In leppott/BCGcalc: Biological Condition Gradient, calculator

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

Purpose

Calculate thermal preference metrics, using thermal preference assignments from Stamp et al. (in progress). The thermal preference assignments are based on an analysis of a large benthic macroinvertebrate dataset from freshwater wadeable streams in Oregon and Washington.

There are seven thermal preference categories:

• Cold stenotherm

• Cold

• Cool

• Cool/warm

• Warm

• Warm stenotherm

• Eurythermal

Three types of metrics are included in the output:

• number of taxa

• % taxa

• % individuals

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_Metrics_Thermal_Input subtab for details).

2. Use the File Builder ‘Taxa Translate and Attribute Assignment’ function to create an input file (minimum required fields = SampleID, TaxonID, Count).

The File Builder option ensures that you are using proper Operational Taxonomic Units (OTUs) and most current thermal preference assignments for Oregon and Washington (Stamp et al. in progress).

Test file

Click here to download an input file that is ready to be run through the thermal metric calculator.

Click here to download the R script for calculating thermal preference metrics.

More metrics (beyond thermal indicators) are available in the BioMonTools R package. You can request the addition of new metrics to the R package or Shiny app by emailing Erik ([e-mail]) or posting your request on the BioMonTools GitHub discussion page.

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

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Last updated 2023-02-03

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