Observation Model Options — obs

Defines a list specifying the structure of the observation model. Custom settings can be supplied which override the defaults.

Usage

obs_opts(
  family = "negbin",
  phi = c(0, 1),
  weight = 1,
  week_effect = TRUE,
  week_length = 7,
  scale = list(),
  likelihood = TRUE,
  return_likelihood = FALSE
)

Arguments

family: Character string defining the observation model. Options are Negative binomial ("negbin"), the default, and Poisson.
phi: A numeric vector of length 2, defaults to 0, 1. Indicates the mean and standard deviation of the normal prior used for the observation process.
weight: Numeric, defaults to 1. Weight to give the observed data in the log density.
week_effect: Logical defaulting to TRUE. Should a day of the week effect be used in the observation model.
week_length: Numeric assumed length of the week in days, defaulting to 7 days. This can be modified if data aggregated over a period other than a week or if data has a non-weekly periodicity.
scale: List, defaulting to an empty list. Should an scaling factor be applied to map latent infections (convolved to date of report). If none empty a mean (mean) and standard deviation (sd) needs to be supplied defining the normally distributed scaling factor.
likelihood: Logical, defaults to TRUE. Should the likelihood be included in the model.
return_likelihood: Logical, defaults to FALSE. Should the likelihood be returned by the model.

Value

A list of observation model settings.

Author

Sam Abbott

Examples

# default settings
obs_opts()
#> $family
#> [1] "negbin"
#> 
#> $phi
#> [1] 0 1
#> 
#> $weight
#> [1] 1
#> 
#> $week_effect
#> [1] TRUE
#> 
#> $week_length
#> [1] 7
#> 
#> $scale
#> list()
#> 
#> $likelihood
#> [1] TRUE
#> 
#> $return_likelihood
#> [1] FALSE
#> 

# Turn off day of the week effect
obs_opts(week_effect = TRUE)
#> $family
#> [1] "negbin"
#> 
#> $phi
#> [1] 0 1
#> 
#> $weight
#> [1] 1
#> 
#> $week_effect
#> [1] TRUE
#> 
#> $week_length
#> [1] 7
#> 
#> $scale
#> list()
#> 
#> $likelihood
#> [1] TRUE
#> 
#> $return_likelihood
#> [1] FALSE
#> 

# Scale reported data
obs_opts(scale = list(mean = 0.2, sd = 0.02))
#> $family
#> [1] "negbin"
#> 
#> $phi
#> [1] 0 1
#> 
#> $weight
#> [1] 1
#> 
#> $week_effect
#> [1] TRUE
#> 
#> $week_length
#> [1] 7
#> 
#> $scale
#> $scale$mean
#> [1] 0.2
#> 
#> $scale$sd
#> [1] 0.02
#> 
#> 
#> $likelihood
#> [1] TRUE
#> 
#> $return_likelihood
#> [1] FALSE
#>