regional_summary | R Documentation |
Used to produce summary output either internally in regional_epinow
or
externally.
regional_summary(
regional_output = NULL,
reported_cases,
results_dir = NULL,
summary_dir = NULL,
target_date = NULL,
region_scale = "Region",
all_regions = TRUE,
return_output = FALSE,
plot = TRUE,
max_plot = 10,
...
)
regional_output |
A list of output as produced by |
reported_cases |
A data frame of confirmed cases (confirm) by date
(date), and region ( |
results_dir |
An optional character string indicating the location of the results directory to extract results from. |
summary_dir |
A character string giving the directory in which to store summary of results. |
target_date |
A character string giving the target date for which to extract results (in the format "yyyy-mm-dd"). Defaults to latest available estimates. |
region_scale |
A character string indicating the name to give the regions being summarised. |
all_regions |
Logical, defaults to |
return_output |
Logical, defaults to FALSE. Should output be returned, this automatically updates to TRUE if no directory for saving is specified. |
plot |
Logical, defaults to |
max_plot |
Numeric, defaults to 10. A multiplicative upper bound on the\ number of cases shown on the plot. Based on the maximum number of reported cases. |
... |
Additional arguments passed to |
A list of summary measures and plots
regional_epinow
# example delays
generation_time <- get_generation_time(
disease = "SARS-CoV-2", source = "ganyani"
)
incubation_period <- get_incubation_period(
disease = "SARS-CoV-2", source = "lauer"
)
reporting_delay <- estimate_delay(rlnorm(100, log(6), 1), max_value = 30)
# example case vector from EpiSoon
cases <- example_confirmed[1:30]
cases <- data.table::rbindlist(list(
data.table::copy(cases)[, region := "testland"],
cases[, region := "realland"]
))
# run basic nowcasting pipeline
out <- regional_epinow(
reported_cases = cases,
generation_time = generation_time_opts(generation_time),
delays = delay_opts(incubation_period + reporting_delay),
output = "region",
rt = NULL
)
regional_summary(
regional_output = out$regional,
reported_cases = cases
)
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