Honours Dissertation Repository by Erica Zaja

Ecological and Environmental Sciences with Management

Last update: 04/04/22

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Research Title: Shrubification in the Western Arctic and its Effects on the Porcupine Caribou Herd Habitat

Repository Structure

Repository includes: datasets, figures, R scripts, statistical output, Markdown structure, backup material, project organisation.

• datasets

  • PCH_Core_Range_2016: PCH core range data (Porcupine Caribou Management Board, 2016)

  • berner_data: Shrub map of North Slope of Alaska (Berner et al, 2021)

  • ITEX_data: plot-based vegetation cover data

  • phenology_data: ITEX phenology data (Prevéy et al, 2021)

  • climate_data: CHELSA temperature and precipitation data

  • anna_data: data used for model RMarkdown dissertation - NOT actual data I need

• main_scripts:

  • RQ1_mapping_EZ.R: script with full shrub raster, full PCH range and cropped shrub map code
  • RQ1_sampling_EZ.R: script with focal study area ID and buffered random sampling method
  • RQ1_models_EZ.R: script with models to answer RQ1
  • RQ2_extraction_EZ.R: script with climate extraction code
  • RQ2_models_EZ.R: script with models to answer RQ2
  • RQ3_mariana_cleaning_EZ: script adapted from Mariana Garcia Criado's ITEX dataset data wranglig script. Modified to keep only functional groups I needed.
  • RQ3_vegcover_EZ.R: script with models for cover of functional groups over time in the ANWR
  • RQ3_shrubcover_EZ.R: script with models for cover of shrubs over time in the ANWR
  • RQ4_wrangle_EZ.R: script with data wrangling for shrub phenology analysis
  • RQ4_models_EZ.R: script with shrub phenology models

• other_scripts

  • RQ1_extras_EZ: NOT USED extra code/analyses for RQ1
  • RQ2_extras_EZ: NOT USED extra code/analyses for RQ2
  • RQ3_extras_EZ: NOT USED extra code/analyses for RQ3
  • RQ3_shrubcover_separate_EZ.R: script with separate models for each shrub genus
  • RQ3_vegcover_separate_EZ.R: script with separate models for each functional group
  • RQ4_extras_EZ: NOT USED extra code/analyses for RQ4
  • other scripts including scraps and experiments

• img:

  • figures produced

• sections:

  • separate Rmd sections of dissertation report

• documents:

  • safety and ethics signed forms, title proposal, outline plan, budget form

• proposals:

  • one page outline, full thesis plan and proposed methods

Requirements

• RStudio version 1.2.5001 or greater
• packages rgdal, sp, raster, ggplot2

My Learning Objectives

• Familiarising with GIS techniques
• Learning spatial analysis
• Working with large datasets and data wrangling
• Using data to answer ecological questions

Feedback Etiquette

• Please use either an issue or a pull request.
• Please use "###" and your initial before your feedback comments.
• Please feel free to comment on anything at all! Be harsh ;)
• I'm happy to answer any questions you might have about my work.

Acknowledgements

I thank the data providers, my supervisor Dr Isla Myers Smith, and Team Shrub members for their support.