25.35 27.03 53.36 10</span></a>
<a class="sourceLine" id="cb7-22" data-line-number="22"><span class="co"># de 22.86 23.16 30.45 27.22 28.33 62.68 10</span></a>
<a class="sourceLine" id="cb7-23" data-line-number="23"><span class="co"># nl 28.99 29.69 34.37 30.32 31.78 65.15 10</span></a>
<a class="sourceLine" id="cb7-24" data-line-number="24"><span class="co"># es 22.45 23.17 30.84 23.73 28.02 64.67 10</span></a>
<a class="sourceLine" id="cb7-25" data-line-number="25"><span class="co"># it 22.76 24.59 30.36 26.23 29.97 66.70 10</span></a>
<a class="sourceLine" id="cb7-26" data-line-number="26"><span class="co"># fr 23.00 24.20 30.70 27.00 29.22 51.23 10</span></a>
<a class="sourceLine" id="cb7-27" data-line-number="27"><span class="co"># pt 23.31 24.41 26.92 27.31 28.39 31.00 10</span></a></code></pre></div>
<p>Currently supported are German, Dutch, Spanish, Italian, French and Portuguese.</p>
</div>
</div>

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2
docs/articles/index.html
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@ -84,7 +84,7 @@
</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="Latest development version">0.8.0.9037</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</span>
</span>
</div>

4
docs/articles/resistance_predict.html
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@ -41,7 +41,7 @@
</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="Latest development version">0.8.0.9032</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</span>
</span>
</div>
@ -187,7 +187,7 @@
<h1>How to predict antimicrobial resistance</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">18 November 2019</h4>
<h4 class="date">29 November 2019</h4>
<div class="hidden name"><code>resistance_predict.Rmd</code></div>

2
docs/authors.html
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@ -84,7 +84,7 @@
</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="Latest development version">0.8.0.9037</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</span>
</span>
</div>

8
docs/extra.css
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@ -200,11 +200,17 @@ table a:not(.btn):hover, .table a:not(.btn):hover {
/* text below header in manual overview */
.template-reference-index h2 ~ p {
font-size: 16px;
font-size: 15px;
}
.template-reference-topic h2 {
font-size: 24px;
}
.template-reference-topic h3 {
font-size: 18px;
}
.template-reference-topic h4 {
font-size: 15px;
}
/* logos on index page */
.logo_img {

2
docs/index.html
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@ -45,7 +45,7 @@
</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="Latest development version">0.8.0.9037</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</span>
</span>
</div>

13
docs/news/index.html
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@ -84,7 +84,7 @@
</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="Latest development version">0.8.0.9037</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</span>
</span>
</div>
@ -231,14 +231,10 @@
</div>
<div id="amr-0-8-0-9037" class="section level1">
<div id="amr-0-9-0" class="section level1">
<h1 class="page-header">
<a href="#amr-0-8-0-9037" class="anchor"></a>AMR 0.8.0.9037<small> Unreleased </small>
<a href="#amr-0-9-0" class="anchor"></a>AMR 0.9.0<small> Unreleased </small>
</h1>
<div id="last-updated-28-nov-2019" class="section level2">
<h2 class="hasAnchor">
<a href="#last-updated-28-nov-2019" class="anchor"></a><small>Last updated: 28-Nov-2019</small>
</h2>
<div id="breaking" class="section level3">
<h3 class="hasAnchor">
<a href="#breaking" class="anchor"></a>Breaking</h3>
@ -333,7 +329,6 @@
<li>Added Dr. Sofia Ny as contributor</li>
</ul>
</div>
</div>
</div>
<div id="amr-0-8-0" class="section level1">
<h1 class="page-header">
@ -1395,7 +1390,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
<div id="tocnav">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#amr-0-8-0-9037">0.8.0.9037</a></li>
<li><a href="#amr-0-9-0">0.9.0</a></li>
<li><a href="#amr-0-8-0">0.8.0</a></li>
<li><a href="#amr-0-7-1">0.7.1</a></li>
<li><a href="#amr-0-7-0">0.7.0</a></li>

2
docs/reference/AMR-deprecated.html
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@ -85,7 +85,7 @@
</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="Latest development version">0.8.0.9036</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</span>
</span>
</div>

2
docs/reference/AMR.html
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@ -85,7 +85,7 @@
</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="Latest development version">0.8.0.9037</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</span>
</span>
</div>

2
docs/reference/WHOCC.html
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@ -85,7 +85,7 @@
</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="Latest development version">0.8.0.9036</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</span>
</span>
</div>

2
docs/reference/WHONET.html
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@ -85,7 +85,7 @@
</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="Latest development version">0.8.0.9036</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</span>
</span>
</div>

2
docs/reference/ab_property.html
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@ -85,7 +85,7 @@
</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="Latest development version">0.8.0.9036</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</span>
</span>
</div>

2
docs/reference/age.html
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@ -85,7 +85,7 @@
</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="Latest development version">0.8.0.9036</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</span>
</span>
</div>

2
docs/reference/age_groups.html
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@ -85,7 +85,7 @@
</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="Latest development version">0.8.0.9036</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</span>
</span>
</div>

2
docs/reference/antibiotics.html
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@ -85,7 +85,7 @@
</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="Latest development version">0.8.0.9036</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</span>
</span>
</div>

2
docs/reference/as.ab.html
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@ -85,7 +85,7 @@
</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="Latest development version">0.8.0.9036</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</span>
</span>
</div>

2
docs/reference/as.disk.html
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@ -85,7 +85,7 @@
</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="Latest development version">0.8.0.9036</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</span>
</span>
</div>

2
docs/reference/as.mic.html
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@ -85,7 +85,7 @@
</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="Latest development version">0.8.0.9037</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</span>
</span>
</div>

2
docs/reference/as.mo.html
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@ -85,7 +85,7 @@
</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="Latest development version">0.8.0.9036</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</span>
</span>
</div>

