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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9057</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9061</small>
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@@ -49,50 +49,82 @@
</div>
<div class="section level2">
<h2 class="pkg-version" data-toc-text="3.0.1.9057" id="amr-3019057">AMR 3.0.1.9057<a class="anchor" aria-label="anchor" href="#amr-3019057"></a></h2>
<p>Planned as v3.1.0, May 2026.</p>
<h2 class="pkg-version" data-toc-text="3.0.1.9061" id="amr-3019061">AMR 3.0.1.9061<a class="anchor" aria-label="anchor" href="#amr-3019061"></a></h2>
<p>Planned as v3.1.0, end of June 2026.</p>
<div class="section level4">
<h4 id="new-3-0-1-9057">New<a class="anchor" aria-label="anchor" href="#new-3-0-1-9057"></a></h4>
<h4 id="breaking-changes-3-0-1-9061">Breaking Changes<a class="anchor" aria-label="anchor" href="#breaking-changes-3-0-1-9061"></a></h4>
<ul><li>The former <em>kingdoms</em> Bacteria and Archaea are now each divided into four kingdoms with new top-level <em>domains</em> ‘Bacteria’ and ‘Archaea’ (Göker and Oren, 2024, DOI: 10.1099/ijsem.0.006242). Following this, a new <code>domain</code> column in the <code>microorganisms</code> data set was added, and more importantly, <code><a href="../reference/mo_property.html">mo_kingdom()</a></code> now returns the formal kingdom (e.g. <code>"Pseudomonadati"</code> instead of <code>"Bacteria"</code>). Use <code><a href="../reference/mo_property.html">mo_domain()</a></code> for the old behaviour. For non-prokaryotic kingdoms (Fungi, Protozoa, etc.), <code>kingdom</code> and <code>domain</code> are identical.</li>
<li>Faster parallel computing via the <code>future</code> package for <code><a href="../reference/as.sir.html">as.sir()</a></code> and <code><a href="../reference/antibiogram.html">wisca()</a></code>: a non-sequential plan (e.g. <code>future::plan(future::multisession)</code>) must be active before using <code>parallel = TRUE</code>.</li>
</ul></div>
<div class="section level4">
<h4 id="new-3-0-1-9061">New<a class="anchor" aria-label="anchor" href="#new-3-0-1-9061"></a></h4>
<ul><li>EUCAST 2026 and CLSI 2026 breakpoints: over 5,700 new breakpoints added to the <code>clinical_breakpoints</code> data set; EUCAST 2026 is now the default for all MIC and disk diffusion interpretations</li>
<li>Wildtype/Non-wildtype (WT/NWT) output when using ECOFF-based interpretation, by setting <code>breakpoint_type = "ECOFF"</code> in <code><a href="../reference/as.sir.html">as.sir()</a></code>; WT/NWT results are fully supported in all resistance/susceptibility functions and plots (<a href="https://github.com/msberends/AMR/issues/254" class="external-link">#254</a>)</li>
<li>Faster parallel computing via the <code>future</code> package; <strong>breaking change</strong>: a non-sequential plan (e.g. <code>future::plan(future::multisession)</code>) must be active before using <code>parallel = TRUE</code>; <code><a href="../reference/antibiogram.html">antibiogram()</a></code> and <code><a href="../reference/antibiogram.html">wisca()</a></code> now also support <code>parallel = TRUE</code> (<a href="https://github.com/msberends/AMR/issues/281" class="external-link">#281</a>)</li>
<li>
<em>tidymodels</em> integration for using SIR, MIC and disk data in modelling pipelines: <code><a href="../reference/amr-tidymodels.html">step_mic_log2()</a></code>, <code><a href="../reference/amr-tidymodels.html">step_sir_numeric()</a></code>, and new column selectors <code><a href="../reference/amr-tidymodels.html">all_sir()</a></code>, <code><a href="../reference/amr-tidymodels.html">all_mic()</a></code>, <code><a href="../reference/amr-tidymodels.html">all_disk()</a></code>
</li>
<li>New <code>esbl_isolates</code> data set for practising AMR modelling</li>
