lvalnegri / workshops-gis_day_2020

Mapping exercise for the GIS DAY 2020, Wednesday November 18, 2020

GIS DAY 2020: Mapping Covid-19 in England using R and Shiny

R Packages

• data.table (or the tidyverse packages readr + dplyr + tidyr) for data collection, wrangling, and engineering

• openxlsx to easily read Excel files

• rgdal to read the boundaries in shapefile format from the ONS Geography Portal

• sp to store the spatial objects as a specific R class (you can also use the more modern sf, that also ties neatly within the tidyverse)

• rgeos, rmapshaper, maptools, raster, and terra are sets of various spatial tools.

• leaflet is the R wrapper for the eponymous Javascript library that allows to build interactive maps (you can also use the more complete tmap or mapview packeages, though they both rely on leaflet anyway for the interactive mapping). leaflet.extras, leaflet.extras2, and leafsync are add-ons packages that allows the R leaflet package to exploit more of the functionalities included in the original JS library.

A good introduction to R for Spatial Data Science can be found here. Lots of resources about GIS in general, and its applications, can be found on the dedicated section of the GIS Day website.

Some of the spatial packages mentioned above can be difficult to install correctly, depending on your configuration. Have a look here for a guide to the installation on a Ubuntu machine.

Boundaries

• MSOA Middle Layer Super Output Areas

• LSOA Lower Layer Super Output Areas

As we are not concerned here with geographical details, both the above boundaries are downloaded in the super generalised form, and can be actually simplified further.

Other boundaries used in the session — LTLA Lower Tier Local Authorities, UTLA Upper Tier LA, RGN Regions, CCG NHS Clinical Commissioning Groups, STP NHS Sustainability and Transformation Partnerships — will be built by dissolving methods using the above boundaries and convenient lookup tables.

You can found here a brief description of the UK Census Geography hierarchy, while this is a more comprehensive starting guide to the whole of UK Geographies.

Covid Data

• Covid Cases by LTLA Total and by Age Class

• Covid Cases by MSOA

• Covid Deaths by NHS Trust

• Hospital Admissions and Bed Occupancy by NHS Trust

• Covid Symptoms (NHS Pathways Calls and Online) by CCG and Sex + Age

• NEW Covid Vaccinations

Ancillary Data

• MSOA House of Commons intelligible Names

• MSOA => LTLA => UTLA => RGN APR-2020

• OA => LSOA => MSOA 2011

• LSOA => CCG => STP => CAL APR-2020

• ONS Postcode Directory AUG-2020

GeoDemographics

• Population by LSOA + MSOA and Sex + Age 2019

• Index of Multiple Deprivation 2019

• Food Shops Locations See [my other github repository] to learn how to collect data related to food shops

• Household Disposable Income FA-2018 by MSOA

• Median House Prices Mar-2020 by MSOA

• Electricity and Gas Consumption 2018

Credits

• Gis Day website

• Contains MSOA names © Open Parliament copyright and database right 2020

• Contains Ordnance Survey data © Crown copyright and database right 2020

• Contains Royal Mail data © Royal Mail copyright and database right 2020

• Contains Public Health England data © Crown copyright and database right 2020

• Office for National Statistics licensed under the Open Government Licence v.3.0