epinow {EpiNow2} | R Documentation |
Real-time Rt Estimation, Forecasting and Reporting
Description
This function wraps the functionality of estimate_infections()
and
forecast_infections()
in order to estimate Rt and cases by date of
infection, forecast into these infections into the future. It also contains
additional functionality to convert forecasts to date of report and produce
summary output useful for reporting results and interpreting them. See
here for
an example of using epinow
to estimate Rt for Covid-19 in a country from
the ECDC data source.
Usage
epinow(
reported_cases,
generation_time = NULL,
delays = delay_opts(),
truncation = trunc_opts(),
rt = rt_opts(),
backcalc = backcalc_opts(),
gp = gp_opts(),
obs = obs_opts(),
stan = stan_opts(),
horizon = 7,
CrIs = c(0.2, 0.5, 0.9),
filter_leading_zeros = TRUE,
zero_threshold = Inf,
return_output = FALSE,
output = c("samples", "plots", "latest", "fit", "timing"),
plot_args = list(),
target_folder = NULL,
target_date,
logs = tempdir(),
id = "epinow",
verbose = interactive()
)
Arguments
reported_cases |
A data frame of confirmed cases (confirm) by date
(date). confirm must be integer and date must be in date format.
|
generation_time |
A call to generation_time_opts() defining the
generation time distribution used. For backwards compatibility a list of
summary parameters can also be passed.
|
delays |
A call to delay_opts() defining delay distributions and
options. See the documentation of delay_opts() and the examples below for
details.
|
truncation |
A call to trunc_opts() defining the truncation of
observed data. Defaults to trunc_opts() . See estimate_truncation() for
an approach to estimating truncation from data.
|
rt |
A list of options as generated by rt_opts() defining Rt
estimation. Defaults to rt_opts() . Set to NULL to switch to using back
calculation rather than generating infections using Rt.
|
backcalc |
A list of options as generated by backcalc_opts() to
define the back calculation. Defaults to backcalc_opts() .
|
gp |
A list of options as generated by gp_opts() to define the
Gaussian process. Defaults to gp_opts() .Set to NULL to disable the
Gaussian process.
|
obs |
A list of options as generated by obs_opts() defining the
observation model. Defaults to obs_opts() .
|
stan |
A list of stan options as generated by stan_opts() . Defaults
to stan_opts() . Can be used to override data , init , and verbose
settings if desired.
|
horizon |
Numeric, defaults to 7. Number of days into the future to
forecast.
|
CrIs |
Numeric vector of credible intervals to calculate.
|
filter_leading_zeros |
Logical, defaults to TRUE. Should zeros at the
start of the time series be filtered out.
|
zero_threshold |
Numeric defaults
to Inf. Indicates if detected zero cases are meaningful by using a threshold
number of cases based on the 7 day average. If the average is above this
threshold then the zero is replaced with the backwards looking rolling
average. If set to infinity then no changes are made.
|
return_output |
Logical, defaults to FALSE. Should output be returned,
this automatically updates to TRUE if no directory for saving is specified.
|
output |
A character vector of optional output to return. Supported
options are samples ("samples"), plots ("plots"), the run time ("timing"),
copying the dated folder into a latest folder (if target_folder is not
null, set using "latest"), and the stan fit ("fit"). The default is to
return all options.
|
plot_args |
A list of optional arguments passed to plot.epinow() .
|
target_folder |
Character string specifying where to save results (will
create if not present).
|
target_date |
Date, defaults to maximum found in the data if not
specified.
|
logs |
Character path indicating the target folder in which to store log
information. Defaults to the temporary directory if not specified. Default
logging can be disabled if logs is set to NULL. If specifying a custom
logging setup then the code for setup_default_logging and the
setup_logging function are a sensible place to start.
|
id |
A character string used to assign logging information on error.
Used by regional_epinow to assign errors to regions. Alter the default to
run with error catching.
|
verbose |
Logical, defaults to TRUE when used interactively and
otherwise FALSE . Should verbose debug progress messages be printed.
Corresponds to the "DEBUG" level from futile.logger . See setup_logging
for more detailed logging options.
|
Value
A list of output from estimate_infections, forecast_infections,
report_cases, and report_summary.
Author(s)
Sam Abbott
See Also
estimate_infections simulate_infections forecast_infections
regional_epinow
Examples
# set number of cores to use
old_opts <- options()
options(mc.cores = ifelse(interactive(), 4, 1))
# construct example distributions
generation_time <- get_generation_time(
disease = "SARS-CoV-2", source = "ganyani"
)
incubation_period <- get_incubation_period(
disease = "SARS-CoV-2", source = "lauer"
)
reporting_delay <- dist_spec(
mean = convert_to_logmean(2, 1),
mean_sd = 0.1,
sd = convert_to_logsd(2, 1),
sd_sd = 0.1,
max = 10
)
# example case data
reported_cases <- example_confirmed[1:40]
# estimate Rt and nowcast/forecast cases by date of infection
out <- epinow(
reported_cases = reported_cases,
generation_time = generation_time_opts(generation_time),
rt = rt_opts(prior = list(mean = 2, sd = 0.1)),
delays = delay_opts(incubation_period + reporting_delay)
)
# summary of the latest estimates
summary(out)
# plot estimates
plot(out)
# summary of R estimates
summary(out, type = "parameters", params = "R")
options(old_opts)
[Package
EpiNow2 version 1.4.0
Index]