<li>New antimicrobial selectors: <code><a href="../reference/antimicrobial_selectors.html">ionophores()</a></code>, <code><a href="../reference/antimicrobial_selectors.html">peptides()</a></code>, <code><a href="../reference/antimicrobial_selectors.html">phosphonics()</a></code>, <code><a href="../reference/antimicrobial_selectors.html">spiropyrimidinetriones()</a></code>
</li>
<li>New antimicrobials: cefepime/taniborbactam (<code>FTA</code>), ceftibuten/avibactam (<code>CTA</code>), clorobiocin (<code>CLB</code>), kasugamycin (<code>KAS</code>), ostreogrycin (<code>OST</code>), taniborbactam (<code>TAN</code>), thiostrepton (<code>THS</code>), xeruborbactam (<code>XER</code>), zorbamycin (<code>ZOR</code>)</li>
<li>New <code><a href="../reference/interpretive_rules.html">interpretive_rules()</a></code>, a unified function for EUCAST and CLSI interpretive rules; <code><a href="../reference/interpretive_rules.html">eucast_rules()</a></code> is now a wrapper around it (<a href="https://github.com/msberends/AMR/issues/235" class="external-link">#235</a>, <a href="https://github.com/msberends/AMR/issues/259" class="external-link">#259</a>)</li>
<li>New <code>morphology</code> column in the <code>microorganisms</code> data set and corresponding <code><a href="../reference/mo_property.html">mo_morphology()</a></code> function, returning the cell shape of bacteria. Data sourced from BacDive; values prefixed with “likely” are extrapolated from genus-level consensus. New <code>add_morphology</code> argument was added to <code><a href="../reference/mo_property.html">mo_gramstain()</a></code> to return combined results such as <code>"Gram-negative rods"</code>.</li>
<li>New <code><a href="../reference/amr_course.html">amr_course()</a></code> to download and unpack course or webinar materials from GitHub in one call</li>
<li>Typed missing value constants <code>NA_ab_</code> and <code>NA_mo_</code>, for use in pipelines that need missing values of a specific class</li>
<li>New <code><a href="../reference/antibiogram.html">wisca_plot()</a></code> to assess the susceptibility and incidence distributions from the Monte Carlo simulations</li>
</ul></div>
<div class="section level4">
<h4 id="fixes-3-0-1-9057">Fixes<a class="anchor" aria-label="anchor" href="#fixes-3-0-1-9057"></a></h4>
<h4 id="fixed-3-0-1-9061">Fixed<a class="anchor" aria-label="anchor" href="#fixed-3-0-1-9061"></a></h4>
<ul><li>
<code><a href="../reference/as.sir.html">as.sir()</a></code> on data frames: already-converted SIR columns no longer dropped on re-run (<a href="https://github.com/msberends/AMR/issues/278" class="external-link">#278</a>); metadata columns (e.g. <code>patient</code>, <code>ward</code>) no longer misidentified as antibiotic columns; <code>info = FALSE</code> now suppresses all messages, including for columns without breakpoints</li>
<code><a href="../reference/as.sir.html">as.sir()</a></code>
<ul><li>On data frames: already-converted SIR columns no longer dropped on re-run (<a href="https://github.com/msberends/AMR/issues/278" class="external-link">#278</a>)</li>
<li>Metadata columns (e.g. <code>patient</code>, <code>ward</code>) no longer misidentified as antibiotic columns</li>
<li>
<code>info = FALSE</code> now suppresses all messages, including for columns without breakpoints</li>
<li>Assumption of disk zones are now preferred over MIC values when input is only whole numbers (<a href="https://github.com/msberends/AMR/issues/291" class="external-link">#291</a>)</li>
</ul></li>
<li>
<code><a href="../reference/as.mic.html">as.mic()</a></code>: values in scientific notation (e.g. <code>1e-3</code>) now handled correctly</li>
<li>
<code><a href="../reference/as.ab.html">as.ab()</a></code>: codes containing “PH” or “TH” (e.g. <code>ETH</code>, <code>PHE</code>) no longer return <code>NA</code> when mixed with unrecognised input (<a href="https://github.com/msberends/AMR/issues/245" class="external-link">#245</a>)</li>
<li>Combined MIC/SIR input values (e.g. <code>"&lt;= 0.002; S"</code> or <code>"S; 0.002"</code>) now parsed correctly (<a href="https://github.com/msberends/AMR/issues/252" class="external-link">#252</a>)</li>
