memory for as.mo()

man/as.mo.Rd

@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/mo.R
+% Please edit documentation in R/mo.R, R/mo_history.R
 \name{as.mo}
 \alias{as.mo}
 \alias{mo}
@@ -7,10 +7,11 @@
 \alias{mo_failures}
 \alias{mo_uncertainties}
 \alias{mo_renamed}
+\alias{clean_mo_history}
 \title{Transform to microorganism ID}
 \usage{
 as.mo(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain = TRUE,
-  reference_df = get_mo_source())
+  reference_df = get_mo_source(), ...)
 
 is.mo(x)
 
@@ -19,6 +20,8 @@ mo_failures()
 mo_uncertainties()
 
 mo_renamed()
+
+clean_mo_history()
 }
 \arguments{
 \item{x}{a character vector or a \code{data.frame} with one or two columns}
@@ -34,6 +37,8 @@ mo_renamed()
 \item{allow_uncertain}{a logical (\code{TRUE} or \code{FALSE}) or a value between 0 and 3 to indicate whether the input should be checked for less possible results, see Details}
 
 \item{reference_df}{a \code{data.frame} to use for extra reference when translating \code{x} to a valid \code{mo}. See \code{\link{set_mo_source}} and \code{\link{get_mo_source}} to automate the usage of your own codes (e.g. used in your analysis or organisation).}
+
+\item{...}{other parameters passed on to functions}
 }
 \value{
 Character (vector) with class \code{"mo"}. Unknown values will return \code{NA}.
@@ -42,6 +47,7 @@ Character (vector) with class \code{"mo"}. Unknown values will return \code{NA}.
 Use this function to determine a valid microorganism ID (\code{mo}). Determination is done using intelligent rules and the complete taxonomic kingdoms Bacteria, Chromista, Protozoa, Archaea, Viruses, and most microbial species from the kingdom Fungi (see Source). The input can be almost anything: a full name (like \code{"Staphylococcus aureus"}), an abbreviated name (like \code{"S. aureus"}), an abbreviation known in the field (like \code{"MRSA"}), or just a genus. Please see Examples.
 }
 \details{
+\strong{General info} \cr
 A microbial ID from this package (class: \code{mo}) typically looks like these examples:\cr
 \preformatted{
   Code              Full name
@@ -60,7 +66,9 @@ A microbial ID from this package (class: \code{mo}) typically looks like these e
 
 Values that cannot be coered will be considered 'unknown' and have an MO code \code{UNKNOWN}.
 
-Use the \code{\link{mo_property}} functions to get properties based on the returned code, see Examples.
+Use the \code{\link{mo_property}_*} functions to get properties based on the returned code, see Examples.
+
+All IDs that are found with zero uncertainty are saved to a local file (\code{"~/.Rhistory_mo"}) to improve speed for every next time. Use \code{clean_mo_history()} to delete this file, which resets the algorithms. Only previous results will be used from this version of the \code{AMR} package, since the taxonomic tree may change in the future for any organism.
 
 \strong{Intelligent rules} \cr
 This function uses intelligent rules to help getting fast and logical results. It tries to find matches in this order: