plot_sync: display synchronized death and confirmed case series

In vjcitn/sars2app: COVID-19 data resources and analysis tools cut down for an interactive app

Description

display synchronized death and confirmed case series

Usage

plot_sync(
  dfr,
  basedate = "2020-05-01",
  maxdate = Inf,
  shift = 26,
  winsize = 14,
  na_pad = TRUE,
  xlim.in = NULL,
  yspan = 0.25
)

Arguments

dfr	data.frame with columns 'date', 'deaths', 'confirmed', where the latter are 'incident', formed by differencing the cumulative counts provided in sars2pack
basedate	minimum date to consider
maxdate	maximum date to use, Inf for no limit relative to available dates
shift	number of days to backshift death counts, coerced to integer
winsize	size of running window for averaging incident counts for plotting
na_pad	logical(1) passed to runner::mean_run
xlim.in	defaults to NULL, standard graphics::plot xlim, or can be a numeric(2)
yspan	log-scale extra padding for y extent, expanding range of log(incident cases)+log cIFR

Value

a list with elements x, y, date, invisibly

Note

The 'IFR' is crudely estimated as exp(mean(log(deaths)-log(confirmed))).

Examples

if (!exists("jh")) jh = enriched_jhu_data()
requireNamespace("dplyr")
us = dplyr::filter(jh, alpha2Code=="US")
usd =  dplyr::filter(us, subset=="deaths")
usc =  dplyr::filter(us, subset=="confirmed")
usd2 = usd[-1,]
usd2$inc = diff(usd$count)
usc2 = usc[-1,]
usc2$inc = diff(usc$count)
uss = rbind(usd2, usc2)
uscd = data.frame(date=usc2$date, confirmed=usc2$inc, deaths=usd2$inc)
plot_sync(uscd)

vjcitn/sars2app documentation built on Jan. 3, 2022, 12:19 a.m.