This BBS.occurrences repository stores functions and datasets for a collaborative project aiming to analyse variation in avian community composition and interspecific 'interactions' by applying Conditional Random Fields (Clark et al. 2018) to count data using North American Breeding Bird Survey data.
Code in the Appendix_S1_CompileBBS script (within the Clark_etal_analysis folder) was used for compiling BBS observations from years 2003 - 2009.
Appendix_S2_CompileLandcover outlines how functions in the repository https://github.com/nicholasjclark/LandcoverMODIS were used for accessing 40 x 40km resolution landcover data from MODIS for each site in each year.
Appendix_S3_FlywayGrouping demonstrates how we group observation sites into recognised migratory flyways and by counties using R's ever-increasing GIS capabilities.
Appendix_S4_PhyloTraitData describes how avian species' phylogenetic and functional
trait datasets were accessed to create pairwise distance matrices.
Appendix_S5_ClimateAltitudeData describes how to download climate data from the PRISM dataset and altitude data from NASA for each sample observation. NDVI data was downloaded at 40km resolution using functions in the gimms package
Appendix_S6_StormData demonstrates how to download storm data from the NOAA storm events database.
Appendix_S7_SpeciesTraits shows functions used to scrape BirdLife International for information on species' migratory status, create binary indicators of species' nesting behaviour and broad habitat category use using data in the Land Condition Trend Analysis Avian Database, calculate Shannon Diversity indices of habitat and diet diversity for each species using data in the EltonTraits database and extract information on average clutch size from the Avian Life History Dataset.
Clark, N.J., Wells, K., Lindberg, O. (2018). Unravelling changing interspecific interactions across environmental gradients using Markov random fields. Ecology DOI: https://doi.org/10.1002/ecy.2221 | [PDF](http://nicholasjclark.weebly.com/uploads/4/4/9/4/44946407/clark_et_al-2018-ecology.pdf)
Poisot, T., Canard, E., Mouillot, D., Mouquet, N. & Gravel, D. (2012). The dissimilarity of species interaction networks. Ecology Letters, 15, 1353-1361.
This project is licensed under the terms of the MIT + file LICENSE