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[Stable] Estimates the relationship between a primary and secondary observation, for example hospital admissions and deaths or hospital admissions and bed occupancy. See secondary_opts() for model structure options. See parameter documentation for model defaults and options. See the examples for case studies using synthetic data and here for an example of forecasting Covid-19 deaths from Covid-19 cases. See here for a prototype function that may be used to estimate and forecast a secondary observation from a primary across multiple regions and here # nolint for an application forecasting Covid-19 deaths in Germany and Poland.

Usage

estimate_secondary(
  reports,
  secondary = secondary_opts(),
  delays = delay_opts(dist_spec(mean = 2.5, mean_sd = 0.5, sd = 0.47, sd_sd = 0.25, max =
    30)),
  truncation = trunc_opts(),
  obs = obs_opts(),
  burn_in = 14,
  CrIs = c(0.2, 0.5, 0.9),
  priors = NULL,
  model = NULL,
  weigh_delay_priors = FALSE,
  verbose = interactive(),
  ...
)

Arguments

reports

A data frame containing the date of report and both primary and secondary reports.

secondary

A call to secondary_opts() or a list containing the following binary variables: cumulative, historic, primary_hist_additive, current, primary_current_additive. These parameters control the structure of the secondary model, see secondary_opts() for details.

delays

A call to delay_opts() defining delay distributions between primary and secondary observations See the documentation of delay_opts() for details. By default a diffuse prior is assumed with a mean of 14 days and standard deviation of 7 days (with a standard deviation of 0.5 and 0.25 respectively on the log scale).

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.

obs

A list of options as generated by obs_opts() defining the observation model. Defaults to obs_opts().

burn_in

Integer, defaults to 14 days. The number of data points to use for estimation but not to fit to at the beginning of the time series. This must be less than the number of observations.

CrIs

Numeric vector of credible intervals to calculate.

priors

A data.frame of named priors to be used in model fitting rather than the defaults supplied from other arguments. This is typically useful if wanting to inform an estimate from the posterior of another model fit.

model

A compiled stan model to override the default model. May be useful for package developers or those developing extensions.

weigh_delay_priors

Logical. If TRUE, all delay distribution priors will be weighted by the number of observation data points, in doing so approximately placing an independent prior at each time step and usually preventing the posteriors from shifting. If FALSE (default), no weight will be applied, i.e. delay distributions will be treated as a single parameters.

verbose

Logical, should model fitting progress be returned. Defaults to interactive().

...

Additional parameters to pass to rstan::sampling.

Value

A list containing: predictions (a data frame ordered by date with the primary, and secondary observations, and a summary of the model estimated secondary observations), posterior which contains a summary of the entire model posterior, data (a list of data used to fit the model), and fit (the stanfit object).

Author

Sam Abbott

Examples

# \donttest{
# set number of cores to use
old_opts <- options()
options(mc.cores = ifelse(interactive(), 4, 1))

# load data.table for manipulation
library(data.table)

#### Incidence data example ####

# make some example secondary incidence data
cases <- example_confirmed
cases <- as.data.table(cases)[, primary := confirm]
# Assume that only 40 percent of cases are reported
cases[, scaling := 0.4]
#>            date confirm primary scaling
#>   1: 2020-02-22      14      14     0.4
#>   2: 2020-02-23      62      62     0.4
#>   3: 2020-02-24      53      53     0.4
#>   4: 2020-02-25      97      97     0.4
#>   5: 2020-02-26      93      93     0.4
#>  ---                                   
#> 126: 2020-06-26     296     296     0.4
#> 127: 2020-06-27     255     255     0.4
#> 128: 2020-06-28     175     175     0.4
#> 129: 2020-06-29     174     174     0.4
#> 130: 2020-06-30     126     126     0.4
# Parameters of the assumed log normal delay distribution
cases[, meanlog := 1.8][, sdlog := 0.5]
#>            date confirm primary scaling meanlog sdlog
#>   1: 2020-02-22      14      14     0.4     1.8   0.5
#>   2: 2020-02-23      62      62     0.4     1.8   0.5
#>   3: 2020-02-24      53      53     0.4     1.8   0.5
#>   4: 2020-02-25      97      97     0.4     1.8   0.5
#>   5: 2020-02-26      93      93     0.4     1.8   0.5
#>  ---                                                 
#> 126: 2020-06-26     296     296     0.4     1.8   0.5
#> 127: 2020-06-27     255     255     0.4     1.8   0.5
#> 128: 2020-06-28     175     175     0.4     1.8   0.5
#> 129: 2020-06-29     174     174     0.4     1.8   0.5
#> 130: 2020-06-30     126     126     0.4     1.8   0.5

# Simulate secondary cases
cases <- simulate_secondary(cases, type = "incidence")
#
# fit model to example data specifying a weak prior for fraction reported
# with a secondary case
inc <- estimate_secondary(cases[1:60],
  obs = obs_opts(scale = list(mean = 0.2, sd = 0.2), week_effect = FALSE)
)
plot(inc, primary = TRUE)


# forecast future secondary cases from primary
inc_preds <- forecast_secondary(
  inc, cases[seq(61, .N)][, value := primary]
)
plot(inc_preds, new_obs = cases, from = "2020-05-01")


#### Prevalence data example ####

# make some example prevalence data
cases <- example_confirmed
cases <- as.data.table(cases)[, primary := confirm]
# Assume that only 30 percent of cases are reported
cases[, scaling := 0.3]
#>            date confirm primary scaling
#>   1: 2020-02-22      14      14     0.3
#>   2: 2020-02-23      62      62     0.3
#>   3: 2020-02-24      53      53     0.3
#>   4: 2020-02-25      97      97     0.3
#>   5: 2020-02-26      93      93     0.3
#>  ---                                   
#> 126: 2020-06-26     296     296     0.3
#> 127: 2020-06-27     255     255     0.3
#> 128: 2020-06-28     175     175     0.3
#> 129: 2020-06-29     174     174     0.3
#> 130: 2020-06-30     126     126     0.3
# Parameters of the assumed log normal delay distribution
cases[, meanlog := 1.6][, sdlog := 0.8]
#>            date confirm primary scaling meanlog sdlog
#>   1: 2020-02-22      14      14     0.3     1.6   0.8
#>   2: 2020-02-23      62      62     0.3     1.6   0.8
#>   3: 2020-02-24      53      53     0.3     1.6   0.8
#>   4: 2020-02-25      97      97     0.3     1.6   0.8
#>   5: 2020-02-26      93      93     0.3     1.6   0.8
#>  ---                                                 
#> 126: 2020-06-26     296     296     0.3     1.6   0.8
#> 127: 2020-06-27     255     255     0.3     1.6   0.8
#> 128: 2020-06-28     175     175     0.3     1.6   0.8
#> 129: 2020-06-29     174     174     0.3     1.6   0.8
#> 130: 2020-06-30     126     126     0.3     1.6   0.8

# Simulate secondary cases
cases <- simulate_secondary(cases, type = "prevalence")

# fit model to example prevalence data
prev <- estimate_secondary(cases[1:100],
  secondary = secondary_opts(type = "prevalence"),
  obs = obs_opts(
    week_effect = FALSE,
    scale = list(mean = 0.4, sd = 0.1)
  )
)
plot(prev, primary = TRUE)


# forecast future secondary cases from primary
prev_preds <- forecast_secondary(
 prev, cases[seq(101, .N)][, value := primary]
)
plot(prev_preds, new_obs = cases, from = "2020-06-01")


options(old_opts)
# }