This package provides functions and Rmarkdown templates for analyzing marine bird tracking data collected for the Oceans Protection Plan. The package implements a workflow for identifying high-use areas around colonial breeding seabird colonies on he coast of British Columbia, using GPS tracking data stored on the Movebank animal tracking data repository.
The package provides functions for data formatting, trip identification, track interpolation, calculating utilization distributions, and identifying high-use areas where multiple individual tracks overlap. The workflow draws on existing functions in the {move}, {adehabitatHR}, and {track2KBA} R packages. The package includes two Rmarkdown templates to produce (1) a diagnostic report summarizing tracking data within a project and (2) a final report on high-use areas with accompanying shapefile exports.
The package is designed so that reports can be esaily updated as new tracking data and projects are added to Movebank.
To install OPPtools on your local machine:
# install.packages("devtools")
devtools::install_github('popovs/OPPtools')
Currently, there are 15 OPP projects on Movebank. Data collected on colonial breeding marine birds are organized by species and colony. Data from non-colonial species and from non-breeding birds are organized by species. A list of Movebank project IDs can be called as a dataset within the package using:
# List of Movebank project IDs
opp_mb_projects()
Before importing data from Movebank, you will need to create a Movebank user account at https://www.movebank.org/cms/movebank-login and be added as a Data collaborator or Data manager by the Project Owner or Project Contact. You may initiate a request to be added to a project through Movebank or by contacting the data owner directly.
Within OPPtools the function opp_movebank_key() uses the {keyring} package to securely add your Movebank credentials to your local keychain. This will allow any functions that call Movebank data to link to Movebank without having to repeatedly re-enter your credentials.
Functions within OPPtools that call Movebank data are wrappers to the {move} package. If you want to pass your credentials directly to functions from the {move} package, you can use:
# Retrieve Movebank credentials from keyring
mb_login <- opp_retrieve_mb_cred()
The package includes two RMarkdown templates that run analysis to identify high-use areas from GPS tracking data collected on colonial breeding seabirds. These reports require a set of input parameters which are stored as a dataset within the package:
cpf_report_params
If these parameters need to be modified to generate additional of updated reports, load the 'cpf_report_params' object into your environment and add or modify parameters. To make permanent changes to the object in the package, submit a pull request to this repo on Github.
The two reports can be generated by running the functions:
opp_render_diagnostic()
opp_render_report()
The diagnostic report provides maps and figures to help you define what parameters to use in data analysis. The final report produces a PDF or HTML summary of analysis results, along with options to export shapefiles of tracking data and identified high-use areas.
The analysis closely follows methods described in:
Beal, M., Oppel, S., Handley, J., Pearmain, E. J., Morera- Pujol, V., Carneiro, A. P. B., Davies, T. E., Phillips, R. A., Taylor, P. R., Miller, M. G. R., Franco, A. M. A., Catry, I., Patrício, A. R., Regalla, A., Staniland, I., Boyd, C., Catry, P., & Dias, M. P. (2021). track2KBA: An R package for identifying important sites for biodiversity from tracking data. Methods in Ecology and Evolution, 12, 2372– 2378. https://doi.org/10.1111/2041- 210X.13713