Pineneedle readme

Overview

• Creating Species Occurence Maps and Species Distribution Models for Species Status Assessment of Monarch Butterflies
• Species Status Assessment Asclepias linaria
• Team Pineneedle (Claire, Mila, Moritz), Spring 2022
• With the help of code by Jeff Oliver https://github.com/jcoliver/biodiversity-sdm-lesson

Dependencies

The following R packages are required (these will be installed by running the setup script, src/setup.R):

• raster
• sp
• dismo
• maptools
• spocc
• rgdal
• sf
• tidyverse
• maps

Structure

• SSA.md: Species Status Assessment for Monarch Butterfly hostplant Pineneedle Milkweed
• Run code with at least 2Gb of RAM
• data
  • wc2-5: climate data at 2.5 minute resolution from WorldClim (note: this folder is not under version control, but will be created by running the setup script (scr/setup.R))
  • cmip5: forcast climate data at 2.5 minute resolution from WorldClim. The data are for the year 2070, based on the GFDL-ESM2G model with an RCP of 4.5 CO₂. For an examination of different forecast models, see McSweeney et al. 2015. (note: this folder is not under version control, but will be created by running the setup script (scr/setup.R))
  • MilkweedCombo.csv: data harvested from GBIF and iNaturalist for Pineneedle Milkweed. This dataset is not under version control, but will be harvested by running src/main.R.
• output (contents are not under version control)
  • pineneedleMilkweedspocc.jpg
  • linaria-single-current-sdm.jpg
  • linaria-single-future-sdm.jpg
• src (directory containing R scripts for gathering occurrence data, running forecast models, and creating map outputs)
  • main.R: this queries data from INAT and GBIF, and creates a csv. file from the data. It then produces a species occurence map and a current and future species distribution model
  • setup.R: this installs important libraries and the worldclim data
  • sdm-functions.R: this prepares the data to be used for creating a SDM
  • linaria-sdm-single.R: this creates a SDM for current climate conditions
  • linaria-future-sdm-single.R: this creates a SDM for 2070 climate conditions

Running the code

• open the src/main.R document
• run the first line of code, source(file = "src/setup.R"), to install all libraries. you might have to restart R in the process
• run the rest of the main.R document (consider runnning the last two lines of code, source "src/linaria-sdm-single.R" and source "src/linaria-future-sdm-single.R", seperately)
• the created maps will be in the output folder

Project DOI