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Automatic Vignette update (#953)
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Co-authored-by: sbfnk <[email protected]>
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github-actions[bot] and sbfnk authored Jan 31, 2025
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100 changes: 50 additions & 50 deletions vignettes/EpiNow2.Rmd
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Expand Up @@ -150,13 +150,13 @@ knitr::kable(summary(estimates))



|measure |estimate |
|:--------------------------------|:------------------------|
|New infections per day |2236 (1329 -- 4036) |
|Expected change in daily reports |Likely decreasing |
|Effective reproduction no. |0.89 (0.71 -- 1.1) |
|Rate of growth |-0.028 (-0.094 -- 0.049) |
|Doubling/halving time (days) |-25 (14 -- -7.4) |
|measure |estimate |
|:----------------------------|:------------------------|
|New infections per day |2246 (1345 -- 3712) |
|Expected change in reports |Likely decreasing |
|Effective reproduction no. |0.9 (0.71 -- 1.1) |
|Rate of growth |-0.028 (-0.097 -- 0.037) |
|Doubling/halving time (days) |-25 (19 -- -7.1) |



Expand All @@ -167,43 +167,43 @@ Summarised parameter estimates can also easily be returned, either filtered for
head(summary(estimates, type = "parameters", params = "R"))
#> date variable strat type median mean sd lower_90
#> <Date> <char> <char> <char> <num> <num> <num> <num>
#> 1: 2020-02-22 R <NA> estimate 2.283241 2.292722 0.14061810 2.075280
#> 2: 2020-02-23 R <NA> estimate 2.247530 2.253561 0.12673725 2.054324
#> 3: 2020-02-24 R <NA> estimate 2.205511 2.212174 0.11519281 2.027170
#> 4: 2020-02-25 R <NA> estimate 2.163334 2.168677 0.10586586 1.999294
#> 5: 2020-02-26 R <NA> estimate 2.119453 2.123228 0.09850283 1.968758
#> 6: 2020-02-27 R <NA> estimate 2.073142 2.076018 0.09275383 1.933010
#> 1: 2020-02-22 R <NA> estimate 2.192146 2.198985 0.11444472 2.024200
#> 2: 2020-02-23 R <NA> estimate 2.155321 2.161326 0.10485587 2.002736
#> 3: 2020-02-24 R <NA> estimate 2.116282 2.122057 0.09752376 1.973624
#> 4: 2020-02-25 R <NA> estimate 2.076851 2.081412 0.09208487 1.944169
#> 5: 2020-02-26 R <NA> estimate 2.034924 2.039632 0.08807288 1.907857
#> 6: 2020-02-27 R <NA> estimate 1.991849 1.996950 0.08500839 1.867559
#> lower_50 lower_20 upper_20 upper_50 upper_90
#> <num> <num> <num> <num> <num>
#> 1: 2.194590 2.249226 2.321517 2.389094 2.535033
#> 2: 2.165231 2.213345 2.278836 2.340448 2.469433
#> 3: 2.130656 2.177294 2.236996 2.289223 2.408927
#> 4: 2.093846 2.137319 2.191361 2.238409 2.350976
#> 5: 2.054041 2.095677 2.145131 2.188372 2.288978
#> 6: 2.010469 2.050364 2.096276 2.137579 2.233775
#> 1: 2.117945 2.163831 2.223016 2.273580 2.398886
#> 2: 2.086968 2.130249 2.182448 2.231471 2.342141
#> 3: 2.053489 2.091872 2.140538 2.184986 2.295274
#> 4: 2.015866 2.053039 2.099319 2.140357 2.242094
#> 5: 1.976725 2.012561 2.056509 2.095363 2.195281
#> 6: 1.936513 1.970944 2.012702 2.051563 2.153084
```

Reported cases are returned in a separate data frame in order to streamline the reporting of forecasts and for model evaluation.