22
docs/reference/as.rsi.html
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@ -51,7 +51,7 @@
<script src="../extra.js"></script>
<meta property="og:title" content="Class 'rsi' — as.rsi" />
<meta property="og:description" content="Interpret MIC values and disk diffusion diameters according to EUCAST or CLSI, or clean up existing RSI values. This transforms the input to a new class rsi, which is an ordered factor with levels S &amp;lt; I &amp;lt; R. Invalid antimicrobial interpretations will be translated as NA with a warning." />
<meta property="og:description" content="Interpret MIC values and disk diffusion diameters according to EUCAST or CLSI, or clean up existing R/SI values. This transforms the input to a new class rsi, which is an ordered factor with levels S &amp;lt; I &amp;lt; R. Invalid antimicrobial interpretations will be translated as NA with a warning." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
<meta name="twitter:card" content="summary" />
@ -85,7 +85,7 @@
</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="Latest development version">0.8.0.9037</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</span>
</span>
</div>
@ -234,7 +234,7 @@
</div>
<div class="ref-description">
<p>Interpret MIC values and disk diffusion diameters according to EUCAST or CLSI, or clean up existing RSI values. This transforms the input to a new class <code>rsi</code>, which is an ordered factor with levels <code>S &lt; I &lt; R</code>. Invalid antimicrobial interpretations will be translated as <code>NA</code> with a warning.</p>
<p>Interpret MIC values and disk diffusion diameters according to EUCAST or CLSI, or clean up existing R/SI values. This transforms the input to a new class <code>rsi</code>, which is an ordered factor with levels <code>S &lt; I &lt; R</code>. Invalid antimicrobial interpretations will be translated as <code>NA</code> with a warning.</p>
</div>
<pre class="usage"><span class='fu'>as.rsi</span>(<span class='no'>x</span>, <span class='no'>...</span>)
@ -293,17 +293,19 @@
<p>Run <code><a href='https://rdrr.io/r/base/unique.html'>unique(AMR::rsi_translation$guideline)</a></code> for a list of all supported guidelines.</p>
<p>After using <code>as.rsi()</code>, you can use <code><a href='eucast_rules.html'>eucast_rules()</a></code> to (1) apply inferred susceptibility and resistance based on results of other antimicrobials and (2) apply intrinsic resistance based on taxonomic properties of a microorganism.</p>
<p>The function <code>is.rsi.eligible()</code> returns <code>TRUE</code> when a columns contains at most 5% invalid antimicrobial interpretations (not S and/or I and/or R), and <code>FALSE</code> otherwise. The threshold of 5% can be set with the <code>threshold</code> parameter.</p>
<h2 class="hasAnchor" id="interpretation-of-s-i-and-r"><a class="anchor" href="#interpretation-of-s-i-and-r"></a>Interpretation of S, I and R</h2>
<h2 class="hasAnchor" id="interpretation-of-r-and-s-i"><a class="anchor" href="#interpretation-of-r-and-s-i"></a>Interpretation of R and S/I</h2>
<p>In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I and R as shown below (<a href='http://www.eucast.org/newsiandr/'>http://www.eucast.org/newsiandr/</a>). Results of several consultations on the new definitions are available on the EUCAST website under "Consultations".</p><ul>
<li><p><strong>S</strong> - Susceptible, standard dosing regimen: A microorganism is categorised as "Susceptible, standard dosing regimen", when there is a high likelihood of therapeutic success using a standard dosing regimen of the agent.</p></li>
<li><p><strong>I</strong> - Susceptible, increased exposure: A microorganism is categorised as "Susceptible, Increased exposure" when there is a high likelihood of therapeutic success because exposure to the agent is increased by adjusting the dosing regimen or by its concentration at the site of infection.</p></li>
<li><p><strong>R</strong> - Resistant: A microorganism is categorised as "Resistant" when there is a high likelihood of therapeutic failure even when there is increased exposure.</p></li>
<p>In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories R and S/I as shown below (<a href='http://www.eucast.org/newsiandr/'>http://www.eucast.org/newsiandr/</a>). Results of several consultations on the new definitions are available on the EUCAST website under "Consultations".</p><ul>
<li><p><strong>R = Resistant</strong><br />
A microorganism is categorised as <em>Resistant</em> when there is a high likelihood of therapeutic failure even when there is increased exposure. Exposure is a function of how the mode of administration, dose, dosing interval, infusion time, as well as distribution and excretion of the antimicrobial agent will influence the infecting organism at the site of infection.</p></li>
<li><p><strong>S = Susceptible</strong><br />
A microorganism is categorised as <em>Susceptible, standard dosing regimen</em>, when there is a high likelihood of therapeutic success using a standard dosing regimen of the agent.</p></li>
<li><p><strong>I = Increased exposure, but still susceptible</strong><br />
A microorganism is categorised as <em>Susceptible, Increased exposure</em> when there is a high likelihood of therapeutic success because exposure to the agent is increased by adjusting the dosing regimen or by its concentration at the site of infection.</p></li>
</ul>
<p>Exposure is a function of how the mode of administration, dose, dosing interval, infusion time, as well as distribution and excretion of the antimicrobial agent will influence the infecting organism at the site of infection.</p>
<p>This AMR package honours this new insight. Use <code><a href='proportion.html'>susceptibility()</a></code> (equal to <code><a href='proportion.html'>proportion_SI()</a></code>) to determine antimicrobial susceptibility and <code><a href='count.html'>count_susceptible()</a></code> (equal to <code><a href='count.html'>count_SI()</a></code>) to count susceptible isolates.</p>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
@ -357,7 +359,7 @@
<li><a href="#arguments">Arguments</a></li>
<li><a href="#value">Value</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#interpretation-of-s-i-and-r">Interpretation of S, I and R</a></li>
<li><a href="#interpretation-of-r-and-s-i">Interpretation of R and S/I</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#see-also">See also</a></li>
<li><a href="#examples">Examples</a></li>

2
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@ -86,7 +86,7 @@ This function requires an internet connection." />
</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="Latest development version">0.8.0.9036</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</span>
</span>
</div>

2
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@ -85,7 +85,7 @@
</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="Latest development version">0.8.0.9036</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</span>
</span>
</div>

2
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@ -85,7 +85,7 @@
</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="Latest development version">0.8.0.9036</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</span>
</span>
</div>

2
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@ -85,7 +85,7 @@
</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="Latest development version">0.8.0.9036</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</span>
</span>
</div>

2
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@ -85,7 +85,7 @@
</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="Latest development version">0.8.0.9036</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</span>
</span>
</div>

22
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@ -86,7 +86,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
</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="Latest development version">0.8.0.9036</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</span>
</span>
</div>
@ -278,7 +278,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
</tr>
<tr>
<th>data</th>
<td><p>a <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code> containing columns with class <code>rsi</code> (see <code><a href='as.rsi.html'>as.rsi()</a></code>)</p></td>
<td><p>a <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code> containing columns with class <code><a href='as.rsi.html'>rsi</a></code> (see <code><a href='as.rsi.html'>as.rsi()</a></code>)</p></td>
</tr>
<tr>
<th>translate_ab</th>
@ -306,18 +306,20 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
<p>These functions are meant to count isolates. Use the <code><a href='proportion.html'>resistance()</a></code>/<code><a href='proportion.html'>susceptibility()</a></code> functions to calculate microbial resistance/susceptibility.</p>
<p>The function <code>count_resistant()</code> is equal to the function <code>count_R()</code>. The function <code>count_susceptible()</code> is equal to the function <code>count_SI()</code>.</p>
<p>The function <code>n_rsi()</code> is an alias of <code>count_all()</code>. They can be used to count all available isolates, i.e. where all input antibiotics have an available result (S, I or R). Their use is equal to <code><a href='https://dplyr.tidyverse.org/reference/n_distinct.html'>n_distinct()</a></code>. Their function is equal to <code>count_susceptible(...) + count_resistant(...)</code>.</p>
<p>The function <code>count_df()</code> takes any variable from <code>data</code> that has an <code>rsi</code> class (created with <code><a href='as.rsi.html'>as.rsi()</a></code>) and counts the number of S's, I's and R's. The function <code><a href='proportion.html'>rsi_df()</a></code> works exactly like <code>count_df()</code>, but adds the percentage of S, I and R.</p>
<h2 class="hasAnchor" id="interpretation-of-s-i-and-r"><a class="anchor" href="#interpretation-of-s-i-and-r"></a>Interpretation of S, I and R</h2>
<p>The function <code>count_df()</code> takes any variable from <code>data</code> that has an <code><a href='as.rsi.html'>rsi</a></code> class (created with <code><a href='as.rsi.html'>as.rsi()</a></code>) and counts the number of S's, I's and R's. The function <code><a href='proportion.html'>rsi_df()</a></code> works exactly like <code>count_df()</code>, but adds the percentage of S, I and R.</p>
<h2 class="hasAnchor" id="interpretation-of-r-and-s-i"><a class="anchor" href="#interpretation-of-r-and-s-i"></a>Interpretation of R and S/I</h2>
<p>In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I and R as shown below (<a href='http://www.eucast.org/newsiandr/'>http://www.eucast.org/newsiandr/</a>). Results of several consultations on the new definitions are available on the EUCAST website under "Consultations".</p><ul>
<li><p><strong>S</strong> - Susceptible, standard dosing regimen: A microorganism is categorised as "Susceptible, standard dosing regimen", when there is a high likelihood of therapeutic success using a standard dosing regimen of the agent.</p></li>
<li><p><strong>I</strong> - Susceptible, increased exposure: A microorganism is categorised as "Susceptible, Increased exposure" when there is a high likelihood of therapeutic success because exposure to the agent is increased by adjusting the dosing regimen or by its concentration at the site of infection.</p></li>
<li><p><strong>R</strong> - Resistant: A microorganism is categorised as "Resistant" when there is a high likelihood of therapeutic failure even when there is increased exposure.</p></li>
<p>In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories R and S/I as shown below (<a href='http://www.eucast.org/newsiandr/'>http://www.eucast.org/newsiandr/</a>). Results of several consultations on the new definitions are available on the EUCAST website under "Consultations".</p><ul>
<li><p><strong>R = Resistant</strong><br />
A microorganism is categorised as <em>Resistant</em> when there is a high likelihood of therapeutic failure even when there is increased exposure. Exposure is a function of how the mode of administration, dose, dosing interval, infusion time, as well as distribution and excretion of the antimicrobial agent will influence the infecting organism at the site of infection.</p></li>
<li><p><strong>S = Susceptible</strong><br />
A microorganism is categorised as <em>Susceptible, standard dosing regimen</em>, when there is a high likelihood of therapeutic success using a standard dosing regimen of the agent.</p></li>
<li><p><strong>I = Increased exposure, but still susceptible</strong><br />
A microorganism is categorised as <em>Susceptible, Increased exposure</em> when there is a high likelihood of therapeutic success because exposure to the agent is increased by adjusting the dosing regimen or by its concentration at the site of infection.</p></li>
</ul>
<p>Exposure is a function of how the mode of administration, dose, dosing interval, infusion time, as well as distribution and excretion of the antimicrobial agent will influence the infecting organism at the site of infection.</p>
<p>This AMR package honours this new insight. Use <code><a href='proportion.html'>susceptibility()</a></code> (equal to <code><a href='proportion.html'>proportion_SI()</a></code>) to determine antimicrobial susceptibility and <code>count_susceptible()</code> (equal to <code>count_SI()</code>) to count susceptible isolates.</p>
<h2 class="hasAnchor" id="combination-therapy"><a class="anchor" href="#combination-therapy"></a>Combination therapy</h2>
@ -423,7 +425,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
<li><a href="#arguments">Arguments</a></li>
<li><a href="#value">Value</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#interpretation-of-s-i-and-r">Interpretation of S, I and R</a></li>
<li><a href="#interpretation-of-r-and-s-i">Interpretation of R and S/I</a></li>
<li><a href="#combination-therapy">Combination therapy</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#see-also">See also</a></li>

