tests/testthat/_snaps/enw_expectation.md
In epiforecasts/epinowcast: Flexible Hierarchical Nowcasting
enw_expectation produces the expected default model
Code
expectation <- enw_expectation(data = pobs)
Message
A random effect using .group is not possible as this variable has fewer than 2 unique values.
i The r design matrix is sparse (>90% zeros). Consider using `sparse_design = TRUE` in `enw_fit_opts()` to potentially reduce memory usage and computation time.
Code
expectation$inits <- NULL
expectation
Output
$formula
$formula$r
[1] "~0 + (1 | day:.group)"
$formula$observation
[1] "~1"
$data_raw
$data_raw$r
date .group location age_group delay day_of_week day week month
1: 2021-07-14 1 DE 00+ 0 Wednesday 1 0 0
2: 2021-07-15 1 DE 00+ 0 Thursday 2 0 0
3: 2021-07-16 1 DE 00+ 0 Friday 3 0 0
4: 2021-07-17 1 DE 00+ 0 Saturday 4 0 0
5: 2021-07-18 1 DE 00+ 0 Sunday 5 0 0
6: 2021-07-19 1 DE 00+ 0 Monday 6 0 0
7: 2021-07-20 1 DE 00+ 0 Tuesday 7 1 0
8: 2021-07-21 1 DE 00+ 0 Wednesday 8 1 0
9: 2021-07-22 1 DE 00+ 0 Thursday 9 1 0
10: 2021-07-23 1 DE 00+ 0 Friday 10 1 0
11: 2021-07-24 1 DE 00+ 0 Saturday 11 1 0
12: 2021-07-25 1 DE 00+ 0 Sunday 12 1 0
13: 2021-07-26 1 DE 00+ 0 Monday 13 1 0
14: 2021-07-27 1 DE 00+ 0 Tuesday 14 2 0
15: 2021-07-28 1 DE 00+ 0 Wednesday 15 2 0
16: 2021-07-29 1 DE 00+ 0 Thursday 16 2 0
17: 2021-07-30 1 DE 00+ 0 Friday 17 2 0
18: 2021-07-31 1 DE 00+ 0 Saturday 18 2 0
19: 2021-08-01 1 DE 00+ 0 Sunday 19 2 1
20: 2021-08-02 1 DE 00+ 0 Monday 20 2 1
21: 2021-08-03 1 DE 00+ 0 Tuesday 21 3 1
22: 2021-08-04 1 DE 00+ 0 Wednesday 22 3 1
23: 2021-08-05 1 DE 00+ 0 Thursday 23 3 1
24: 2021-08-06 1 DE 00+ 0 Friday 24 3 1
25: 2021-08-07 1 DE 00+ 0 Saturday 25 3 1
26: 2021-08-08 1 DE 00+ 0 Sunday 26 3 1
27: 2021-08-09 1 DE 00+ 0 Monday 27 3 1
28: 2021-08-10 1 DE 00+ 0 Tuesday 28 4 1
29: 2021-08-11 1 DE 00+ 0 Wednesday 29 4 1
30: 2021-08-12 1 DE 00+ 0 Thursday 30 4 1
31: 2021-08-13 1 DE 00+ 0 Friday 31 4 1
32: 2021-08-14 1 DE 00+ 0 Saturday 32 4 1
33: 2021-08-15 1 DE 00+ 0 Sunday 33 4 1
34: 2021-08-16 1 DE 00+ 0 Monday 34 4 1
35: 2021-08-17 1 DE 00+ 0 Tuesday 35 5 1
36: 2021-08-18 1 DE 00+ 0 Wednesday 36 5 1
37: 2021-08-19 1 DE 00+ 0 Thursday 37 5 1
38: 2021-08-20 1 DE 00+ 0 Friday 38 5 1
39: 2021-08-21 1 DE 00+ 0 Saturday 39 5 1
40: 2021-08-22 1 DE 00+ 0 Sunday 40 5 1
date .group location age_group delay day_of_week day week month
$data_raw$observation
date .group location age_group delay day_of_week day week month
1: 2021-07-13 1 DE 00+ 0 Tuesday 0 0 0
2: 2021-07-14 1 DE 00+ 0 Wednesday 1 0 0
3: 2021-07-15 1 DE 00+ 0 Thursday 2 0 0
4: 2021-07-16 1 DE 00+ 0 Friday 3 0 0
5: 2021-07-17 1 DE 00+ 0 Saturday 4 0 0
6: 2021-07-18 1 DE 00+ 0 Sunday 5 0 0
7: 2021-07-19 1 DE 00+ 0 Monday 6 0 0
8: 2021-07-20 1 DE 00+ 0 Tuesday 7 1 0
9: 2021-07-21 1 DE 00+ 0 Wednesday 8 1 0
10: 2021-07-22 1 DE 00+ 0 Thursday 9 1 0
11: 2021-07-23 1 DE 00+ 0 Friday 10 1 0
12: 2021-07-24 1 DE 00+ 0 Saturday 11 1 0
13: 2021-07-25 1 DE 00+ 0 Sunday 12 1 0
14: 2021-07-26 1 DE 00+ 0 Monday 13 1 0
15: 2021-07-27 1 DE 00+ 0 Tuesday 14 2 0
16: 2021-07-28 1 DE 00+ 0 Wednesday 15 2 0
17: 2021-07-29 1 DE 00+ 0 Thursday 16 2 0
18: 2021-07-30 1 DE 00+ 0 Friday 17 2 0
19: 2021-07-31 1 DE 00+ 0 Saturday 18 2 0
20: 2021-08-01 1 DE 00+ 0 Sunday 19 2 1
21: 2021-08-02 1 DE 00+ 0 Monday 20 2 1
22: 2021-08-03 1 DE 00+ 0 Tuesday 21 3 1
23: 2021-08-04 1 DE 00+ 0 Wednesday 22 3 1
24: 2021-08-05 1 DE 00+ 0 Thursday 23 3 1
25: 2021-08-06 1 DE 00+ 0 Friday 24 3 1
26: 2021-08-07 1 DE 00+ 0 Saturday 25 3 1
27: 2021-08-08 1 DE 00+ 0 Sunday 26 3 1
28: 2021-08-09 1 DE 00+ 0 Monday 27 3 1
29: 2021-08-10 1 DE 00+ 0 Tuesday 28 4 1
30: 2021-08-11 1 DE 00+ 0 Wednesday 29 4 1
31: 2021-08-12 1 DE 00+ 0 Thursday 30 4 1
32: 2021-08-13 1 DE 00+ 0 Friday 31 4 1
33: 2021-08-14 1 DE 00+ 0 Saturday 32 4 1
34: 2021-08-15 1 DE 00+ 0 Sunday 33 4 1
35: 2021-08-16 1 DE 00+ 0 Monday 34 4 1
36: 2021-08-17 1 DE 00+ 0 Tuesday 35 5 1
37: 2021-08-18 1 DE 00+ 0 Wednesday 36 5 1
38: 2021-08-19 1 DE 00+ 0 Thursday 37 5 1
39: 2021-08-20 1 DE 00+ 0 Friday 38 5 1
40: 2021-08-21 1 DE 00+ 0 Saturday 39 5 1
41: 2021-08-22 1 DE 00+ 0 Sunday 40 5 1
date .group location age_group delay day_of_week day week month
$data
$data$expr_r_seed
[1] 1
$data$expr_gt_n
[1] 1
$data$expr_lrgt
[1] 0
$data$expr_t
[1] 40
$data$expr_obs
[1] 0
$data$expr_g
[1] 0
$data$expr_ft
[1] 41
$data$expr_fintercept
[1] 0
$data$expr_fnrow
[1] 40
$data$expr_findex
[1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25
[26] 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40
$data$expr_fnindex
[1] 40
$data$expr_fncol
[1] 40
$data$expr_rncol
[1] 1
$data$expr_fdesign
day1 day2 day3 day4 day5 day6 day7 day8 day9 day10 day11 day12 day13 day14
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day15 day16 day17 day18 day19 day20 day21 day22 day23 day24 day25 day26
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39 0 0 0 0 0 0 0 0 0 0 0 0
40 0 0 0 0 0 0 0 0 0 0 0 0
day27 day28 day29 day30 day31 day32 day33 day34 day35 day36 day37 day38
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day39 day40
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2 0 0
3 0 0
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5 0 0
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12 0 0
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24 0 0
25 0 0
26 0 0
27 0 0
28 0 0
29 0 0
30 0 0
31 0 0
32 0 0
33 0 0
34 0 0
35 0 0
36 0 0
37 0 0
38 0 0
39 1 0
40 0 1
attr(,"assign")
[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 1 1 1 1 1 1 1 1
[39] 1 1
attr(,"contrasts")
attr(,"contrasts")$day
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28
1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
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29 30 31 32 33 34 35 36 37 38 39 40
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$data$expr_rdesign
fixed day
1 0 1
2 0 1
3 0 1
4 0 1
5 0 1
6 0 1
7 0 1
8 0 1
9 0 1
10 0 1
11 0 1
12 0 1
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15 0 1
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31 0 1
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36 0 1
37 0 1
38 0 1
39 0 1
40 0 1
attr(,"assign")
[1] 1 2
$data$expl_lrd_n
[1] 1
$data$expl_lrd
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
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[9,] 0 0 0 0 0 0 0 0 0 0 0 0
[10,] 0 0 0 0 0 0 0 0 0 0 0 0