<li>
<code><a href="../reference/as.mo.html">as.mo()</a></code>:
<ul><li>Input of the form <code>"X complex"</code> now falls back to <code>"X"</code> when the complex is not a distinct taxon in the database, preventing <code>NA</code> results for valid clinical descriptions such as <code>"Proteus vulgaris complex"</code> (<a href="https://github.com/msberends/AMR/issues/287" class="external-link">#287</a>)</li>
<li>Abbreviated-genus input (e.g. <code>"S. apiospermum"</code>) now correctly ranks candidates whose species epithet exactly matches the input above more-prevalent organisms whose species does not match; fixes <code>"S. apiospermum"</code> resolving to <em>Staphylococcus</em> instead of <em>Scedosporium apiospermum</em> (<a href="https://github.com/msberends/AMR/issues/288" class="external-link">#288</a>)</li>
</ul></li>
<li>
<code>get_author_year()</code> in the microorganism reproduction script now strips <code>emend.</code> and everything after it, so <code>ref</code> reflects the combination authority rather than the emendation author (e.g. <em>Rhodococcus equi</em> now returns “Goodfellow et al., 1977” instead of “Nouioui et al., 2018”)</li>
<li>BRMO classification now includes bacterial complexes (<a href="https://github.com/msberends/AMR/issues/275" class="external-link">#275</a>)</li>
<li>Translation fixes for Italian CoNS/CoPS names (<a href="https://github.com/msberends/AMR/issues/256" class="external-link">#256</a>), Dutch antimicrobials, and <code><a href="../reference/proportion.html">sir_df()</a></code> foreign-language output (<a href="https://github.com/msberends/AMR/issues/272" class="external-link">#272</a>)</li>
<li>Fixed some EUCAST Expert Rules, mostly on <em>S. pneumoniae</em>
</li>
</ul></div>
<div class="section level4">
<h4 id="updates-3-0-1-9057">Updates<a class="anchor" aria-label="anchor" href="#updates-3-0-1-9057"></a></h4>
<ul><li>
<h4 id="updated-3-0-1-9061">Updated<a class="anchor" aria-label="anchor" href="#updated-3-0-1-9061"></a></h4>
<ul><li>Taxonomic update for all microorganisms, now updated to June 2026</li>
<li>
<code><a href="../reference/mo_property.html">mo_kingdom()</a></code> now returns the formal taxonomic kingdom; a one-time note per session explains the change when querying bacterial or archaeal records.</li>
<li>
<code><a href="../reference/mo_property.html">mo_taxonomy()</a></code> and <code><a href="../reference/mo_property.html">mo_info()</a></code> gained <code>domain</code> for the list output</li>
<li>
<code><a href="../reference/antibiogram.html">antibiogram()</a></code> and <code><a href="../reference/antibiogram.html">wisca()</a></code> now also support parallel computing via the argument <code>parallel = TRUE</code> (<a href="https://github.com/msberends/AMR/issues/281" class="external-link">#281</a>)</li>
<li>
<code><a href="../reference/AMR-deprecated.html">custom_eucast_rules()</a></code> renamed to <code><a href="../reference/custom_interpretive_rules.html">custom_interpretive_rules()</a></code>; old name deprecated but still works (<a href="https://github.com/msberends/AMR/issues/268" class="external-link">#268</a>)</li>
<li>
<code><a href="../reference/mdro.html">mdro()</a></code> can now infer resistance from a drug+inhibitor combination when the base drug column is absent (e.g. piperacillin inferred from piperacillin/tazobactam); controlled via new <code>infer_from_combinations</code> argument (default <code>TRUE</code>) (<a href="https://github.com/msberends/AMR/issues/209" class="external-link">#209</a>)</li>
<li>
<code><a href="../reference/antibiogram.html">wisca()</a></code> now more strictly follows Bielicki et al. (2016) by using <math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mtext mathvariant="normal">Beta</mtext><mo stretchy="false" form="prefix">(</mo><mn>1</mn><mo>,</mo><mn>9999</mn><mo stretchy="false" form="postfix">)</mo></mrow><annotation encoding="application/x-tex">\text{Beta}(1, 9999)</annotation></semantics></math> for intrinsically resistant pairs, forcing near-zero susceptibility regardless of observed data (based on EUCAST Expected Resistant Phenotypes)</li>
