Skip to content

Commit

Permalink
set seed in vignettes
Browse files Browse the repository at this point in the history
  • Loading branch information
@sbfnk
sbfnk committed May 10, 2024
1 parent ac3bc24 commit 45d290a
Show file tree
Hide file tree
Showing 24 changed files with 181 additions and 172 deletions.
Binary file modified vignettes/EpiNow2-unnamed-chunk-11-1.png
View file
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file modified vignettes/EpiNow2-unnamed-chunk-15-1.png
View file
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
90 changes: 45 additions & 45 deletions vignettes/EpiNow2.Rmd
View file
Original file line number Diff line number Diff line change
Expand Up @@ -138,11 +138,11 @@ knitr::kable(summary(estimates))

|measure |estimate |
|:--------------------------------|:-----------------------|
|New infections per day |2194 (959 -- 4537) |
|New infections per day |2199 (962 -- 4757) |
|Expected change in daily reports |Likely decreasing |
|Effective reproduction no. |0.88 (0.57 -- 1.2) |
|Rate of growth |-0.035 (-0.16 -- 0.071) |
|Doubling/halving time (days) |-20 (9.7 -- -4.3) |
|Effective reproduction no. |0.88 (0.58 -- 1.2) |
|Rate of growth |-0.034 (-0.15 -- 0.076) |
|Doubling/halving time (days) |-20 (9.1 -- -4.6) |



Expand All @@ -153,20 +153,20 @@ 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 2.282341 2.287029 0.1578993 2.039580
#> 2: 2020-02-23 R <NA> estimate 2.247501 2.253287 0.1365203 2.036124
#> 3: 2020-02-24 R <NA> estimate 2.211478 2.216927 0.1209953 2.028704
#> 4: 2020-02-25 R <NA> estimate 2.173422 2.177949 0.1107091 2.003955
#> 5: 2020-02-26 R <NA> estimate 2.130907 2.136457 0.1045656 1.976722
#> 6: 2020-02-27 R <NA> estimate 2.085150 2.092644 0.1012598 1.935996
#> 1: 2020-02-22 R <NA> estimate 2.288484 2.293707 0.1613209 2.044132
#> 2: 2020-02-23 R <NA> estimate 2.254878 2.259642 0.1403568 2.040359
#> 3: 2020-02-24 R <NA> estimate 2.217611 2.222709 0.1251234 2.026980
#> 4: 2020-02-25 R <NA> estimate 2.174854 2.182984 0.1150322 2.002758
#> 5: 2020-02-26 R <NA> estimate 2.132196 2.140643 0.1089983 1.974475
#> 6: 2020-02-27 R <NA> estimate 2.088958 2.095945 0.1056741 1.933753
#> lower_50 lower_20 upper_20 upper_50 upper_90
#> <num> <num> <num> <num> <num>
#> 1: 2.178184 2.244453 2.321996 2.388252 2.546907
#> 2: 2.161279 2.216246 2.280849 2.342883 2.476179
#> 3: 2.136466 2.182567 2.241605 2.298582 2.414471
#> 4: 2.105387 2.144891 2.201741 2.250736 2.370276
#> 5: 2.065872 2.105379 2.158661 2.204257 2.318660
#> 6: 2.024025 2.062980 2.111543 2.156906 2.268855
#> 1: 2.181696 2.246458 2.328439 2.398968 2.574407
#> 2: 2.162459 2.217716 2.289158 2.349965 2.508728
#> 3: 2.136181 2.184912 2.247679 2.303535 2.440930
#> 4: 2.101307 2.148035 2.204825 2.256175 2.381675
#> 5: 2.064946 2.108764 2.160005 2.207901 2.331636
#> 6: 2.023783 2.062603 2.114298 2.159626 2.285821
```

Reported cases are returned in a separate data frame in order to streamline the reporting of forecasts and for model evaluation.
Expand All @@ -176,20 +176,20 @@ 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 76 77.6780 21.93549 46 62 71
#> 2: 2020-02-23 gp_rt 86 89.8400 25.68136 54 72 80
#> 3: 2020-02-24 gp_rt 86 89.4875 25.31927 53 72 80
#> 4: 2020-02-25 gp_rt 80 82.6275 23.54659 49 66 75
#> 5: 2020-02-26 gp_rt 79 82.3555 23.43305 50 66 74
#> 6: 2020-02-27 gp_rt 108 110.0040 29.95643 66 88 101
#> 1: 2020-02-22 gp_rt 74.0 76.9430 21.47422 46 62 70.0
#> 2: 2020-02-23 gp_rt 87.0 89.5820 24.71017 54 72 82.0
#> 3: 2020-02-24 gp_rt 86.0 88.6670 24.76764 53 71 80.6
#> 4: 2020-02-25 gp_rt 81.0 82.6625 22.56520 49 66 75.0
#> 5: 2020-02-26 gp_rt 79.0 81.8240 23.31905 48 65 75.0
#> 6: 2020-02-27 gp_rt 107.5 111.2375 30.27595 69 89 101.0
#> upper_20 upper_50 upper_90
#> <num> <num> <num>
#> 1: 81 90 116.00
#> 2: 93 105 136.05
#> 3: 93 104 137.00
#> 4: 86 96 126.00
#> 5: 85 96 126.00
#> 6: 115 128 165.00
#> 1: 79 89 116.00
#> 2: 92 104 135.00
#> 3: 92 103 133.00
#> 4: 87 96 121.00
#> 5: 85 96 121.05
#> 6: 115 129 166.00
```