[11,] 0 0 0 0 0 0 0 0 0 0 0 0
[12,] 0 0 0 0 0 0 0 0 0 0 0 0
[13,] 0 0 0 0 0 0 0 0 0 0 0 0
[14,] 0 0 0 0 0 0 0 0 0 0 0 0
[15,] 0 0 0 0 0 0 0 0 0 0 0 0
[16,] 0 0 0 0 0 0 0 0 0 0 0 0
[17,] 0 0 0 0 0 0 0 0 0 0 0 0
[18,] 0 0 0 0 0 0 0 0 0 0 0 0
[19,] 0 0 0 0 0 0 0 0 0 0 0 0
[20,] 0 0 0 0 0 0 0 0 0 0 0 0
[21,] 0 0 0 0 0 0 0 0 0 0 0 0
[22,] 0 0 0 0 0 0 0 0 0 0 0 0
[23,] 0 0 0 0 0 0 0 0 0 0 0 0
[24,] 0 0 0 0 0 0 0 0 0 0 0 0
[25,] 0 0 0 0 0 0 0 0 0 0 0 0
[26,] 1 0 0 0 0 0 0 0 0 0 0 0
[27,] 0 1 0 0 0 0 0 0 0 0 0 0
[28,] 0 0 1 0 0 0 0 0 0 0 0 0
[29,] 0 0 0 1 0 0 0 0 0 0 0 0
[30,] 0 0 0 0 1 0 0 0 0 0 0 0
[31,] 0 0 0 0 0 1 0 0 0 0 0 0
[32,] 0 0 0 0 0 0 1 0 0 0 0 0
[33,] 0 0 0 0 0 0 0 1 0 0 0 0
[34,] 0 0 0 0 0 0 0 0 1 0 0 0
[35,] 0 0 0 0 0 0 0 0 0 1 0 0
[36,] 0 0 0 0 0 0 0 0 0 0 1 0
[37,] 0 0 0 0 0 0 0 0 0 0 0 1
[38,] 0 0 0 0 0 0 0 0 0 0 0 0
[39,] 0 0 0 0 0 0 0 0 0 0 0 0
[40,] 0 0 0 0 0 0 0 0 0 0 0 0
[41,] 0 0 0 0 0 0 0 0 0 0 0 0
[,38] [,39] [,40] [,41]
[1,] 0 0 0 0
[2,] 0 0 0 0
[3,] 0 0 0 0
[4,] 0 0 0 0
[5,] 0 0 0 0
[6,] 0 0 0 0
[7,] 0 0 0 0
[8,] 0 0 0 0
[9,] 0 0 0 0
[10,] 0 0 0 0
[11,] 0 0 0 0
[12,] 0 0 0 0
[13,] 0 0 0 0
[14,] 0 0 0 0
[15,] 0 0 0 0
[16,] 0 0 0 0
[17,] 0 0 0 0
[18,] 0 0 0 0
[19,] 0 0 0 0
[20,] 0 0 0 0
[21,] 0 0 0 0
[22,] 0 0 0 0
[23,] 0 0 0 0
[24,] 0 0 0 0
[25,] 0 0 0 0
[26,] 0 0 0 0
[27,] 0 0 0 0
[28,] 0 0 0 0
[29,] 0 0 0 0
[30,] 0 0 0 0
[31,] 0 0 0 0
[32,] 0 0 0 0
[33,] 0 0 0 0
[34,] 0 0 0 0
[35,] 0 0 0 0
[36,] 0 0 0 0
[37,] 0 0 0 0
[38,] 1 0 0 0
[39,] 0 1 0 0
[40,] 0 0 1 0
[41,] 0 0 0 1
$data$expl_obs
[1] 0
$data$expl_fintercept
[1] 1
$data$expl_fnrow
[1] 41
$data$expl_findex
[1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25
[26] 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41
$data$expl_fnindex
[1] 41
$data$expl_fncol
[1] 0
$data$expl_rncol
[1] 0
$data$expl_fdesign
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
$data$expl_rdesign
(Intercept)
attr(,"assign")
[1] 0
$priors
variable dimension
1: expr_r_int 1
2: expr_beta_sd 1
3: expr_lelatent_int 1
4: expl_beta_sd 1
description
1: Intercept of the log growth rate
2: Standard deviation of scaled pooled log growth rate effects
3: Intercept for initial log observations (ordered by group and then\n time)
4: Standard deviation of scaled pooled log growth rate effects
distribution mean sd
1: Normal 0.0 0.2
2: Zero truncated normal 0.0 1.0
3: Normal 4.1 1.0
4: Zero truncated normal 0.0 1.0
enw_expectation supports custom expectation models
Code
expectation <- enw_expectation(~ 1 + (1 | day_of_week), data = pobs)
expectation$inits <- NULL
expectation
Output
$formula
$formula$r
[1] "~1 + (1 | day_of_week)"
$formula$observation
[1] "~1"
$data_raw
$data_raw$r
date .group location age_group delay day_of_week day week month
1: 2021-07-14 1 DE 00+ 0 Wednesday 1 0 0
2: 2021-07-15 1 DE 00+ 0 Thursday 2 0 0
3: 2021-07-16 1 DE 00+ 0 Friday 3 0 0
4: 2021-07-17 1 DE 00+ 0 Saturday 4 0 0
5: 2021-07-18 1 DE 00+ 0 Sunday 5 0 0
6: 2021-07-19 1 DE 00+ 0 Monday 6 0 0
7: 2021-07-20 1 DE 00+ 0 Tuesday 7 1 0
8: 2021-07-21 1 DE 00+ 0 Wednesday 8 1 0
9: 2021-07-22 1 DE 00+ 0 Thursday 9 1 0
10: 2021-07-23 1 DE 00+ 0 Friday 10 1 0
11: 2021-07-24 1 DE 00+ 0 Saturday 11 1 0
12: 2021-07-25 1 DE 00+ 0 Sunday 12 1 0
13: 2021-07-26 1 DE 00+ 0 Monday 13 1 0
14: 2021-07-27 1 DE 00+ 0 Tuesday 14 2 0
15: 2021-07-28 1 DE 00+ 0 Wednesday 15 2 0
16: 2021-07-29 1 DE 00+ 0 Thursday 16 2 0
17: 2021-07-30 1 DE 00+ 0 Friday 17 2 0
18: 2021-07-31 1 DE 00+ 0 Saturday 18 2 0
19: 2021-08-01 1 DE 00+ 0 Sunday 19 2 1
20: 2021-08-02 1 DE 00+ 0 Monday 20 2 1
21: 2021-08-03 1 DE 00+ 0 Tuesday 21 3 1
22: 2021-08-04 1 DE 00+ 0 Wednesday 22 3 1
23: 2021-08-05 1 DE 00+ 0 Thursday 23 3 1
24: 2021-08-06 1 DE 00+ 0 Friday 24 3 1
25: 2021-08-07 1 DE 00+ 0 Saturday 25 3 1
26: 2021-08-08 1 DE 00+ 0 Sunday 26 3 1
27: 2021-08-09 1 DE 00+ 0 Monday 27 3 1
28: 2021-08-10 1 DE 00+ 0 Tuesday 28 4 1
29: 2021-08-11 1 DE 00+ 0 Wednesday 29 4 1
30: 2021-08-12 1 DE 00+ 0 Thursday 30 4 1
31: 2021-08-13 1 DE 00+ 0 Friday 31 4 1
32: 2021-08-14 1 DE 00+ 0 Saturday 32 4 1
33: 2021-08-15 1 DE 00+ 0 Sunday 33 4 1
34: 2021-08-16 1 DE 00+ 0 Monday 34 4 1
35: 2021-08-17 1 DE 00+ 0 Tuesday 35 5 1
36: 2021-08-18 1 DE 00+ 0 Wednesday 36 5 1
37: 2021-08-19 1 DE 00+ 0 Thursday 37 5 1
38: 2021-08-20 1 DE 00+ 0 Friday 38 5 1
39: 2021-08-21 1 DE 00+ 0 Saturday 39 5 1
40: 2021-08-22 1 DE 00+ 0 Sunday 40 5 1
date .group location age_group delay day_of_week day week month
$data_raw$observation
date .group location age_group delay day_of_week day week month
1: 2021-07-13 1 DE 00+ 0 Tuesday 0 0 0
2: 2021-07-14 1 DE 00+ 0 Wednesday 1 0 0
3: 2021-07-15 1 DE 00+ 0 Thursday 2 0 0
4: 2021-07-16 1 DE 00+ 0 Friday 3 0 0
5: 2021-07-17 1 DE 00+ 0 Saturday 4 0 0
6: 2021-07-18 1 DE 00+ 0 Sunday 5 0 0
7: 2021-07-19 1 DE 00+ 0 Monday 6 0 0
8: 2021-07-20 1 DE 00+ 0 Tuesday 7 1 0
9: 2021-07-21 1 DE 00+ 0 Wednesday 8 1 0
10: 2021-07-22 1 DE 00+ 0 Thursday 9 1 0
11: 2021-07-23 1 DE 00+ 0 Friday 10 1 0
12: 2021-07-24 1 DE 00+ 0 Saturday 11 1 0
13: 2021-07-25 1 DE 00+ 0 Sunday 12 1 0
14: 2021-07-26 1 DE 00+ 0 Monday 13 1 0
15: 2021-07-27 1 DE 00+ 0 Tuesday 14 2 0
16: 2021-07-28 1 DE 00+ 0 Wednesday 15 2 0
17: 2021-07-29 1 DE 00+ 0 Thursday 16 2 0
18: 2021-07-30 1 DE 00+ 0 Friday 17 2 0
19: 2021-07-31 1 DE 00+ 0 Saturday 18 2 0
20: 2021-08-01 1 DE 00+ 0 Sunday 19 2 1
21: 2021-08-02 1 DE 00+ 0 Monday 20 2 1
22: 2021-08-03 1 DE 00+ 0 Tuesday 21 3 1
23: 2021-08-04 1 DE 00+ 0 Wednesday 22 3 1
24: 2021-08-05 1 DE 00+ 0 Thursday 23 3 1
25: 2021-08-06 1 DE 00+ 0 Friday 24 3 1
26: 2021-08-07 1 DE 00+ 0 Saturday 25 3 1
27: 2021-08-08 1 DE 00+ 0 Sunday 26 3 1
28: 2021-08-09 1 DE 00+ 0 Monday 27 3 1
29: 2021-08-10 1 DE 00+ 0 Tuesday 28 4 1
30: 2021-08-11 1 DE 00+ 0 Wednesday 29 4 1
31: 2021-08-12 1 DE 00+ 0 Thursday 30 4 1
32: 2021-08-13 1 DE 00+ 0 Friday 31 4 1
33: 2021-08-14 1 DE 00+ 0 Saturday 32 4 1
34: 2021-08-15 1 DE 00+ 0 Sunday 33 4 1
35: 2021-08-16 1 DE 00+ 0 Monday 34 4 1
36: 2021-08-17 1 DE 00+ 0 Tuesday 35 5 1
37: 2021-08-18 1 DE 00+ 0 Wednesday 36 5 1
38: 2021-08-19 1 DE 00+ 0 Thursday 37 5 1
39: 2021-08-20 1 DE 00+ 0 Friday 38 5 1
40: 2021-08-21 1 DE 00+ 0 Saturday 39 5 1
41: 2021-08-22 1 DE 00+ 0 Sunday 40 5 1
date .group location age_group delay day_of_week day week month
$data
$data$expr_r_seed
[1] 1
$data$expr_gt_n
[1] 1
$data$expr_lrgt
[1] 0
$data$expr_t
[1] 40
$data$expr_obs
[1] 0
$data$expr_g
