check_and_report_missing_taxa()

check_and_report_missing_taxa

R Documentation

Check for missing taxa and stop pipeline if any are found

Description

Validates that all community taxa have been classified. When missing taxa are found, stops with an informative error message listing the count of unclassified taxa. Returns ‘TRUE’ invisibly when no taxa are missing.

Usage

check_and_report_missing_taxa(vec_taxa_without_classification)

Arguments

vec_taxa_without_classification

A character vector of taxon names that could not be classified automatically or via the auxiliary table. An empty vector (‘character(0)’) signals full coverage and causes the function to return silently.

Details

The missing taxa are stored as a targets object ‘data_missing_taxa_template’ in the pipeline store. Inspect them with ‘targets::tar_read("data_missing_taxa_template")’. The object is a ‘tibble’ with columns ‘sel_name’, ‘kingdom’, ‘phylum’, ‘class’, ‘order’, ‘family’, ‘genus’, and ‘species’; rank columns are left as ‘NA’ for manual completion. Fill in the missing classifications and copy or append rows to ‘Data/Input/aux_classification_table.csv’, then re-run the pipeline. Use ‘R/03_Supplementary_analyses/Make_auxiliary_classification_table.R’ to coalesce templates across all pipeline stores into one CSV.

Value

‘TRUE’ invisibly when every taxon is classified. Stops with an error when any taxa are missing.