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[Stable] Takes the output of stan_opts() and converts it into a list understood by stan. Internally calls the other create_ family of functions to construct a single list for input into stan with all data required present.

Usage

create_stan_data(
  reported_cases,
  seeding_time,
  rt,
  gp,
  obs,
  horizon,
  backcalc,
  shifted_cases
)

Arguments

reported_cases

A <data.frame> of confirmed cases (confirm) by date (date). confirm must be integer and date must be in date format.

seeding_time

Integer; seeding time, usually obtained using get_seeding_time().

rt

A list of options as generated by rt_opts() defining Rt estimation. Defaults to rt_opts(). Set to NULL to switch to using back calculation rather than generating infections using Rt.

gp

A list of options as generated by gp_opts() to define the Gaussian process. Defaults to gp_opts(). Set to NULL to disable the Gaussian process.

obs

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

horizon

Numeric, forecast horizon.

backcalc

A list of options as generated by backcalc_opts() to define the back calculation. Defaults to backcalc_opts().

shifted_cases

A <data.frame> of delay shifted cases

Value

A list of stan data

Author

Sam Abbott

Sebastian Funk

Examples

create_stan_data(
 example_confirmed, 7, rt_opts(), gp_opts(), obs_opts(), 7,
 backcalc_opts(), create_shifted_cases(example_confirmed, 7, 14, 7)
)
#> $cases
#>   [1]  238  240  561  347  466  587  769  778 1247 1492 1797  977 2313 2651 2547
#>  [16] 3497 2823 4000 3526 4207 5322 5986 6557 5560 4789 5249 5210 6153 5959 5974
#>  [31] 5217 4050 4053 4782 4668 4585 4805 4316 3599 3039 3836 4204 3951 4694 4092
#>  [46] 3153 2972 2667 3786 3493 3491 3047 2256 2729 3370 2646 3021 2357 2324 1739
#>  [61] 2091 2086 1872 1965 1900 1389 1221 1075 1444 1401 1327 1083  802  744 1402
#>  [76]  888  992  789  875  675  451  813  665  642  652  669  531  300  397  584
#>  [91]  593  516  416  355  178  318  321  177  518  270  197  280  283  202  379
#> [106]  163  346  338  301  210  328  331    0  264  224  221
#> 
#> $cases_time
#>   [1]   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18
#>  [19]  19  20  21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36
#>  [37]  37  38  39  40  41  42  43  44  45  46  47  48  49  50  51  52  53  54
#>  [55]  55  56  57  58  59  60  61  62  63  64  65  66  67  68  69  70  71  72
#>  [73]  73  74  75  76  77  78  79  80  81  82  83  84  85  86  87  88  89  90
#>  [91]  91  92  93  94  95  96  97  98  99 100 101 102 103 104 105 106 107 108
#> [109] 109 110 111 112 113 114 115 116
#> 
#> $lt
#> [1] 116
#> 
#> $shifted_cases
#>            date confirm
#>          <Date>   <num>
#>   1: 2020-03-07    3028
#>   2: 2020-03-08    3407
#>   3: 2020-03-09    3698
#>   4: 2020-03-10    3912
#>   5: 2020-03-11    4217
#>  ---                   
#> 112: 2020-06-26     224
#> 113: 2020-06-27     222
#> 114: 2020-06-28     219
#> 115: 2020-06-29     217
#> 116: 2020-06-30     215
#> 
#> $t
#> [1] 130
#> 
#> $horizon
#> [1] 7
#> 
#> $burn_in
#> [1] 0
#> 
#> $seeding_time
#> [1] 7
#> 
#> $r_mean
#> [1] 1
#> 
#> $r_sd
#> [1] 1
#> 
#> $estimate_r
#> [1] 1
#> 
#> $bp_n
#> [1] 0
#> 
#> $breakpoints
#> NULL
#> 
#> $future_fixed
#> [1] 1
#> 
#> $fixed_from
#> [1] 0
#> 
#> $pop
#> [1] 0
#> 
#> $stationary
#> [1] 0
#> 
#> $future_time
#> [1] 7
#> 
#> $prior_infections
#> [1] 6.127493
#> 
#> $prior_growth
#> [1] 0.1829178
#> 
#> $rt_half_window
#> [1] 0
#> 
#> $backcalc_prior
#> [1] 1
#> 
#> $fixed
#> [1] 0
#> 
#> $M
#> [1] 24
#> 
#> $L
#> [1] 1.5
#> 
#> $ls_meanlog
#> [1] 2.991842
#> 
#> $ls_sdlog
#> [1] 0.3245928
#> 
#> $ls_min
#> [1] 0
#> 
#> $ls_max
#> [1] 116
#> 
#> $alpha_sd
#> [1] 0.05
#> 
#> $gp_type
#> [1] 0
#> 
#> $model_type
#> [1] 1
#> 
#> $phi_mean
#> [1] 0
#> 
#> $phi_sd
#> [1] 1
#> 
#> $week_effect
#> [1] 7
#> 
#> $obs_weight
#> [1] 1
#> 
#> $obs_scale
#> [1] 0
#> 
#> $obs_scale_mean
#> [1] 1
#> 
#> $obs_scale_sd
#> [1] 0
#> 
#> $accumulate
#> [1] 0
#> 
#> $likelihood
#> [1] 1
#> 
#> $return_likelihood
#> [1] 0
#> 
#> $day_of_week
#>   [1] 6 7 1 2 3 4 5 6 7 1 2 3 4 5 6 7 1 2 3 4 5 6 7 1 2 3 4 5 6 7 1 2 3 4 5 6 7
#>  [38] 1 2 3 4 5 6 7 1 2 3 4 5 6 7 1 2 3 4 5 6 7 1 2 3 4 5 6 7 1 2 3 4 5 6 7 1 2
#>  [75] 3 4 5 6 7 1 2 3 4 5 6 7 1 2 3 4 5 6 7 1 2 3 4 5 6 7 1 2 3 4 5 6 7 1 2 3 4
#> [112] 5 6 7 1 2 3 4 5 6 7 1 2
#>