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 @@ -238,19 +238,19 @@ estimates <- regional_epinow(
gp = NULL,
stan = stan_opts(cores = 4, warmup = 250, samples = 1000)
)
#> INFO [2024-05-08 10:30:10] Producing following optional outputs: regions, summary, samples, plots, latest
#> INFO [2024-05-08 10:30:10] Reporting estimates using data up to: 2020-04-21
#> INFO [2024-05-08 10:30:10] No target directory specified so returning output
#> INFO [2024-05-08 10:30:10] Producing estimates for: testland, realland
#> INFO [2024-05-08 10:30:10] Regions excluded: none
#> INFO [2024-05-08 10:30:17] Completed estimates for: testland
#> INFO [2024-05-08 10:30:25] Completed estimates for: realland
#> INFO [2024-05-08 10:30:25] Completed regional estimates
#> INFO [2024-05-08 10:30:25] Regions with estimates: 2
#> INFO [2024-05-08 10:30:25] Regions with runtime errors: 0
#> INFO [2024-05-08 10:30:25] Producing summary
#> INFO [2024-05-08 10:30:25] No summary directory specified so returning summary output
#> INFO [2024-05-08 10:30:25] No target directory specified so returning timings
#> INFO [2024-05-10 07:58:14] Producing following optional outputs: regions, summary, samples, plots, latest
#> INFO [2024-05-10 07:58:14] Reporting estimates using data up to: 2020-04-21
#> INFO [2024-05-10 07:58:14] No target directory specified so returning output
#> INFO [2024-05-10 07:58:14] Producing estimates for: testland, realland
#> INFO [2024-05-10 07:58:14] Regions excluded: none
#> INFO [2024-05-10 07:58:29] Completed estimates for: testland
#> INFO [2024-05-10 07:58:41] Completed estimates for: realland
#> INFO [2024-05-10 07:58:41] Completed regional estimates
#> INFO [2024-05-10 07:58:41] Regions with estimates: 2
#> INFO [2024-05-10 07:58:41] Regions with runtime errors: 0
#> INFO [2024-05-10 07:58:41] Producing summary
#> INFO [2024-05-10 07:58:41] No summary directory specified so returning summary output
#> INFO [2024-05-10 07:58:41] 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 @@ -264,10 +264,10 @@ 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 |2073 (997 -- 4424) |Likely decreasing |0.86 (0.6 -- 1.2) |-0.04 (-0.12 -- 0.048) |-17 (14 -- -6) |
|testland |2047 (1018 -- 4236) |Likely decreasing |0.86 (0.6 -- 1.2) |-0.04 (-0.12 -- 0.042) |-17 (17 -- -6) |
|Region |New infections per day |Expected change in daily reports |Effective reproduction no. |Rate of growth |Doubling/halving time (days) |
|:--------|:----------------------|:--------------------------------|:--------------------------|:-----------------------|:----------------------------|
|realland |2060 (1007 -- 4579) |Likely decreasing |0.86 (0.59 -- 1.2) |-0.039 (-0.12 -- 0.056) |-18 (12 -- -5.9) |
|testland |2136 (1050 -- 4356) |Likely decreasing |0.86 (0.62 -- 1.2) |-0.036 (-0.11 -- 0.048) |-19 (14 -- -6.4) |



