* Any progress bar will now only show in interactive mode (i.e. not in R Markdown)
* Speed improvement for `mdro()` and `filter_ab_class()`
* New option `arrows_textangled` for `ggplot_pca()` to indicate whether the text at the end of the arrows should be angled (defaults to `TRUE`, as it was in previous versions)
* Added parenteral DDD to benzylpenicillin
* Fixed a bug where `as.mic()` could not handle dots without a leading zero (like `"<=.25`)
### Other
* Moved primary location of this project from GitLab to [GitHub](https://github.com/msberends/AMR), giving us native support for automated syntax checking without being dependent on external services such as AppVeyor and Travis CI.
@ -132,7 +134,7 @@ This software is now out of beta and considered stable. Nonetheless, this packag
### New
* Support for the newest [EUCAST Clinical Breakpoint Tables v.10.0](http://www.eucast.org/clinical_breakpoints/), valid from 1 January 2020. This affects translation of MIC and disk zones using `as.rsi()` and inferred resistance and susceptibility using `eucast_rules()`.
* The repository of this package now contains a clean version of the EUCAST and CLSI guidelines from 2011-2020 to translate MIC and disk diffusion values to R/SI: <https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt>. This **allows for machine reading these guidelines**, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. This file used to process the EUCAST Clinical Breakpoints Excel file [can be found here](https://gitlab.com/msberends/AMR/blob/master/data-raw/read_EUCAST.R).
* The repository of this package now contains a clean version of the EUCAST and CLSI guidelines from 2011-2020 to translate MIC and disk diffusion values to R/SI: <https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt>. This **allows for machine reading these guidelines**, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. This file used to process the EUCAST Clinical Breakpoints Excel file [can be found here](https://github.com/msberends/AMR/blob/master/data-raw/read_EUCAST.R).
* Support for LOINC and SNOMED codes
* Support for LOINC codes in the `antibiotics` data set. Use `ab_loinc()` to retrieve LOINC codes, or use a LOINC code for input in any `ab_*` function:
```r
@ -449,9 +451,7 @@ This software is now out of beta and considered stable. Nonetheless, this packag
* All references to antibiotics in our package now use EARS-Net codes, like `AMX` for amoxicillin
* Functions `atc_certe`, `ab_umcg` and `atc_trivial_nl` have been removed
* All `atc_*` functions are superceded by `ab_*` functions
* All output will be translated by using an included translation file which [can be viewed here](https://gitlab.com/msberends/AMR/blob/master/data-raw/translations.tsv).
Please [create an issue in one of our repositories](https://gitlab.com/msberends/AMR/issues/new?issue[title]=Translation%20suggestion) if you want additions in this file.
* All output will be translated by using an included translation file which [can be viewed here](https://github.com/msberends/AMR/blob/master/data-raw/translations.tsv)
* Improvements to plotting AMR results with `ggplot_rsi()`:
* New parameter `colours` to set the bar colours
* New parameters `title`, `subtitle`, `caption`, `x.title` and `y.title` to set titles and axis descriptions
@ -475,9 +475,7 @@ This software is now out of beta and considered stable. Nonetheless, this packag
freq(age) %>%
boxplot()
```
* Removed all hardcoded EUCAST rules and replaced them with a new reference file which [can be viewed here](https://gitlab.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv).
Please [create an issue in one of our repositories](https://gitlab.com/msberends/AMR/issues/new?issue[title]=EUCAST%20edit) if you want changes in this file.
* Removed all hardcoded EUCAST rules and replaced them with a new reference file which [can be viewed here](https://github.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv)
* Added ceftazidim intrinsic resistance to *Streptococci*
* Changed default settings for `age_groups()`, to let groups of fives and tens end with 100+ instead of 120+
* Fix for `freq()` for when all values are `NA`
@ -694,7 +692,7 @@ We've got a new website: [https://msberends.gitlab.io/AMR](https://msberends.git
# AMR 0.5.0
#### New
* Repository moved to GitLab: https://gitlab.com/msberends/AMR
* Repository moved to GitLab
* Function `count_all` to get all available isolates (that like all `portion_*` and `count_*` functions also supports `summarise` and `group_by`), the old `n_rsi` is now an alias of `count_all`
* Function `get_locale` to determine language for language-dependent output for some `mo_*` functions. This is now the default value for their `language` parameter, by which the system language will be used at default.
* Data sets `microorganismsDT`, `microorganisms.prevDT`, `microorganisms.unprevDT` and `microorganisms.oldDT` to improve the speed of `as.mo`. They are for reference only, since they are primarily for internal use of `as.mo`.
