Ticks sampled using drag cloths

This dataset was derived from NEON data portal with data product ID 'DP1.10093.001'. Details about this data product can be found at https://data.neonscience.org/data-products/DP1.10093.001.

data_tick

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 (plotID_collectDate).

  • observation_datetime: Observation date and time.

  • 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 square meter).

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

  • LifeStage: Life stage of the tick (Larva, Nymph, or Adult).

  • release: Version of data release by NEON.

  • remarks_field: Technician notes; free text comments accompanying the record.

  • samplingMethod: Name or code for the method used to collect or test a sample.

  • targetTaxaPresent: Indicator of whether the sample contained individuals of the target taxa ('Y' or 'N').

  • totalSampledArea: Total area sampled (square meter).

  • 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.

  • plotType: NEON plot type in which sampling occurred: tower, distributed or gradient.

Details

To clean the data, we:

  1. Mapped life stage from tck_taxonomyProcessed sex/age codes to Larva, Nymph, or Adult; rows with unmappable values are dropped.

  2. Aggregated taxonomy counts by sampleID, acceptedTaxonID, and LifeStage; concatenated release values.

  3. Applied the IXOSP2 reconciliation fix: when field counts (from tck_fielddata) exceed lab counts for a given life stage, the difference is assigned to Order Ixodida (IXOSP2, "Ixodida sp.") rather than using fragile string-matching.

  4. Left-joined downward from field effort to lab taxonomy to preserve empty drag events (targetTaxaPresent == "N"), which receive individualCount = 0.

  5. Abundance = individualCount / totalSampledArea (count per square meter); invalid or non-finite values are dropped except for empty drag rows.

Note

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

Author

Wynne Moss, Melissa Chen, Brendan Hobart, Matt Bitters