VenomMaps: Updated Species Distribution Maps and Models for New World Pitvipers (Crotalinae)

Rhett M. Rautsaw, Gustavo Jiménez-Velázquez, Erich P. Hofmann, Laura R. V. Alencar, Christoph I. Grünwald, Marcio Martins, Paola Carrasco, Tiffany M. Doan, & Christopher L. Parkinson

Cleaned occurrence records for Viperidae from GBIF, HerpMapper, Bison, Brazil Snake Atlas, BioWeb Ecuador, and custom databases/georeferencing.
- data/occurrence
Updated distribution maps in geojson format for all New World Pitvipers as well as distribution maps for Old World Vipers from Roll et al. 2017.
- data/distributions
Final species distribution models for all New World pitvipers
- data/sdms
Code used to clean occurrence records, construct distribution maps, and summarize sdm results.
- code/*
Code used to construct species distribution models
- code/autokuenm/*
Shiny App to visualize results
- app.R
- User Guide found below

Shiny App

You can view the VenomMaps Shiny App for free on my Digital Ocean Droplet: RhettRautsaw.app/shiny/VenomMaps

User Guide

After opening the app you should be greeted with the following page:

Next, (1) enter a Species into the box on the right and (2) hit Update to plot the distribution. Multiple species can be input at once!

You can filter the list of species in the Species box by country and available SDMs. For example, (1) entering "United States of America" in the Country box and (2) checking the box for the Logistic Model will filter the (4) Species box to only show species that fit these criteria.

If you only want to view the SDM rather than the distribution polygon + SDM, you can (3) check the Clear Distribution box. Remember to (5) Update to make the changes.

Please note that SDMs are large and take a long time to plot. Please be patient. Alternatively, you can download this repository and run the Shiny App locally for faster plotting (see below).

The box in the lower left corner (6) has alternate basemaps on which to view the data. We recommend changing to the "Terrain" map to view SDMs.

Lastly, a table with SDM statistics (7) will continuously update based on the (4) Species selected.

You can also plot the 10th percentile training threshold models and although it is not shown, you can also add Occurrence Records.

You can download the distribution map using the Download Shapefile option. There is also a second tab at the top of the page (General Information) which will give you some more information such as the common name, tell you when the species was described, subspecies, and the maximum length for the species compared to all other viper species:

Running the Application Locally

This app can also be run through R:

library(shiny)

# Easiest way is to use runGitHub
runGitHub("VenomMaps", "RhettRautsaw")

# Run a tar or zip file directly
runUrl("https://github.com/RhettRautsaw/VenomMaps/archive/master.tar.gz")
runUrl("https://github.com/RhettRautsaw/VenomMaps/archive/master.zip")

To run a Shiny app from a subdirectory in the repo or zip file, you can use the subdir argument. This repository happens to contain another copy of the app in inst/shinyapp/.

runGitHub("VenomMaps", "RhettRautsaw", subdir = "inst/shinyapp/")

runUrl("https://github.com/RhettRautsaw/VenomMaps/archive/master.tar.gz",
  subdir = "inst/shinyapp/")

Download the Data

You can clone this GitHub repository to run the Shiny App or to download all the geojson files.

# First clone the repository with git. If you have cloned it into
# ~/VenomMaps, first go to that directory, then use runApp().
setwd("~/VenomMaps")
runApp()

Todo List (Additions)

Update distribution maps for Old World Vipers and other venomous snake species.
Add phylogeographic tracing/playback
Venom Information
Diet Information

RhettRautsaw/VenomMaps