#' Use these functions to return a specific property of an antibiotic from the [antibiotics] data set. All input values will be evaluated internally with [as.ab()].
#' @inheritSection lifecycle Stable lifecycle
#' @param x any (vector of) text that can be coerced to a valid microorganism code with [as.ab()]
#' @param x any (vector of) text that can be coerced to a valid antibiotic code with [as.ab()]
#' @param tolower logical to indicate whether the first character of every output should be transformed to a lower case character. This will lead to e.g. "polymyxin B" and not "polymyxin b".
#' @param property one of the column names of one of the [antibiotics] data set
#' @param language language of the returned text, defaults to system language (see [get_locale()]) and can also be set with `getOption("AMR_locale")`. Use `language = NULL` or `language = ""` to prevent translation.
<li><p>Any progress bar will now only show in interactive mode (i.e.not in R Markdown)</p></li>
<li><p>Speed improvement for <code><ahref="../reference/mdro.html">mdro()</a></code> and <code><ahref="../reference/filter_ab_class.html">filter_ab_class()</a></code></p></li>
<li><p>New option <code>arrows_textangled</code> for <code><ahref="../reference/ggplot_pca.html">ggplot_pca()</a></code> to indicate whether the text at the end of the arrows should be angled (defaults to <code>TRUE</code>, as it was in previous versions)</p></li>
<li><p>Added parenteral DDD to benzylpenicillin</p></li>
<li><p>Fixed a bug where <code><ahref="../reference/as.mic.html">as.mic()</a></code> could not handle dots without a leading zero (like <code>"<=.25</code>)</p></li>
</ul>
</div>
<divid="other"class="section level3">
@ -447,7 +449,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<ahref="#new-2"class="anchor"></a>New</h3>
<ul>
<li>Support for the newest <ahref="http://www.eucast.org/clinical_breakpoints/">EUCAST Clinical Breakpoint Tables v.10.0</a>, valid from 1 January 2020. This affects translation of MIC and disk zones using <code><ahref="../reference/as.rsi.html">as.rsi()</a></code> and inferred resistance and susceptibility using <code><ahref="../reference/eucast_rules.html">eucast_rules()</a></code>.</li>
<li>The repository of this package now contains a clean version of the EUCAST and CLSI guidelines from 2011-2020 to translate MIC and disk diffusion values to R/SI: <ahref="https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt" class="uri">https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt</a>. This <strong>allows for machine reading these guidelines</strong>, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. This file used to process the EUCAST Clinical Breakpoints Excel file <ahref="https://gitlab.com/msberends/AMR/blob/master/data-raw/read_EUCAST.R">can be found here</a>.</li>
<li>The repository of this package now contains a clean version of the EUCAST and CLSI guidelines from 2011-2020 to translate MIC and disk diffusion values to R/SI: <ahref="https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt" class="uri">https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt</a>. This <strong>allows for machine reading these guidelines</strong>, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. This file used to process the EUCAST Clinical Breakpoints Excel file <ahref="https://github.com/msberends/AMR/blob/master/data-raw/read_EUCAST.R">can be found here</a>.</li>
<li>Support for LOINC and SNOMED codes
<ul>
<li>
@ -865,43 +867,39 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<li><p>Fixed a critical bug in <code><ahref="../reference/first_isolate.html">first_isolate()</a></code> where missing species would lead to incorrect FALSEs. This bug was not present in AMR v0.5.0, but was in v0.6.0 and v0.6.1.</p></li>
<li><p>Fixed a bug in <code><ahref="../reference/eucast_rules.html">eucast_rules()</a></code> where antibiotics from WHONET software would not be recognised</p></li>
<li>
<p>Completely reworked the <code>antibiotics</code> data set:</p>
<li>Fixed a critical bug in <code><ahref="../reference/first_isolate.html">first_isolate()</a></code> where missing species would lead to incorrect FALSEs. This bug was not present in AMR v0.5.0, but was in v0.6.0 and v0.6.1.</li>
<li>Fixed a bug in <code><ahref="../reference/eucast_rules.html">eucast_rules()</a></code> where antibiotics from WHONET software would not be recognised</li>
<li>Completely reworked the <code>antibiotics</code> data set:
<ul>
<li>
<p>All entries now have 3 different identifiers:</p>
<li>All entries now have 3 different identifiers:
<ul>
<li>Column <code>ab</code> contains a human readable EARS-Net code, used by ECDC and WHO/WHONET - this is the primary identifier used in this package</li>
