In leppott/BCGcalc: Biological Condition Gradient, calculator

knitr::opts_chunk$set(echo = FALSE
                      , results = 'asis'
                      , warning = FALSE
                      , message = FALSE)

Purpose

Calculate outputs for the Pacific Northwest Maritime Region (PNMR) BCG model (Stamp 2022).

The PNMR BCG model is intended to be applied to samples that meet the following criteria:

Freshwater wadeable streams
Within the following Omernik Level 3 ecoregions: Coast Range, Puget Lowland, Willamette Valley, Cascades, and North Cascades, excluding xeric regions (< 650 mm mean annual precipitation) (Figure 1)
Total watershed area: 5 to 260 km2 (2 to 100 mi2)
Target number of organisms: 500. The number of individuals should not exceed 600; if it does, random subsampling should be applied
Sampling effort: at least 8 ft2 sampling area
Lowest practical taxonomic resolution based on current PNMR Standard Taxonomic Effort guidelines
Collection gear: D-Frame kick-nets or Surber net with 500-micrometer mesh net
Collection method: targeted-riffle or reachwide, multihabitat ( Hayslip 2007 )
Collection period: summer baseflow period (typically June through mid-October)

The PNMR BCG model was calibrated for macroinvertebrate communities in three classes of freshwater wadeable streams:

low gradient/lower elevation (LoGrad-LoElev)
higher gradient/lower elevation (HiGrad-LoElev)
higher gradient/higher elevation (HiGrad-HiElev)

The classification thresholds are 1% for gradient and 750-m for elevation.

During BCG model development, we derived gradient and elevation information from the following sources:

Gradient - NHDPlusV2 flowline slope (x 100) from the NHDPlus Attributes table (McKay et a. 2016)
Elevation - EPA StreamCat elevation, local catchment scale (Hill et al. 2016)

When running the BCG model, we encourage you to use gradient and elevation data from the same sources that the BCG model was calibrated with. However, that is not a required and we know occasional situations will arise when it’s more appropriate to use other data sources

Input File

There are two pathways to creating the input file:

Generate a file outside of the Shiny app that is ready to go (has all the required fields, with exact column heading names – see the Calc_BCG_Input subtab for details)
Use the File Builder functions to create an input file (minimum required fields = SampleID, TaxonID, Count, elevation and percent slope)

Using the File Builder option ensures that you are using proper Operational Taxonomic Units (OTUs) and attributes for the BCG model calculation.