Ground beetle abundance data

This dataset was derived from NEON data portal with data product ID 'DP1.10022.001'. Details about this data product can be found at https://data.neonscience.org/data-products/DP1.10022.001.

data_beetle

Format

A data frame (also a tibble) with the following columns:

  • location_id: Location id.

  • siteID: NEON site code.

  • plotID: Plot identifier (NEON site code_XXX).

  • unique_sample_id: Identity of unique samples (equals sampleID).

  • trapID: Identifier for the trap.

  • observation_datetime: Observation date (collection date).

  • taxon_id: Accepted species code, based on one or more sources.

  • taxon_name: Scientific name, associated with the taxonID. This is the name of the lowest level taxonomic rank that can be determined.

  • taxon_rank: The lowest level taxonomic rank that can be determined for the individual or specimen.

  • variable_name: The variable name(s) represented by the value column.

  • value: Abundance (count per trap day); NA for zero-catch events.

  • unit: Unit of the values in the value column.

  • boutID: Sampling bout identifier (siteID_collectDate).

  • nativeStatusCode: The process by which the taxon became established in the location. 'A': Presumed absent; 'N': Native; 'I': Introduced; 'UNK': Status unknown.

  • release: Version of data release by NEON.

  • remarks: Remarks (technical notes) of record.

  • samplingProtocolVersion: The NEON document number and version where detailed information regarding the sampling method used is available; format 'NEON.DOC.######vX'.

  • samplingImpractical: Flag indicating whether sampling was impractical.

  • trapConditionFlag: Consolidated trap condition flag from cup, lid, and fluid level status.

  • trappingDays: Number of days between trap setting and collecting events.

  • latitude: The geographic latitude (in decimal degrees, WGS84) of the geographic center of the reference area.

  • longitude: The geographic longitude (in decimal degrees, WGS84) of the geographic center of the reference area.

  • elevation: Elevation (in meters) above sea level.

  • nlcdClass: National Land Cover Database Vegetation Type Name.

Details

To clean the data, we:

  1. Filtered bet_fielddata to sampleCollected == "Y"; computed trappingDays from set/collect dates; adjusted for traps collected multiple times from the same set date; consolidated trap condition issues into trapConditionFlag from cupStatus, lidStatus, and fluidLevel.

  2. Built a taxonomy resolution hierarchy: Expert ID overrides Parataxonomist ID; both override Sorting taxonomy. Unpinned other carabid individuals are excluded because their sorting-level taxonomy is too coarse (2013-2016 protocol).

  3. Computed unpinned counts per subsample (sorting total minus pinned individuals); clamped to zero where anomalous.

  4. Left-joined downward from field effort to taxonomy to preserve zero-catch trap events (value = NA).

  5. Abundance = count / trappingDays (count per trap day).

Note

Details of locations (e.g. latitude/longitude coordinates can be found in neon_location).

Author

Kari Norman