In leppott/BCGcalc: Biological Condition Gradient, calculator

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

Purpose

The fuzzy set temperature model is an exploratory model. Instead of assigning macroinvertebrate samples to a BCG level, it assigns them to one of the following temperature classes:

• VERY COLD

• COLD

• COOL

• WARM

The model works the same way as a BCG model, with an output that includes probability of membership in a primary and secondary class. Input metrics include:

• number cold stenotherm taxa

• number cold stenotherm + cold taxa

• percent cold stenotherm + cold taxa

• percent cold stenotherm + cold indiv

• percent warm + warm stenotherm taxa

• percent warm + warm stenotherm indiv

The thermal preference metrics are based on assignments from Stamp et al. (in progress), which were derived from an analysis of a large benthic macroinvertebrate dataset from freshwater wadeable streams in Oregon and Washington coupled with the Maximum Weekly Maximum Temperature (MWMT) metric from the NorWeST modeled stream temperature dataset.

Click here to read more about the model and to view the box plots that helped inform selection of metrics and thresholds. For more information, contact Jen Stamp (Tetra Tech) ([e-mail]).

Input File

There are two pathways to creating the input file:

1. 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_FuzzySet_Input subtab for details)

2. Use the File Builder functions to create an input file (minimum required fields = SampleID, TaxonID, Count)

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

IMPORTANT: Your input file needs to include the following two fields (which the File Builder function does not automatically populate - you’ll need to add them in manually) -

• INDEX_NAME = Therm_ORWA_Bugs500ct

• INDEX_CLASS = orwa

Test File

Click here to download a test file.

Click here to download example R scripts and data (all functions).

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Last updated 2023-06-07

leppott/BCGcalc documentation built on May 17, 2024, 5:55 p.m.