/landscape_bird_homogenization

Processed data and analysis for paper on landscape and bird population homogenization using Mountain Legacy Project photograph pairs

landscape_bird_homogenization

Processed data and analysis for paper on landscape and bird population homogenization using Mountain Legacy Project photograph pairs

Summary

This project studies landscape and bird diversity change in a mountainous area (the Willmore Wilderness Park in Alberta, Canada) over the last century.

We have data on past and current land cover composition (historic and repeat photos & their land cover classifications). The 10 land cover categories are: Coniferous forest, Broadleaf forest, Mixedwood forest, Wetland, Shrub, Herbaceous, Rock, Water, Regenerating area, Snow/Ice.

We have species distribution models (made from auditory survey data and Landsat-based land cover map). The 13 bird species are: American pipit, American robin, Chipping sparrow, Dark-eyed junco, Golden-crowned kinglet, Golden-crowned sparrow, Gray jay, Hermit thrush, Pine siskin, Ruby-crowned kinglet, Savannah sparrow, Wilson's warbler, Yellow-rumped warbler.

Data

The data is split into two folders:

  • RawData
    • Birddata.xls contains the expert transcription of bird survey recordings
    • LandCoverClassifications.zip contains the land cover classifications of those photographs
    • LandsatBasedClassifiedMap.tif contains the Landsat-based classified map used to generate the species distribution models
    • LandsatBasedClassifiedMapClasses.txt is the legend for the Landsat-based raster
    • Photographs.zip contains the 46 photograph pairs as found on the Mountain Legacy Project website
  • ProcessedData
    • assessment-table-full.xlsx is external data downloaded from NABCI's State of North America's Birds 2016 Report which lists breeding habitat, non-breeding habitat and level of conservation concern for various bird species
    • ImageAnalysis.xlsx is a summary of the processed data from LandCoverClassifications.zip as well as the backtransformations from the species distribution models. It contains both land cover proportions in the photograph pairs as well as bird occurrence probabilities at each site
    • ImageAnalysis_SensitivityAnalysis_MinusSE.xlsx and ImageAnalysis_SensitivityAnalysis_PlusSE.xlsx are the same as ImageAnalysis.xlsx except that the values are generated using the species distribution model's beta-coefficients minus the standard error, and plus the standard error, respectively, to be used for sensitivity analysis
    • LandcoverLookup.csv is a lookup table for the different land cover category codes
    • SpeciesLookup.csv is a lookup table for the different bird species codes

Code

  • BirdDiversityAnalysis.Rmd
    • This file walks through the code that analyzes land cover and bird diversity change
    • This file also generates the figures in the associated publication
    • The pdf is the knitted (formatted) output of this Rmd file