Alberta mountain pine beetle r values

Code	Data (Alberta)	Data (national parks)

Background

Code for data retrieval and analyses of Alberta mountain pine beetle population recruitment rates (r values).

In support of the following manuscripts:

• Cooke, B. J., Chubaty, A. M., and A. L. Carroll (submitted) The mountain pine beetle in a marginal boreal landscape: Cross-scale collapse triggered by population removal.

• Cooke, B. J., Brett, R., Olesinski, J., Chubaty, A. M., and A. L. Carroll (submitted) Weather, climate, and the rise and fall of an unprecedented outbreak of mountain pine beetle in Alberta's Mountain Parks, 1999-2023.

Data availability

Data are retrieved from public sources, or shared via Google Drive.

Additionally, data used for analyses of the national parks are archived at , and those used for analyses of the provincial commercially managed forests are archived at .

Initial project setup

0. Prerequisites:

   a. install a suitable Java Runtime Environment following instructions at https://github.com/CWFC-CCFB/J4R/wiki#requirements

1. Clone the repository:

   git clone https://github.com/FOR-CAST/r-values

2. Install required packages to project library:

   renv::restore()

3. Install PhantomJS:

   webshot::install_phantomjs()

Running the code

Open the primary script (00-main.R) and run the lines sequentially.

• select the spatial extent of the analyses by setting run_for = "AB" for provincial scale, or run_for = "NP" for running the national parks analyses;
• setting extract_mdb = TRUE requires running on Windows to be able to open the Access database files;
• setting plot_all = TRUE will build all plots, including intermediate ones;
• setting rerun_all = TRUE will rebuild all local intermediate datasets (use carefully!);
• running 01-download-data.R will prompt for Google credentials to access several data sets;
• mdb extraction is skipped gets skipped if extract_mdb = FALSE;
• most of the mdb import gets skipped unless the outputs it creates are missing or rerun_all = TRUE;
• sourcing 03-Jasper-analyses.R can be done after the '01-download-data.R' script has been run (it does not need the 01a,b nor 02 scripts to have been run);

References

Alberta Agriculture and Forestry (2020) Mountain pine beetle detection and management in Alberta. Updated January 31, 2023. https://open.alberta.ca/dataset/1b872329-6f35-4c11-9ee8-ec35976f4631/resource/3569fff2-b385-4d5e-889f-8192e725b558/

Cooke, B. J., Brett, R., Olesinski, J., Chubaty, A. M., and A. L. Carroll (submitted) Weather, climate, and the rise and fall of an unprecedented outbreak of mountain pine beetle in Alberta’s Mountain Parks, 1999-2023.

Cooke, B. J., Chubaty, A. M., and A. L. Carroll (submitted) The mountain pine beetle in a marginal boreal landscape: Cross-scale collapse triggered by population removal.