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(v1.3.0.9016) mo_uncertainties() overhaul

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dr. M.S. (Matthijs) Berends
2020-09-12 08:49:01 +02:00
parent 68e9cb78e9
commit 3ff871afeb
71 changed files with 820 additions and 169 deletions
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man/as.mo.Rd
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@@ -106,7 +106,7 @@ With the default setting (\code{allow_uncertain = TRUE}, level 2), below example
There are three helper functions that can be run after using the \code{\link[=as.mo]{as.mo()}} function:
\itemize{
\item Use \code{\link[=mo_uncertainties]{mo_uncertainties()}} to get a \code{\link{data.frame}} with all values that were coerced to a valid value, but with uncertainty. The output contains a score, that is calculated as \eqn{(n - 0.5 * L) / n}, where \emph{n} is the number of characters of the full taxonomic name of the microorganism, and \emph{L} is the \href{https://en.wikipedia.org/wiki/Levenshtein_distance}{Levenshtein distance} between that full name and the user input.
\item Use \code{\link[=mo_uncertainties]{mo_uncertainties()}} to get a \code{\link{data.frame}} that prints in a pretty format with all taxonomic names that were guessed. The output contains a score that is based on the human pathogenic prevalence and the \href{https://en.wikipedia.org/wiki/Levenshtein_distance}{Levenshtein distance} between the full taxonomic name and the user input.
\item Use \code{\link[=mo_failures]{mo_failures()}} to get a \code{\link{character}} \code{\link{vector}} with all values that could not be coerced to a valid value.
\item Use \code{\link[=mo_renamed]{mo_renamed()}} to get a \code{\link{data.frame}} with all values that could be coerced based on old, previously accepted taxonomic names.
}