In leppott/BCGcalc: Biological Condition Gradient, calculator

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

Purpose

Create an input file with the proper Operational Taxonomic Units (OTUs) and attributes for each calculation.

OTUs differ across calculations. For example, for the BCG model calculation, worms are collapsed to Subclass and mites to Order-level. For the thermal preference metric calculations, mites and worms are kept at the lowest practical taxonomic level.

This function performs two steps to the input file:

1. "Translates" the original TaxonID to the proper OTU based on the selected calculation

2. Appends the Pacific Northwest taxa attributes, which include the Maritime Region BCG taxa attributes, functional feeding group and thermal preference assignments, and more.

The ‘taxa translator’ and attribute tables are based on stream biomonitoring data from Oregon and Washington and will be updated on an annual basis. If you have questions or comments about these tables, or want to request the addition of new taxa, please email Sean Sullivan ([e-mail]).

Click here to download the tables and associated metadata files from GitHub.

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Input File

There are three required fields:

• SampleID

  • Unique sample identifier. Includes any replicate/duplicate information.

• TaxaID

  • Unique taxa name

• Count of individuals (e.g., N_Taxa)

  • Count of taxa individuals

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.

Optional - if there are additional fields in the input file that you want to carry through into the output file (e.g., stationID, collection date, latitude, longitude), click on the ‘Columns to keep in output’ box. The list of fields in your input file will appear. Click on the fields that you want to include. If you change your mind and want to remove a field, click on it and hit ‘delete.’

IMPORTANT: Do not repeat the required columns. Do not include Life Stage or other fields that are unique to the taxa and not the sample (such as notes from the taxonomist). If a taxon occurs in more than one row for a given sample, it will lead to double-counting of that taxon in the richness metrics.

Test File

Click here to download a test file.

Note that there is one taxon (Atherix) in the input file that comes out as a ‘nonmatch.’ This is because it has a trailing space. R is sensitive to leading and trailing spaces and is also case sensitive (for example, it recognizes 'A' and 'a' as different variables).

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

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Last updated 2023-02-02

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