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add_custom_microorganisms.Rd
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antimicrobials.Rd
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mo_property.Rd
mo_source.Rd
pca.Rd
plot.Rd
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skewness.Rd
top_n_microorganisms.Rd
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CRAN-SUBMISSION
DESCRIPTION
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48 lines
2.6 KiB
R
48 lines
2.6 KiB
R
% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/top_n_microorganisms.R
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\name{top_n_microorganisms}
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\alias{top_n_microorganisms}
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\title{Filter Top \emph{n} Microorganisms}
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\usage{
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top_n_microorganisms(x, n, property = "fullname", n_for_each = NULL,
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col_mo = NULL, ...)
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}
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\arguments{
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\item{x}{A data frame containing microbial data.}
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\item{n}{An integer specifying the maximum number of unique values of the \code{property} to include in the output.}
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\item{property}{A character string indicating the microorganism property to use for filtering. Must be one of the column names of the \link{microorganisms} data set: "mo", "fullname", "status", "kingdom", "phylum", "class", "order", "family", "genus", "species", "subspecies", "rank", "ref", "oxygen_tolerance", "source", "lpsn", "lpsn_parent", "lpsn_renamed_to", "mycobank", "mycobank_parent", "mycobank_renamed_to", "gbif", "gbif_parent", "gbif_renamed_to", "prevalence", or "snomed". If \code{NULL}, the raw values from \code{col_mo} will be used without transformation.}
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\item{n_for_each}{An optional integer specifying the maximum number of rows to retain for each value of the selected property. If \code{NULL}, all rows within the top \emph{n} groups will be included.}
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\item{col_mo}{A character string indicating the column in \code{x} that contains microorganism names or codes. Defaults to the first column of class \code{\link{mo}}. Values will be coerced using \code{\link[=as.mo]{as.mo()}}.}
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\item{...}{Additional arguments passed on to \code{\link[=mo_property]{mo_property()}} when \code{property} is not \code{NULL}.}
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}
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\description{
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This function filters a data set to include only the top \emph{n} microorganisms based on a specified property, such as taxonomic family or genus. For example, it can filter a data set to the top 3 species, or to any species in the top 5 genera, or to the top 3 species in each of the top 5 genera.
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}
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\details{
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This function is useful for preprocessing data before creating \link[=antibiogram]{antibiograms} or other analyses that require focused subsets of microbial data. For example, it can filter a data set to only include isolates from the top 10 species.
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}
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\examples{
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# filter to the top 3 species:
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top_n_microorganisms(example_isolates,
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n = 3
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)
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# filter to any species in the top 5 genera:
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top_n_microorganisms(example_isolates,
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n = 5, property = "genus"
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)
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# filter to the top 3 species in each of the top 5 genera:
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top_n_microorganisms(example_isolates,
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n = 5, property = "genus", n_for_each = 3
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)
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}
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\seealso{
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\code{\link[=mo_property]{mo_property()}}, \code{\link[=as.mo]{as.mo()}}, \code{\link[=antibiogram]{antibiogram()}}
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}
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