<li>
<code><a href="../reference/proportion.html">susceptibility()</a></code> / <code><a href="../reference/proportion.html">resistance()</a></code>: new <code>guideline</code> argument (default EUCAST) to ensure the ‘I’ category is interpreted correctly per guideline</li>
<li>Capped MIC handling in <code><a href="../reference/as.sir.html">as.sir()</a></code> reworked into four clearly defined options: <code>"none"</code>, <code>"conservative"</code> (new default), <code>"standard"</code>, <code>"lenient"</code> (<a href="https://github.com/msberends/AMR/issues/243" class="external-link">#243</a>)</li>
<li>
<code><a href="../reference/as.mic.html">as.mic()</a></code> / <code><a href="../reference/as.mic.html">rescale_mic()</a></code>: new <code>round_to_next_log2</code> argument to round values up to the nearest log2 dilution level (<a href="https://github.com/msberends/AMR/issues/255" class="external-link">#255</a>)</li>
<li>
<code>antimicrobials$group</code> now a <code>list</code>, so drugs belonging to multiple groups are fully represented; use <code>ab_group(all_groups = TRUE)</code> to retrieve all groups for a drug (<a href="https://github.com/msberends/AMR/issues/246" class="external-link">#246</a>)</li>
<li>New antimicrobials added: cefepime/taniborbactam (<code>FTA</code>), ceftibuten/avibactam (<code>CTA</code>), clorobiocin (<code>CLB</code>), kasugamycin (<code>KAS</code>), ostreogrycin (<code>OST</code>), taniborbactam (<code>TAN</code>), thiostrepton (<code>THS</code>), xeruborbactam (<code>XER</code>), zorbamycin (<code>ZOR</code>)</li>
<li>Improved console messages with clickable links throughout, powered by <code>cli</code> (<a href="https://github.com/msberends/AMR/issues/191" class="external-link">#191</a>, <a href="https://github.com/msberends/AMR/issues/265" class="external-link">#265</a>)</li>
<code>antimicrobials$group</code> is now a <code>list</code>, so that drugs belonging to multiple groups are fully represented; use <code>ab_group(all_groups = TRUE)</code> to retrieve all groups for a drug (<a href="https://github.com/msberends/AMR/issues/246" class="external-link">#246</a>)</li>
<li>Improved console messages with clickable links throughout, powered by <code>cli</code> if it is installed (<a href="https://github.com/msberends/AMR/issues/191" class="external-link">#191</a>, <a href="https://github.com/msberends/AMR/issues/265" class="external-link">#265</a>)</li>
<li>
<code><a href="../reference/as.disk.html">as.disk()</a></code>: input validation is now more strict, rejecting values that are not recognisable as a numeric disk zone diameter</li>
</ul></div>
</div>
<div class="section level2">

116
news/index.md
View File

@@ -1,8 +1,27 @@
# Changelog
## AMR 3.0.1.9057
## AMR 3.0.1.9061
Planned as v3.1.0, May 2026.
Planned as v3.1.0, end of June 2026.
#### Breaking Changes
- The former *kingdoms* Bacteria and Archaea are now each divided into
four kingdoms with new top-level *domains* ‘Bacteria’ and ‘Archaea’
(Göker and Oren, 2024, DOI: 10.1099/ijsem.0.006242). Following this, a
new `domain` column in the `microorganisms` data set was added, and
more importantly,
[`mo_kingdom()`](https://amr-for-r.org/reference/mo_property.md) now
returns the formal kingdom (e.g. `"Pseudomonadati"` instead of
`"Bacteria"`). Use
[`mo_domain()`](https://amr-for-r.org/reference/mo_property.md) for
the old behaviour. For non-prokaryotic kingdoms (Fungi, Protozoa,
etc.), `kingdom` and `domain` are identical.
- Faster parallel computing via the `future` package for
[`as.sir()`](https://amr-for-r.org/reference/as.sir.md) and
[`wisca()`](https://amr-for-r.org/reference/antibiogram.md): a
non-sequential plan (e.g. `future::plan(future::multisession)`) must
be active before using `parallel = TRUE`.
#### New
@@ -14,14 +33,6 @@ Planned as v3.1.0, May 2026.
[`as.sir()`](https://amr-for-r.org/reference/as.sir.md); WT/NWT
results are fully supported in all resistance/susceptibility functions
and plots ([\#254](https://github.com/msberends/AMR/issues/254))
- Faster parallel computing via the `future` package; **breaking
change**: a non-sequential plan
(e.g. `future::plan(future::multisession)`) must be active before
using `parallel = TRUE`;
[`antibiogram()`](https://amr-for-r.org/reference/antibiogram.md) and
[`wisca()`](https://amr-for-r.org/reference/antibiogram.md) now also
support `parallel = TRUE`
([\#281](https://github.com/msberends/AMR/issues/281))
- *tidymodels* integration for using SIR, MIC and disk data in modelling
pipelines:
[`step_mic_log2()`](https://amr-for-r.org/reference/amr-tidymodels.md),
@@ -36,6 +47,10 @@ Planned as v3.1.0, May 2026.
[`peptides()`](https://amr-for-r.org/reference/antimicrobial_selectors.md),
[`phosphonics()`](https://amr-for-r.org/reference/antimicrobial_selectors.md),
[`spiropyrimidinetriones()`](https://amr-for-r.org/reference/antimicrobial_selectors.md)
- New antimicrobials: cefepime/taniborbactam (`FTA`),
ceftibuten/avibactam (`CTA`), clorobiocin (`CLB`), kasugamycin
(`KAS`), ostreogrycin (`OST`), taniborbactam (`TAN`), thiostrepton
(`THS`), xeruborbactam (`XER`), zorbamycin (`ZOR`)
- New
[`interpretive_rules()`](https://amr-for-r.org/reference/interpretive_rules.md),
a unified function for EUCAST and CLSI interpretive rules;
@@ -43,20 +58,35 @@ Planned as v3.1.0, May 2026.
is now a wrapper around it
([\#235](https://github.com/msberends/AMR/issues/235),
[\#259](https://github.com/msberends/AMR/issues/259))
- New `morphology` column in the `microorganisms` data set and
corresponding
[`mo_morphology()`](https://amr-for-r.org/reference/mo_property.md)
function, returning the cell shape of bacteria. Data sourced from
BacDive; values prefixed with “likely” are extrapolated from
genus-level consensus. New `add_morphology` argument was added to
[`mo_gramstain()`](https://amr-for-r.org/reference/mo_property.md) to
return combined results such as `"Gram-negative rods"`.
- New [`amr_course()`](https://amr-for-r.org/reference/amr_course.md) to
download and unpack course or webinar materials from GitHub in one
call
- Typed missing value constants `NA_ab_` and `NA_mo_`, for use in
pipelines that need missing values of a specific class
- New [`wisca_plot()`](https://amr-for-r.org/reference/antibiogram.md)
to assess the susceptibility and incidence distributions from the
Monte Carlo simulations
#### Fixes
#### Fixed
- [`as.sir()`](https://amr-for-r.org/reference/as.sir.md) on data
frames: already-converted SIR columns no longer dropped on re-run
([\#278](https://github.com/msberends/AMR/issues/278)); metadata
columns (e.g. `patient`, `ward`) no longer misidentified as antibiotic
columns; `info = FALSE` now suppresses all messages, including for
columns without breakpoints
- [`as.sir()`](https://amr-for-r.org/reference/as.sir.md)
- On data frames: already-converted SIR columns no longer dropped on
re-run ([\#278](https://github.com/msberends/AMR/issues/278))
- Metadata columns (e.g. `patient`, `ward`) no longer misidentified as
antibiotic columns
- `info = FALSE` now suppresses all messages, including for columns
without breakpoints
- Assumption of disk zones are now preferred over MIC values when
input is only whole numbers
([\#291](https://github.com/msberends/AMR/issues/291))
- [`as.mic()`](https://amr-for-r.org/reference/as.mic.md): values in
scientific notation (e.g. `1e-3`) now handled correctly
- [`as.ab()`](https://amr-for-r.org/reference/as.ab.md): codes
@@ -66,6 +96,23 @@ Planned as v3.1.0, May 2026.