2
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@ -86,7 +86,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
</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="Latest development version">0.8.0.9036</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</span>
</span>
</div>

4
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@ -85,7 +85,7 @@
</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="Latest development version">0.8.0.9036</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</span>
</span>
</div>
@ -252,7 +252,7 @@
<li><p><code>gender</code><br /> gender of the patient</p></li>
<li><p><code>patient_id</code><br /> ID of the patient</p></li>
<li><p><code>mo</code><br /> ID of microorganism created with <code><a href='as.mo.html'>as.mo()</a></code>, see also <a href='microorganisms.html'>microorganisms</a></p></li>
<li><p><code>PEN:RIF</code><br /> 40 different antibiotics with class <code>rsi</code> (see <code><a href='as.rsi.html'>as.rsi()</a></code>); these column names occur in <a href='antibiotics.html'>antibiotics</a> data set and can be translated with <code><a href='ab_property.html'>ab_name()</a></code></p></li>
<li><p><code>PEN:RIF</code><br /> 40 different antibiotics with class <code><a href='as.rsi.html'>rsi</a></code> (see <code><a href='as.rsi.html'>as.rsi()</a></code>); these column names occur in <a href='antibiotics.html'>antibiotics</a> data set and can be translated with <code><a href='ab_property.html'>ab_name()</a></code></p></li>
</ul>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>

2
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@ -85,7 +85,7 @@
</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="Latest development version">0.8.0.9032</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</span>
</span>
</div>

2
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@ -85,7 +85,7 @@
</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="Latest development version">0.8.0.9036</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</span>
</span>
</div>

2
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@ -85,7 +85,7 @@
</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="Latest development version">0.8.0.9037</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</span>
</span>
</div>

2
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@ -85,7 +85,7 @@
</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="Latest development version">0.8.0.9037</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</span>
</span>
</div>

6
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@ -85,7 +85,7 @@
</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="Latest development version">0.8.0.9036</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</span>
</span>
</div>
@ -300,7 +300,7 @@
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>data</th>
<td><p>a <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code> with column(s) of class <code>rsi</code> (see <code><a href='as.rsi.html'>as.rsi()</a></code>)</p></td>
<td><p>a <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code> with column(s) of class <code><a href='as.rsi.html'>rsi</a></code> (see <code><a href='as.rsi.html'>as.rsi()</a></code>)</p></td>
</tr>
<tr>
<th>position</th>
@ -393,7 +393,7 @@
<p>At default, the names of antibiotics will be shown on the plots using <code><a href='ab_property.html'>ab_name()</a></code>. This can be set with the <code>translate_ab</code> parameter. See <code><a href='count.html'>count_df()</a></code>.</p><h3>The functions</h3>
<p><code>geom_rsi()</code> will take any variable from the data that has an <code>rsi</code> class (created with <code><a href='as.rsi.html'>as.rsi()</a></code>) using <code><a href='proportion.html'>rsi_df()</a></code> and will plot bars with the percentage R, I and S. The default behaviour is to have the bars stacked and to have the different antibiotics on the x axis.</p>
<p><code>geom_rsi()</code> will take any variable from the data that has an <code><a href='as.rsi.html'>rsi</a></code> class (created with <code><a href='as.rsi.html'>as.rsi()</a></code>) using <code><a href='proportion.html'>rsi_df()</a></code> and will plot bars with the percentage R, I and S. The default behaviour is to have the bars stacked and to have the different antibiotics on the x axis.</p>
<p><code>facet_rsi()</code> creates 2d plots (at default based on S/I/R) using <code><a href='https://ggplot2.tidyverse.org/reference/facet_wrap.html'>ggplot2::facet_wrap()</a></code>.</p>
<p><code>scale_y_percent()</code> transforms the y axis to a 0 to 100% range using <code>ggplot2::scale_continuous()</code>.</p>
<p><code>scale_rsi_colours()</code> sets colours to the bars: pastel blue for S, pastel turquoise for I and pastel red for R, using <code>ggplot2::scale_brewer()</code>.</p>

2
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@ -85,7 +85,7 @@
</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="Latest development version">0.8.0.9036</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</span>
</span>
</div>

2
docs/reference/index.html
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@ -84,7 +84,7 @@
</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="Latest development version">0.8.0.9037</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</span>
</span>
</div>

2
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@ -85,7 +85,7 @@
</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="Latest development version">0.8.0.9037</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</span>
</span>
</div>

2
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@ -85,7 +85,7 @@
</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="Latest development version">0.8.0.9036</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</span>
</span>
</div>

2
docs/reference/kurtosis.html
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@ -85,7 +85,7 @@
</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="Latest development version">0.8.0.9037</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</span>
</span>
</div>

17
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@ -85,7 +85,7 @@
</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="Latest development version">0.8.0.9036</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</span>
</span>
</div>
@ -248,24 +248,15 @@
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>x</th>
<td><p>a character vector where matches are sought, or an
object which can be coerced by <code>as.character</code> to a character
vector. <a href='https://rdrr.io/r/base/LongVectors.html'>Long vectors</a> are supported.</p></td>
<td><p>a character vector where matches are sought, or an object which can be coerced by <code><a href='https://rdrr.io/r/base/character.html'>as.character()</a></code> to a character vector.</p></td>
</tr>
<tr>
<th>pattern</th>
<td><p>character string containing a <a href='https://rdrr.io/r/base/regex.html'>regular expression</a>
(or character string for <code>fixed = TRUE</code>) to be matched
in the given character vector. Coerced by
<code><a href='https://rdrr.io/r/base/character.html'>as.character</a></code> to a character string if possible. If a
character vector of length 2 or more is supplied, the first element
is used with a warning. Missing values are allowed except for
<code>regexpr</code> and <code>gregexpr</code>.</p></td>
<td><p>a character string containing a regular expression (or <code><a href='https://rdrr.io/r/base/character.html'>character</a></code> string for <code>fixed = TRUE</code>) to be matched in the given character vector. Coerced by <code><a href='https://rdrr.io/r/base/character.html'>as.character()</a></code> to a character string if possible. If a <code><a href='https://rdrr.io/r/base/character.html'>character</a></code> vector of length 2 or more is supplied, the first element is used with a warning.</p></td>
</tr>
<tr>
<th>ignore.case</th>
<td><p>if <code>FALSE</code>, the pattern matching is <em>case
sensitive</em> and if <code>TRUE</code>, case is ignored during matching.</p></td>
<td><p>if <code>FALSE</code>, the pattern matching is <em>case sensitive</em> and if <code>TRUE</code>, case is ignored during matching.</p></td>
</tr>
</table>

