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Importing macroinvertebrate abundance data from the EA Ecology and Fish Data Explorer

import_inv_taxa.Rd

The import_inv_taxa function imports macroinvertebrate taxon abundance information from the Environment Agency's Ecology and Fish Data Explorer (EDE). The function downloads and merges two files: one listing taxon abundances by sample, and one with details of each taxon (e.g. full taxon name, taxonomic rank). The data can be optionally filtered by site and/or sample ID, and the filtered data saved as a .rds file.

Usage

import_inv_taxa(sites = NULL,
                samples = NULL,
                save = FALSE)

Arguments

sites

Vector of site ids to filter by. Default = NULL

samples

Vector of sample ids to filter by. Default = NULL

save

Specifies whether (TRUE) or not (FALSE) the filtered data should be saved as an rds file (for future use, or audit trail). Default = FALSE.

Value

A tibble containing the imported macroinvertebrate taxonomic abundance data.

Details

If saving a copy of the filtered taxa data, the name of the rds file is hard-wired to INV_OPEN_DATA_TAXA_F.RDS.

Downloaded raw data files will be automatically removed from the working directory following execution of the function.

The function automatically modifies the output from EDE, renaming "SITE_ID" to "biol_site_id" (hetoolkit's standardised column header for biology site ids).

Please note that that approaches to sample processing, such as abundance recording, have changed over time. For details, please see page 5 of this pdf document

Examples


# Import data from EDE for specific sites
taxa_data <- import_inv_taxa(sites = c("34310", "34343"))
#> Warning: The following named parsers don't match the column names: REPLICATE_CODE

# Import data using sample IDs
biol_data <- hetoolkit::import_inv(sites = c("34310", "34343"))
sample_IDs <- unique(biol_data$SAMPLE_ID)

taxa_data <- import_inv_taxa(samples = sample_IDs)
#> Warning: The following named parsers don't match the column names: REPLICATE_CODE