Expand Down
1 change: 1 addition & 0 deletions vignettes/EpiNow2.Rmd.orig
View file
Original file line number Diff line number Diff line change
Expand Up @@ -20,6 +20,7 @@ knitr::opts_chunk$set(
fig.height = 6.5,
fig.path = "EpiNow2-"
)
set.seed(9876)
```
## Quick start

Expand Down
Binary file modified vignettes/epinow-regional_epinow-1.png
View file
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file modified vignettes/epinow-regional_epinow_multiple-1.png
View file
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
93 changes: 46 additions & 47 deletions vignettes/epinow.Rmd
View file
Original file line number Diff line number Diff line change
Expand Up @@ -50,16 +50,15 @@ res <- epinow(reported_cases,
rt = rt_opts(prior = rt_prior)
)
#> Logging threshold set at INFO for the EpiNow2 logger
#> Writing EpiNow2 logs to the console and: /var/folders/n9/h_419gjj2mg3d208nplgvbg40000gp/T//RtmpV4gG8k/regional-epinow/2020-04-21.log
#> Writing EpiNow2 logs to the console and: /tmp/RtmpJDlhZu/regional-epinow/2020-04-21.log
#> Logging threshold set at INFO for the EpiNow2.epinow logger
#> Writing EpiNow2.epinow logs to the console and: /var/folders/n9/h_419gjj2mg3d208nplgvbg40000gp/T//RtmpV4gG8k/epinow/2020-04-21.log
#> WARN [2024-05-08 10:27:26] epinow: There were 12 divergent transitions after warmup. See
#> Writing EpiNow2.epinow logs to the console and: /tmp/RtmpJDlhZu/epinow/2020-04-21.log
#> WARN [2024-05-10 07:52:36] epinow: There were 11 divergent transitions after warmup. See
#> https://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them. -
#> WARN [2024-05-08 10:27:26] epinow: Examine the pairs() plot to diagnose sampling problems
#> WARN [2024-05-10 07:52:36] epinow: Examine the pairs() plot to diagnose sampling problems
#> -
res$plots$R
#> NULL
```

