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Automatic Vignette update (#873)
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Co-authored-by: github-merge-queue <[email protected]>
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96 changes: 48 additions & 48 deletions vignettes/EpiNow2.Rmd
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Expand Up @@ -150,13 +150,13 @@ knitr::kable(summary(estimates))



|measure |estimate |
|:--------------------------------|:----------------------|
|New infections per day |2275 (1102 -- 4554) |
|Expected change in daily reports |Likely decreasing |
|Effective reproduction no. |0.89 (0.63 -- 1.2) |
|Rate of growth |-0.029 (-0.13 -- 0.07) |
|Doubling/halving time (days) |-24 (10 -- -5.4) |
|measure |estimate |
|:--------------------------------|:------------------------|
|New infections per day |2266 (1324 -- 4172) |
|Expected change in daily reports |Likely decreasing |
|Effective reproduction no. |0.9 (0.71 -- 1.2) |
|Rate of growth |-0.027 (-0.093 -- 0.051) |
|Doubling/halving time (days) |-26 (14 -- -7.5) |



Expand All @@ -165,22 +165,22 @@ Summarised parameter estimates can also easily be returned, either filtered for

``` r
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 2.306013 2.310790 0.1540239 2.056853
#> 2: 2020-02-23 R <NA> estimate 2.266565 2.271512 0.1360063 2.049787
#> 3: 2020-02-24 R <NA> estimate 2.226070 2.230026 0.1222073 2.028592
#> 4: 2020-02-25 R <NA> estimate 2.183114 2.186413 0.1121909 2.004851
#> 5: 2020-02-26 R <NA> estimate 2.137137 2.140814 0.1052495 1.974622
#> 6: 2020-02-27 R <NA> estimate 2.090623 2.093424 0.1005494 1.940482
#> date variable strat type median mean sd lower_90
#> <Date> <char> <char> <char> <num> <num> <num> <num>
#> 1: 2020-02-22 R <NA> estimate 2.287987 2.290720 0.14678968 2.056834
#> 2: 2020-02-23 R <NA> estimate 2.247641 2.251922 0.13171390 2.038763
#> 3: 2020-02-24 R <NA> estimate 2.208073 2.210936 0.11891193 2.016136
#> 4: 2020-02-25 R <NA> estimate 2.165172 2.167861 0.10846265 1.991208
#> 5: 2020-02-26 R <NA> estimate 2.120656 2.122831 0.10027192 1.960414
#> 6: 2020-02-27 R <NA> estimate 2.074142 2.076024 0.09406499 1.925058
#> lower_50 lower_20 upper_20 upper_50 upper_90
#> <num> <num> <num> <num> <num>
#> 1: 2.205403 2.268372 2.343532 2.415484 2.562332
#> 2: 2.179397 2.233646 2.305061 2.365446 2.495602
#> 3: 2.143963 2.197360 2.260493 2.313351 2.438623
#> 4: 2.109778 2.155150 2.213032 2.262105 2.377589
#> 5: 2.068317 2.112241 2.163534 2.210975 2.317693
#> 6: 2.024142 2.064680 2.115606 2.160040 2.261932
#> 1: 2.190162 2.251441 2.327439 2.390297 2.536828
#> 2: 2.160845 2.215980 2.283736 2.342490 2.473291
#> 3: 2.128236 2.177448 2.239422 2.293251 2.412534
#> 4: 2.093381 2.137557 2.193825 2.242761 2.348207
#> 5: 2.054260 2.096437 2.145255 2.189826 2.291795
#> 6: 2.009842 2.050170 2.095696 2.137567 2.233805
```