18
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@ -85,7 +85,7 @@
</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="Latest development version">0.8.0.9037</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</span>
</span>
</div>
@ -415,17 +415,19 @@ The Dutch national guideline - Rijksinstituut voor Volksgezondheid en Milieu "WI
<strong>TMP</strong>: trimethoprim (<a href='https://www.whocc.no/atc_ddd_index/?code=J01EA01'>J01EA01</a>),
<strong>SXT</strong>: trimethoprim/sulfamethoxazole (<a href='https://www.whocc.no/atc_ddd_index/?code=J01EE01'>J01EE01</a>),
<strong>VAN</strong>: vancomycin (<a href='https://www.whocc.no/atc_ddd_index/?code=J01XA01'>J01XA01</a>).</p>
<h2 class="hasAnchor" id="interpretation-of-s-i-and-r"><a class="anchor" href="#interpretation-of-s-i-and-r"></a>Interpretation of S, I and R</h2>
<h2 class="hasAnchor" id="interpretation-of-r-and-s-i"><a class="anchor" href="#interpretation-of-r-and-s-i"></a>Interpretation of R and S/I</h2>
<p>In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I and R as shown below (<a href='http://www.eucast.org/newsiandr/'>http://www.eucast.org/newsiandr/</a>). Results of several consultations on the new definitions are available on the EUCAST website under "Consultations".</p><ul>
<li><p><strong>S</strong> - Susceptible, standard dosing regimen: A microorganism is categorised as "Susceptible, standard dosing regimen", when there is a high likelihood of therapeutic success using a standard dosing regimen of the agent.</p></li>
<li><p><strong>I</strong> - Susceptible, increased exposure: A microorganism is categorised as "Susceptible, Increased exposure" when there is a high likelihood of therapeutic success because exposure to the agent is increased by adjusting the dosing regimen or by its concentration at the site of infection.</p></li>
<li><p><strong>R</strong> - Resistant: A microorganism is categorised as "Resistant" when there is a high likelihood of therapeutic failure even when there is increased exposure.</p></li>
<p>In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories R and S/I as shown below (<a href='http://www.eucast.org/newsiandr/'>http://www.eucast.org/newsiandr/</a>). Results of several consultations on the new definitions are available on the EUCAST website under "Consultations".</p><ul>
<li><p><strong>R = Resistant</strong><br />
A microorganism is categorised as <em>Resistant</em> when there is a high likelihood of therapeutic failure even when there is increased exposure. Exposure is a function of how the mode of administration, dose, dosing interval, infusion time, as well as distribution and excretion of the antimicrobial agent will influence the infecting organism at the site of infection.</p></li>
<li><p><strong>S = Susceptible</strong><br />
A microorganism is categorised as <em>Susceptible, standard dosing regimen</em>, when there is a high likelihood of therapeutic success using a standard dosing regimen of the agent.</p></li>
<li><p><strong>I = Increased exposure, but still susceptible</strong><br />
A microorganism is categorised as <em>Susceptible, Increased exposure</em> when there is a high likelihood of therapeutic success because exposure to the agent is increased by adjusting the dosing regimen or by its concentration at the site of infection.</p></li>
</ul>
<p>Exposure is a function of how the mode of administration, dose, dosing interval, infusion time, as well as distribution and excretion of the antimicrobial agent will influence the infecting organism at the site of infection.</p>
<p>This AMR package honours this new insight. Use <code><a href='proportion.html'>susceptibility()</a></code> (equal to <code><a href='proportion.html'>proportion_SI()</a></code>) to determine antimicrobial susceptibility and <code><a href='count.html'>count_susceptible()</a></code> (equal to <code><a href='count.html'>count_SI()</a></code>) to count susceptible isolates.</p>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
@ -455,7 +457,7 @@ The Dutch national guideline - Rijksinstituut voor Volksgezondheid en Milieu "WI
<li><a href="#value">Value</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#antibiotics">Antibiotics</a></li>
<li><a href="#interpretation-of-s-i-and-r">Interpretation of S, I and R</a></li>
<li><a href="#interpretation-of-r-and-s-i">Interpretation of R and S/I</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#examples">Examples</a></li>
</ul>

2
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@ -85,7 +85,7 @@
</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="Latest development version">0.8.0.9036</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</span>
</span>
</div>

2
docs/reference/microorganisms.html
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@ -85,7 +85,7 @@
</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="Latest development version">0.8.0.9037</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</span>
</span>
</div>

2
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@ -85,7 +85,7 @@
</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="Latest development version">0.8.0.9036</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</span>
</span>
</div>

2
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@ -85,7 +85,7 @@
</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="Latest development version">0.8.0.9036</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</span>
</span>
</div>

2
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@ -86,7 +86,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
</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="Latest development version">0.8.0.9036</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</span>
</span>
</div>

2
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@ -85,7 +85,7 @@
</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="Latest development version">0.8.0.9036</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</span>
</span>
</div>

22
docs/reference/proportion.html
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@ -86,7 +86,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
</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="Latest development version">0.8.0.9036</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</span>
</span>
</div>
@ -294,7 +294,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
</tr>
<tr>
<th>data</th>
<td><p>a <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code> containing columns with class <code>rsi</code> (see <code><a href='as.rsi.html'>as.rsi()</a></code>)</p></td>
<td><p>a <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code> containing columns with class <code><a href='as.rsi.html'>rsi</a></code> (see <code><a href='as.rsi.html'>as.rsi()</a></code>)</p></td>
</tr>
<tr>
<th>translate_ab</th>
@ -325,7 +325,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
<p>The function <code>resistance()</code> is equal to the function <code>proportion_R()</code>. The function <code>susceptibility()</code> is equal to the function <code>proportion_SI()</code>.</p>
<p><strong>Remember that you should filter your table to let it contain only first isolates!</strong> This is needed to exclude duplicates and to reduce selection bias. Use <code><a href='first_isolate.html'>first_isolate()</a></code> to determine them in your data set.</p>
<p>These functions are not meant to count isolates, but to calculate the proportion of resistance/susceptibility. Use the <code><a href='count.html'>AMR::count()</a></code> functions to count isolates. The function <code>susceptibility()</code> is essentially equal to <code>count_susceptible() / count_all()</code>. <em>Low counts can infuence the outcome - the <code>proportion</code> functions may camouflage this, since they only return the proportion (albeit being dependent on the <code>minimum</code> parameter).</em></p>
<p>The function <code>proportion_df()</code> takes any variable from <code>data</code> that has an <code>rsi</code> class (created with <code><a href='as.rsi.html'>as.rsi()</a></code>) and calculates the proportions R, I and S. The function <code>rsi_df()</code> works exactly like <code>proportion_df()</code>, but adds the number of isolates.</p>
<p>The function <code>proportion_df()</code> takes any variable from <code>data</code> that has an <code><a href='as.rsi.html'>rsi</a></code> class (created with <code><a href='as.rsi.html'>as.rsi()</a></code>) and calculates the proportions R, I and S. The function <code>rsi_df()</code> works exactly like <code>proportion_df()</code>, but adds the number of isolates.</p>
<h2 class="hasAnchor" id="combination-therapy"><a class="anchor" href="#combination-therapy"></a>Combination therapy</h2>
@ -357,17 +357,19 @@ resistance() should be used to calculate resistance, susceptibility() should be
</pre>
<p>Using <code>only_all_tested</code> has no impact when only using one antibiotic as input.</p>
<h2 class="hasAnchor" id="interpretation-of-s-i-and-r"><a class="anchor" href="#interpretation-of-s-i-and-r"></a>Interpretation of S, I and R</h2>
<h2 class="hasAnchor" id="interpretation-of-r-and-s-i"><a class="anchor" href="#interpretation-of-r-and-s-i"></a>Interpretation of R and S/I</h2>
<p>In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I and R as shown below (<a href='http://www.eucast.org/newsiandr/'>http://www.eucast.org/newsiandr/</a>). Results of several consultations on the new definitions are available on the EUCAST website under "Consultations".</p><ul>
<li><p><strong>S</strong> - Susceptible, standard dosing regimen: A microorganism is categorised as "Susceptible, standard dosing regimen", when there is a high likelihood of therapeutic success using a standard dosing regimen of the agent.</p></li>
<li><p><strong>I</strong> - Susceptible, increased exposure: A microorganism is categorised as "Susceptible, Increased exposure" when there is a high likelihood of therapeutic success because exposure to the agent is increased by adjusting the dosing regimen or by its concentration at the site of infection.</p></li>
<li><p><strong>R</strong> - Resistant: A microorganism is categorised as "Resistant" when there is a high likelihood of therapeutic failure even when there is increased exposure.</p></li>
<p>In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories R and S/I as shown below (<a href='http://www.eucast.org/newsiandr/'>http://www.eucast.org/newsiandr/</a>). Results of several consultations on the new definitions are available on the EUCAST website under "Consultations".</p><ul>
<li><p><strong>R = Resistant</strong><br />
A microorganism is categorised as <em>Resistant</em> when there is a high likelihood of therapeutic failure even when there is increased exposure. Exposure is a function of how the mode of administration, dose, dosing interval, infusion time, as well as distribution and excretion of the antimicrobial agent will influence the infecting organism at the site of infection.</p></li>
<li><p><strong>S = Susceptible</strong><br />
A microorganism is categorised as <em>Susceptible, standard dosing regimen</em>, when there is a high likelihood of therapeutic success using a standard dosing regimen of the agent.</p></li>
<li><p><strong>I = Increased exposure, but still susceptible</strong><br />
A microorganism is categorised as <em>Susceptible, Increased exposure</em> when there is a high likelihood of therapeutic success because exposure to the agent is increased by adjusting the dosing regimen or by its concentration at the site of infection.</p></li>
</ul>
<p>Exposure is a function of how the mode of administration, dose, dosing interval, infusion time, as well as distribution and excretion of the antimicrobial agent will influence the infecting organism at the site of infection.</p>
<p>This AMR package honours this new insight. Use <code>susceptibility()</code> (equal to <code>proportion_SI()</code>) to determine antimicrobial susceptibility and <code><a href='count.html'>count_susceptible()</a></code> (equal to <code><a href='count.html'>count_SI()</a></code>) to count susceptible isolates.</p>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
@ -468,7 +470,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
<li><a href="#value">Value</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#combination-therapy">Combination therapy</a></li>
<li><a href="#interpretation-of-s-i-and-r">Interpretation of S, I and R</a></li>
<li><a href="#interpretation-of-r-and-s-i">Interpretation of R and S/I</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#see-also">See also</a></li>
<li><a href="#examples">Examples</a></li>