``` r
head(summary(estimates, output = "estimated_reported_cases"))
#> date type median mean sd lower_90 lower_50 lower_20
#> <Date> <char> <num> <num> <num> <num> <num> <num>
#> 1: 2020-02-22 gp_rt 75 76.6065 21.32979 45.00 62 70
#> 2: 2020-02-23 gp_rt 88 89.4765 23.85403 55.00 73 82
#> 3: 2020-02-24 gp_rt 88 90.1225 24.67288 54.00 73 82
#> 4: 2020-02-25 gp_rt 80 82.5340 22.61151 49.95 67 75
#> 5: 2020-02-26 gp_rt 80 82.4475 22.69676 49.00 66 75
#> 6: 2020-02-27 gp_rt 109 111.4705 28.76635 69.00 92 103
#> date type median mean sd lower_90 lower_50 lower_20
#> <Date> <char> <num> <num> <num> <num> <num> <num>
#> 1: 2020-02-22 gp_rt 36 36.2210 9.597511 22.00 30 33
#> 2: 2020-02-23 gp_rt 52 53.4375 13.289635 34.00 44 50
#> 3: 2020-02-24 gp_rt 64 65.6005 15.262941 42.00 55 61
#> 4: 2020-02-25 gp_rt 72 73.3265 16.283718 48.95 62 68
#> 5: 2020-02-26 gp_rt 82 83.0275 19.168972 54.00 70 77
#> 6: 2020-02-27 gp_rt 119 121.2740 25.328851 83.00 103 113
#> upper_20 upper_50 upper_90
#> <num> <num> <num>
#> 1: 80 90 114
#> 2: 94 104 132
#> 3: 94 105 133
#> 4: 86 95 124
#> 5: 86 97 123
#> 6: 116 129 163
#> 1: 38 42 53.00
#> 2: 56 61 77.00
#> 3: 68 75 92.05
#> 4: 76 83 102.00
#> 5: 87 94 116.05
#> 6: 126 136 167.00
```

A range of plots are returned (with the single summary plot shown below). These plots can also be generated using the following `plot` method.
Expand Down Expand Up @@ -252,19 +252,19 @@ estimates <- regional_epinow(
gp = NULL,
stan = stan_opts(cores = 4, warmup = 250, samples = 1000)
)
#> INFO [2024-12-06 15:15:15] Producing following optional outputs: regions, summary, samples, plots, latest
#> INFO [2024-12-06 15:15:15] Reporting estimates using data up to: 2020-04-21
#> INFO [2024-12-06 15:15:15] No target directory specified so returning output
#> INFO [2024-12-06 15:15:15] Producing estimates for: testland, realland
#> INFO [2024-12-06 15:15:15] Regions excluded: none
#> INFO [2024-12-06 15:15:39] Completed estimates for: testland
#> INFO [2024-12-06 15:16:01] Completed estimates for: realland
#> INFO [2024-12-06 15:16:01] Completed regional estimates
#> INFO [2024-12-06 15:16:01] Regions with estimates: 2
#> INFO [2024-12-06 15:16:01] Regions with runtime errors: 0
#> INFO [2024-12-06 15:16:01] Producing summary
#> INFO [2024-12-06 15:16:01] No summary directory specified so returning summary output
#> INFO [2024-12-06 15:16:02] No target directory specified so returning timings
#> INFO [2025-01-31 17:34:01] Producing following optional outputs: regions, summary, samples, plots, latest
#> INFO [2025-01-31 17:34:01] Reporting estimates using data up to: 2020-04-21
#> INFO [2025-01-31 17:34:01] No target directory specified so returning output
#> INFO [2025-01-31 17:34:01] Producing estimates for: testland, realland
#> INFO [2025-01-31 17:34:01] Regions excluded: none
#> INFO [2025-01-31 17:34:21] Completed estimates for: testland
#> INFO [2025-01-31 17:34:41] Completed estimates for: realland
#> INFO [2025-01-31 17:34:41] Completed regional estimates
#> INFO [2025-01-31 17:34:41] Regions with estimates: 2
#> INFO [2025-01-31 17:34:41] Regions with runtime errors: 0
#> INFO [2025-01-31 17:34:41] Producing summary
#> INFO [2025-01-31 17:34:41] No summary directory specified so returning summary output
#> INFO [2025-01-31 17:34:41] No target directory specified so returning timings
```

Results from each region are stored in a `regional` list with across region summary measures and plots stored in a `summary` list. All results can be set to be internally saved by setting the `target_folder` and `summary_dir` arguments. Each region can be estimated in parallel using the `{future}` package (when in most scenarios `cores` should be set to 1). For routine use each MCMC chain can also be run in parallel (with `future` = TRUE) with a time out (`max_execution_time`) allowing for partial results to be returned if a subset of chains is running longer than expected. See the documentation for the `{future}` package for details on nested futures.
Expand All @@ -278,10 +278,10 @@ knitr::kable(estimates$summary$summarised_results$table)



|Region |New infections per day |Expected change in daily reports |Effective reproduction no. |Rate of growth |Doubling/halving time (days) |
|:--------|:----------------------|:--------------------------------|:--------------------------|:-----------------------|:----------------------------|
|realland |2090 (1075 -- 4374) |Likely decreasing |0.86 (0.63 -- 1.2) |-0.038 (-0.11 -- 0.045) |-18 (15 -- -6.3) |
|testland |2111 (1040 -- 4336) |Likely decreasing |0.86 (0.62 -- 1.2) |-0.038 (-0.11 -- 0.043) |-18 (16 -- -6.2) |
|Region |New infections per day |Expected change in reports |Effective reproduction no. |Rate of growth |Doubling/halving time (days) |
|:--------|:----------------------|:--------------------------|:--------------------------|:-----------------------|:----------------------------|
|realland |2017 (1029 -- 3866) |Likely decreasing |0.85 (0.6 -- 1.1) |-0.042 (-0.11 -- 0.036) |-17 (19 -- -6.1) |
|testland |2026 (1026 -- 4222) |Likely decreasing |0.86 (0.6 -- 1.2) |-0.04 (-0.12 -- 0.042) |-17 (17 -- -5.9) |



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