README.md

Introduction

This repository contains the code that implements the Shiny app for the Predicting bat dispersion through urban environments project. Most of the calculations are performed by R to set up the inputs to the Circuitscape calculation that is implemented in Julia. The app queries a PostGIS database for the vector and raster data required to perform the calculations.

Installation

Centos Packages

Install the following Centos packages with yum:

sudo yum install udunits2-devel
sudo yum install geos geos-devel
sudo yum install postgresql-devel

R Packages

Run the following commands in the R console to install the required packages:

install.packages("glue")
install.packages("JuliaCall")
install.packages("leaflet")
install.packages("R6")
install.packages("raster")
install.packages("rpostgis")
install.packages("sf")
install.packages("shiny")
install.packages("shinyBS")
install.packages("shinyjs")
install.packages("stringr")
install.packages("uuid")
install.packages("vroom")

Julia Package

Run the following commands in the Julia console to install the required Circuitscape package:

using Pkg
Pkg.add("Circuitscape")

Environment Variables

The default values for the PostgreSQL database name and the PostgreSQL port are:

DATABASE_NAME="os"
DATABASE_PORT=5432

Configure any of these values by creating a .env file with different values, e.g.:

DATABASE_PORT=5555
DATABASE_NAME="my-bat-data"

Software Versions

The app runs with the following software versions:

Software	Version
R	4.0.4
Julia	1.5.4
Postgres	13.2
PostGIS	3.1.1

Data

The data is all open source. The shapefiles for buildings, rivers and roads are from Ordnance Survey:

• https://www.ordnancesurvey.co.uk/business-government/products/open-map-rivers
• https://www.ordnancesurvey.co.uk/business-government/products/open-map-roads
• https://www.ordnancesurvey.co.uk/business-government/products/open-map-local

The landcover is from the CEH landcover map:

• https://www.ceh.ac.uk/services/land-cover-map-2015

Lidar DTM/DSM is also used to figure out where hedgerows/forest is, which is available from the government:

• https://data.gov.uk/dataset/fba12e80-519f-4be2-806f-41be9e26ab96/lidar-composite-dsm-2017-2m
• https://data.gov.uk/dataset/002d24f0-0056-4176-b55e-171ba7f0e0d5/lidar-composite-dtm-2017-2m

Resources

Some useful articles:

• How can Postgis and R be used as a GIS?