incidence (version 1.7.4)

get_fit: Accessors for incidence_fit objects

Description

Accessors for incidence_fit objects

Usage

get_fit(x)
# S3 method for incidence_fit
get_fit(x)
# S3 method for incidence_fit_list
get_fit(x)
get_info(x, what = "r", ...)
# S3 method for incidence_fit
get_info(x, what = "r", ...)
# S3 method for incidence_fit_list
get_info(x, what = "r", groups = NULL, na.rm = TRUE, ...)

Value

a list of incidence_fit objects.

Arguments

x

an incidence_fit or incidence_fit_list object.

what

the name of the item in the "info" element of the incidence_fit object.

...

currently unused.

groups

if what = "pred" and x is an incidence_fit_list object, then this indicates what part of the nesting hierarchy becomes the column named "groups". Defaults to NULL, indicating that no groups column will be added/modified.

na.rm

when TRUE (default), missing values will be excluded from the results.

Examples

if (require(outbreaks)) { withAutoprint({

 dat <- ebola_sim$linelist$date_of_onset

 ## EXAMPLE WITH A SINGLE MODEL

 ## compute weekly incidence
 sex <- ebola_sim$linelist$gender
 i.sex <- incidence(dat, interval = 7, group = sex)
 
 ## Compute the optimal split for each group separately
 fits  <- fit_optim_split(i.sex, separate_split = TRUE)

 ## `fits` contains an `incidence_fit_list` object
 fits$fit
 
 ## Grab the list of `incidence_fit` objects
 get_fit(fits$fit)
 
 ## Get the predictions for all groups
 get_info(fits$fit, "pred", groups = 1)
 
 ## Get the predictions, but set `groups` to "before" and "after"
 get_info(fits$fit, "pred", groups = 2)
 
 ## Get the reproduction number
 get_info(fits$fit, "r")

 ## Get the doubling confidence interval
 get_info(fits$fit, "doubling.conf")

 ## Get the halving confidence interval
 get_info(fits$fit, "halving.conf")
})}