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(v1.7.1.9011) subsetting taxonomy fix

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dr. M.S. (Matthijs) Berends
2021-07-04 15:26:50 +02:00
parent 3bd50710e8
commit 5b5741f681
20 changed files with 94 additions and 86 deletions
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2
man/bug_drug_combinations.Rd
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@ -58,7 +58,7 @@ bug_drug_combinations(x, col_mo = NULL, FUN = mo_shortname, ...)
The function \code{\link[=bug_drug_combinations]{bug_drug_combinations()}} returns a \link{data.frame} with columns "mo", "ab", "S", "I", "R" and "total".
}
\description{
Determine antimicrobial resistance (AMR) of all bug-drug combinations in your data set where at least 30 (default) isolates are available per species. Use \code{\link[=format]{format()}} on the result to prettify it to a publicable/printable format, see \emph{Examples}.
Determine antimicrobial resistance (AMR) of all bug-drug combinations in your data set where at least 30 (default) isolates are available per species. Use \code{\link[=format]{format()}} on the result to prettify it to a publishable/printable format, see \emph{Examples}.
}
\details{
The function \code{\link[=format]{format()}} calculates the resistance per bug-drug combination. Use \code{combine_IR = FALSE} (default) to test R vs. S+I and \code{combine_IR = TRUE} to test R+I vs. S.

7
man/mo_property.Rd
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@ -106,6 +106,7 @@ mo_property(x, property = "fullname", language = get_locale(), ...)
\item A \link{list} in case of \code{\link[=mo_taxonomy]{mo_taxonomy()}} and \code{\link[=mo_info]{mo_info()}}
\item A named \link{character} in case of \code{\link[=mo_url]{mo_url()}}
\item A \link{numeric} in case of \code{\link[=mo_snomed]{mo_snomed()}}
\item A \link{character} with additional class \code{taxonomic_name} in case of \code{\link[=mo_family]{mo_family()}}, \code{\link[=mo_genus]{mo_genus()}}, \code{\link[=mo_name]{mo_name()}}, \code{\link[=mo_fullname]{mo_fullname()}} and \code{\link[=mo_shortname]{mo_shortname()}}
\item A \link{character} in all other cases
}
}
@ -130,11 +131,13 @@ Determination of yeasts - \code{\link[=mo_is_yeast]{mo_is_yeast()}} - will be ba
Intrinsic resistance - \code{\link[=mo_is_intrinsic_resistant]{mo_is_intrinsic_resistant()}} - will be determined based on the \link{intrinsic_resistant} data set, which is based on \href{https://www.eucast.org/expert_rules_and_intrinsic_resistance/}{'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.2} (2020). The \code{\link[=mo_is_intrinsic_resistant]{mo_is_intrinsic_resistant()}} functions can be vectorised over arguments \code{x} (input for microorganisms) and over \code{ab} (input for antibiotics).
The functions \code{\link[=mo_family]{mo_family()}}, \code{\link[=mo_genus]{mo_genus()}}, \code{\link[=mo_name]{mo_name()}}, \code{\link[=mo_fullname]{mo_fullname()}} and \code{\link[=mo_shortname]{mo_shortname()}} are returned with an additional class \code{taxonomic_name}, which allows italic printing in \link[tibble:tibble]{tibbles}.
All output \link[=translate]{will be translated} where possible.
The function \code{\link[=mo_url]{mo_url()}} will return the direct URL to the online database entry, which also shows the scientific reference of the concerned species.
SNOMED codes - \code{\link[=mo_snomed]{mo_snomed()}} - are from the US Edition of SNOMED CT from 1 September 2020. See the \link{microorganisms} data set for more info.
SNOMED codes - \code{\link[=mo_snomed]{mo_snomed()}} - are from the US Edition of SNOMED CT from 1 September 2020. See \emph{Source} and the \link{microorganisms} data set for more info.
}
\section{Stable Lifecycle}{
@ -299,5 +302,5 @@ mo_info("E. coli")
}
}
\seealso{
\link{microorganisms}
Data set \link{microorganisms}
}