library("EpiNow2")
library("here")
options(mc.cores = 4)
set.seed(12345)
# get example case counts
reported_cases <- example_confirmed[1:60]
#' # use example distributions
reporting_delay <- LogNormal(mean = 2, sd = 1, max = 10L)
example_estimate_infections <- estimate_infections(reported_cases,
generation_time = gt_opts(example_generation_time),
delays = delay_opts(example_incubation_period + reporting_delay),
rt = rt_opts(prior = list(mean = 2, sd = 0.1)),
stan = stan_opts(samples = 200, control = list(adapt_delta = 0.95))
)
cases <- example_confirmed[1:60]
cases <- data.table::rbindlist(list(
data.table::copy(cases)[, region := "testland"],
cases[, region := "realland"]
))
example_regional_epinow <- regional_epinow(
generation_time = gt_opts(example_generation_time),
data = cases,
delays = delay_opts(example_incubation_period + reporting_delay),
rt = rt_opts(prior = list(mean = 2, sd = 0.2)),
stan = stan_opts(samples = 200, control = list(adapt_delta = 0.95))
)
saveRDS(
example_estimate_infections,
here("inst", "extdata", "example_estimate_infections.rds"),
compress = "xz"
)
saveRDS(
example_regional_epinow,
here("inst", "extdata", "example_regional_epinow.rds"),
compress = "xz"
)
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