Reported cases are returned in a separate data frame in order to streamline the reporting of forecasts and for model evaluation.
Expand All @@ -190,20 +190,20 @@ Reported cases are returned in a separate data frame in order to streamline the
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 74 76.8805 21.41765 46 62 69
#> 2: 2020-02-23 gp_rt 85 88.0035 24.36979 53 71 80
#> 3: 2020-02-24 gp_rt 87 89.3710 24.82584 53 72 81
#> 4: 2020-02-25 gp_rt 79 81.6050 23.06389 48 66 74
#> 5: 2020-02-26 gp_rt 80 82.3575 22.85603 50 66 74
#> 6: 2020-02-27 gp_rt 107 110.2845 30.84153 66 88 100
#> 1: 2020-02-22 gp_rt 75 76.6790 20.61666 46 63.00 70.0
#> 2: 2020-02-23 gp_rt 88 90.2305 24.69604 55 73.00 82.0
#> 3: 2020-02-24 gp_rt 87 89.9430 25.24045 55 72.75 81.0
#> 4: 2020-02-25 gp_rt 81 82.7225 23.10631 50 66.00 75.0
#> 5: 2020-02-26 gp_rt 81 82.8090 22.82214 49 67.00 75.0
#> 6: 2020-02-27 gp_rt 110 112.3805 29.06563 69 92.00 103.6
#> upper_20 upper_50 upper_90
#> <num> <num> <num>
#> 1: 80 89 116
#> 2: 92 102 132
#> 3: 93 104 135
#> 4: 85 95 124
#> 5: 86 95 124
#> 6: 115 129 166
#> 1: 80 89 113.00
#> 2: 94 105 135.05
#> 3: 94 104 134.00
#> 4: 86 96 123.00
#> 5: 87 97 121.00
#> 6: 117 130 163.00
```

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 [2024-11-01 00:25:14] Producing following optional outputs: regions, summary, samples, plots, latest
#> INFO [2024-11-01 00:25:14] Reporting estimates using data up to: 2020-04-21
#> INFO [2024-11-01 00:25:14] No target directory specified so returning output
#> INFO [2024-11-01 00:25:14] Producing estimates for: testland, realland
#> INFO [2024-11-01 00:25:14] Regions excluded: none
#> INFO [2024-11-01 00:25:36] Completed estimates for: testland
#> INFO [2024-11-01 00:26:00] Completed estimates for: realland
#> INFO [2024-11-01 00:26:00] Completed regional estimates
#> INFO [2024-11-01 00:26:00] Regions with estimates: 2
#> INFO [2024-11-01 00:26:00] Regions with runtime errors: 0
#> INFO [2024-11-01 00:26:00] Producing summary
#> INFO [2024-11-01 00:26:00] No summary directory specified so returning summary output
#> INFO [2024-11-01 00:26:00] No target directory specified so returning timings
#> INFO [2024-12-01 00:25:55] Producing following optional outputs: regions, summary, samples, plots, latest
#> INFO [2024-12-01 00:25:55] Reporting estimates using data up to: 2020-04-21
#> INFO [2024-12-01 00:25:55] No target directory specified so returning output
#> INFO [2024-12-01 00:25:55] Producing estimates for: testland, realland
#> INFO [2024-12-01 00:25:55] Regions excluded: none
#> INFO [2024-12-01 00:26:16] Completed estimates for: testland
#> INFO [2024-12-01 00:26:36] Completed estimates for: realland
#> INFO [2024-12-01 00:26:36] Completed regional estimates
#> INFO [2024-12-01 00:26:36] Regions with estimates: 2
#> INFO [2024-12-01 00:26:36] Regions with runtime errors: 0
#> INFO [2024-12-01 00:26:36] Producing summary
#> INFO [2024-12-01 00:26:36] No summary directory specified so returning summary output
#> INFO [2024-12-01 00:26:37] 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 @@ -280,8 +280,8 @@ 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 |2107 (1035 -- 4584) |Likely decreasing |0.87 (0.62 -- 1.2) |-0.037 (-0.11 -- 0.049) |-19 (14 -- -6.2) |
|testland |2084 (1062 -- 4392) |Likely decreasing |0.85 (0.61 -- 1.2) |-0.04 (-0.11 -- 0.048) |-18 (15 -- -6.4) |
|realland |2110 (999 -- 4398) |Likely decreasing |0.87 (0.6 -- 1.2) |-0.037 (-0.12 -- 0.047) |-19 (15 -- -5.9) |
|testland |2140 (985 -- 4505) |Likely decreasing |0.87 (0.61 -- 1.2) |-0.036 (-0.11 -- 0.052) |-19 (13 -- -6.1) |



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