2
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@ -85,7 +85,7 @@
</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="Latest development version">0.8.0.9036</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</span>
</span>
</div>

2
docs/reference/reexports.html
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@ -90,7 +90,7 @@ below to see their documentation.
</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="Latest development version">0.8.0.9032</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</span>
</span>
</div>

18
docs/reference/resistance_predict.html
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@ -85,7 +85,7 @@
</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="Latest development version">0.8.0.9036</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</span>
</span>
</div>
@ -359,17 +359,19 @@
<li><p><code>"lin"</code> or <code>"linear"</code>: a linear regression model</p></li>
</ul>
<h2 class="hasAnchor" id="interpretation-of-s-i-and-r"><a class="anchor" href="#interpretation-of-s-i-and-r"></a>Interpretation of S, I and R</h2>
<h2 class="hasAnchor" id="interpretation-of-r-and-s-i"><a class="anchor" href="#interpretation-of-r-and-s-i"></a>Interpretation of R and S/I</h2>
<p>In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I and R as shown below (<a href='http://www.eucast.org/newsiandr/'>http://www.eucast.org/newsiandr/</a>). Results of several consultations on the new definitions are available on the EUCAST website under "Consultations".</p><ul>
<li><p><strong>S</strong> - Susceptible, standard dosing regimen: A microorganism is categorised as "Susceptible, standard dosing regimen", when there is a high likelihood of therapeutic success using a standard dosing regimen of the agent.</p></li>
<li><p><strong>I</strong> - Susceptible, increased exposure: A microorganism is categorised as "Susceptible, Increased exposure" when there is a high likelihood of therapeutic success because exposure to the agent is increased by adjusting the dosing regimen or by its concentration at the site of infection.</p></li>
<li><p><strong>R</strong> - Resistant: A microorganism is categorised as "Resistant" when there is a high likelihood of therapeutic failure even when there is increased exposure.</p></li>
<p>In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories R and S/I as shown below (<a href='http://www.eucast.org/newsiandr/'>http://www.eucast.org/newsiandr/</a>). Results of several consultations on the new definitions are available on the EUCAST website under "Consultations".</p><ul>
<li><p><strong>R = Resistant</strong><br />
A microorganism is categorised as <em>Resistant</em> when there is a high likelihood of therapeutic failure even when there is increased exposure. Exposure is a function of how the mode of administration, dose, dosing interval, infusion time, as well as distribution and excretion of the antimicrobial agent will influence the infecting organism at the site of infection.</p></li>
<li><p><strong>S = Susceptible</strong><br />
A microorganism is categorised as <em>Susceptible, standard dosing regimen</em>, when there is a high likelihood of therapeutic success using a standard dosing regimen of the agent.</p></li>
<li><p><strong>I = Increased exposure, but still susceptible</strong><br />
A microorganism is categorised as <em>Susceptible, Increased exposure</em> when there is a high likelihood of therapeutic success because exposure to the agent is increased by adjusting the dosing regimen or by its concentration at the site of infection.</p></li>
</ul>
<p>Exposure is a function of how the mode of administration, dose, dosing interval, infusion time, as well as distribution and excretion of the antimicrobial agent will influence the infecting organism at the site of infection.</p>
<p>This AMR package honours this new insight. Use <code><a href='proportion.html'>susceptibility()</a></code> (equal to <code><a href='proportion.html'>proportion_SI()</a></code>) to determine antimicrobial susceptibility and <code><a href='count.html'>count_susceptible()</a></code> (equal to <code><a href='count.html'>count_SI()</a></code>) to count susceptible isolates.</p>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
@ -437,7 +439,7 @@
<li><a href="#arguments">Arguments</a></li>
<li><a href="#value">Value</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#interpretation-of-s-i-and-r">Interpretation of S, I and R</a></li>
<li><a href="#interpretation-of-r-and-s-i">Interpretation of R and S/I</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#see-also">See also</a></li>
<li><a href="#examples">Examples</a></li>

2
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@ -85,7 +85,7 @@
</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="Latest development version">0.8.0.9036</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</span>
</span>
</div>

2
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@ -86,7 +86,7 @@ When negative: the left tail is longer; the mass of the distribution is concentr
</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="Latest development version">0.8.0.9036</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</span>
</span>
</div>

2
docs/reference/translate.html
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@ -85,7 +85,7 @@
</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="Latest development version">0.8.0.9036</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.9.0</span>
</span>
</div>

38
git_commit.sh
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@ -1,38 +0,0 @@
#######################################################################
# To push new commits to the premaster branch, run: #
# bash git_premaster.sh "commit message" #
# #
# After successful CRAN checks, merge it to the master branch with: #
# bash git_merge.sh #
#######################################################################
if [ -z "$1" ]; then
echo "FATAL - no commit message"
exit 1
fi
echo "••••••••••••••••••••••••••••••••••••••••••••"
echo "• Updating package date and version number •"
echo "••••••••••••••••••••••••••••••••••••••••••••"
sed -i -- "s/^Date: .*/Date: $(date '+%Y-%m-%d')/" DESCRIPTION
# get latest tags
git pull --tags --quiet
# get version number: latest tag + .90 + number of commits (like 0.6.1.9033)
newversion=`git describe --tags | sed 's/-/.90/' | sed 's/-.*//' | sed 's/v//'`
sed -i -- "s/^Version: .*/Version: ${newversion}/" DESCRIPTION
echo "First 3 lines of DESCRIPTION:"
head -3 DESCRIPTION
echo
echo "•••••••••••••••••••••••"
echo "• Documenting package •"
echo "•••••••••••••••••••••••"
Rscript -e "devtools::document()"
echo
echo "••••••••••••••"
echo "• Committing •"
echo "••••••••••••••"
git add .
git commit -a -m "$1" --quiet
echo
echo "Done."

