Defines a list specifying the structure of the observation
model. Custom settings can be supplied which override the defaults.
Character string defining the observation model. Options are Negative binomial ("negbin"), the default, and Poisson.
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.
Numeric, defaults to 1. Weight to give the observed data in the log density.
Logical defaulting to TRUE
. Should a day of the week effect
be used in the observation model.
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.
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.
Logical, defaults to TRUE
. Should the likelihood be
included in the model
Logical, defaults to FALSE
. Should the likelihood
be returned by the model.
A list of observation model settings.
# 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
#>