top_n_microorganisms: Filter Top _n_ Microorganisms

In msberends/AMR: Antimicrobial Resistance Data Analysis

Filter Top n Microorganisms

Description

This function filters a data set to include only the top 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.

Usage

top_n_microorganisms(x, n, property = "fullname", n_for_each = NULL,
  col_mo = NULL, ...)

Arguments

x	a data frame containing microbial data
n	an integer specifying the maximum number of unique values of the property to include in the output
property	a character string indicating the microorganism property to use for filtering. Must be one of the column names of the 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 NULL, the raw values from col_mo will be used without transformation.
n_for_each	an optional integer specifying the maximum number of rows to retain for each value of the selected property. If NULL, all rows within the top n groups will be included.
col_mo	A character string indicating the column in x that contains microorganism names or codes. Defaults to the first column of class mo. Values will be coerced using as.mo().
...	Additional arguments passed on to mo_property() when property is not NULL.

Details

This function is useful for preprocessing data before creating 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.

See Also

mo_property(), as.mo(), antibiogram()

Examples

# filter to the top 3 species:
top_n_microorganisms(example_isolates,
  n = 3
)

# filter to any species in the top 5 genera:
top_n_microorganisms(example_isolates,
  n = 5, property = "genus"
)

# filter to the top 3 species in each of the top 5 genera:
top_n_microorganisms(example_isolates,
  n = 5, property = "genus", n_for_each = 3
)

msberends/AMR documentation built on March 5, 2025, 2:28 p.m.