4
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View File

@ -1,9 +1,13 @@
#######################################################################
# To push new commits to the premaster branch, run: #
# bash git_premaster.sh "commit message" #
# This creates auto version numbering in DESCRIPTION and NEWS.md. #
# #
# After successful CRAN checks, merge it to the master branch with: #
# bash git_merge.sh #
# #
# To prerelease a new version number, run: #
# bash git_premaster.sh "v0.x.x" FALSE "0.x.x" #
#######################################################################
# stash current changes

37
git_premaster.sh
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@ -20,24 +20,31 @@ echo "••••••••••••••••••••••••
echo "• Updating package date and version number •"
echo "••••••••••••••••••••••••••••••••••••••••••••"
sed -i -- "s/^Date: .*/Date: $(date '+%Y-%m-%d')/" DESCRIPTION
# get latest tags
git pull --tags --quiet
current_tag=`git describe --tags --abbrev=0 | sed 's/v//'`
current_commit=`git describe --tags | sed 's/.*-\(.*\)-.*/\1/'`
# combine tag (e.g. 0.1.0) and commit number (like 40) increased by 9000 to indicate beta version
new_version="$current_tag.$((current_commit + 9000))" # results in 0.1.0.9040
if [ -z "$new_version" ]; then
new_version="$current_tag.9000"
echo
echo "** COULD NOT CREATE NEW VERSION NUMBER! **"
echo "Are there some unpushed changes in a new tag? Then mind NEWS.md. Assuming sequence number 9000."
echo
if [ -z "$3" ]; then
# no version number set, so get latest tags to create it
git pull --tags --quiet
current_tag=`git describe --tags --abbrev=0 | sed 's/v//'`
current_commit=`git describe --tags | sed 's/.*-\(.*\)-.*/\1/'`
# combine tag (e.g. 0.1.0) and commit number (like 40) increased by 9000 to indicate beta version
new_version="$current_tag.$((current_commit + 9000))" # results in 0.1.0.9040
if [ -z "$new_version" ]; then
new_version="$current_tag.9000"
echo
echo "** COULD NOT CREATE NEW VERSION NUMBER! **"
echo "Are there some unpushed changes in a new tag? Then mind NEWS.md. Assuming sequence number 9000."
echo
fi
# add date to 2nd line of NEWS.md when no version number was set
sed -i -- "2s/.*/## \<small\>Last updated: $(date '+%d-%b-%Y')\<\/small\>/" NEWS.md
else
new_version=$3
# rmove 2nd line of NEWS.md (the last changed date)
sed -i -- "2s/.*//" NEWS.md
echo "Run devtools::release() or devtools::submit_cran() after this script. Non-interactive mode will not work."
fi
# set version number to DESCRIPTION and NEWS files
sed -i -- "s/^Version: .*/Version: ${new_version}/" DESCRIPTION
# update 1st line of NEWS.md
sed -i -- "1s/.*/# AMR ${new_version}/" NEWS.md
# add date to 2nd line of NEWS.md
sed -i -- "2s/.*/## \<small\>Last updated: $(date '+%d-%b-%Y')\<\/small\>/" NEWS.md
rm *-- || true
echo "• First 3 lines of DESCRIPTION:"
head -3 DESCRIPTION

46
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@ -1,46 +0,0 @@
#######################################################################
# To push new commits to the premaster branch, run: #
# bash git_premaster.sh "commit message" #
# #
# After successful CRAN checks, merge it to the master branch with: #
# bash git_merge.sh #
# #
# Initiate a new release with: #
# bash git_release.sh "new_version_number" #
# This will edit the DESCRIPTION file and the NEWS.md file. #
#######################################################################
if [ -z "$1" ]; then
echo "FATAL - no version number"
exit 1
fi
echo "••••••••••••••••••••••••••••••••••••••••••••"
echo "• Updating package date and version number •"
echo "••••••••••••••••••••••••••••••••••••••••••••"
new_version=${1}
sed -i -- "s/^Date: .*/Date: $(date '+%Y-%m-%d')/" DESCRIPTION
sed -i -- "s/^Version: .*/Version: ${new_version}/" DESCRIPTION
# update 1st line of NEWS.md
sed -i -- "1s/.*/# AMR ${new_version}/" NEWS.md
# rmove 2nd line of NEWS.md
sed -i -- "2s/.*//" NEWS.md
rm *-- || true
echo "• First 3 lines of DESCRIPTION:"
head -3 DESCRIPTION
echo
echo "• First 2 lines of NEWS.md:"
head -2 NEWS.md
echo
echo "••••••••••••••••••••••••••"
echo "• Building complete site •"
echo "••••••••••••••••••••••••••"
echo "• Installing..."
Rscript -e "devtools::load_all(quiet = TRUE)"
Rscript -e "devtools::install(quiet = TRUE, dependencies = FALSE)"
rm -rf docs
Rscript -e "pkgdown::init_site()"
Rscript -e "suppressMessages(pkgdown::build_site(lazy = FALSE, examples = FALSE))"
echo
echo "Run devtools::release() or devtools::submit_cran(). Non-interactive mode (this script) will not work."

4
git_siteonly.sh
View File

@ -1,9 +1,13 @@
#######################################################################
# To push new commits to the premaster branch, run: #
# bash git_premaster.sh "commit message" #
# This creates auto version numbering in DESCRIPTION and NEWS.md. #
# #
# After successful CRAN checks, merge it to the master branch with: #
# bash git_merge.sh #
# #
# To prerelease a new version number, run: #
# bash git_premaster.sh "v0.x.x" FALSE "0.x.x" #
#######################################################################
bash git_premaster.sh "website update" FALSE

17
man/as.rsi.Rd
View File

@ -41,7 +41,7 @@ is.rsi.eligible(x, threshold = 0.05)
Ordered factor with new class \code{\link{rsi}}
}
\description{
Interpret MIC values and disk diffusion diameters according to EUCAST or CLSI, or clean up existing RSI values. This transforms the input to a new class \code{\link{rsi}}, which is an ordered factor with levels \verb{S < I < R}. Invalid antimicrobial interpretations will be translated as \code{NA} with a warning.
Interpret MIC values and disk diffusion diameters according to EUCAST or CLSI, or clean up existing R/SI values. This transforms the input to a new class \code{\link{rsi}}, which is an ordered factor with levels \verb{S < I < R}. Invalid antimicrobial interpretations will be translated as \code{NA} with a warning.
}
\details{
Run \code{unique(AMR::rsi_translation$guideline)} for a list of all supported guidelines.
@ -50,17 +50,18 @@ After using \code{\link[=as.rsi]{as.rsi()}}, you can use \code{\link[=eucast_rul
The function \code{\link[=is.rsi.eligible]{is.rsi.eligible()}} returns \code{TRUE} when a columns contains at most 5\% invalid antimicrobial interpretations (not S and/or I and/or R), and \code{FALSE} otherwise. The threshold of 5\% can be set with the \code{threshold} parameter.
}
\section{Interpretation of S, I and R}{
\section{Interpretation of R and S/I}{
In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I and R as shown below (\url{http://www.eucast.org/newsiandr/}). Results of several consultations on the new definitions are available on the EUCAST website under "Consultations".
In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories R and S/I as shown below (\url{http://www.eucast.org/newsiandr/}). Results of several consultations on the new definitions are available on the EUCAST website under "Consultations".
\itemize{
\item \strong{S} - Susceptible, standard dosing regimen: A microorganism is categorised as "Susceptible, standard dosing regimen", when there is a high likelihood of therapeutic success using a standard dosing regimen of the agent.
\item \strong{I} - Susceptible, increased exposure: A microorganism is categorised as "Susceptible, Increased exposure" when there is a high likelihood of therapeutic success because exposure to the agent is increased by adjusting the dosing regimen or by its concentration at the site of infection.
\item \strong{R} - Resistant: A microorganism is categorised as "Resistant" when there is a high likelihood of therapeutic failure even when there is increased exposure.
\item \strong{R = Resistant}\cr
A microorganism is categorised as \emph{Resistant} when there is a high likelihood of therapeutic failure even when there is increased exposure. Exposure is a function of how the mode of administration, dose, dosing interval, infusion time, as well as distribution and excretion of the antimicrobial agent will influence the infecting organism at the site of infection.
\item \strong{S = Susceptible}\cr
A microorganism is categorised as \emph{Susceptible, standard dosing regimen}, when there is a high likelihood of therapeutic success using a standard dosing regimen of the agent.
\item \strong{I = Increased exposure, but still susceptible}\cr
A microorganism is categorised as \emph{Susceptible, Increased exposure} when there is a high likelihood of therapeutic success because exposure to the agent is increased by adjusting the dosing regimen or by its concentration at the site of infection.
}
Exposure is a function of how the mode of administration, dose, dosing interval, infusion time, as well as distribution and excretion of the antimicrobial agent will influence the infecting organism at the site of infection.
This AMR package honours this new insight. Use \code{\link[=susceptibility]{susceptibility()}} (equal to \code{\link[=proportion_SI]{proportion_SI()}}) to determine antimicrobial susceptibility and \code{\link[=count_susceptible]{count_susceptible()}} (equal to \code{\link[=count_SI]{count_SI()}}) to count susceptible isolates.
}

