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dr. M.S. (Matthijs) Berends 2023-01-07 01:54:46 +01:00
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DESCRIPTION
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Package: AMR Package: AMR
Version: 1.8.2.9087 Version: 1.8.2.9088
Date: 2023-01-07 Date: 2023-01-07
Title: Antimicrobial Resistance Data Analysis Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR) Description: Functions to simplify and standardise antimicrobial resistance (AMR)

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NEWS.md
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# AMR 1.8.2.9087 # AMR 1.8.2.9088
*(this beta version will eventually become v2.0! We're happy to reach a new major milestone soon!)* *(this beta version will eventually become v2.0! We're happy to reach a new major milestone soon!)*

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R/mo_matching_score.R
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#' * \eqn{x} is the user input; #' * \eqn{x} is the user input;
#' * \eqn{n} is a taxonomic name (genus, species, and subspecies); #' * \eqn{n} is a taxonomic name (genus, species, and subspecies);
#' * \eqn{l_n} is the length of \eqn{n}; #' * \eqn{l_n} is the length of \eqn{n};
#' * \ifelse{html}{\out{<i>lev</i> is the
#' * \eqn{lev} is the [Levenshtein distance function](https://en.wikipedia.org/wiki/Levenshtein_distance) (counting any insertion as 1, and any deletion or substitution as 2) that is needed to change \eqn{x} into \eqn{n}; #' * \eqn{lev} is the [Levenshtein distance function](https://en.wikipedia.org/wiki/Levenshtein_distance) (counting any insertion as 1, and any deletion or substitution as 2) that is needed to change \eqn{x} into \eqn{n};
#' * \eqn{p_{n}} is the human pathogenic prevalence group of \eqn{n}, as described below; #' * \eqn{p_{n}} is the human pathogenic prevalence group of \eqn{n}, as described below;
#' * \eqn{k_n} is the taxonomic kingdom of \eqn{n}, set as Bacteria = 1, Fungi = 2, Protozoa = 3, Archaea = 4, others = 5. #' * \eqn{k_n} is the taxonomic kingdom of \eqn{n}, set as Bacteria = 1, Fungi = 2, Protozoa = 3, Archaea = 4, others = 5.

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man/as.mo.Rd
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@ -138,7 +138,6 @@ where:
\item \eqn{x} is the user input; \item \eqn{x} is the user input;
\item \eqn{n} is a taxonomic name (genus, species, and subspecies); \item \eqn{n} is a taxonomic name (genus, species, and subspecies);
\item \eqn{l_n} is the length of \eqn{n}; \item \eqn{l_n} is the length of \eqn{n};
\item \ifelse{html}{\out{\if{html}{\out{<i>}}lev\if{html}{\out{</i>}} is the
\item \eqn{lev} is the \href{https://en.wikipedia.org/wiki/Levenshtein_distance}{Levenshtein distance function} (counting any insertion as 1, and any deletion or substitution as 2) that is needed to change \eqn{x} into \eqn{n}; \item \eqn{lev} is the \href{https://en.wikipedia.org/wiki/Levenshtein_distance}{Levenshtein distance function} (counting any insertion as 1, and any deletion or substitution as 2) that is needed to change \eqn{x} into \eqn{n};
\item \eqn{p_{n}} is the human pathogenic prevalence group of \eqn{n}, as described below; \item \eqn{p_{n}} is the human pathogenic prevalence group of \eqn{n}, as described below;
\item \eqn{k_n} is the taxonomic kingdom of \eqn{n}, set as Bacteria = 1, Fungi = 2, Protozoa = 3, Archaea = 4, others = 5. \item \eqn{k_n} is the taxonomic kingdom of \eqn{n}, set as Bacteria = 1, Fungi = 2, Protozoa = 3, Archaea = 4, others = 5.

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man/mo_matching_score.Rd
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@ -30,7 +30,6 @@ where:
\item \eqn{x} is the user input; \item \eqn{x} is the user input;
\item \eqn{n} is a taxonomic name (genus, species, and subspecies); \item \eqn{n} is a taxonomic name (genus, species, and subspecies);
\item \eqn{l_n} is the length of \eqn{n}; \item \eqn{l_n} is the length of \eqn{n};
\item \ifelse{html}{\out{\if{html}{\out{<i>}}lev\if{html}{\out{</i>}} is the
\item \eqn{lev} is the \href{https://en.wikipedia.org/wiki/Levenshtein_distance}{Levenshtein distance function} (counting any insertion as 1, and any deletion or substitution as 2) that is needed to change \eqn{x} into \eqn{n}; \item \eqn{lev} is the \href{https://en.wikipedia.org/wiki/Levenshtein_distance}{Levenshtein distance function} (counting any insertion as 1, and any deletion or substitution as 2) that is needed to change \eqn{x} into \eqn{n};
\item \eqn{p_{n}} is the human pathogenic prevalence group of \eqn{n}, as described below; \item \eqn{p_{n}} is the human pathogenic prevalence group of \eqn{n}, as described below;
\item \eqn{k_n} is the taxonomic kingdom of \eqn{n}, set as Bacteria = 1, Fungi = 2, Protozoa = 3, Archaea = 4, others = 5. \item \eqn{k_n} is the taxonomic kingdom of \eqn{n}, set as Bacteria = 1, Fungi = 2, Protozoa = 3, Archaea = 4, others = 5.