Calculate a risk ratio from incidence — infer_rate

This enables incidence rates are able to be compared to a baseline figure for incidence. The baseline could come for example from a population average or average incidence over time. The output is an incidence rate ratio. The incidence_baseline column is a rate of events per unit time. The time unit is expected to be the same as that of the date in modelled and this is not checked.

Usage

infer_rate_ratio(
  modelled = i_incidence_model,
  base = i_baseline_incidence_data,
  ...
)

Arguments

modelled

Model output from something like poisson_locfit_model(). It really makes sense if this is a grouped model. - a dataframe with columns:

time (ggoutbreak::time_period + group_unique) - A (usually complete) set of singular observations per unit time as a `time_period`
incidence.fit (double) - an estimate of the incidence rate on a log scale
incidence.se.fit (positive_double) - the standard error of the incidence rate estimate on a log scale
incidence.0.025 (positive_double) - lower confidence limit of the incidence rate (true scale)
incidence.0.5 (positive_double) - median estimate of the incidence rate (true scale)
incidence.0.975 (positive_double) - upper confidence limit of the incidence rate (true scale)

Any grouping allowed.

base

The baseline data must be grouped in the same way as modelled. It may be a time series but does not have to be. See the example and note this may change in the future. - a dataframe with columns:

baseline_incidence (positive_double) - Baseline raw incidence rate as count data

Any grouping allowed.

...

not used

Value

a dataframe with incidence rate ratios for each of the classes in modelled. A dataframe containing the following columns:

time (ggoutbreak::time_period + group_unique) - A (usually complete) set of singular observations per unit time as a time_period
rate_ratio.0.025 (positive_double) - lower confidence limit of the rate ratio for a population group
rate_ratio.0.5 (positive_double) - median estimate of the rate ratio for a population group
rate_ratio.0.975 (positive_double) - upper confidence limit of the rate ratio for a population group

Any grouping allowed.

Examples


baseline = ggoutbreak::england_covid_poisson %>%
  dplyr::mutate(baseline_incidence = incidence.0.5)


tmp = ggoutbreak::england_covid_poisson_age_stratified %>%
  ggoutbreak::infer_rate_ratio(baseline) %>%
  dplyr::glimpse()
#> Rows: 26,790
#> Columns: 24
#> Groups: class [19]
#> $ class              <fct> 00_04, 00_04, 00_04, 00_04, 00_04, 00_04, 00_04, 00…
#> $ time               <time_prd> 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, …
#> $ incidence.fit      <dbl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, -97…
#> $ incidence.se.fit   <dbl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 0.0…
#> $ incidence.0.025    <dbl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 0.0…
#> $ incidence.0.05     <dbl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 0.0…
#> $ incidence.0.25     <dbl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 0.0…
#> $ incidence.0.5      <dbl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 0.0…
#> $ incidence.0.75     <dbl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 0.0…
#> $ incidence.0.95     <dbl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 0.0…
#> $ incidence.0.975    <dbl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 0.0…
#> $ growth.fit         <dbl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 0.0…
#> $ growth.se.fit      <dbl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 0.0…
#> $ growth.0.025       <dbl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 0.0…
#> $ growth.0.05        <dbl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 0.0…
#> $ growth.0.25        <dbl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 0.0…
#> $ growth.0.5         <dbl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 0.0…
#> $ growth.0.75        <dbl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 0.0…
#> $ growth.0.95        <dbl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 0.0…
#> $ growth.0.975       <dbl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 0.0…
#> $ baseline_incidence <dbl> 3.1078399, 2.8905742, 2.6931935, 2.5110697, 2.34049…
#> $ rate_ratio.0.025   <dbl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 0.0…
#> $ rate_ratio.0.5     <dbl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 0.0…
#> $ rate_ratio.0.975   <dbl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 0.0…