15
man/count.Rd
View File

@ -72,17 +72,18 @@ The function \code{\link[=n_rsi]{n_rsi()}} is an alias of \code{\link[=count_all
The function \code{\link[=count_df]{count_df()}} takes any variable from \code{data} that has an \code{\link{rsi}} class (created with \code{\link[=as.rsi]{as.rsi()}}) and counts the number of S's, I's and R's. The function \code{\link[=rsi_df]{rsi_df()}} works exactly like \code{\link[=count_df]{count_df()}}, but adds the percentage of S, I and R.
}
\section{Interpretation of S, I and R}{
\section{Interpretation of R and S/I}{
In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I and R as shown below (\url{http://www.eucast.org/newsiandr/}). Results of several consultations on the new definitions are available on the EUCAST website under "Consultations".
In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories R and S/I as shown below (\url{http://www.eucast.org/newsiandr/}). Results of several consultations on the new definitions are available on the EUCAST website under "Consultations".
\itemize{
\item \strong{S} - Susceptible, standard dosing regimen: A microorganism is categorised as "Susceptible, standard dosing regimen", when there is a high likelihood of therapeutic success using a standard dosing regimen of the agent.
\item \strong{I} - Susceptible, increased exposure: A microorganism is categorised as "Susceptible, Increased exposure" when there is a high likelihood of therapeutic success because exposure to the agent is increased by adjusting the dosing regimen or by its concentration at the site of infection.
\item \strong{R} - Resistant: A microorganism is categorised as "Resistant" when there is a high likelihood of therapeutic failure even when there is increased exposure.
\item \strong{R = Resistant}\cr
A microorganism is categorised as \emph{Resistant} when there is a high likelihood of therapeutic failure even when there is increased exposure. Exposure is a function of how the mode of administration, dose, dosing interval, infusion time, as well as distribution and excretion of the antimicrobial agent will influence the infecting organism at the site of infection.
\item \strong{S = Susceptible}\cr
A microorganism is categorised as \emph{Susceptible, standard dosing regimen}, when there is a high likelihood of therapeutic success using a standard dosing regimen of the agent.
\item \strong{I = Increased exposure, but still susceptible}\cr
A microorganism is categorised as \emph{Susceptible, Increased exposure} when there is a high likelihood of therapeutic success because exposure to the agent is increased by adjusting the dosing regimen or by its concentration at the site of infection.
}
Exposure is a function of how the mode of administration, dose, dosing interval, infusion time, as well as distribution and excretion of the antimicrobial agent will influence the infecting organism at the site of infection.
This AMR package honours this new insight. Use \code{\link[=susceptibility]{susceptibility()}} (equal to \code{\link[=proportion_SI]{proportion_SI()}}) to determine antimicrobial susceptibility and \code{\link[=count_susceptible]{count_susceptible()}} (equal to \code{\link[=count_SI]{count_SI()}}) to count susceptible isolates.
}

15
man/like.Rd
View File

@ -16,20 +16,11 @@ x \%like\% pattern
x \%like_case\% pattern
}
\arguments{
\item{x}{a character vector where matches are sought, or an
object which can be coerced by \code{as.character} to a character
vector. \link[base]{Long vectors} are supported.}
\item{x}{a character vector where matches are sought, or an object which can be coerced by \code{\link[=as.character]{as.character()}} to a character vector.}
\item{pattern}{character string containing a \link[base]{regular expression}
(or character string for \code{fixed = TRUE}) to be matched
in the given character vector. Coerced by
\code{\link[base]{as.character}} to a character string if possible. If a
character vector of length 2 or more is supplied, the first element
is used with a warning. Missing values are allowed except for
\code{regexpr} and \code{gregexpr}.}
\item{pattern}{a character string containing a regular expression (or \code{\link{character}} string for \code{fixed = TRUE}) to be matched in the given character vector. Coerced by \code{\link[=as.character]{as.character()}} to a character string if possible. If a \code{\link{character}} vector of length 2 or more is supplied, the first element is used with a warning.}
\item{ignore.case}{if \code{FALSE}, the pattern matching is \emph{case
sensitive} and if \code{TRUE}, case is ignored during matching.}
\item{ignore.case}{if \code{FALSE}, the pattern matching is \emph{case sensitive} and if \code{TRUE}, case is ignored during matching.}
}
\value{
A \code{\link{logical}} vector

15
man/mdro.Rd
View File

@ -179,17 +179,18 @@ The following antibiotics are used for the functions \code{\link[=eucast_rules]{
\strong{VAN}: vancomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XA01}{J01XA01}).
}
\section{Interpretation of S, I and R}{
\section{Interpretation of R and S/I}{
In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I and R as shown below (\url{http://www.eucast.org/newsiandr/}). Results of several consultations on the new definitions are available on the EUCAST website under "Consultations".
In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories R and S/I as shown below (\url{http://www.eucast.org/newsiandr/}). Results of several consultations on the new definitions are available on the EUCAST website under "Consultations".
\itemize{
\item \strong{S} - Susceptible, standard dosing regimen: A microorganism is categorised as "Susceptible, standard dosing regimen", when there is a high likelihood of therapeutic success using a standard dosing regimen of the agent.
\item \strong{I} - Susceptible, increased exposure: A microorganism is categorised as "Susceptible, Increased exposure" when there is a high likelihood of therapeutic success because exposure to the agent is increased by adjusting the dosing regimen or by its concentration at the site of infection.
\item \strong{R} - Resistant: A microorganism is categorised as "Resistant" when there is a high likelihood of therapeutic failure even when there is increased exposure.
\item \strong{R = Resistant}\cr
A microorganism is categorised as \emph{Resistant} when there is a high likelihood of therapeutic failure even when there is increased exposure. Exposure is a function of how the mode of administration, dose, dosing interval, infusion time, as well as distribution and excretion of the antimicrobial agent will influence the infecting organism at the site of infection.
\item \strong{S = Susceptible}\cr
A microorganism is categorised as \emph{Susceptible, standard dosing regimen}, when there is a high likelihood of therapeutic success using a standard dosing regimen of the agent.
\item \strong{I = Increased exposure, but still susceptible}\cr
A microorganism is categorised as \emph{Susceptible, Increased exposure} when there is a high likelihood of therapeutic success because exposure to the agent is increased by adjusting the dosing regimen or by its concentration at the site of infection.
}
Exposure is a function of how the mode of administration, dose, dosing interval, infusion time, as well as distribution and excretion of the antimicrobial agent will influence the infecting organism at the site of infection.
This AMR package honours this new insight. Use \code{\link[=susceptibility]{susceptibility()}} (equal to \code{\link[=proportion_SI]{proportion_SI()}}) to determine antimicrobial susceptibility and \code{\link[=count_susceptible]{count_susceptible()}} (equal to \code{\link[=count_SI]{count_SI()}}) to count susceptible isolates.
}