[1] 0
$data$expr_ft
[1] 41
$data$expr_fintercept
[1] 1
$data$expr_fnrow
[1] 40
$data$expr_findex
[1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25
[26] 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40
$data$expr_fnindex
[1] 40
$data$expr_fncol
[1] 7
$data$expr_rncol
[1] 1
$data$expr_fdesign
day_of_weekFriday day_of_weekMonday day_of_weekSaturday day_of_weekSunday
1 0 0 0 0
2 0 0 0 0
3 1 0 0 0
4 0 0 1 0
5 0 0 0 1
6 0 1 0 0
7 0 0 0 0
8 0 0 0 0
9 0 0 0 0
10 1 0 0 0
11 0 0 1 0
12 0 0 0 1
13 0 1 0 0
14 0 0 0 0
15 0 0 0 0
16 0 0 0 0
17 1 0 0 0
18 0 0 1 0
19 0 0 0 1
20 0 1 0 0
21 0 0 0 0
22 0 0 0 0
23 0 0 0 0
24 1 0 0 0
25 0 0 1 0
26 0 0 0 1
27 0 1 0 0
28 0 0 0 0
29 0 0 0 0
30 0 0 0 0
31 1 0 0 0
32 0 0 1 0
33 0 0 0 1
34 0 1 0 0
35 0 0 0 0
36 0 0 0 0
37 0 0 0 0
38 1 0 0 0
39 0 0 1 0
40 0 0 0 1
day_of_weekThursday day_of_weekTuesday day_of_weekWednesday
1 0 0 1
2 1 0 0
3 0 0 0
4 0 0 0
5 0 0 0
6 0 0 0
7 0 1 0
8 0 0 1
9 1 0 0
10 0 0 0
11 0 0 0
12 0 0 0
13 0 0 0
14 0 1 0
15 0 0 1
16 1 0 0
17 0 0 0
18 0 0 0
19 0 0 0
20 0 0 0
21 0 1 0
22 0 0 1
23 1 0 0
24 0 0 0
25 0 0 0
26 0 0 0
27 0 0 0
28 0 1 0
29 0 0 1
30 1 0 0
31 0 0 0
32 0 0 0
33 0 0 0
34 0 0 0
35 0 1 0
36 0 0 1
37 1 0 0
38 0 0 0
39 0 0 0
40 0 0 0
$data$expr_rdesign
fixed day_of_week
1 0 1
2 0 1
3 0 1
4 0 1
5 0 1
6 0 1
7 0 1
attr(,"assign")
[1] 1 2
$data$expl_lrd_n
[1] 1
$data$expl_lrd
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
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[13,] 0 0 0 0 0 0 0 0 0 0 0 0 1
[14,] 0 0 0 0 0 0 0 0 0 0 0 0 0
[15,] 0 0 0 0 0 0 0 0 0 0 0 0 0
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[27,] 0 0 0 0 0 0 0 0 0 0 0 0 0
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[40,] 0 0 0 0 0 0 0 0 0 0 0 0 0
[41,] 0 0 0 0 0 0 0 0 0 0 0 0 0
[,14] [,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22] [,23] [,24] [,25]
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[11,] 0 0 0 0 0 0 0 0 0 0 0 0
[12,] 0 0 0 0 0 0 0 0 0 0 0 0
[13,] 0 0 0 0 0 0 0 0 0 0 0 0
[14,] 1 0 0 0 0 0 0 0 0 0 0 0
[15,] 0 1 0 0 0 0 0 0 0 0 0 0
[16,] 0 0 1 0 0 0 0 0 0 0 0 0
[17,] 0 0 0 1 0 0 0 0 0 0 0 0
[18,] 0 0 0 0 1 0 0 0 0 0 0 0
[19,] 0 0 0 0 0 1 0 0 0 0 0 0
[20,] 0 0 0 0 0 0 1 0 0 0 0 0
[21,] 0 0 0 0 0 0 0 1 0 0 0 0
[22,] 0 0 0 0 0 0 0 0 1 0 0 0
[23,] 0 0 0 0 0 0 0 0 0 1 0 0
[24,] 0 0 0 0 0 0 0 0 0 0 1 0
[25,] 0 0 0 0 0 0 0 0 0 0 0 1
[26,] 0 0 0 0 0 0 0 0 0 0 0 0
[27,] 0 0 0 0 0 0 0 0 0 0 0 0
[28,] 0 0 0 0 0 0 0 0 0 0 0 0
[29,] 0 0 0 0 0 0 0 0 0 0 0 0
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[31,] 0 0 0 0 0 0 0 0 0 0 0 0
[32,] 0 0 0 0 0 0 0 0 0 0 0 0
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[34,] 0 0 0 0 0 0 0 0 0 0 0 0
[35,] 0 0 0 0 0 0 0 0 0 0 0 0
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[37,] 0 0 0 0 0 0 0 0 0 0 0 0
[38,] 0 0 0 0 0 0 0 0 0 0 0 0
[39,] 0 0 0 0 0 0 0 0 0 0 0 0
[40,] 0 0 0 0 0 0 0 0 0 0 0 0
[41,] 0 0 0 0 0 0 0 0 0 0 0 0
[,26] [,27] [,28] [,29] [,30] [,31] [,32] [,33] [,34] [,35] [,36] [,37]
[1,] 0 0 0 0 0 0 0 0 0 0 0 0
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[25,] 0 0 0 0 0 0 0 0 0 0 0 0
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[27,] 0 1 0 0 0 0 0 0 0 0 0 0
[28,] 0 0 1 0 0 0 0 0 0 0 0 0
[29,] 0 0 0 1 0 0 0 0 0 0 0 0
[30,] 0 0 0 0 1 0 0 0 0 0 0 0
[31,] 0 0 0 0 0 1 0 0 0 0 0 0
[32,] 0 0 0 0 0 0 1 0 0 0 0 0
[33,] 0 0 0 0 0 0 0 1 0 0 0 0
[34,] 0 0 0 0 0 0 0 0 1 0 0 0
[35,] 0 0 0 0 0 0 0 0 0 1 0 0
[36,] 0 0 0 0 0 0 0 0 0 0 1 0
[37,] 0 0 0 0 0 0 0 0 0 0 0 1
[38,] 0 0 0 0 0 0 0 0 0 0 0 0
[39,] 0 0 0 0 0 0 0 0 0 0 0 0
[40,] 0 0 0 0 0 0 0 0 0 0 0 0
[41,] 0 0 0 0 0 0 0 0 0 0 0 0
[,38] [,39] [,40] [,41]
[1,] 0 0 0 0
[2,] 0 0 0 0
[3,] 0 0 0 0
[4,] 0 0 0 0
[5,] 0 0 0 0
[6,] 0 0 0 0
[7,] 0 0 0 0
[8,] 0 0 0 0
[9,] 0 0 0 0
[10,] 0 0 0 0
[11,] 0 0 0 0
[12,] 0 0 0 0
[13,] 0 0 0 0
[14,] 0 0 0 0
[15,] 0 0 0 0
[16,] 0 0 0 0
[17,] 0 0 0 0
[18,] 0 0 0 0
[19,] 0 0 0 0
[20,] 0 0 0 0
[21,] 0 0 0 0
[22,] 0 0 0 0
[23,] 0 0 0 0
[24,] 0 0 0 0
[25,] 0 0 0 0
[26,] 0 0 0 0
[27,] 0 0 0 0
[28,] 0 0 0 0
[29,] 0 0 0 0
[30,] 0 0 0 0
[31,] 0 0 0 0
[32,] 0 0 0 0
[33,] 0 0 0 0
[34,] 0 0 0 0
[35,] 0 0 0 0
[36,] 0 0 0 0
[37,] 0 0 0 0
[38,] 1 0 0 0
[39,] 0 1 0 0
[40,] 0 0 1 0
[41,] 0 0 0 1
$data$expl_obs
[1] 0
$data$expl_fintercept
[1] 1
$data$expl_fnrow
[1] 41
$data$expl_findex
[1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25
[26] 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41
$data$expl_fnindex
[1] 41
$data$expl_fncol
[1] 0
$data$expl_rncol
[1] 0
$data$expl_fdesign
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
$data$expl_rdesign
(Intercept)
attr(,"assign")
[1] 0
$priors
variable dimension
1: expr_r_int 1
2: expr_beta_sd 1
3: expr_lelatent_int 1
4: expl_beta_sd 1
description
1: Intercept of the log growth rate
2: Standard deviation of scaled pooled log growth rate effects
3: Intercept for initial log observations (ordered by group and then\n time)
4: Standard deviation of scaled pooled log growth rate effects
distribution mean sd
1: Normal 0.0 0.2
2: Zero truncated normal 0.0 1.0
3: Normal 4.1 1.0
4: Zero truncated normal 0.0 1.0
enw_expectation works as expected when multiple timeseries are present
Code
expectation_module[setdiff(names(expectation_module), "inits")]
Output
$formula
$formula$r
[1] "~1 + (1 | .group)"
$formula$observation
[1] "~(1 | week:.group)"
$data_raw
$data_raw$r
date .group location age_group delay day_of_week day week month
1: 2021-08-13 1 DE 00-04 0 Friday 1 0 0
2: 2021-08-14 1 DE 00-04 0 Saturday 2 0 0
3: 2021-08-15 1 DE 00-04 0 Sunday 3 0 0
4: 2021-08-16 1 DE 00-04 0 Monday 4 0 0
5: 2021-08-17 1 DE 00-04 0 Tuesday 5 0 0
6: 2021-08-18 1 DE 00-04 0 Wednesday 6 0 0
7: 2021-08-19 1 DE 00-04 0 Thursday 7 1 0
8: 2021-08-20 1 DE 00-04 0 Friday 8 1 0
9: 2021-08-21 1 DE 00-04 0 Saturday 9 1 0
10: 2021-08-22 1 DE 00-04 0 Sunday 10 1 0
11: 2021-08-13 2 DE 00+ 0 Friday 1 0 0
12: 2021-08-14 2 DE 00+ 0 Saturday 2 0 0
13: 2021-08-15 2 DE 00+ 0 Sunday 3 0 0
14: 2021-08-16 2 DE 00+ 0 Monday 4 0 0
15: 2021-08-17 2 DE 00+ 0 Tuesday 5 0 0
16: 2021-08-18 2 DE 00+ 0 Wednesday 6 0 0
17: 2021-08-19 2 DE 00+ 0 Thursday 7 1 0
18: 2021-08-20 2 DE 00+ 0 Friday 8 1 0
19: 2021-08-21 2 DE 00+ 0 Saturday 9 1 0
20: 2021-08-22 2 DE 00+ 0 Sunday 10 1 0
21: 2021-08-13 3 DE 80+ 0 Friday 1 0 0
22: 2021-08-14 3 DE 80+ 0 Saturday 2 0 0
23: 2021-08-15 3 DE 80+ 0 Sunday 3 0 0
24: 2021-08-16 3 DE 80+ 0 Monday 4 0 0
