Overview

This project aims to support Monarch butterfly conservation by modeling a species of milkweed in the southwest of North America. Using publicly available occurence data of the horsetail milkweed species (Asclepius subverticillata) from GBIF and iNaturalist, as well as and future climate data, we forecast current and future distribution of the horsetail milkweed. These deliverables are contained in this Species Status Assessment (SSA)

Some code described below is borrowed from Jeff Oliver https://github.com/jcoliver/biodiversity-sdm-lesson.

Dependencies

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

• spocc
• sp
• raster
• maptools
• rdgal
• dismo
• sf
• tidyverse

Structure

SSA-Asclepias-subverticillata.md: Host Plant Information For Monarch (Danaus plexippus) Species Status Assessment

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: forcast 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.
• horsetail.csv: data harvested from GBIF and iNaturalist for Asclepias subverticillata. This dataset is not under version control, but will be harvested by running src/occuranceMap.R

output (contents are not under version control): populated with maps when the scripts below are run.

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

• futureSpeciesDistributionModel.R: contains the code that runs horsetail-future-sdm-single.R and produces the future species distribution model map
• horsetail-future-sdm-single.R: contains the code that creates a future species distribution model map using projected climate data; to execute, run src/futureSpeciesDistributionModel.R
• horsetail-sdm-single.R: contains the code that creates a current species distribution model map; to execute, run src/speciesDistributionModel.R
• occuranceMap.R: contains the code that will create an occurence map using GBIF and iNaturalist data; run this script itself
• project.Rproj: This code was created in a R project, the details of this are shown here.
• sdm-functions.R: contains code that produces the species distribution models themselves; both horsetail-sdm-single.R and horsetail-future-sdm-single.R call on this file, no need to run on its own
• setup.R: contains code that installs necessary packages and and downloads climate data. Run this script first
• speciesDistributionModel.R: contains the code that runs horsetail-sdm-single.R and produces the current species distribution model map

Running the code

Instructions to clone this repository, run the code, and replicate the output.

1. Copy the URL to this Spidertail-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. Run scripts in the src folder in the following order:
   1. setup.R
   2. occuranceMap.R (this creates the species occurence map)
   3. speciesDistributionModel.R (this creates a current species distribution model map)
   4. futureSpeciesDistributionModel.R (this creates a future species distribution model map)
4. Browse the output folder for the three maps you just created