filter_non_plantae_taxa()

filter_non_plantae_taxa

R Documentation

Filter Non-Plantae Taxa

Description

Removes taxa that do not belong to the kingdom Plantae from a community data frame, using a classification table to determine the kingdom assignment for each taxon.

Usage

filter_non_plantae_taxa(data, data_classification_table)

Arguments

data

A data frame containing community data with at minimum a column named ‘taxon’.

data_classification_table

A data frame with columns ‘sel_name’ and ‘kingdom’, mapping taxon names to their kingdom classification.

Details

Performs a left join between ‘data’ and ‘data_classification_table’ on ‘taxon == sel_name’ to retrieve the kingdom for each taxon. Any taxon where ‘kingdom’ is not exactly ‘"Plantae"’, including taxa with ‘kingdom = NA’, is treated as non-plant and removed. When any taxa are dropped, ‘cli::cli_warn()’ is issued reporting the count and the full vector of removed taxon names. Note: the upstream ‘get_taxa_classification()’ already filters to Plantae during the taxospace lookup, so in practice this function mainly catches taxa that are genuinely unclassifiable (i.e. not found in any classification source).

Value

A data frame identical in structure to ‘data’ but with all rows belonging to non-Plantae taxa removed. Taxa with ‘kingdom = NA’ (unclassifiable) are also removed.