<li>Function <code><ahref="../reference/AMR-deprecated.html">guess_mo()</a></code> is now deprecated in favour of <code><ahref="../reference/as.mo.html">as.mo()</a></code> and will be remover in future versions</li>
<li>Fixed a critical bug in <code><ahref="../reference/eucast_rules.html">eucast_rules()</a></code> where some rules that depend on previous applied rules would not be applied adequately</li>
<li>Improvements for <code><ahref="../reference/as.mo.html">as.mo()</a></code>:</li>
<li>Finds better results when input is in other languages</li>
<li><p><code>"S. aureus - please mind: MRSA"</code>. The last word will be stripped, after which the function will try to find a match. If it does not, the second last word will be stripped, etc. Again, a warning will be thrown that the result <em>Staphylococcus aureus</em> (<code>B_STPHY_AUR</code>) needs review.</p></li>
<li><p><code>"D. spartina"</code>. This is the abbreviation of an old taxonomic name: <em>Didymosphaeria spartinae</em> (the last "e" was missing from the input). This fungus was renamed to <em>Leptosphaeria obiones</em>, so a warning will be thrown that this result (<code>F_LPTSP_OBI</code>) needs review.</p></li>
</ul>
<p><code>guess_mo</code> is an alias of <code>as.mo</code>.</p>
@ -341,12 +337,11 @@ The <code><a href='mo_property.html'>mo_property</a></code> functions (like <cod
<spanclass='fu'>as.mo</span>(<spanclass='st'>"GAS"</span>) <spanclass='co'># Group A Streptococci</span>
<spanclass='fu'>as.mo</span>(<spanclass='st'>"GBS"</span>) <spanclass='co'># Group B Streptococci</span>
<spanclass='co'># guess_mo is an alias of as.mo and works the same</span>
<spanclass='fu'>guess_mo</span>(<spanclass='st'>"S. epidermidis"</span>) <spanclass='co'># will remain species: B_STPHY_EPI</span>
<spanclass='fu'>guess_mo</span>(<spanclass='st'>"S. epidermidis"</span>, <spanclass='kw'>Becker</span><spanclass='kw'>=</span><spanclass='fl'>TRUE</span>) <spanclass='co'># will not remain species: B_STPHY_CNS</span>
<spanclass='fu'>as.mo</span>(<spanclass='st'>"S. epidermidis"</span>) <spanclass='co'># will remain species: B_STPHY_EPI</span>
<spanclass='fu'>as.mo</span>(<spanclass='st'>"S. epidermidis"</span>, <spanclass='kw'>Becker</span><spanclass='kw'>=</span><spanclass='fl'>TRUE</span>) <spanclass='co'># will not remain species: B_STPHY_CNS</span>
<spanclass='fu'>guess_mo</span>(<spanclass='st'>"S. pyogenes"</span>) <spanclass='co'># will remain species: B_STRPTC_PYO</span>
<spanclass='fu'>guess_mo</span>(<spanclass='st'>"S. pyogenes"</span>, <spanclass='kw'>Lancefield</span><spanclass='kw'>=</span><spanclass='fl'>TRUE</span>) <spanclass='co'># will not remain species: B_STRPTC_GRA</span>
<spanclass='fu'>as.mo</span>(<spanclass='st'>"S. pyogenes"</span>) <spanclass='co'># will remain species: B_STRPTC_PYO</span>
<spanclass='fu'>as.mo</span>(<spanclass='st'>"S. pyogenes"</span>, <spanclass='kw'>Lancefield</span><spanclass='kw'>=</span><spanclass='fl'>TRUE</span>) <spanclass='co'># will not remain species: B_STRPTC_GRA</span>
<spanclass='co'># Use mo_* functions to get a specific property based on `mo`</span>
These functions are \link{Deprecated}. They will be removed in a future release. Using the functions will give a warning with the name of the function it has been replaced by.
\item{x}{a character vector or a \code{data.frame} with one or two columns}
@ -77,8 +73,6 @@ When using \code{allow_uncertain = TRUE} (which is the default setting), it will
\item{\code{"S. aureus - please mind: MRSA"}. The last word will be stripped, after which the function will try to find a match. If it does not, the second last word will be stripped, etc. Again, a warning will be thrown that the result \emph{Staphylococcus aureus} (\code{B_STPHY_AUR}) needs review.}
\item{\code{"D. spartina"}. This is the abbreviation of an old taxonomic name: \emph{Didymosphaeria spartinae} (the last "e" was missing from the input). This fungus was renamed to \emph{Leptosphaeria obiones}, so a warning will be thrown that this result (\code{F_LPTSP_OBI}) needs review.}
}
\code{guess_mo} is an alias of \code{as.mo}.
}
\section{Source}{
@ -124,12 +118,11 @@ as.mo("Streptococcus group A")
as.mo("GAS") # Group A Streptococci
as.mo("GBS") # Group B Streptococci
# guess_mo is an alias of as.mo and works the same
guess_mo("S. epidermidis") # will remain species: B_STPHY_EPI
guess_mo("S. epidermidis", Becker = TRUE) # will not remain species: B_STPHY_CNS
as.mo("S. epidermidis") # will remain species: B_STPHY_EPI
as.mo("S. epidermidis", Becker = TRUE) # will not remain species: B_STPHY_CNS
guess_mo("S. pyogenes") # will remain species: B_STRPTC_PYO
guess_mo("S. pyogenes", Lancefield = TRUE) # will not remain species: B_STRPTC_GRA
as.mo("S. pyogenes") # will remain species: B_STRPTC_PYO
as.mo("S. pyogenes", Lancefield = TRUE) # will not remain species: B_STRPTC_GRA
# Use mo_* functions to get a specific property based on `mo`
