Lemmonhead's Repository

Overview

This repository draws on data from GBIF to create distribution models of the monarch butterfly host species, Asclepias Lemmonii (Lemmon's Milkweed). The code creates an occurrence map, species distribution model, and climate forecast model for this species of milkweed.

Link to Species Status Assessment.

Thank you to Jeff Oliver, from whom we have borrowed code.

Dependencies

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

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

Structure

• SSA-asclepias-lemmonii.md: Species Status Assessment for Asclepias Lemmonii

• data: directory containing necessary 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 (scripts/setup.R)).
  • cmip5: forecast climate data at 2.5 minute resolution from WorldClim. These data were originally downloaded from the WorldClim website, but stored in the .RData format for ease of use. 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.
  • lemmonii.csv: data harvested from GBIF for Asclepias Lemmonii. This dataset is not under version control, but will be harvested by running src/main.R.
  • worldClimVariables.csv: list of climate data used from WorldClim

• output: directory containing image outputs

  • lemmonii-single-prediction.pdf: SDF with both current and future data
  • lemmonii-single-current-future-sdm.jpg: SDM with both current and future data
  • occurence_map.jpg: occurrence map
  • sdm.jpg: screenshot of SDM

• src: directory containing R scripts for gathering occurrence data, running forecast models, and creating map outputs.

  • main.R: creates an occurence map, SDM, and SDF
  • functions.R: contains commonly used functions
  • setup.R: load packages and run setup for creating SDMs and SDFs
  • sdm-functions.R: required functions for creating SDMs
  • lemmonii-sdm-single.R: create an SDM
  • future-sdm-single.R: create an SDF

Running the code

1. Copy the URL to this lemmonheads-mapping Github repository by clicking on the green "Code" button above

2. Clone the repository by opening a "New Project from Git Repository" in RStudio or rstudio.cloud and pasting the URL

3. Open main.R

4. Run the following lines in order to run the necessary setup

• source("src/setup.R")
• source("src/functions.R")

3. Run the following lines in order to query and clean the data

• lemmonData <- query()
• lemmonData <- clean(lemmonData)

4. To create an occurence map, run occurenceMap(lemmonData)
5. To create either an SDM or an SDF, run modelPrep(lemmonData)

• For an SDM, run source("src/lemmonii-sdm-single.R")
• For an SDF, run source("src/future-sdm-single.R") after you have ran the previous line