Periphyton, seston, and phytoplankton collection

This dataset was derived from NEON data portal with data product ID 'DP1.20166.001'. Details about this data product can be found at https://data.neonscience.org/data-products/DP1.20166.001.

data_algae

Format

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

  • location_id: Location id.

  • siteID: NEON site code.

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

  • observation_datetime: Observation date and time.

  • taxon_id: Accepted taxon code.

  • taxon_name: Scientific name associated with the taxon ID.

  • 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: Cell density value.

  • unit: Either cells/mL (water column) or cells/cm2 (benthic).

  • sampleCondition: Condition of the sample (all "Condition OK").

  • perBottleSampleVolume: Sample volume per bottle (milliliter); fallback-filled where originally missing.

  • release: Version of data release by NEON.

  • habitatType: Habitat type sampled.

  • algalSampleType: Type of algal sample collected.

  • samplerType: Type of sampler used to collect the sample.

  • benthicArea: Area of the benthos sampled (square meter).

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

  • substratumSizeClass: Size class of the substratum sampled.

  • phytoDepth1: First phytoplankton sample depth (meter) at sampling location.

  • phytoDepth2: Second phytoplankton sample depth (meter) at sampling location.

  • phytoDepth3: Third phytoplankton sample depth (meter) at sampling location.

  • 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.

Details

To clean the data, we:

  1. Filtered alg_biomass to analysisType == "taxonomy" records only.

  2. Computed a fallback bottle volume (preservativeVolume + labSampleVolume) used when perBottleSampleVolume is NA or 0.

  3. Joined alg_taxonomyProcessed to alg_biomass to alg_fieldData via sampleID and parentSampleID.

  4. Filtered to algalParameterUnit == "cellsPerBottle" and sampleCondition == "Condition OK".

  5. Computed cell density: water column samples (seston/phytoplankton) as cells/mL; benthic samples as cells/cm².

  6. Resolved within-sample duplicates by summing density across records sharing the same sampleID and acceptedTaxonID.

Note

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

Author

Lara Jansen