Tick-borne pathogen status

This dataset was derived from NEON data portal with data product ID 'DP1.10092.001'. Details about this data product can be found at https://data.neonscience.org/data-products/DP1.10092.001.

data_tick_pathogen

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, usually it has location and date information.

  • 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: Value of the variable(s) specified by variable_name.

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

  • lifeStage: Life stage of the host (all Nymph).

  • testProtocolVersion: The protocol version used to test the sample.

  • release: Version of data release by NEON.

  • n_tests: Number of tests conducted.

  • n_positive_test: Number of tests that were positive.

  • 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. Removed samples with flagged quality checks

  2. Removed samples with missing metadata (domain/site/plotID; Lat/Long; plotType; nlcdClass, elevation, collectDate, subsampleID, batchID, testingID, testPathogenName

  3. Removed samples where sampleCondition!=“OK”

  4. Removed samples where testResult==NA

  5. Removed samples where HardTick DNA Quality (under testPathogenName) are not ‘Positive’, and then removed hardtack DNA and Ixodes pacificus tests.

  6. Combined B. burgdeferi and B burgdeferi sensu lato into a single test pathogen type (B. burgedferi sensu lato)

Note

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

Author

Melissa Chen, Wynne Moss, Brendan Hobart, Matt Bitters