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Tutorials for BAM Folks

What is this?

A place to store tutorials, scripts, and documentation for steps that most BAM Team Members will need at some point.

Each tutorial below explains a particular data processing/analysis step in the overall BAM Modelling Workflow.

BAM Team Members: If you have a new tutorial to share with the group, do the following:

  1. check if the tutorial exists
    • if yes: contact the person who last committed to it and then work out how to improve it
    • if no: create a new one
  2. To create a tutorial, create a new folder that has lower case letters and dashes (slugified), like new-folder (i.e. not New Folder),
  3. Include your tutorial within the folder, for file options follow some of the existing tutorials.
  4. Once a tutorial is started, add the link below and let Nicole know so it can be added to BAM News.

BAM Team Members: If you have any questions about the database or a given processing step, do the following:

  1. Review the open issues to see if your question has already been asked
    • if yes: Add a comment describing your question in the already open issue
    • if no: Open a new issue describing your question
  2. Be sure to 'watch' the repo so you receive notifications when people reply

Tutorials

BAM Workflow

BAM Data and Data Structure

Data Processing

Data analysis

Coming soon...

TODO

  1. Establishing ODBC connection (DONE)
  2. Fetch data from db (DONE)
  3. Database structure (next!)
  4. Pre-process long format (next!)
  5. Joining tables and filtering
  6. Species cross tabulation
  7. Calculating species offsets
  8. Analyzing point count data with QPAD offsets

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Tutorials describing BAM's analytical workflow (!= SOP)

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