25: 2021-08-17 3 DE 80+ 0 Tuesday 5 0 0
26: 2021-08-18 3 DE 80+ 0 Wednesday 6 0 0
27: 2021-08-19 3 DE 80+ 0 Thursday 7 1 0
28: 2021-08-20 3 DE 80+ 0 Friday 8 1 0
29: 2021-08-21 3 DE 80+ 0 Saturday 9 1 0
30: 2021-08-22 3 DE 80+ 0 Sunday 10 1 0
date .group location age_group delay day_of_week day week month
observed
1: TRUE
2: TRUE
3: TRUE
4: TRUE
5: TRUE
6: TRUE
7: TRUE
8: TRUE
9: TRUE
10: TRUE
11: TRUE
12: TRUE
13: TRUE
14: TRUE
15: TRUE
16: TRUE
17: TRUE
18: TRUE
19: TRUE
20: TRUE
21: TRUE
22: TRUE
23: TRUE
24: TRUE
25: TRUE
26: TRUE
27: TRUE
28: TRUE
29: TRUE
30: TRUE
observed
$data_raw$observation
date .group location age_group delay day_of_week day week month
1: 2021-08-12 1 DE 00-04 0 Thursday 0 0 0
2: 2021-08-13 1 DE 00-04 0 Friday 1 0 0
3: 2021-08-14 1 DE 00-04 0 Saturday 2 0 0
4: 2021-08-15 1 DE 00-04 0 Sunday 3 0 0
5: 2021-08-16 1 DE 00-04 0 Monday 4 0 0
6: 2021-08-17 1 DE 00-04 0 Tuesday 5 0 0
7: 2021-08-18 1 DE 00-04 0 Wednesday 6 0 0
8: 2021-08-19 1 DE 00-04 0 Thursday 7 1 0
9: 2021-08-20 1 DE 00-04 0 Friday 8 1 0
10: 2021-08-21 1 DE 00-04 0 Saturday 9 1 0
11: 2021-08-22 1 DE 00-04 0 Sunday 10 1 0
12: 2021-08-12 2 DE 00+ 0 Thursday 0 0 0
13: 2021-08-13 2 DE 00+ 0 Friday 1 0 0
14: 2021-08-14 2 DE 00+ 0 Saturday 2 0 0
15: 2021-08-15 2 DE 00+ 0 Sunday 3 0 0
16: 2021-08-16 2 DE 00+ 0 Monday 4 0 0
17: 2021-08-17 2 DE 00+ 0 Tuesday 5 0 0
18: 2021-08-18 2 DE 00+ 0 Wednesday 6 0 0
19: 2021-08-19 2 DE 00+ 0 Thursday 7 1 0
20: 2021-08-20 2 DE 00+ 0 Friday 8 1 0
21: 2021-08-21 2 DE 00+ 0 Saturday 9 1 0
22: 2021-08-22 2 DE 00+ 0 Sunday 10 1 0
23: 2021-08-12 3 DE 80+ 0 Thursday 0 0 0
24: 2021-08-13 3 DE 80+ 0 Friday 1 0 0
25: 2021-08-14 3 DE 80+ 0 Saturday 2 0 0
26: 2021-08-15 3 DE 80+ 0 Sunday 3 0 0
27: 2021-08-16 3 DE 80+ 0 Monday 4 0 0
28: 2021-08-17 3 DE 80+ 0 Tuesday 5 0 0
29: 2021-08-18 3 DE 80+ 0 Wednesday 6 0 0
30: 2021-08-19 3 DE 80+ 0 Thursday 7 1 0
31: 2021-08-20 3 DE 80+ 0 Friday 8 1 0
32: 2021-08-21 3 DE 80+ 0 Saturday 9 1 0
33: 2021-08-22 3 DE 80+ 0 Sunday 10 1 0
date .group location age_group delay day_of_week day week month
$data
$data$expr_r_seed
[1] 2
$data$expr_gt_n
[1] 2
$data$expr_lrgt
[1] -0.1053605 -2.3025851
$data$expr_t
[1] 10
$data$expr_obs
[1] 0
$data$expr_g
[1] 0 10 20
$data$expr_ft
[1] 12
$data$expr_fintercept
[1] 1
$data$expr_fnrow
[1] 30
$data$expr_findex
[1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25
[26] 26 27 28 29 30
$data$expr_fnindex
[1] 30
$data$expr_fncol
[1] 3
$data$expr_rncol
[1] 1
$data$expr_fdesign
.group1 .group2 .group3
1 1 0 0
2 1 0 0
3 1 0 0
4 1 0 0
5 1 0 0
6 1 0 0
7 1 0 0
8 1 0 0
9 1 0 0
10 1 0 0
11 0 1 0
12 0 1 0
13 0 1 0
14 0 1 0
15 0 1 0
16 0 1 0
17 0 1 0
18 0 1 0
19 0 1 0
20 0 1 0
21 0 0 1
22 0 0 1
23 0 0 1
24 0 0 1
25 0 0 1
26 0 0 1
27 0 0 1
28 0 0 1
29 0 0 1
30 0 0 1
$data$expr_rdesign
fixed .group
1 0 1
2 0 1
3 0 1
attr(,"assign")
[1] 1 2
$data$expl_lrd_n
[1] 2
$data$expl_lrd
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12]
[1,] 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
[2,] 0.9 0.1 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
[3,] 0.0 0.9 0.1 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
[4,] 0.0 0.0 0.9 0.1 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
[5,] 0.0 0.0 0.0 0.9 0.1 0.0 0.0 0.0 0.0 0.0 0.0 0.0
[6,] 0.0 0.0 0.0 0.0 0.9 0.1 0.0 0.0 0.0 0.0 0.0 0.0
[7,] 0.0 0.0 0.0 0.0 0.0 0.9 0.1 0.0 0.0 0.0 0.0 0.0
[8,] 0.0 0.0 0.0 0.0 0.0 0.0 0.9 0.1 0.0 0.0 0.0 0.0
[9,] 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.9 0.1 0.0 0.0 0.0
[10,] 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.9 0.1 0.0 0.0
[11,] 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.9 0.1 0.0
[12,] 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.9 0.1
$data$expl_obs
[1] 1
$data$expl_fintercept
[1] 1
$data$expl_fnrow
[1] 33
$data$expl_findex
[1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25
[26] 26 27 28 29 30 31 32 33
$data$expl_fnindex
[1] 33
$data$expl_fncol
[1] 6
$data$expl_rncol
[1] 3
$data$expl_fdesign
week0:.group1 week1:.group1 week0:.group2 week1:.group2 week0:.group3
1 1 0 0 0 0
2 1 0 0 0 0
3 1 0 0 0 0
4 1 0 0 0 0
5 1 0 0 0 0
6 1 0 0 0 0
7 1 0 0 0 0
8 0 1 0 0 0
9 0 1 0 0 0
10 0 1 0 0 0
11 0 1 0 0 0
12 0 0 1 0 0
13 0 0 1 0 0
14 0 0 1 0 0
15 0 0 1 0 0
16 0 0 1 0 0
17 0 0 1 0 0
18 0 0 1 0 0
19 0 0 0 1 0
20 0 0 0 1 0
21 0 0 0 1 0
22 0 0 0 1 0
23 0 0 0 0 1
24 0 0 0 0 1
25 0 0 0 0 1
26 0 0 0 0 1
27 0 0 0 0 1
28 0 0 0 0 1
29 0 0 0 0 1
30 0 0 0 0 0
31 0 0 0 0 0
32 0 0 0 0 0
33 0 0 0 0 0
week1:.group3
1 0
2 0
3 0
4 0
5 0
6 0
7 0
8 0
9 0
10 0
11 0
12 0
13 0
14 0
15 0
16 0
17 0
18 0
19 0
20 0
21 0
22 0
23 0
24 0
25 0
26 0
27 0
28 0
29 0
30 1
31 1
32 1
33 1
$data$expl_rdesign
fixed week__.group1 week__.group2 week__.group3
1 0 1 0 0
2 0 1 0 0
3 0 0 1 0
4 0 0 1 0
5 0 0 0 1
6 0 0 0 1
attr(,"assign")
[1] 1 2 3 4
$priors
variable dimension
1: expr_r_int 1
2: expr_beta_sd 1
3: expr_lelatent_int 1
4: expr_lelatent_int 2
5: expr_lelatent_int 3
6: expr_lelatent_int 4
7: expr_lelatent_int 5
8: expr_lelatent_int 6
9: expl_beta_sd 1
description
1: Intercept of the log growth rate
2: Standard deviation of scaled pooled log growth rate effects
3: Intercept for initial log observations (ordered by group and then\n time)
4: Intercept for initial log observations (ordered by group and then\n time)
5: Intercept for initial log observations (ordered by group and then\n time)
6: Intercept for initial log observations (ordered by group and then\n time)
7: Intercept for initial log observations (ordered by group and then\n time)
8: Intercept for initial log observations (ordered by group and then\n time)
9: Standard deviation of scaled pooled log growth rate effects
distribution mean sd
1: Normal 0.0 0.2
2: Zero truncated normal 0.0 1.0
3: Normal 2.1 1.0
4: Normal 2.1 1.0
5: Normal 5.5 1.0
6: Normal 5.5 1.0
7: Normal 3.4 1.0
8: Normal 3.4 1.0
9: Zero truncated normal 0.0 1.0
epiforecasts/epinowcast documentation built on Feb. 3, 2025, 4:17 p.m.
R Package Documentation
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enw_expectation produces the expected default model
Code
expectation <- enw_expectation(data = pobs)
Message
A random effect using .group is not possible as this variable has fewer than 2 unique values.
i The r design matrix is sparse (>90% zeros). Consider using `sparse_design = TRUE` in `enw_fit_opts()` to potentially reduce memory usage and computation time.
