Painting a portrait

How do COVID-19 admissions evolve over time?

‘Protect the NHS’ is the appeal from the UK government, ordering people to stay at home. Pressure on healthcare services is important to understand during a pandemic.

This is part of the government campaign. (Image: Public Health England)

How do COVID-19 admissions and patient levels change over time?

Evolving over time

We can plot COVID-19 admissions and COVID-19 patients in hospitals in England. NHS England use the following definitions:

• COVID-19 admission: admissions with positive tests plus in-patient diagnoses. For hospital admissions, the person must have a positive SARS-CoV-2 test in the prior 14 days. NHS England counts in-patient diagnoses against the day before their diagnosis.
• COVID-19 patients (or hospital cases): the number of confirmed COVID-19 patients in hospital at 8am. This measure includes all hospitals.

Prof Johnson (Bristol) produces graphs showing admissions and patients over time.

Each dot represents a day. (Image: Twitter/BristOliver)

Using R, we are going to produce a similar graph using ggplot2.

Straight from the API

Public Health England provide an interface for their data-set. That means we can download an R package, rather than upload data via spreadsheets.

library(tidyverse)
library(lubridate)
library(scales)
library(ukcovid19)

Depending on your version, you may need to use remotes to install the PHE package:

library(remotes)
remotes::install_github("publichealthengland/coronavirus-dashboard-api-R-sdk")

That allows to draw numbers straight from the interface.

First, we have to set the ‘structure’ of our data request:

covid19_structure <- list(
  date = "date",
  areaType = "areaType",
  areaName = "areaName",
  areaCode = "areaCode",
  newAdmissions = "newAdmissions",
  hospitalCases = "hospitalCases")

The two measures of interest are newAdmissions and hospitalCases .