biodivercity

Make spatial predictions of biodiversity across city landscapes. Refer to package website for demonstrations of how the package may be used.

Overview

Many frameworks to assess ‘biodiversity’ have been proposed in research and practice. Some offer a more holistic view, by including parts of the ecosystem (e.g., climate, soil, air, water, landscape structure, genetic variation) that may contribute to ‘total biodiversity’ within a given region. However, such conceptualisations of ‘biodiversity’ may include components with low causal proximity (e.g., indirect effect of the landscape on species diversity), and may be difficult to measure at wide spatial scales (e.g., genetic diversity, plant species diversity). In decision-making, unnecessary complexity may also risk contributing to mistrust or ignorance of the overall assessment.

biodivercity is an R package for assessing the diversity of animal species in urban areas. It provides a way to directly assess the habitat value of urban landscapes, based on their empirical effect on chosen animal groups (e.g., taxa such as birds, butterflies, odonates, amphibians, etc.). The key features include:

• Step-by-step protocols for random point sampling of an animal group within areas of interest
• Generate data summaries of the animals surveyed, at multiple levels of granularity (e.g., areas, periods, animal groups, species)
• Download and process landscape data within areas of interest (e.g., remotely sensed data, OpenStreetMap data, manually mapped data)
• Build predictive models to assess local (Alpha), community (Beta) and total (Gamma) diversity for an animal group (currently available only for Alpha diversity); respectively, these three types of diversity represent the local quantity of species, variety of species, and total quantity of species within an area of interest
• Use models to make pixel-based spatial predictions across new areas and time periods
• Convert vector data generated from future design scenarios into formats suitable for model predictions
• Summarise spatial predictions to benchmark and compare biodiversity ‘performance’ between planning units across the city

Figure: Broad overview of the data workflow for a chosen animal group

Setup

Install the development version from GitHub with:

# install.packages("devtools")
devtools::install_github("ecological-cities/biodivercity", ref = "main")

Load the package:

library(biodivercity)

Citation

To cite biodivercity or acknowledge its use, please cite the following:

Song, X. P., Tan, E. Y. W., Lee, S. K. R., Sim, H. J., Nai, J., Chong, K. Y. (2022). biodivercity: An R package for spatial assessment of biodiversity across city landscapes. R Package version 0.1.0. https://doi.org/10.5281/zenodo.7410414.

To get a BibTex entry, run citation("biodivercity").

Data sources

Development of a Biodiversity Index for Residential Towns using Biodiversity Field Surveys, 2016–2022. Ministry of National Development Research Fund (MNDRF) Grant. Awarded to the National University of Singapore and the Singapore Housing & Development Board.

References

Baker, D. J., Maclean, I. M., Goodall, M., & Gaston, K. J. (2021). Species distribution modelling is needed to support ecological impact assessments. Journal of Applied Ecology, 58(1), 21-26.

Soto-Navarro, C. A., Harfoot, M., Hill, S. L. L., Campbell, J., Mora, F., Campos, C., … & Burgess, N. D. (2021). Towards a multidimensional biodiversity index for national application. Nature Sustainability, 1-10.