Code
expectation$inits <- NULL
expectation
Output
$formula
$formula$r
[1] "~0 + (1 | day:.group)"
$formula$observation
[1] "~1"
$data_raw
$data_raw$r
date .group location age_group delay day_of_week day week month
1: 2021-07-14 1 DE 00+ 0 Wednesday 1 0 0
2: 2021-07-15 1 DE 00+ 0 Thursday 2 0 0
3: 2021-07-16 1 DE 00+ 0 Friday 3 0 0
4: 2021-07-17 1 DE 00+ 0 Saturday 4 0 0
5: 2021-07-18 1 DE 00+ 0 Sunday 5 0 0
6: 2021-07-19 1 DE 00+ 0 Monday 6 0 0
7: 2021-07-20 1 DE 00+ 0 Tuesday 7 1 0
8: 2021-07-21 1 DE 00+ 0 Wednesday 8 1 0
9: 2021-07-22 1 DE 00+ 0 Thursday 9 1 0
10: 2021-07-23 1 DE 00+ 0 Friday 10 1 0
11: 2021-07-24 1 DE 00+ 0 Saturday 11 1 0
12: 2021-07-25 1 DE 00+ 0 Sunday 12 1 0
13: 2021-07-26 1 DE 00+ 0 Monday 13 1 0
14: 2021-07-27 1 DE 00+ 0 Tuesday 14 2 0
15: 2021-07-28 1 DE 00+ 0 Wednesday 15 2 0
16: 2021-07-29 1 DE 00+ 0 Thursday 16 2 0
17: 2021-07-30 1 DE 00+ 0 Friday 17 2 0
18: 2021-07-31 1 DE 00+ 0 Saturday 18 2 0
19: 2021-08-01 1 DE 00+ 0 Sunday 19 2 1
20: 2021-08-02 1 DE 00+ 0 Monday 20 2 1
21: 2021-08-03 1 DE 00+ 0 Tuesday 21 3 1
22: 2021-08-04 1 DE 00+ 0 Wednesday 22 3 1
23: 2021-08-05 1 DE 00+ 0 Thursday 23 3 1
24: 2021-08-06 1 DE 00+ 0 Friday 24 3 1
25: 2021-08-07 1 DE 00+ 0 Saturday 25 3 1
26: 2021-08-08 1 DE 00+ 0 Sunday 26 3 1
27: 2021-08-09 1 DE 00+ 0 Monday 27 3 1
28: 2021-08-10 1 DE 00+ 0 Tuesday 28 4 1
29: 2021-08-11 1 DE 00+ 0 Wednesday 29 4 1
30: 2021-08-12 1 DE 00+ 0 Thursday 30 4 1
31: 2021-08-13 1 DE 00+ 0 Friday 31 4 1
32: 2021-08-14 1 DE 00+ 0 Saturday 32 4 1
33: 2021-08-15 1 DE 00+ 0 Sunday 33 4 1
34: 2021-08-16 1 DE 00+ 0 Monday 34 4 1
35: 2021-08-17 1 DE 00+ 0 Tuesday 35 5 1
36: 2021-08-18 1 DE 00+ 0 Wednesday 36 5 1
37: 2021-08-19 1 DE 00+ 0 Thursday 37 5 1
38: 2021-08-20 1 DE 00+ 0 Friday 38 5 1
39: 2021-08-21 1 DE 00+ 0 Saturday 39 5 1
40: 2021-08-22 1 DE 00+ 0 Sunday 40 5 1
date .group location age_group delay day_of_week day week month
$data_raw$observation
date .group location age_group delay day_of_week day week month
1: 2021-07-13 1 DE 00+ 0 Tuesday 0 0 0
2: 2021-07-14 1 DE 00+ 0 Wednesday 1 0 0
3: 2021-07-15 1 DE 00+ 0 Thursday 2 0 0
4: 2021-07-16 1 DE 00+ 0 Friday 3 0 0
5: 2021-07-17 1 DE 00+ 0 Saturday 4 0 0
6: 2021-07-18 1 DE 00+ 0 Sunday 5 0 0
7: 2021-07-19 1 DE 00+ 0 Monday 6 0 0
8: 2021-07-20 1 DE 00+ 0 Tuesday 7 1 0
9: 2021-07-21 1 DE 00+ 0 Wednesday 8 1 0
10: 2021-07-22 1 DE 00+ 0 Thursday 9 1 0
11: 2021-07-23 1 DE 00+ 0 Friday 10 1 0
12: 2021-07-24 1 DE 00+ 0 Saturday 11 1 0
13: 2021-07-25 1 DE 00+ 0 Sunday 12 1 0
14: 2021-07-26 1 DE 00+ 0 Monday 13 1 0
15: 2021-07-27 1 DE 00+ 0 Tuesday 14 2 0
16: 2021-07-28 1 DE 00+ 0 Wednesday 15 2 0
17: 2021-07-29 1 DE 00+ 0 Thursday 16 2 0
18: 2021-07-30 1 DE 00+ 0 Friday 17 2 0
19: 2021-07-31 1 DE 00+ 0 Saturday 18 2 0
20: 2021-08-01 1 DE 00+ 0 Sunday 19 2 1
21: 2021-08-02 1 DE 00+ 0 Monday 20 2 1
22: 2021-08-03 1 DE 00+ 0 Tuesday 21 3 1
23: 2021-08-04 1 DE 00+ 0 Wednesday 22 3 1
24: 2021-08-05 1 DE 00+ 0 Thursday 23 3 1
25: 2021-08-06 1 DE 00+ 0 Friday 24 3 1
26: 2021-08-07 1 DE 00+ 0 Saturday 25 3 1
27: 2021-08-08 1 DE 00+ 0 Sunday 26 3 1
28: 2021-08-09 1 DE 00+ 0 Monday 27 3 1
29: 2021-08-10 1 DE 00+ 0 Tuesday 28 4 1
30: 2021-08-11 1 DE 00+ 0 Wednesday 29 4 1
31: 2021-08-12 1 DE 00+ 0 Thursday 30 4 1
32: 2021-08-13 1 DE 00+ 0 Friday 31 4 1
33: 2021-08-14 1 DE 00+ 0 Saturday 32 4 1
34: 2021-08-15 1 DE 00+ 0 Sunday 33 4 1
35: 2021-08-16 1 DE 00+ 0 Monday 34 4 1
36: 2021-08-17 1 DE 00+ 0 Tuesday 35 5 1
37: 2021-08-18 1 DE 00+ 0 Wednesday 36 5 1
38: 2021-08-19 1 DE 00+ 0 Thursday 37 5 1
39: 2021-08-20 1 DE 00+ 0 Friday 38 5 1
40: 2021-08-21 1 DE 00+ 0 Saturday 39 5 1
41: 2021-08-22 1 DE 00+ 0 Sunday 40 5 1
date .group location age_group delay day_of_week day week month
$data
$data$expr_r_seed
[1] 1
$data$expr_gt_n
[1] 1
$data$expr_lrgt
[1] 0
$data$expr_t
[1] 40
$data$expr_obs
[1] 0
$data$expr_g
[1] 0
$data$expr_ft
[1] 41
$data$expr_fintercept
[1] 0
$data$expr_fnrow
[1] 40
$data$expr_findex
[1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25
[26] 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40
$data$expr_fnindex
[1] 40
$data$expr_fncol
[1] 40
$data$expr_rncol
[1] 1
$data$expr_fdesign
day1 day2 day3 day4 day5 day6 day7 day8 day9 day10 day11 day12 day13 day14
1 1 0 0 0 0 0 0 0 0 0 0 0 0 0
2 0 1 0 0 0 0 0 0 0 0 0 0 0 0
3 0 0 1 0 0 0 0 0 0 0 0 0 0 0
4 0 0 0 1 0 0 0 0 0 0 0 0 0 0
5 0 0 0 0 1 0 0 0 0 0 0 0 0 0
6 0 0 0 0 0 1 0 0 0 0 0 0 0 0
7 0 0 0 0 0 0 1 0 0 0 0 0 0 0
8 0 0 0 0 0 0 0 1 0 0 0 0 0 0
9 0 0 0 0 0 0 0 0 1 0 0 0 0 0
10 0 0 0 0 0 0 0 0 0 1 0 0 0 0
11 0 0 0 0 0 0 0 0 0 0 1 0 0 0
12 0 0 0 0 0 0 0 0 0 0 0 1 0 0
13 0 0 0 0 0 0 0 0 0 0 0 0 1 0
14 0 0 0 0 0 0 0 0 0 0 0 0 0 1
15 0 0 0 0 0 0 0 0 0 0 0 0 0 0
16 0 0 0 0 0 0 0 0 0 0 0 0 0 0
17 0 0 0 0 0 0 0 0 0 0 0 0 0 0
18 0 0 0 0 0 0 0 0 0 0 0 0 0 0
19 0 0 0 0 0 0 0 0 0 0 0 0 0 0
20 0 0 0 0 0 0 0 0 0 0 0 0 0 0
21 0 0 0 0 0 0 0 0 0 0 0 0 0 0
22 0 0 0 0 0 0 0 0 0 0 0 0 0 0
23 0 0 0 0 0 0 0 0 0 0 0 0 0 0
24 0 0 0 0 0 0 0 0 0 0 0 0 0 0
25 0 0 0 0 0 0 0 0 0 0 0 0 0 0
26 0 0 0 0 0 0 0 0 0 0 0 0 0 0
27 0 0 0 0 0 0 0 0 0 0 0 0 0 0
28 0 0 0 0 0 0 0 0 0 0 0 0 0 0
29 0 0 0 0 0 0 0 0 0 0 0 0 0 0
30 0 0 0 0 0 0 0 0 0 0 0 0 0 0
31 0 0 0 0 0 0 0 0 0 0 0 0 0 0
32 0 0 0 0 0 0 0 0 0 0 0 0 0 0
33 0 0 0 0 0 0 0 0 0 0 0 0 0 0
34 0 0 0 0 0 0 0 0 0 0 0 0 0 0
35 0 0 0 0 0 0 0 0 0 0 0 0 0 0
36 0 0 0 0 0 0 0 0 0 0 0 0 0 0
37 0 0 0 0 0 0 0 0 0 0 0 0 0 0
38 0 0 0 0 0 0 0 0 0 0 0 0 0 0
39 0 0 0 0 0 0 0 0 0 0 0 0 0 0
40 0 0 0 0 0 0 0 0 0 0 0 0 0 0
day15 day16 day17 day18 day19 day20 day21 day22 day23 day24 day25 day26
1 0 0 0 0 0 0 0 0 0 0 0 0
2 0 0 0 0 0 0 0 0 0 0 0 0
3 0 0 0 0 0 0 0 0 0 0 0 0
4 0 0 0 0 0 0 0 0 0 0 0 0
5 0 0 0 0 0 0 0 0 0 0 0 0
6 0 0 0 0 0 0 0 0 0 0 0 0
7 0 0 0 0 0 0 0 0 0 0 0 0
8 0 0 0 0 0 0 0 0 0 0 0 0
9 0 0 0 0 0 0 0 0 0 0 0 0
10 0 0 0 0 0 0 0 0 0 0 0 0
11 0 0 0 0 0 0 0 0 0 0 0 0
12 0 0 0 0 0 0 0 0 0 0 0 0
13 0 0 0 0 0 0 0 0 0 0 0 0
14 0 0 0 0 0 0 0 0 0 0 0 0
15 1 0 0 0 0 0 0 0 0 0 0 0
16 0 1 0 0 0 0 0 0 0 0 0 0
17 0 0 1 0 0 0 0 0 0 0 0 0
18 0 0 0 1 0 0 0 0 0 0 0 0
19 0 0 0 0 1 0 0 0 0 0 0 0
20 0 0 0 0 0 1 0 0 0 0 0 0
21 0 0 0 0 0 0 1 0 0 0 0 0
22 0 0 0 0 0 0 0 1 0 0 0 0
23 0 0 0 0 0 0 0 0 1 0 0 0
24 0 0 0 0 0 0 0 0 0 1 0 0
25 0 0 0 0 0 0 0 0 0 0 1 0
26 0 0 0 0 0 0 0 0 0 0 0 1
27 0 0 0 0 0 0 0 0 0 0 0 0
28 0 0 0 0 0 0 0 0 0 0 0 0
29 0 0 0 0 0 0 0 0 0 0 0 0
30 0 0 0 0 0 0 0 0 0 0 0 0
31 0 0 0 0 0 0 0 0 0 0 0 0
32 0 0 0 0 0 0 0 0 0 0 0 0
33 0 0 0 0 0 0 0 0 0 0 0 0
34 0 0 0 0 0 0 0 0 0 0 0 0
35 0 0 0 0 0 0 0 0 0 0 0 0
36 0 0 0 0 0 0 0 0 0 0 0 0
37 0 0 0 0 0 0 0 0 0 0 0 0
38 0 0 0 0 0 0 0 0 0 0 0 0
39 0 0 0 0 0 0 0 0 0 0 0 0
40 0 0 0 0 0 0 0 0 0 0 0 0
day27 day28 day29 day30 day31 day32 day33 day34 day35 day36 day37 day38
1 0 0 0 0 0 0 0 0 0 0 0 0
2 0 0 0 0 0 0 0 0 0 0 0 0
3 0 0 0 0 0 0 0 0 0 0 0 0
4 0 0 0 0 0 0 0 0 0 0 0 0
5 0 0 0 0 0 0 0 0 0 0 0 0
6 0 0 0 0 0 0 0 0 0 0 0 0
7 0 0 0 0 0 0 0 0 0 0 0 0
8 0 0 0 0 0 0 0 0 0 0 0 0
9 0 0 0 0 0 0 0 0 0 0 0 0
10 0 0 0 0 0 0 0 0 0 0 0 0
11 0 0 0 0 0 0 0 0 0 0 0 0
