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 (named location).

  • siteID: NEON site code.

  • plotID: Plot identifier.

  • unique_sample_id: Identity of unique samples (namedLocation_collectDate).

  • observation_datetime: Observation date and time.

  • taxon_id: Pathogen name (standardized).

  • taxon_name: Pathogen name (same as taxon_id).

  • taxon_rank: Taxonomic rank inferred from name ("genus" for sp./spp. names, otherwise "species").

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

  • value: Positivity rate (n_positive_test / n_tests).

  • unit: Unit of the values in the value column ("positive tests per pathogen per sampling event").

  • lifeStage: Life stage of the host tick (extracted from subsampleID).

  • 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 tests from batches that failed quality criteria (criteriaMet != "Y" in tck_pathogenqa).

  2. Removed samples where sampleCondition != "OK" or testResult is NA.

  3. Applied the DNA quality fix: identified ticks (testingID) whose HardTick DNA Quality test was not "Positive" and dropped all test rows for those ticks (not just the DNA quality row itself), because pathogen results from ticks with degraded DNA are unreliable.

  4. Removed HardTick DNA Quality and Ixodes pacificus test rows; unified "Borrelia burgdorferi" into "Borrelia burgdorferi sensu lato".

  5. Extracted lifeStage from the last dot-delimited segment of subsampleID.

  6. Aggregated to one row per location x date x pathogen x life stage: value = n_positive_test / n_tests.

Note

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

Author

Melissa Chen, Wynne Moss, Brendan Hobart, Matt Bitters