borealbirds/tutorials

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

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

• Overall BAM Modelling Workflow: Understanding this will give you a better sense of what other tutorials you need to review.

BAM Data and Data Structure

• Description of the BAM Avian Database
• BAM Biophysical Database (redirect)
• Variables needed for Offset calculation

Data Processing

• Connecting to BAM SQL Server via ODBC
• Test fetch data from Access datbase via RODBC
• Fetch data from SQL server via RODBC
• Step A1. Prep data for offset calculation
• [Step A2. Prep other covariates for analyses]
• Apply QPAD
• Step B. Calculate Offsets
• [Step F. Generate prediction grids]

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