<li>Column <code>atc</code> contains the ATC code, used by WHO/WHOCC</li>
<li>Column <code>cid</code> contains the CID code (Compound ID), used by PubChem</li>
</ul>
</li>
<li><p>Based on the Compound ID, almost 5,000 official brand names have been added from many different countries</p></li>
<li><p>All references to antibiotics in our package now use EARS-Net codes, like <code>AMX</code> for amoxicillin</p></li>
<li><p>Functions <code>atc_certe</code>, <code>ab_umcg</code> and <code>atc_trivial_nl</code> have been removed</p></li>
<li><p>All <code>atc_*</code> functions are superceded by <code>ab_*</code> functions</p></li>
<li>
<p>All output will be translated by using an included translation file which <ahref="https://gitlab.com/msberends/AMR/blob/master/data-raw/translations.tsv">can be viewed here</a>.</p>
<p>Please <ahref="https://gitlab.com/msberends/AMR/issues/new?issue%5Btitle%5D=Translation%20suggestion">create an issue in one of our repositories</a> if you want additions in this file.</p>
<li>Based on the Compound ID, almost 5,000 official brand names have been added from many different countries</li>
<li>All references to antibiotics in our package now use EARS-Net codes, like <code>AMX</code> for amoxicillin</li>
<li>Functions <code>atc_certe</code>, <code>ab_umcg</code> and <code>atc_trivial_nl</code> have been removed</li>
<li>All <code>atc_*</code> functions are superceded by <code>ab_*</code> functions</li>
<li>All output will be translated by using an included translation file which <ahref="https://github.com/msberends/AMR/blob/master/data-raw/translations.tsv">can be viewed here</a>
</li>
</ul>
</li>
<li>
<p>Improvements to plotting AMR results with <code><ahref="../reference/ggplot_rsi.html">ggplot_rsi()</a></code>:</p>
<li>Improvements to plotting AMR results with <code><ahref="../reference/ggplot_rsi.html">ggplot_rsi()</a></code>:
<ul>
<li>New parameter <code>colours</code> to set the bar colours</li>
<li>New parameters <code>title</code>, <code>subtitle</code>, <code>caption</code>, <code>x.title</code> and <code>y.title</code> to set titles and axis descriptions</li>
</ul>
</li>
<li><p>Improved intelligence of looking up antibiotic columns in a data set using <code><ahref="../reference/guess_ab_col.html">guess_ab_col()</a></code></p></li>
<li><p>Added ~5,000 more old taxonomic names to the <code>microorganisms.old</code> data set, which leads to better results finding when using the <code><ahref="../reference/as.mo.html">as.mo()</a></code> function</p></li>
<li><p>This package now honours the new EUCAST insight (2019) that S and I are but classified as susceptible, where I is defined as ‘increased exposure’ and not ‘intermediate’ anymore. For functions like <code><ahref="../reference/AMR-deprecated.html">portion_df()</a></code> and <code><ahref="../reference/count.html">count_df()</a></code> this means that their new parameter <code>combine_SI</code> is TRUE at default. Our plotting function <code><ahref="../reference/ggplot_rsi.html">ggplot_rsi()</a></code> also reflects this change since it uses <code><ahref="../reference/count.html">count_df()</a></code> internally.</p></li>
<li><p>The <code><ahref="../reference/age.html">age()</a></code> function gained a new parameter <code>exact</code> to determine ages with decimals</p></li>
<li>Improved intelligence of looking up antibiotic columns in a data set using <code><ahref="../reference/guess_ab_col.html">guess_ab_col()</a></code>
</li>
<li>Added ~5,000 more old taxonomic names to the <code>microorganisms.old</code> data set, which leads to better results finding when using the <code><ahref="../reference/as.mo.html">as.mo()</a></code> function</li>
<li>This package now honours the new EUCAST insight (2019) that S and I are but classified as susceptible, where I is defined as ‘increased exposure’ and not ‘intermediate’ anymore. For functions like <code><ahref="../reference/AMR-deprecated.html">portion_df()</a></code> and <code><ahref="../reference/count.html">count_df()</a></code> this means that their new parameter <code>combine_SI</code> is TRUE at default. Our plotting function <code><ahref="../reference/ggplot_rsi.html">ggplot_rsi()</a></code> also reflects this change since it uses <code><ahref="../reference/count.html">count_df()</a></code> internally.</li>
<li>The <code><ahref="../reference/age.html">age()</a></code> function gained a new parameter <code>exact</code> to determine ages with decimals</li>
<li><p>speed improvement for microbial IDs</p></li>
<li><p>fixed factor level names for R Markdown</p></li>