- Combined MIC/SIR input values (e.g. `"<= 0.002; S"` or `"S; 0.002"`)
now parsed correctly
([\#252](https://github.com/msberends/AMR/issues/252))
- [`as.mo()`](https://amr-for-r.org/reference/as.mo.md):
- Input of the form `"X complex"` now falls back to `"X"` when the
complex is not a distinct taxon in the database, preventing `NA`
results for valid clinical descriptions such as
`"Proteus vulgaris complex"`
([\#287](https://github.com/msberends/AMR/issues/287))
- Abbreviated-genus input (e.g. `"S. apiospermum"`) now correctly
ranks candidates whose species epithet exactly matches the input
above more-prevalent organisms whose species does not match; fixes
`"S. apiospermum"` resolving to *Staphylococcus* instead of
*Scedosporium apiospermum*
([\#288](https://github.com/msberends/AMR/issues/288))
- `get_author_year()` in the microorganism reproduction script now
strips `emend.` and everything after it, so `ref` reflects the
combination authority rather than the emendation author
(e.g. *Rhodococcus equi* now returns “Goodfellow et al., 1977” instead
of “Nouioui et al., 2018”)
- BRMO classification now includes bacterial complexes
([\#275](https://github.com/msberends/AMR/issues/275))
- Translation fixes for Italian CoNS/CoPS names
@@ -74,9 +121,21 @@ Planned as v3.1.0, May 2026.
[`sir_df()`](https://amr-for-r.org/reference/proportion.md)
foreign-language output
([\#272](https://github.com/msberends/AMR/issues/272))
- Fixed some EUCAST Expert Rules, mostly on *S. pneumoniae*
#### Updates
#### Updated
- Taxonomic update for all microorganisms, now updated to June 2026
- [`mo_kingdom()`](https://amr-for-r.org/reference/mo_property.md) now
returns the formal taxonomic kingdom; a one-time note per session
explains the change when querying bacterial or archaeal records.
- [`mo_taxonomy()`](https://amr-for-r.org/reference/mo_property.md) and
[`mo_info()`](https://amr-for-r.org/reference/mo_property.md) gained
`domain` for the list output
- [`antibiogram()`](https://amr-for-r.org/reference/antibiogram.md) and
[`wisca()`](https://amr-for-r.org/reference/antibiogram.md) now also
support parallel computing via the argument `parallel = TRUE`
([\#281](https://github.com/msberends/AMR/issues/281))
- [`custom_eucast_rules()`](https://amr-for-r.org/reference/AMR-deprecated.md)
renamed to
[`custom_interpretive_rules()`](https://amr-for-r.org/reference/custom_interpretive_rules.md);
@@ -87,6 +146,11 @@ Planned as v3.1.0, May 2026.
is absent (e.g. piperacillin inferred from piperacillin/tazobactam);
controlled via new `infer_from_combinations` argument (default `TRUE`)
([\#209](https://github.com/msberends/AMR/issues/209))
- [`wisca()`](https://amr-for-r.org/reference/antibiogram.md) now more
strictly follows Bielicki et al. (2016) by using
$`\text{Beta}(1, 9999)`$ for intrinsically resistant pairs, forcing
near-zero susceptibility regardless of observed data (based on EUCAST
Expected Resistant Phenotypes)
- [`susceptibility()`](https://amr-for-r.org/reference/proportion.md) /
[`resistance()`](https://amr-for-r.org/reference/proportion.md): new
`guideline` argument (default EUCAST) to ensure the ‘I’ category is
@@ -100,17 +164,17 @@ Planned as v3.1.0, May 2026.
[`rescale_mic()`](https://amr-for-r.org/reference/as.mic.md): new
`round_to_next_log2` argument to round values up to the nearest log2
dilution level ([\#255](https://github.com/msberends/AMR/issues/255))
- `antimicrobials$group` now a `list`, so drugs belonging to multiple
groups are fully represented; use `ab_group(all_groups = TRUE)` to
retrieve all groups for a drug
- `antimicrobials$group` is now a `list`, so that drugs belonging to
multiple groups are fully represented; use
`ab_group(all_groups = TRUE)` to retrieve all groups for a drug
([\#246](https://github.com/msberends/AMR/issues/246))
- New antimicrobials added: cefepime/taniborbactam (`FTA`),
ceftibuten/avibactam (`CTA`), clorobiocin (`CLB`), kasugamycin
(`KAS`), ostreogrycin (`OST`), taniborbactam (`TAN`), thiostrepton
(`THS`), xeruborbactam (`XER`), zorbamycin (`ZOR`)
- Improved console messages with clickable links throughout, powered by
`cli` ([\#191](https://github.com/msberends/AMR/issues/191),
`cli` if it is installed
([\#191](https://github.com/msberends/AMR/issues/191),
[\#265](https://github.com/msberends/AMR/issues/265))
- [`as.disk()`](https://amr-for-r.org/reference/as.disk.md): input
validation is now more strict, rejecting values that are not
recognisable as a numeric disk zone diameter
## AMR 3.0.1