12 0 0 0 0 0 0 0 0 0 0 0 0
13 0 0 0 0 0 0 0 0 0 0 0 0
14 0 0 0 0 0 0 0 0 0 0 0 0
15 0 0 0 0 0 0 0 0 0 0 0 0
16 0 0 0 0 0 0 0 0 0 0 0 0
17 0 0 0 0 0 0 0 0 0 0 0 0
18 0 0 0 0 0 0 0 0 0 0 0 0
19 0 0 0 0 0 0 0 0 0 0 0 0
20 0 0 0 0 0 0 0 0 0 0 0 0
21 0 0 0 0 0 0 0 0 0 0 0 0
22 0 0 0 0 0 0 0 0 0 0 0 0
23 0 0 0 0 0 0 0 0 0 0 0 0
24 0 0 0 0 0 0 0 0 0 0 0 0
25 0 0 0 0 0 0 0 0 0 0 0 0
26 0 0 0 0 0 0 0 0 0 0 0 0
27 1 0 0 0 0 0 0 0 0 0 0 0
28 0 1 0 0 0 0 0 0 0 0 0 0
29 0 0 1 0 0 0 0 0 0 0 0 0
30 0 0 0 1 0 0 0 0 0 0 0 0
31 0 0 0 0 1 0 0 0 0 0 0 0
32 0 0 0 0 0 1 0 0 0 0 0 0
33 0 0 0 0 0 0 1 0 0 0 0 0
34 0 0 0 0 0 0 0 1 0 0 0 0
35 0 0 0 0 0 0 0 0 1 0 0 0
36 0 0 0 0 0 0 0 0 0 1 0 0
37 0 0 0 0 0 0 0 0 0 0 1 0
38 0 0 0 0 0 0 0 0 0 0 0 1
39 0 0 0 0 0 0 0 0 0 0 0 0
40 0 0 0 0 0 0 0 0 0 0 0 0
day39 day40
1 0 0
2 0 0
3 0 0
4 0 0
5 0 0
6 0 0
7 0 0
8 0 0
9 0 0
10 0 0
11 0 0
12 0 0
13 0 0
14 0 0
15 0 0
16 0 0
17 0 0
18 0 0
19 0 0
20 0 0
21 0 0
22 0 0
23 0 0
24 0 0
25 0 0
26 0 0
27 0 0
28 0 0
29 0 0
30 0 0
31 0 0
32 0 0
33 0 0
34 0 0
35 0 0
36 0 0
37 0 0
38 0 0
39 1 0
40 0 1
attr(,"assign")
[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 1 1 1 1 1 1 1 1
[39] 1 1
attr(,"contrasts")
attr(,"contrasts")$day
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28
1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
2 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
3 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
4 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
5 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
6 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
7 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
8 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
9 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
10 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
11 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
12 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
13 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
14 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0
15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0
16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0
17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0
18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0
19 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0
20 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0
21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0
22 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0
23 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0
24 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0
25 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0
26 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0
27 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0
28 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1
29 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
30 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
31 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
32 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
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$data$expr_rdesign
fixed day
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2 0 1
3 0 1
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5 0 1
6 0 1
7 0 1
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11 0 1
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37 0 1
38 0 1
39 0 1
40 0 1
attr(,"assign")
[1] 1 2
$data$expl_lrd_n
[1] 1
$data$expl_lrd
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$data$expl_obs
[1] 0
$data$expl_fintercept
[1] 1
$data$expl_fnrow
[1] 41
$data$expl_findex
[1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25
[26] 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41
$data$expl_fnindex
[1] 41
$data$expl_fncol
[1] 0
$data$expl_rncol
[1] 0
$data$expl_fdesign
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
$data$expl_rdesign
(Intercept)
attr(,"assign")
[1] 0
$priors
variable dimension
1: expr_r_int 1
2: expr_beta_sd 1
3: expr_lelatent_int 1
4: expl_beta_sd 1
description
1: Intercept of the log growth rate
2: Standard deviation of scaled pooled log growth rate effects
3: Intercept for initial log observations (ordered by group and then\n time)
4: Standard deviation of scaled pooled log growth rate effects
distribution mean sd
1: Normal 0.0 0.2
2: Zero truncated normal 0.0 1.0
3: Normal 4.1 1.0
4: Zero truncated normal 0.0 1.0
enw_expectation supports custom expectation models
Code
expectation <- enw_expectation(~ 1 + (1 | day_of_week), data = pobs)
expectation$inits <- NULL
expectation
Output
$formula
$formula$r
[1] "~1 + (1 | day_of_week)"
$formula$observation
[1] "~1"
$data_raw
$data_raw$r
date .group location age_group delay day_of_week day week month
1: 2021-07-14 1 DE 00+ 0 Wednesday 1 0 0
2: 2021-07-15 1 DE 00+ 0 Thursday 2 0 0
3: 2021-07-16 1 DE 00+ 0 Friday 3 0 0
4: 2021-07-17 1 DE 00+ 0 Saturday 4 0 0
5: 2021-07-18 1 DE 00+ 0 Sunday 5 0 0
6: 2021-07-19 1 DE 00+ 0 Monday 6 0 0
7: 2021-07-20 1 DE 00+ 0 Tuesday 7 1 0
8: 2021-07-21 1 DE 00+ 0 Wednesday 8 1 0
9: 2021-07-22 1 DE 00+ 0 Thursday 9 1 0
10: 2021-07-23 1 DE 00+ 0 Friday 10 1 0
11: 2021-07-24 1 DE 00+ 0 Saturday 11 1 0
12: 2021-07-25 1 DE 00+ 0 Sunday 12 1 0
13: 2021-07-26 1 DE 00+ 0 Monday 13 1 0
14: 2021-07-27 1 DE 00+ 0 Tuesday 14 2 0
15: 2021-07-28 1 DE 00+ 0 Wednesday 15 2 0
16: 2021-07-29 1 DE 00+ 0 Thursday 16 2 0
17: 2021-07-30 1 DE 00+ 0 Friday 17 2 0
18: 2021-07-31 1 DE 00+ 0 Saturday 18 2 0
19: 2021-08-01 1 DE 00+ 0 Sunday 19 2 1
20: 2021-08-02 1 DE 00+ 0 Monday 20 2 1
21: 2021-08-03 1 DE 00+ 0 Tuesday 21 3 1
22: 2021-08-04 1 DE 00+ 0 Wednesday 22 3 1
23: 2021-08-05 1 DE 00+ 0 Thursday 23 3 1
24: 2021-08-06 1 DE 00+ 0 Friday 24 3 1
25: 2021-08-07 1 DE 00+ 0 Saturday 25 3 1
26: 2021-08-08 1 DE 00+ 0 Sunday 26 3 1
27: 2021-08-09 1 DE 00+ 0 Monday 27 3 1
28: 2021-08-10 1 DE 00+ 0 Tuesday 28 4 1
29: 2021-08-11 1 DE 00+ 0 Wednesday 29 4 1
30: 2021-08-12 1 DE 00+ 0 Thursday 30 4 1
31: 2021-08-13 1 DE 00+ 0 Friday 31 4 1
32: 2021-08-14 1 DE 00+ 0 Saturday 32 4 1
33: 2021-08-15 1 DE 00+ 0 Sunday 33 4 1
34: 2021-08-16 1 DE 00+ 0 Monday 34 4 1
35: 2021-08-17 1 DE 00+ 0 Tuesday 35 5 1
36: 2021-08-18 1 DE 00+ 0 Wednesday 36 5 1
37: 2021-08-19 1 DE 00+ 0 Thursday 37 5 1
38: 2021-08-20 1 DE 00+ 0 Friday 38 5 1
39: 2021-08-21 1 DE 00+ 0 Saturday 39 5 1
40: 2021-08-22 1 DE 00+ 0 Sunday 40 5 1
date .group location age_group delay day_of_week day week month
$data_raw$observation
date .group location age_group delay day_of_week day week month
1: 2021-07-13 1 DE 00+ 0 Tuesday 0 0 0
2: 2021-07-14 1 DE 00+ 0 Wednesday 1 0 0
3: 2021-07-15 1 DE 00+ 0 Thursday 2 0 0
4: 2021-07-16 1 DE 00+ 0 Friday 3 0 0
5: 2021-07-17 1 DE 00+ 0 Saturday 4 0 0
6: 2021-07-18 1 DE 00+ 0 Sunday 5 0 0
7: 2021-07-19 1 DE 00+ 0 Monday 6 0 0
8: 2021-07-20 1 DE 00+ 0 Tuesday 7 1 0
9: 2021-07-21 1 DE 00+ 0 Wednesday 8 1 0
10: 2021-07-22 1 DE 00+ 0 Thursday 9 1 0
11: 2021-07-23 1 DE 00+ 0 Friday 10 1 0
