Add species information to CA and HL tables

Adds one or more columns from species_info to the CA and/or HL elements of a DATRAS-like object by matching Valid_Aphia in the table to WoRMS_AphiaID in species_info.

The function preserves the original row order of each table and performs a left join, meaning that rows with no matching species information are retained and receive NA in the added columns.

For this type of lookup, the function uses base::match(), which is typically faster and simpler than base::merge() when only selected columns need to be appended and the original row order should be kept.

Usage

add_species_info(x, vars = NULL, verbose = TRUE)

Arguments

x

A DATRAS-like object containing at least optional CA and/or HL data frames.

vars

Character vector giving the names of columns in species_info to add. If NULL, all columns except WoRMS_AphiaID are added.

verbose

Logical; if TRUE, progress messages are printed.

Value

The input object x, with the requested columns added to the CA and/or HL elements where present.

Details

The lookup is based on the correspondence between:

• x[["CA"]][["Valid_Aphia"]] or x[["HL"]][["Valid_Aphia"]]

• species_info[["WoRMS_AphiaID"]]

If any requested columns already exist in CA or HL, they are overwritten.

Examples

## Add all available species information
## x <- add_species_info(x)

## Add only selected columns
## x <- add_species_info(x, vars = c("ScientificName", "FishBase"))