S3 generic for computing proportions from fitted models
Usage
proportion(
fitted_model,
numerator_combination = NULL,
denominator_combination = NULL,
...
)
# S3 method for class 'ps'
proportion(
fitted_model,
numerator_combination = NULL,
denominator_combination = NULL,
...
)
# S3 method for class 'rw'
proportion(
fitted_model,
numerator_combination = NULL,
denominator_combination = NULL,
...
)Arguments
- fitted_model
Fitted model object with class `EpiStrainDynamics.fit` with `multiple` or `subtyped` pathogen structure.
- numerator_combination
Named pathogens or subtypes to be included in proportion numerator.
- denominator_combination
Named pathogens or subtypes to be included in proportion denominator, or 'all'.
- ...
Additional arguments passed to metrics calculation
Value
named list of class `EpiStrainDynamics.metric` containing a dataframe of the calculated metric outcome (`$measure`), the fit object (`$fit`), and the constructed model object (`$constructed_model`). The `measure` data frame contains the median of the epidemiological quantity (`y`), the 50 interval of the quantity (`lb_50` & `ub_50`), the 95 (`lb_95` & `ub_95`), the proportion greater than a defined threshold value (`prop`), the pathogen name (`pathogen`), and the time label (`time`).
Examples
if (FALSE) { # \dontrun{
mod <- construct_model(
method = p_spline(),
pathogen_structure = multiple(
case_timeseries = sarscov2$cases,
time = sarscov2$date,
component_pathogen_timeseries = list(
alpha = sarscov2$alpha,
delta = sarscov2$delta,
omicron = sarscov2$omicron,
other = sarscov2$other))
)
fit <- fit_model(mod)
prop <- proportion(fit)
# or a unique combination, compared to all pathogens
prop2 <- proportion(fit,
numerator_combination = c('alpha', 'delta', 'omicron'),
denominator_combination = 'all'
)
# or a user-specified combination in both numerator and denominator
prop3 <- proportion(fit,
numerator_combination = 'alpha',
denominator_combination = c('alpha', 'delta', 'omicron')
)
} # }