@ -919,20 +917,22 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
</li>
</ul>
</li>
<li>
<p>Removed all hardcoded EUCAST rules and replaced them with a new reference file which <ahref="https://gitlab.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv">can be viewed here</a>.</p>
<p>Please <ahref="https://gitlab.com/msberends/AMR/issues/new?issue%5Btitle%5D=EUCAST%20edit">create an issue in one of our repositories</a> if you want changes in this file.</p>
</li>
<li><p>Added ceftazidim intrinsic resistance to <em>Streptococci</em></p></li>
<li><p>Changed default settings for <code><ahref="../reference/age_groups.html">age_groups()</a></code>, to let groups of fives and tens end with 100+ instead of 120+</p></li>
<li><p>Fix for <code>freq()</code> for when all values are <code>NA</code></p></li>
<li><p>Fix for <code><ahref="../reference/first_isolate.html">first_isolate()</a></code> for when dates are missing</p></li>
<li><p>Improved speed of <code><ahref="../reference/guess_ab_col.html">guess_ab_col()</a></code></p></li>
<li><p>Function <code><ahref="../reference/as.mo.html">as.mo()</a></code> now gently interprets any number of whitespace characters (like tabs) as one space</p></li>
<li><p>Function <code><ahref="../reference/as.mo.html">as.mo()</a></code> now returns <code>UNKNOWN</code> for <code>"con"</code> (WHONET ID of ‘contamination’) and returns <code>NA</code> for <code>"xxx"</code>(WHONET ID of ‘no growth’)</p></li>
<li><p>Small algorithm fix for <code><ahref="../reference/as.mo.html">as.mo()</a></code></p></li>
<li><p>Removed viruses from data set <code>microorganisms.codes</code> and cleaned it up</p></li>
<li><p>Fix for <code><ahref="../reference/mo_property.html">mo_shortname()</a></code> where species would not be determined correctly</p></li>
<li>Removed all hardcoded EUCAST rules and replaced them with a new reference file which <ahref="https://github.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv">can be viewed here</a>
</li>
<li>Added ceftazidim intrinsic resistance to <em>Streptococci</em>
</li>
<li>Changed default settings for <code><ahref="../reference/age_groups.html">age_groups()</a></code>, to let groups of fives and tens end with 100+ instead of 120+</li>
<li>Fix for <code>freq()</code> for when all values are <code>NA</code>
</li>
<li>Fix for <code><ahref="../reference/first_isolate.html">first_isolate()</a></code> for when dates are missing</li>
<li>Improved speed of <code><ahref="../reference/guess_ab_col.html">guess_ab_col()</a></code>
</li>
<li>Function <code><ahref="../reference/as.mo.html">as.mo()</a></code> now gently interprets any number of whitespace characters (like tabs) as one space</li>
<li>Function <code><ahref="../reference/as.mo.html">as.mo()</a></code> now returns <code>UNKNOWN</code> for <code>"con"</code> (WHONET ID of ‘contamination’) and returns <code>NA</code> for <code>"xxx"</code>(WHONET ID of ‘no growth’)</li>
<li>Small algorithm fix for <code><ahref="../reference/as.mo.html">as.mo()</a></code>
</li>
<li>Removed viruses from data set <code>microorganisms.codes</code> and cleaned it up</li>
<li>Fix for <code><ahref="../reference/mo_property.html">mo_shortname()</a></code> where species would not be determined correctly</li>
</ul>
</div>
<divid="other-7"class="section level4">
@ -1198,8 +1198,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
<h4class="hasAnchor">
<ahref="#new-8"class="anchor"></a>New</h4>
<ul>
<li>Repository moved to GitLab: <ahref="https://gitlab.com/msberends/AMR"class="uri">https://gitlab.com/msberends/AMR</a>
</li>
<li>Repository moved to GitLab</li>
<li>Function <code>count_all</code> to get all available isolates (that like all <code>portion_*</code> and <code>count_*</code> functions also supports <code>summarise</code> and <code>group_by</code>), the old <code>n_rsi</code> is now an alias of <code>count_all</code>
</li>
<li>Function <code>get_locale</code> to determine language for language-dependent output for some <code>mo_*</code> functions. This is now the default value for their <code>language</code> parameter, by which the system language will be used at default.</li>
ab_property(x, property = "name", language = get_locale(), ...)
}
\arguments{
\item{x}{any (vector of) text that can be coerced to a valid microorganism code with \code{\link[=as.ab]{as.ab()}}}
\item{x}{any (vector of) text that can be coerced to a valid antibiotic code with \code{\link[=as.ab]{as.ab()}}}
\item{language}{language of the returned text, defaults to system language (see \code{\link[=get_locale]{get_locale()}}) and can also be set with \code{getOption("AMR_locale")}. Use \code{language = NULL} or \code{language = ""} to prevent translation.}
