ccviR

The ccviR package implements the NatureServe Climate Change Vulnerability Index (CCVI) version 3.02 in an R package and Shiny App. The package allows all of the geospatial aspects of calculating the CCVI to be done in R, removing the need for separate GIS calculations. The app provides an interactive application designed to offer a user-friendly and simple interface for calculating the NatureServe CCVI.

The NatureServe CCVI is a rapid assessment tool designed to allow a relative grouping of unrelated taxa by vulnerability to climate change and to highlight which factors contribute to the climate change vulnerability of individual species or groups of taxa. This information can be used to inform conservation decision making and to help identify actions to increase species resilience to climate change. See Young et. al (2012), Young et. al. (2015) and the NatureServe CCVI Guidelines for more detailed descriptions of the index and how it was created.

Installation

You can install the development version of ccviR from GitHub with:

# install.packages("devtools")
devtools::install_github("LandSciTech/ccviR")

Launching the app

The code below will open the app in your default browser with an example data set available.

While the following will open the app with the current working directory as the default data location.

Comparison to the NatureServe CCVI tool

ccviR uses the same vulnerability factors and scoring algorithm as the original NatureServe Excel spreadsheet. The index values, scores and Monte Carlo uncertainty analysis produced are the same.

New Features

  • Spatial analyses are included in the package so only minimal GIS skills are needed
  • Uses climate data from the whole species range rather than the range in the assessment area to score thermal and hydrological niche factors
  • Simultaneously calculates the index for multiple scenarios such as, emissions scenarios, time horizons or GCMs
  • A function and Shiny app to classify new climate data sets into exposure categories
  • Plots that explain the drivers of the index value
  • Allows the full assessment to be carried out in a reproducible environment
  • Simplifies synthetic analyses across many species, groups or regions
  • The Shiny app provides a Graphical User Interface to calculate the NatureServe CCVI
  • The Shiny app allows users to calculate the index without knowing R
  • Makes the NatureServe CCVI accessible to a wider audience

Vignettes/tutorials available

See vignette("app_vignette", package = "ccviR") for an introduction to how to use the app with a demo data set, vignette("app_details_vignette", package = "ccviR") for a more detailed look at how to use the app in practice, vignette("data_prep_vignette", package = "ccviR") for how to use an app to prepare custom climate data sets, and vignette("package_vignette", package = "ccviR") for a tutorial on how to use the package to calculate the index directly in R.

Citation

Endicott, S., Naujokaitis-Lewis, I., 2024. ccviR: an R package and Shiny app to implement the NatureServe Climate Change Vulnerability Index. Journal of Open Source Software 9, 7150. https://doi.org/10.21105/joss.07150