15
man/proportion.Rd
View File

@ -118,17 +118,18 @@ and that, in combination therapies, for \code{only_all_tested = FALSE} applies t
Using \code{only_all_tested} has no impact when only using one antibiotic as input.
}
\section{Interpretation of S, I and R}{
\section{Interpretation of R and S/I}{
In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I and R as shown below (\url{http://www.eucast.org/newsiandr/}). Results of several consultations on the new definitions are available on the EUCAST website under "Consultations".
In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories R and S/I as shown below (\url{http://www.eucast.org/newsiandr/}). Results of several consultations on the new definitions are available on the EUCAST website under "Consultations".
\itemize{
\item \strong{S} - Susceptible, standard dosing regimen: A microorganism is categorised as "Susceptible, standard dosing regimen", when there is a high likelihood of therapeutic success using a standard dosing regimen of the agent.
\item \strong{I} - Susceptible, increased exposure: A microorganism is categorised as "Susceptible, Increased exposure" when there is a high likelihood of therapeutic success because exposure to the agent is increased by adjusting the dosing regimen or by its concentration at the site of infection.
\item \strong{R} - Resistant: A microorganism is categorised as "Resistant" when there is a high likelihood of therapeutic failure even when there is increased exposure.
\item \strong{R = Resistant}\cr
A microorganism is categorised as \emph{Resistant} when there is a high likelihood of therapeutic failure even when there is increased exposure. Exposure is a function of how the mode of administration, dose, dosing interval, infusion time, as well as distribution and excretion of the antimicrobial agent will influence the infecting organism at the site of infection.
\item \strong{S = Susceptible}\cr
A microorganism is categorised as \emph{Susceptible, standard dosing regimen}, when there is a high likelihood of therapeutic success using a standard dosing regimen of the agent.
\item \strong{I = Increased exposure, but still susceptible}\cr
A microorganism is categorised as \emph{Susceptible, Increased exposure} when there is a high likelihood of therapeutic success because exposure to the agent is increased by adjusting the dosing regimen or by its concentration at the site of infection.
}
Exposure is a function of how the mode of administration, dose, dosing interval, infusion time, as well as distribution and excretion of the antimicrobial agent will influence the infecting organism at the site of infection.
This AMR package honours this new insight. Use \code{\link[=susceptibility]{susceptibility()}} (equal to \code{\link[=proportion_SI]{proportion_SI()}}) to determine antimicrobial susceptibility and \code{\link[=count_susceptible]{count_susceptible()}} (equal to \code{\link[=count_SI]{count_SI()}}) to count susceptible isolates.
}

15
man/resistance_predict.Rd
View File

@ -100,17 +100,18 @@ Valid options for the statistical model (parameter \code{model}) are:
\item \code{"lin"} or \code{"linear"}: a linear regression model
}
}
\section{Interpretation of S, I and R}{
\section{Interpretation of R and S/I}{
In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I and R as shown below (\url{http://www.eucast.org/newsiandr/}). Results of several consultations on the new definitions are available on the EUCAST website under "Consultations".
In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories R and S/I as shown below (\url{http://www.eucast.org/newsiandr/}). Results of several consultations on the new definitions are available on the EUCAST website under "Consultations".
\itemize{
\item \strong{S} - Susceptible, standard dosing regimen: A microorganism is categorised as "Susceptible, standard dosing regimen", when there is a high likelihood of therapeutic success using a standard dosing regimen of the agent.
\item \strong{I} - Susceptible, increased exposure: A microorganism is categorised as "Susceptible, Increased exposure" when there is a high likelihood of therapeutic success because exposure to the agent is increased by adjusting the dosing regimen or by its concentration at the site of infection.
\item \strong{R} - Resistant: A microorganism is categorised as "Resistant" when there is a high likelihood of therapeutic failure even when there is increased exposure.
\item \strong{R = Resistant}\cr
A microorganism is categorised as \emph{Resistant} when there is a high likelihood of therapeutic failure even when there is increased exposure. Exposure is a function of how the mode of administration, dose, dosing interval, infusion time, as well as distribution and excretion of the antimicrobial agent will influence the infecting organism at the site of infection.
\item \strong{S = Susceptible}\cr
A microorganism is categorised as \emph{Susceptible, standard dosing regimen}, when there is a high likelihood of therapeutic success using a standard dosing regimen of the agent.
\item \strong{I = Increased exposure, but still susceptible}\cr
A microorganism is categorised as \emph{Susceptible, Increased exposure} when there is a high likelihood of therapeutic success because exposure to the agent is increased by adjusting the dosing regimen or by its concentration at the site of infection.
}
Exposure is a function of how the mode of administration, dose, dosing interval, infusion time, as well as distribution and excretion of the antimicrobial agent will influence the infecting organism at the site of infection.
This AMR package honours this new insight. Use \code{\link[=susceptibility]{susceptibility()}} (equal to \code{\link[=proportion_SI]{proportion_SI()}}) to determine antimicrobial susceptibility and \code{\link[=count_susceptible]{count_susceptible()}} (equal to \code{\link[=count_SI]{count_SI()}}) to count susceptible isolates.
}

8
pkgdown/extra.css
View File

@ -200,11 +200,17 @@ table a:not(.btn):hover, .table a:not(.btn):hover {
/* text below header in manual overview */
.template-reference-index h2 ~ p {
font-size: 16px;
font-size: 15px;
}
.template-reference-topic h2 {
font-size: 24px;
}
.template-reference-topic h3 {
font-size: 18px;
}
.template-reference-topic h4 {
font-size: 15px;
}
/* logos on index page */
.logo_img {

2
vignettes/AMR.Rmd
View File

@ -431,7 +431,7 @@ ggplot(data_1st %>% group_by(genus)) +
geom_rsi(x = "genus") +
# split plots on antibiotic
facet_rsi(facet = "antibiotic") +
# make R red, I yellow and S green
# set colours to the R/SI interpretations
scale_rsi_colours() +
# show percentages on y axis
scale_y_percent(breaks = 0:4 * 25) +

26
vignettes/WHONET.Rmd
View File

@ -67,9 +67,10 @@ We also created a package dedicated to data cleaning and checking, called the `c
So let's check our data, with a couple of frequency tables:
```{r, results = 'asis'}
# our newly created `mo` variable
data %>% freq(mo, nmax = 10)
# our newly created `mo` variable, put in the mo_name() function
data %>% freq(mo_name(mo), nmax = 10)
```
```{r, results = 'asis'}
# our transformed antibiotic columns
# amoxicillin/clavulanic acid (J01CR02) as an example
data %>% freq(AMC_ND2)
@ -77,8 +78,21 @@ data %>% freq(AMC_ND2)
### A first glimpse at results
An easy ggplot will already give a lot of information, using the included `ggplot_rsi()` function:
An easy `ggplot` will already give a lot of information, using the included `ggplot_rsi()` function:
```{r}
ggplot_rsi(data, translate_ab = 'ab')
```{r, eval = FALSE}
data %>%
group_by(Country) %>%
select(Country, AMP_ND2, AMC_ED20, CAZ_ED10, CIP_ED5) %>%
ggplot_rsi(translate_ab = 'ab', facet = "Country", datalabels = FALSE)
```
```{r, echo = FALSE}
# on very old and some new releases of R, this may lead to an error
tryCatch(data %>%
group_by(Country) %>%
select(Country, AMP_ND2, AMC_ED20, CAZ_ED10, CIP_ED5) %>%
ggplot_rsi(translate_ab = 'ab', facet = "Country", datalabels = FALSE) %>%
print(),
error = function(e) base::invisible())
```