create_stan_data {EpiNow2} | R Documentation |
Create Stan Data Required for estimate_infections
Description
Takes the output of stan_opts()
and converts it into a list understood by
stan. Internally calls the other create_
family of functions to
construct a single list for input into stan with all data required
present.
Usage
create_stan_data(
data,
seeding_time,
rt,
gp,
obs,
backcalc,
shifted_cases,
forecast
)
Arguments
data |
A <data.frame> of disease reports (confirm) by date (date).
confirm must be numeric and date must be in date format. Optionally
this can also have a logical accumulate column which indicates whether
data should be added to the next data point. This is useful when modelling
e.g. weekly incidence data. See also the fill_missing() function which
helps add the accumulate column with the desired properties when dealing
with non-daily data. If any accumulation is done this happens after
truncation as specified by the truncation argument.
|
seeding_time |
Integer; seeding time, usually obtained using
get_seeding_time() .
|
rt |
A list of options as generated by rt_opts() defining Rt
estimation. Defaults to rt_opts() . To generate new infections using
the non-mechanistic model instead of the renewal equation model, use
rt = NULL . The non-mechanistic model internally uses the setting
rt = rt_opts(use_rt = FALSE, future = "project", gp_on = "R0") .
|
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() .
|
backcalc |
A list of options as generated by backcalc_opts() to
define the back calculation. Defaults to backcalc_opts() .
|
shifted_cases |
A <data.frame> of delay shifted cases
|
forecast |
A list of options as generated by forecast_opts() defining
the forecast opitions. Defaults to forecast_opts() . If NULL then no
forecasting will be done.
|
Value
A list of stan data
Examples
## Not run:
create_stan_data(
example_confirmed, 7, rt_opts(), gp_opts(), obs_opts(), 7,
backcalc_opts(), create_shifted_cases(example_confirmed, 7, 14, 7)
)
## End(Not run)
[Package
EpiNow2 version 1.7.1
Index]