From 08fe5a88c07878acc59e7a1c4dd149d1a0c545b9 Mon Sep 17 00:00:00 2001 From: Matthijs Berends Date: Sat, 7 Jan 2023 01:54:46 +0100 Subject: [PATCH] documentation --- DESCRIPTION | 2 +- NEWS.md | 2 +- R/mo_matching_score.R | 1 - man/as.mo.Rd | 1 - man/mo_matching_score.Rd | 1 - 5 files changed, 2 insertions(+), 5 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 814afd2f..d091855e 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 1.8.2.9087 +Version: 1.8.2.9088 Date: 2023-01-07 Title: Antimicrobial Resistance Data Analysis Description: Functions to simplify and standardise antimicrobial resistance (AMR) diff --git a/NEWS.md b/NEWS.md index e79808e4..436c3797 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# 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!)* diff --git a/R/mo_matching_score.R b/R/mo_matching_score.R index 78a48f7f..50da212e 100755 --- a/R/mo_matching_score.R +++ b/R/mo_matching_score.R @@ -46,7 +46,6 @@ #' * \eqn{x} is the user input; #' * \eqn{n} is a taxonomic name (genus, species, and subspecies); #' * \eqn{l_n} is the length of \eqn{n}; -#' * \ifelse{html}{\out{lev 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{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. diff --git a/man/as.mo.Rd b/man/as.mo.Rd index 6b69e3f4..9b6ba030 100644 --- a/man/as.mo.Rd +++ b/man/as.mo.Rd @@ -138,7 +138,6 @@ where: \item \eqn{x} is the user input; \item \eqn{n} is a taxonomic name (genus, species, and subspecies); \item \eqn{l_n} is the length of \eqn{n}; -\item \ifelse{html}{\out{\if{html}{\out{}}lev\if{html}{\out{}} 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{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. diff --git a/man/mo_matching_score.Rd b/man/mo_matching_score.Rd index 4e6cbc9c..5f8629a4 100644 --- a/man/mo_matching_score.Rd +++ b/man/mo_matching_score.Rd @@ -30,7 +30,6 @@ where: \item \eqn{x} is the user input; \item \eqn{n} is a taxonomic name (genus, species, and subspecies); \item \eqn{l_n} is the length of \eqn{n}; -\item \ifelse{html}{\out{\if{html}{\out{}}lev\if{html}{\out{}} 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{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.