prepare.RdPrepare data for modelling with idbrm
Default method used when preparing data
prepare(data, ...)
# S3 method for default
prepare(data, model, ...)| data | A dataframe to be used for modelling |
|---|---|
| ... | Additional arguments passed to model specific prepare functions |
| model | Character string, model type to prepare to use. Supported options are "convolution". |
Sam Abbott
Sam Abbott
# define some example data
library(data.table)
dt <- data.table(
region = "France", cases = seq(10, 500, by = 10),
date = seq(as.Date("2020-10-01"), by = "days", length.out = 50)
)
dt <- dt[, deaths := as.integer(shift(cases, 5) * 0.1)]
dt <- dt[is.na(deaths), deaths := 0]
dt <- prepare(
dt, model = "convolution", location = "region",
primary = "cases", secondary = "deaths",
)
dt[]
#> location date time index init_obs cstart cmax primary secondary
#> 1: France 2020-10-01 0 1 1 1 1 10 0
#> 2: France 2020-10-02 1 2 1 1 2 20 0
#> 3: France 2020-10-03 2 3 1 1 3 30 0
#> 4: France 2020-10-04 3 4 1 1 4 40 0
#> 5: France 2020-10-05 4 5 1 1 5 50 0
#> 6: France 2020-10-06 5 6 1 1 6 60 1
#> 7: France 2020-10-07 6 7 1 1 7 70 2
#> 8: France 2020-10-08 7 8 1 1 8 80 3
#> 9: France 2020-10-09 8 9 1 1 9 90 4
#> 10: France 2020-10-10 9 10 1 1 10 100 5
#> 11: France 2020-10-11 10 11 1 1 11 110 6
#> 12: France 2020-10-12 11 12 1 1 12 120 7
#> 13: France 2020-10-13 12 13 1 1 13 130 8
#> 14: France 2020-10-14 13 14 1 1 14 140 9
#> 15: France 2020-10-15 14 15 0 1 15 150 10
#> 16: France 2020-10-16 15 16 0 1 16 160 11
#> 17: France 2020-10-17 16 17 0 1 17 170 12
#> 18: France 2020-10-18 17 18 0 1 18 180 13
#> 19: France 2020-10-19 18 19 0 1 19 190 14
#> 20: France 2020-10-20 19 20 0 1 20 200 15
#> 21: France 2020-10-21 20 21 0 1 21 210 16
#> 22: France 2020-10-22 21 22 0 1 22 220 17
#> 23: France 2020-10-23 22 23 0 1 23 230 18
#> 24: France 2020-10-24 23 24 0 1 24 240 19
#> 25: France 2020-10-25 24 25 0 1 25 250 20
#> 26: France 2020-10-26 25 26 0 1 26 260 21
#> 27: France 2020-10-27 26 27 0 1 27 270 22
#> 28: France 2020-10-28 27 28 0 1 28 280 23
#> 29: France 2020-10-29 28 29 0 1 29 290 24
#> 30: France 2020-10-30 29 30 0 1 30 300 25
#> 31: France 2020-10-31 30 31 0 1 31 310 26
#> 32: France 2020-11-01 31 32 0 2 31 320 27
#> 33: France 2020-11-02 32 33 0 3 31 330 28
#> 34: France 2020-11-03 33 34 0 4 31 340 29
#> 35: France 2020-11-04 34 35 0 5 31 350 30
#> 36: France 2020-11-05 35 36 0 6 31 360 31
#> 37: France 2020-11-06 36 37 0 7 31 370 32
#> 38: France 2020-11-07 37 38 0 8 31 380 33
#> 39: France 2020-11-08 38 39 0 9 31 390 34
#> 40: France 2020-11-09 39 40 0 10 31 400 35
#> 41: France 2020-11-10 40 41 0 11 31 410 36
#> 42: France 2020-11-11 41 42 0 12 31 420 37
#> 43: France 2020-11-12 42 43 0 13 31 430 38
#> 44: France 2020-11-13 43 44 0 14 31 440 39
#> 45: France 2020-11-14 44 45 0 15 31 450 40
#> 46: France 2020-11-15 45 46 0 16 31 460 41
#> 47: France 2020-11-16 46 47 0 17 31 470 42
#> 48: France 2020-11-17 47 48 0 18 31 480 43
#> 49: France 2020-11-18 48 49 0 19 31 490 44
#> 50: France 2020-11-19 49 50 0 20 31 500 45
#> location date time index init_obs cstart cmax primary secondary