check_nematode_genus: Check validity of nematode genus names against reference...

In Nematode: Ecological Indices Calculator for Nematode Communities

Check validity of nematode genus names against reference database

Description

This generic function validates nematode genus names by checking their existence in a reference database (nematode.info). It supports multiple input types and provides flexible output formats.

Usage

check_nematode_genus(Query.genus, Query.col = NULL, show.details = TRUE, ...)

## S3 method for class 'character'
check_nematode_genus(Query.genus, Query.col = NULL, show.details = TRUE, ...)

## S3 method for class 'data.frame'
check_nematode_genus(Query.genus, Query.col, show.details = TRUE, ...)

## Default S3 method:
check_nematode_genus(Query.genus, Query.col = NULL, show.details = TRUE, ...)

Arguments

Query.genus	Input to check: can be character vector or data.frame
Query.col	When input is data.frame, specifies column name containing genus names (ignored for character input)
show.details	Logical controlling output format: TRUE: returns data.frame with query, existence status, and full reference info FALSE: returns only invalid/missing genus names
...	Additional arguments (currently unused).

Value

Output varies by input type and show.details:

• For character vector input:

  • show.details = TRUE: data.frame with query, existence, and reference data

  • show.details = FALSE: character vector of invalid genera

• For data.frame input: same as character input for the specified column

• For unsupported types: error message

Examples

# Check character vector
check_nematode_genus(c("Caenorhabditis", "Wrong"))

# Check data.frame column
df <- data.frame(genus = c("Meloidogyne", "XXX"))
check_nematode_genus(Query.genus = df, Query.col = "genus")

Nematode documentation built on Aug. 21, 2025, 5:58 p.m.