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Update EpiNow2 vignette #880

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Dec 10, 2024
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Update EpiNow2 vignette #880

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90 changes: 45 additions & 45 deletions vignettes/EpiNow2.Rmd
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Expand Up @@ -131,7 +131,7 @@ estimates <- epinow(
data = reported_cases,
generation_time = gt_opts(example_generation_time),
delays = delay_opts(example_incubation_period + reporting_delay),
rt = rt_opts(prior = list(mean = 2, sd = 0.2)),
rt = rt_opts(prior = LogNormal(mean = 2, sd = 0.2)),
stan = stan_opts(cores = 4, control = list(adapt_delta = 0.99)),
verbose = interactive()
)
Expand All @@ -152,11 +152,11 @@ knitr::kable(summary(estimates))

|measure |estimate |
|:--------------------------------|:------------------------|
|New infections per day |2266 (1324 -- 4172) |
|New infections per day |2236 (1329 -- 4036) |
|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) |
|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) |



Expand All @@ -167,20 +167,20 @@ 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 2.287987 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
#> 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
#> lower_50 lower_20 upper_20 upper_50 upper_90
#> <num> <num> <num> <num> <num>
#> 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
#> 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
```

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 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
#> 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
#> upper_20 upper_50 upper_90
#> <num> <num> <num>
#> 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
#> 1: 80 90 114
#> 2: 94 104 132
#> 3: 94 105 133
#> 4: 86 95 124
#> 5: 86 97 123
#> 6: 116 129 163
```

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 @@ -248,23 +248,23 @@ estimates <- regional_epinow(
data = reported_cases,
generation_time = gt_opts(example_generation_time),
delays = delay_opts(example_incubation_period + reporting_delay),
rt = rt_opts(prior = list(mean = 2, sd = 0.2), rw = 7),
rt = rt_opts(prior = LogNormal(mean = 2, sd = 0.2), rw = 7),
gp = NULL,
stan = stan_opts(cores = 4, warmup = 250, samples = 1000)
)
#> 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
#> 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
```

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 |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) |
|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) |



Expand Down
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