Format data for use with stan

Usage

fv_as_data_list(
  obs,
  horizon = 4,
  r_init = c(0, 0.25),
  r_step = 1,
  r_forecast = TRUE,
  beta = c(0, 0.5),
  lkj = 0.5,
  voc_scale = c(0, 0.2),
  period = NULL,
  special_periods = c(),
  variant_relationship = "correlated",
  overdispersion = TRUE,
  likelihood = TRUE,
  output_loglik = TRUE,
  debug = FALSE
)

Arguments

obs: A data frame with the following variables: date, cases, seq_voc, and seq_total.
horizon: Integer forecast horizon. Defaults to 4.
r_init: Numeric vector of length 2. Mean and standard deviation for the normal prior on the initial log growth rate.
r_step: Integer, defaults to 1. The number of observations between each change in the growth rate.
r_forecast: Logical, defaults TRUE. Should the growth rate be forecast beyond the data horizon.
beta: Numeric vector, defaults to c(0, 0.5). Represents the mean and standard deviation of the normal prior (truncated at 1 and -1) on the weighting in the differenced AR process of the previous difference. Placing a tight prior around zero effectively reduces the AR process to a random walk on the growth rate.
lkj: Numeric defaults to 0.5. The assumed prior covariance between variants growth rates when using the "correlated" model. This sets the shape parameter for the Lewandowski-Kurowicka-Joe (LKJ) prior distribution. If set to 1 assigns a uniform prior for all correlations, values less than 1 indicate increased belief in strong correlations and values greater than 1 indicate increased belief weaker correlations. Our default setting places increased weight on some correlation between strains.
voc_scale: Numeric vector of length 2. Prior mean and standard deviation for the initial growth rate modifier due to the variant of concern.
period: Logical defaults to NULL. If specified should be a function that accepts a vector of dates. This can be used to assign periodic effects to dates which will then be adjusted for in the case model. An example is adjusting for day of the week effects for which the fv_dow_period() can be used.
special_periods: A vector of dates to pass to the period function argument with the same name to be treated as "special" for example holidays being treated as sundays in fv_dow_period().
variant_relationship: Character string, defaulting to "correlated". Controls the relationship of strains with options being "correlated" (strains growth rates are correlated over time), "scaled" (a fixed scaling between strains), and "independent" (fully independent strains after initial scaling).
overdispersion: Logical, defaults to TRUE. Should the observations used include overdispersion.
likelihood: Logical, defaults to TRUE. Should the likelihood be included in the model
output_loglik: Logical, defaults to FALSE. Should the log-likelihood be output. Disabling this will speed up fitting if evaluating the model fit is not required.
debug: Logical, defaults to FALSE. Should within model debug information be returned.

Value

A list as required by stan.

Examples

fv_as_data_list(latest_obs(germany_covid19_delta_obs))
#> $t
#> [1] 30
#> 
#> $t_nots
#> [1] 26
#> 
#> $t_nseq
#> [1] 4
#> 
#> $t_seq
#> [1] 14
#> 
#> $t_seqf
#> [1] 26
#> 
#> $X
#>  [1]  87328 109442 117965 107223 142664 145568 131887 107141  77261  57310
#> [11]  33052  22631  15553   7659   5033   4181   5067   7969  11122  14654
#> [21]  18474  28646  44862  62984  71057  75107
#> 
#> $N
#>  [1] 4108 4539 3667 4547 3688 3817 2781 2197 1566  991  706  803  735  564
#> 
#> $Y
#>  [1]   6  34  54  89 101 119 102 181 309 414 451 631 643 521
#> 
#> $start_date
#> [1] "2021-03-20"
#> 
#> $seq_start_date
#> [1] "2021-04-17"
#> 
#> $r_init_mean
#> [1] 0
#> 
#> $r_init_sd
#> [1] 0.25
#> 
#> $beta_mean
#> [1] 0
#> 
#> $beta_sd
#> [1] 0.5
#> 
#> $voc_mean
#> [1] 0
#> 
#> $voc_sd
#> [1] 0.2
#> 
#> $relat
#> [1] 2
#> 
#> $overdisp
#> [1] 1
#> 
#> $likelihood
#> [1] 1
#> 
#> $output_loglik
#> [1] 1
#> 
#> $debug
#> [1] 0
#> 
#> $period
#> [1] 1
#> 
#> $periodic
#>  [1] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
#> 
#> $eta_n
#> [1] 28
#> 
#> $eta_loc
#>  [1] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
#> 
#> $voc_eta_n
#> [1] 24
#> 
#> $voc_eta_loc
#>  [1] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
#> 
#> $lkj_prior
#> [1] 0.5
#>

Format data for use with stan

Usage

Arguments

Value

See also

Examples