12: 2021-07-24 1 DE 00+ 0 Saturday 11 1 0
13: 2021-07-25 1 DE 00+ 0 Sunday 12 1 0
14: 2021-07-26 1 DE 00+ 0 Monday 13 1 0
15: 2021-07-27 1 DE 00+ 0 Tuesday 14 2 0
16: 2021-07-28 1 DE 00+ 0 Wednesday 15 2 0
17: 2021-07-29 1 DE 00+ 0 Thursday 16 2 0
18: 2021-07-30 1 DE 00+ 0 Friday 17 2 0
19: 2021-07-31 1 DE 00+ 0 Saturday 18 2 0
20: 2021-08-01 1 DE 00+ 0 Sunday 19 2 1
21: 2021-08-02 1 DE 00+ 0 Monday 20 2 1
22: 2021-08-03 1 DE 00+ 0 Tuesday 21 3 1
23: 2021-08-04 1 DE 00+ 0 Wednesday 22 3 1
24: 2021-08-05 1 DE 00+ 0 Thursday 23 3 1
25: 2021-08-06 1 DE 00+ 0 Friday 24 3 1
26: 2021-08-07 1 DE 00+ 0 Saturday 25 3 1
27: 2021-08-08 1 DE 00+ 0 Sunday 26 3 1
28: 2021-08-09 1 DE 00+ 0 Monday 27 3 1
29: 2021-08-10 1 DE 00+ 0 Tuesday 28 4 1
30: 2021-08-11 1 DE 00+ 0 Wednesday 29 4 1
31: 2021-08-12 1 DE 00+ 0 Thursday 30 4 1
32: 2021-08-13 1 DE 00+ 0 Friday 31 4 1
33: 2021-08-14 1 DE 00+ 0 Saturday 32 4 1
34: 2021-08-15 1 DE 00+ 0 Sunday 33 4 1
35: 2021-08-16 1 DE 00+ 0 Monday 34 4 1
36: 2021-08-17 1 DE 00+ 0 Tuesday 35 5 1
37: 2021-08-18 1 DE 00+ 0 Wednesday 36 5 1
38: 2021-08-19 1 DE 00+ 0 Thursday 37 5 1
39: 2021-08-20 1 DE 00+ 0 Friday 38 5 1
40: 2021-08-21 1 DE 00+ 0 Saturday 39 5 1
41: 2021-08-22 1 DE 00+ 0 Sunday 40 5 1
date .group location age_group delay day_of_week day week month
$data
$data$expr_r_seed
[1] 1
$data$expr_gt_n
[1] 1
$data$expr_lrgt
[1] 0
$data$expr_t
[1] 40
$data$expr_obs
[1] 0
$data$expr_g
[1] 0
$data$expr_ft
[1] 41
$data$expr_fintercept
[1] 1
$data$expr_fnrow
[1] 40
$data$expr_findex
[1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25
[26] 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40
$data$expr_fnindex
[1] 40
$data$expr_fncol
[1] 7
$data$expr_rncol
[1] 1
$data$expr_fdesign
day_of_weekFriday day_of_weekMonday day_of_weekSaturday day_of_weekSunday
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2 0 0 0 0
3 1 0 0 0
4 0 0 1 0
5 0 0 0 1
6 0 1 0 0
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11 0 0 1 0
12 0 0 0 1
13 0 1 0 0
14 0 0 0 0
15 0 0 0 0
16 0 0 0 0
17 1 0 0 0
18 0 0 1 0
19 0 0 0 1
20 0 1 0 0
21 0 0 0 0
22 0 0 0 0
23 0 0 0 0
24 1 0 0 0
25 0 0 1 0
26 0 0 0 1
27 0 1 0 0
28 0 0 0 0
29 0 0 0 0
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31 1 0 0 0
32 0 0 1 0
33 0 0 0 1
34 0 1 0 0
35 0 0 0 0
36 0 0 0 0
37 0 0 0 0
38 1 0 0 0
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40 0 0 0 1
day_of_weekThursday day_of_weekTuesday day_of_weekWednesday
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2 1 0 0
3 0 0 0
4 0 0 0
5 0 0 0
6 0 0 0
7 0 1 0
8 0 0 1
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10 0 0 0
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15 0 0 1
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18 0 0 0
19 0 0 0
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25 0 0 0
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27 0 0 0
28 0 1 0
29 0 0 1
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31 0 0 0
32 0 0 0
33 0 0 0
34 0 0 0
35 0 1 0
36 0 0 1
37 1 0 0
38 0 0 0
39 0 0 0
40 0 0 0
$data$expr_rdesign
fixed day_of_week
1 0 1
2 0 1
3 0 1
4 0 1
5 0 1
6 0 1
7 0 1
attr(,"assign")
[1] 1 2
$data$expl_lrd_n
[1] 1
$data$expl_lrd
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[18,] 0 0 0 0 1 0 0 0 0 0 0 0
[19,] 0 0 0 0 0 1 0 0 0 0 0 0
[20,] 0 0 0 0 0 0 1 0 0 0 0 0
[21,] 0 0 0 0 0 0 0 1 0 0 0 0
[22,] 0 0 0 0 0 0 0 0 1 0 0 0
[23,] 0 0 0 0 0 0 0 0 0 1 0 0
[24,] 0 0 0 0 0 0 0 0 0 0 1 0
[25,] 0 0 0 0 0 0 0 0 0 0 0 1
[26,] 0 0 0 0 0 0 0 0 0 0 0 0
[27,] 0 0 0 0 0 0 0 0 0 0 0 0
[28,] 0 0 0 0 0 0 0 0 0 0 0 0
[29,] 0 0 0 0 0 0 0 0 0 0 0 0
[30,] 0 0 0 0 0 0 0 0 0 0 0 0
[31,] 0 0 0 0 0 0 0 0 0 0 0 0
[32,] 0 0 0 0 0 0 0 0 0 0 0 0
[33,] 0 0 0 0 0 0 0 0 0 0 0 0
[34,] 0 0 0 0 0 0 0 0 0 0 0 0
[35,] 0 0 0 0 0 0 0 0 0 0 0 0
[36,] 0 0 0 0 0 0 0 0 0 0 0 0
[37,] 0 0 0 0 0 0 0 0 0 0 0 0
[38,] 0 0 0 0 0 0 0 0 0 0 0 0
[39,] 0 0 0 0 0 0 0 0 0 0 0 0
[40,] 0 0 0 0 0 0 0 0 0 0 0 0
[41,] 0 0 0 0 0 0 0 0 0 0 0 0
[,26] [,27] [,28] [,29] [,30] [,31] [,32] [,33] [,34] [,35] [,36] [,37]
[1,] 0 0 0 0 0 0 0 0 0 0 0 0
[2,] 0 0 0 0 0 0 0 0 0 0 0 0
[3,] 0 0 0 0 0 0 0 0 0 0 0 0
[4,] 0 0 0 0 0 0 0 0 0 0 0 0
[5,] 0 0 0 0 0 0 0 0 0 0 0 0
[6,] 0 0 0 0 0 0 0 0 0 0 0 0
[7,] 0 0 0 0 0 0 0 0 0 0 0 0
[8,] 0 0 0 0 0 0 0 0 0 0 0 0
[9,] 0 0 0 0 0 0 0 0 0 0 0 0
[10,] 0 0 0 0 0 0 0 0 0 0 0 0
[11,] 0 0 0 0 0 0 0 0 0 0 0 0
[12,] 0 0 0 0 0 0 0 0 0 0 0 0
[13,] 0 0 0 0 0 0 0 0 0 0 0 0
[14,] 0 0 0 0 0 0 0 0 0 0 0 0
[15,] 0 0 0 0 0 0 0 0 0 0 0 0
[16,] 0 0 0 0 0 0 0 0 0 0 0 0
[17,] 0 0 0 0 0 0 0 0 0 0 0 0
[18,] 0 0 0 0 0 0 0 0 0 0 0 0
[19,] 0 0 0 0 0 0 0 0 0 0 0 0
[20,] 0 0 0 0 0 0 0 0 0 0 0 0
[21,] 0 0 0 0 0 0 0 0 0 0 0 0
[22,] 0 0 0 0 0 0 0 0 0 0 0 0
[23,] 0 0 0 0 0 0 0 0 0 0 0 0
[24,] 0 0 0 0 0 0 0 0 0 0 0 0
[25,] 0 0 0 0 0 0 0 0 0 0 0 0
[26,] 1 0 0 0 0 0 0 0 0 0 0 0
[27,] 0 1 0 0 0 0 0 0 0 0 0 0
[28,] 0 0 1 0 0 0 0 0 0 0 0 0
[29,] 0 0 0 1 0 0 0 0 0 0 0 0
[30,] 0 0 0 0 1 0 0 0 0 0 0 0
[31,] 0 0 0 0 0 1 0 0 0 0 0 0
[32,] 0 0 0 0 0 0 1 0 0 0 0 0
[33,] 0 0 0 0 0 0 0 1 0 0 0 0
[34,] 0 0 0 0 0 0 0 0 1 0 0 0
[35,] 0 0 0 0 0 0 0 0 0 1 0 0
[36,] 0 0 0 0 0 0 0 0 0 0 1 0
[37,] 0 0 0 0 0 0 0 0 0 0 0 1
[38,] 0 0 0 0 0 0 0 0 0 0 0 0
[39,] 0 0 0 0 0 0 0 0 0 0 0 0
[40,] 0 0 0 0 0 0 0 0 0 0 0 0
[41,] 0 0 0 0 0 0 0 0 0 0 0 0
[,38] [,39] [,40] [,41]
[1,] 0 0 0 0
[2,] 0 0 0 0
[3,] 0 0 0 0
[4,] 0 0 0 0
[5,] 0 0 0 0
[6,] 0 0 0 0
[7,] 0 0 0 0
[8,] 0 0 0 0
[9,] 0 0 0 0
[10,] 0 0 0 0
[11,] 0 0 0 0
[12,] 0 0 0 0
[13,] 0 0 0 0
[14,] 0 0 0 0
[15,] 0 0 0 0
[16,] 0 0 0 0
[17,] 0 0 0 0
[18,] 0 0 0 0
[19,] 0 0 0 0
[20,] 0 0 0 0
[21,] 0 0 0 0
[22,] 0 0 0 0
[23,] 0 0 0 0
[24,] 0 0 0 0
[25,] 0 0 0 0
[26,] 0 0 0 0
[27,] 0 0 0 0
[28,] 0 0 0 0
[29,] 0 0 0 0
[30,] 0 0 0 0
[31,] 0 0 0 0
[32,] 0 0 0 0
[33,] 0 0 0 0
[34,] 0 0 0 0
[35,] 0 0 0 0
[36,] 0 0 0 0
[37,] 0 0 0 0
[38,] 1 0 0 0
[39,] 0 1 0 0
[40,] 0 0 1 0
[41,] 0 0 0 1
$data$expl_obs
[1] 0
$data$expl_fintercept
[1] 1
$data$expl_fnrow
[1] 41
$data$expl_findex
[1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25
[26] 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41
$data$expl_fnindex
[1] 41
$data$expl_fncol
[1] 0
$data$expl_rncol
[1] 0
$data$expl_fdesign
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
$data$expl_rdesign
(Intercept)
attr(,"assign")
[1] 0
$priors
variable dimension
1: expr_r_int 1
2: expr_beta_sd 1
3: expr_lelatent_int 1
4: expl_beta_sd 1
description
1: Intercept of the log growth rate
2: Standard deviation of scaled pooled log growth rate effects
3: Intercept for initial log observations (ordered by group and then\n time)
4: Standard deviation of scaled pooled log growth rate effects
distribution mean sd
1: Normal 0.0 0.2
2: Zero truncated normal 0.0 1.0
3: Normal 4.1 1.0
4: Zero truncated normal 0.0 1.0
enw_expectation works as expected when multiple timeseries are present
Code
expectation_module[setdiff(names(expectation_module), "inits")]
Output
$formula
$formula$r
[1] "~1 + (1 | .group)"
$formula$observation
[1] "~(1 | week:.group)"
$data_raw
