Verion 2020
The code in this repo originates from the https://github.com/psolymos/abmianalytics project.
This repository contains code to reproduce the 2020 version of Alberta bird models presented on the ABMI data and mapping portals.
The numbered R scripts are the distinct steps in the process (functions that all steps might need, data processing, data packaging, model summaries, prediction/mapping).
The cc folder contains code to run the models on WestGrid computing cluster.
The sector-effects folder contains code for calculating sector effects with partial backfilling.
- Combine all the data inputs into a common format (
01-data-processing.R):
- species data: BAM and BBS species code can be found in the borealbirds organization, ABMI data processing is documented in the ABbiodiversity/abmidata repo
- Veg/soil/HF info: ABbiodiversity/veg-hf-soil-summaries repo
- QPAD offsets: borealbirds/qpad-offsets repo
- Lookup tables, etc.: ABbiodiversity/abmianalytics, inside the
lookupfolder
- Create a data package that can be copied over to other machines to run the models (north, south separately) (
02-data-packaging.R):
- Various ID, methods related variables (ARU, ROAD, date/time etc), spatial predictors, veg/soil/HF info at various scales
- Species matrix
- Offsets matrix
- Models list
- Matrix with bootstrap indices
- Run models and save the output for each species (scripts in the
ccfolder: these will run locally or on a cumpute cluster) - Check results (
03-model-summaries.R) - Prediction maps, sector effects, figures, etc. are described in the
pipeline/2020folder of the ABbiodiversity/abmianalytics repo. - Final coefficients are wrapped in the ABbiodiversity/allinone and ABbiodiversity/allinone-coefsrepos for easy distribution and reproducibility.