In leppott/BCGcalc: Biological Condition Gradient, calculator

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

Purpose

The BCG calculator requires the inclusion of Index Name and Index Class fields in the input file (otherwise the R code won’t know which BCG rules to apply). These are not fields that users normally have in their data files, so we added this function to make that step easier.

Assign Index Class workflow {width=80%}

Index_Name

At this time, there is only one Index_Name option for the MaritimeNW model: BCG_MariNW_Bugs500ct. This is set as the default. In the future, if there are refinements to version 1 of the BCG model, users will have the option of selecting version 1 or version 2 of the model.

Index_Class

The MaritimeNW model has three classes based on elevation and gradient/slope:

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.

Required Fields

SampleID or SiteID– unique identifier
- Tip: pick an identifier that can be linked to other files (such as the file coming out of the File Builder – Taxa Translator/Attribute function)
Gradient of the stream segment/flowline – units must be percent (0-100)
Elevation – units must be meters

If you named the required fields differently in your input file, it’s ok. Click on the drop-down menus. The list of fields in your input file will appear. Select the correct column headings.

IMPORTANT NOTE:

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

• Gradient - NHDPlusV2 flowline slope (x 100) from the NHDPlusV2 Attributes table (McKay et a. 2016)

• Elevation - EPA 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. For example, if the stream is too small to show up in the NHDPlusV2 dataset but you can obtain flowline slope elsewhere, do so (it is better than leaving it blank and not being able to generate a BCG model output). Another scenario you might encounter is that you have NHDPlusV2 slope but you disagree with the slope class assignment (low vs high gradient). In those situations, investigate further. If you find that the NHDPlusV2 slope is not representative of the stream reach where the biological sampling took place, and you have a better, alternate source of slope for that site, use that instead.