$data_raw$r
date .group location age_group delay day_of_week day week month
1: 2021-08-13 1 DE 00-04 0 Friday 1 0 0
2: 2021-08-14 1 DE 00-04 0 Saturday 2 0 0
3: 2021-08-15 1 DE 00-04 0 Sunday 3 0 0
4: 2021-08-16 1 DE 00-04 0 Monday 4 0 0
5: 2021-08-17 1 DE 00-04 0 Tuesday 5 0 0
6: 2021-08-18 1 DE 00-04 0 Wednesday 6 0 0
7: 2021-08-19 1 DE 00-04 0 Thursday 7 1 0
8: 2021-08-20 1 DE 00-04 0 Friday 8 1 0
9: 2021-08-21 1 DE 00-04 0 Saturday 9 1 0
10: 2021-08-22 1 DE 00-04 0 Sunday 10 1 0
11: 2021-08-13 2 DE 00+ 0 Friday 1 0 0
12: 2021-08-14 2 DE 00+ 0 Saturday 2 0 0
13: 2021-08-15 2 DE 00+ 0 Sunday 3 0 0
14: 2021-08-16 2 DE 00+ 0 Monday 4 0 0
15: 2021-08-17 2 DE 00+ 0 Tuesday 5 0 0
16: 2021-08-18 2 DE 00+ 0 Wednesday 6 0 0
17: 2021-08-19 2 DE 00+ 0 Thursday 7 1 0
18: 2021-08-20 2 DE 00+ 0 Friday 8 1 0
19: 2021-08-21 2 DE 00+ 0 Saturday 9 1 0
20: 2021-08-22 2 DE 00+ 0 Sunday 10 1 0
21: 2021-08-13 3 DE 80+ 0 Friday 1 0 0
22: 2021-08-14 3 DE 80+ 0 Saturday 2 0 0
23: 2021-08-15 3 DE 80+ 0 Sunday 3 0 0
24: 2021-08-16 3 DE 80+ 0 Monday 4 0 0
25: 2021-08-17 3 DE 80+ 0 Tuesday 5 0 0
26: 2021-08-18 3 DE 80+ 0 Wednesday 6 0 0
27: 2021-08-19 3 DE 80+ 0 Thursday 7 1 0
28: 2021-08-20 3 DE 80+ 0 Friday 8 1 0
29: 2021-08-21 3 DE 80+ 0 Saturday 9 1 0
30: 2021-08-22 3 DE 80+ 0 Sunday 10 1 0
date .group location age_group delay day_of_week day week month
observed
1: TRUE
2: TRUE
3: TRUE
4: TRUE
5: TRUE
6: TRUE
7: TRUE
8: TRUE
9: TRUE
10: TRUE
11: TRUE
12: TRUE
13: TRUE
14: TRUE
15: TRUE
16: TRUE
17: TRUE
18: TRUE
19: TRUE
20: TRUE
21: TRUE
22: TRUE
23: TRUE
24: TRUE
25: TRUE
26: TRUE
27: TRUE
28: TRUE
29: TRUE
30: TRUE
observed
$data_raw$observation
date .group location age_group delay day_of_week day week month
1: 2021-08-12 1 DE 00-04 0 Thursday 0 0 0
2: 2021-08-13 1 DE 00-04 0 Friday 1 0 0
3: 2021-08-14 1 DE 00-04 0 Saturday 2 0 0
4: 2021-08-15 1 DE 00-04 0 Sunday 3 0 0
5: 2021-08-16 1 DE 00-04 0 Monday 4 0 0
6: 2021-08-17 1 DE 00-04 0 Tuesday 5 0 0
7: 2021-08-18 1 DE 00-04 0 Wednesday 6 0 0
8: 2021-08-19 1 DE 00-04 0 Thursday 7 1 0
9: 2021-08-20 1 DE 00-04 0 Friday 8 1 0
10: 2021-08-21 1 DE 00-04 0 Saturday 9 1 0
11: 2021-08-22 1 DE 00-04 0 Sunday 10 1 0
12: 2021-08-12 2 DE 00+ 0 Thursday 0 0 0
13: 2021-08-13 2 DE 00+ 0 Friday 1 0 0
14: 2021-08-14 2 DE 00+ 0 Saturday 2 0 0
15: 2021-08-15 2 DE 00+ 0 Sunday 3 0 0
16: 2021-08-16 2 DE 00+ 0 Monday 4 0 0
17: 2021-08-17 2 DE 00+ 0 Tuesday 5 0 0
18: 2021-08-18 2 DE 00+ 0 Wednesday 6 0 0
19: 2021-08-19 2 DE 00+ 0 Thursday 7 1 0
20: 2021-08-20 2 DE 00+ 0 Friday 8 1 0
21: 2021-08-21 2 DE 00+ 0 Saturday 9 1 0
22: 2021-08-22 2 DE 00+ 0 Sunday 10 1 0
23: 2021-08-12 3 DE 80+ 0 Thursday 0 0 0
24: 2021-08-13 3 DE 80+ 0 Friday 1 0 0
25: 2021-08-14 3 DE 80+ 0 Saturday 2 0 0
26: 2021-08-15 3 DE 80+ 0 Sunday 3 0 0
27: 2021-08-16 3 DE 80+ 0 Monday 4 0 0
28: 2021-08-17 3 DE 80+ 0 Tuesday 5 0 0
29: 2021-08-18 3 DE 80+ 0 Wednesday 6 0 0
30: 2021-08-19 3 DE 80+ 0 Thursday 7 1 0
31: 2021-08-20 3 DE 80+ 0 Friday 8 1 0
32: 2021-08-21 3 DE 80+ 0 Saturday 9 1 0
33: 2021-08-22 3 DE 80+ 0 Sunday 10 1 0
date .group location age_group delay day_of_week day week month
$data
$data$expr_r_seed
[1] 2
$data$expr_gt_n
[1] 2
$data$expr_lrgt
[1] -0.1053605 -2.3025851
$data$expr_t
[1] 10
$data$expr_obs
[1] 0
$data$expr_g
[1] 0 10 20
$data$expr_ft
[1] 12
$data$expr_fintercept
[1] 1
$data$expr_fnrow
[1] 30
$data$expr_findex
[1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25
[26] 26 27 28 29 30
$data$expr_fnindex
[1] 30
$data$expr_fncol
[1] 3
$data$expr_rncol
[1] 1
$data$expr_fdesign
.group1 .group2 .group3
1 1 0 0
2 1 0 0
3 1 0 0
4 1 0 0
5 1 0 0
6 1 0 0
7 1 0 0
8 1 0 0
9 1 0 0
10 1 0 0
11 0 1 0
12 0 1 0
13 0 1 0
14 0 1 0
15 0 1 0
16 0 1 0
17 0 1 0
18 0 1 0
19 0 1 0
20 0 1 0
21 0 0 1
22 0 0 1
23 0 0 1
24 0 0 1
25 0 0 1
26 0 0 1
27 0 0 1
28 0 0 1
29 0 0 1
30 0 0 1
$data$expr_rdesign
fixed .group
1 0 1
2 0 1
3 0 1
attr(,"assign")
[1] 1 2
$data$expl_lrd_n
[1] 2
$data$expl_lrd
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12]
[1,] 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
[2,] 0.9 0.1 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
[3,] 0.0 0.9 0.1 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
[4,] 0.0 0.0 0.9 0.1 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
[5,] 0.0 0.0 0.0 0.9 0.1 0.0 0.0 0.0 0.0 0.0 0.0 0.0
[6,] 0.0 0.0 0.0 0.0 0.9 0.1 0.0 0.0 0.0 0.0 0.0 0.0
[7,] 0.0 0.0 0.0 0.0 0.0 0.9 0.1 0.0 0.0 0.0 0.0 0.0
[8,] 0.0 0.0 0.0 0.0 0.0 0.0 0.9 0.1 0.0 0.0 0.0 0.0
[9,] 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.9 0.1 0.0 0.0 0.0
[10,] 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.9 0.1 0.0 0.0
[11,] 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.9 0.1 0.0
[12,] 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.9 0.1
$data$expl_obs
[1] 1
$data$expl_fintercept
[1] 1
$data$expl_fnrow
[1] 33
$data$expl_findex
[1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25
[26] 26 27 28 29 30 31 32 33
$data$expl_fnindex
[1] 33
$data$expl_fncol
[1] 6
$data$expl_rncol
[1] 3
$data$expl_fdesign
week0:.group1 week1:.group1 week0:.group2 week1:.group2 week0:.group3
1 1 0 0 0 0
2 1 0 0 0 0
3 1 0 0 0 0
4 1 0 0 0 0
5 1 0 0 0 0
6 1 0 0 0 0
7 1 0 0 0 0
8 0 1 0 0 0
9 0 1 0 0 0
10 0 1 0 0 0
11 0 1 0 0 0
12 0 0 1 0 0
13 0 0 1 0 0
14 0 0 1 0 0
15 0 0 1 0 0
16 0 0 1 0 0
17 0 0 1 0 0
18 0 0 1 0 0
19 0 0 0 1 0
20 0 0 0 1 0
21 0 0 0 1 0
22 0 0 0 1 0
23 0 0 0 0 1
24 0 0 0 0 1
25 0 0 0 0 1
26 0 0 0 0 1
27 0 0 0 0 1
28 0 0 0 0 1
29 0 0 0 0 1
30 0 0 0 0 0
31 0 0 0 0 0
32 0 0 0 0 0
33 0 0 0 0 0
week1:.group3
1 0
2 0
3 0
4 0
5 0
6 0
7 0
8 0
9 0
10 0
11 0
12 0
13 0
14 0
15 0
16 0
17 0
18 0
19 0
20 0
21 0
22 0
23 0
24 0
25 0
26 0
27 0
28 0
29 0
30 1
31 1
32 1
33 1
$data$expl_rdesign
fixed week__.group1 week__.group2 week__.group3
1 0 1 0 0
2 0 1 0 0
3 0 0 1 0
4 0 0 1 0
5 0 0 0 1
6 0 0 0 1
attr(,"assign")
[1] 1 2 3 4
$priors
variable dimension
1: expr_r_int 1
2: expr_beta_sd 1
3: expr_lelatent_int 1
4: expr_lelatent_int 2
5: expr_lelatent_int 3
6: expr_lelatent_int 4
7: expr_lelatent_int 5
8: expr_lelatent_int 6
9: expl_beta_sd 1
description
1: Intercept of the log growth rate
2: Standard deviation of scaled pooled log growth rate effects
3: Intercept for initial log observations (ordered by group and then\n time)
4: Intercept for initial log observations (ordered by group and then\n time)
5: Intercept for initial log observations (ordered by group and then\n time)
6: Intercept for initial log observations (ordered by group and then\n time)
7: Intercept for initial log observations (ordered by group and then\n time)
8: Intercept for initial log observations (ordered by group and then\n time)
9: Standard deviation of scaled pooled log growth rate effects
distribution mean sd
1: Normal 0.0 0.2
2: Zero truncated normal 0.0 1.0
3: Normal 2.1 1.0
4: Normal 2.1 1.0
5: Normal 5.5 1.0
6: Normal 5.5 1.0
7: Normal 3.4 1.0
8: Normal 3.4 1.0
9: Zero truncated normal 0.0 1.0
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