![plot of chunk epinow](epinow-epinow-1.png)
Expand Down Expand Up @@ -98,37 +97,37 @@ region_rt <- regional_epinow(
#> ℹ The argument will be removed completely in the next version.
#> This warning is displayed once every 8 hours.
#> Call `lifecycle::last_lifecycle_warnings()` to see where this warning was generated.
#> INFO [2024-05-08 10:27:30] Producing following optional outputs: regions, summary, samples, plots, latest
#> INFO [2024-05-10 07:52:38] Producing following optional outputs: regions, summary, samples, plots, latest
#> Logging threshold set at INFO for the EpiNow2 logger
#> Writing EpiNow2 logs to the console and: /var/folders/n9/h_419gjj2mg3d208nplgvbg40000gp/T//RtmpV4gG8k/regional-epinow/2020-04-21.log
#> Writing EpiNow2 logs to the console and: /tmp/RtmpJDlhZu/regional-epinow/2020-04-21.log
#> Logging threshold set at INFO for the EpiNow2.epinow logger
#> Writing EpiNow2.epinow logs to: /var/folders/n9/h_419gjj2mg3d208nplgvbg40000gp/T//RtmpV4gG8k/epinow/2020-04-21.log
#> INFO [2024-05-08 10:27:30] Reporting estimates using data up to: 2020-04-21
#> INFO [2024-05-08 10:27:30] No target directory specified so returning output
#> INFO [2024-05-08 10:27:30] Producing estimates for: testland, realland
#> INFO [2024-05-08 10:27:30] Regions excluded: none
#> INFO [2024-05-08 10:27:59] Completed estimates for: testland
#> INFO [2024-05-08 10:28:27] Completed estimates for: realland
#> INFO [2024-05-08 10:28:27] Completed regional estimates
#> INFO [2024-05-08 10:28:27] Regions with estimates: 2
#> INFO [2024-05-08 10:28:27] Regions with runtime errors: 0
#> INFO [2024-05-08 10:28:27] Producing summary
#> INFO [2024-05-08 10:28:27] No summary directory specified so returning summary output
#> INFO [2024-05-08 10:28:27] No target directory specified so returning timings
#> Writing EpiNow2.epinow logs to: /tmp/RtmpJDlhZu/epinow/2020-04-21.log
#> INFO [2024-05-10 07:52:38] Reporting estimates using data up to: 2020-04-21
#> INFO [2024-05-10 07:52:38] No target directory specified so returning output
#> INFO [2024-05-10 07:52:38] Producing estimates for: testland, realland
#> INFO [2024-05-10 07:52:38] Regions excluded: none
#> INFO [2024-05-10 07:53:40] Completed estimates for: testland
#> INFO [2024-05-10 07:54:29] Completed estimates for: realland
#> INFO [2024-05-10 07:54:29] Completed regional estimates
#> INFO [2024-05-10 07:54:29] Regions with estimates: 2
#> INFO [2024-05-10 07:54:29] Regions with runtime errors: 0
#> INFO [2024-05-10 07:54:29] Producing summary
#> INFO [2024-05-10 07:54:29] No summary directory specified so returning summary output
#> INFO [2024-05-10 07:54:29] No target directory specified so returning timings
## summary
region_rt$summary$summarised_results$table
#> Region New infections per day Expected change in daily reports
#> <char> <char> <fctr>
#> 1: realland 2215 (948 -- 4737) Likely decreasing
#> 2: testland 2222 (962 -- 4772) Likely decreasing
#> 1: realland 2211 (921 -- 4610) Likely decreasing
#> 2: testland 2238 (980 -- 4646) Likely decreasing
#> Effective reproduction no. Rate of growth
#> <char> <char>
#> 1: 0.88 (0.57 -- 1.2) -0.034 (-0.16 -- 0.075)
#> 2: 0.88 (0.57 -- 1.2) -0.034 (-0.16 -- 0.076)
#> 1: 0.87 (0.57 -- 1.2) -0.036 (-0.16 -- 0.076)
#> 2: 0.88 (0.58 -- 1.2) -0.034 (-0.16 -- 0.076)
#> Doubling/halving time (days)
#> <char>
#> 1: -20 (9.3 -- -4.2)
#> 2: -21 (9.1 -- -4.4)
#> 1: -19 (9.2 -- -4.3)
#> 2: -20 (9.1 -- -4.4)
## plot
region_rt$summary$plots$R
```
Expand All @@ -148,37 +147,37 @@ region_separate_rt <- regional_epinow(
delays = delay_opts(delay),
rt = rt, gp = gp,
)
#> INFO [2024-05-08 10:28:27] Producing following optional outputs: regions, summary, samples, plots, latest
#> INFO [2024-05-10 07:54:30] Producing following optional outputs: regions, summary, samples, plots, latest
#> Logging threshold set at INFO for the EpiNow2 logger
#> Writing EpiNow2 logs to the console and: /var/folders/n9/h_419gjj2mg3d208nplgvbg40000gp/T//RtmpV4gG8k/regional-epinow/2020-04-21.log
#> Writing EpiNow2 logs to the console and: /tmp/RtmpJDlhZu/regional-epinow/2020-04-21.log
#> Logging threshold set at INFO for the EpiNow2.epinow logger
#> Writing EpiNow2.epinow logs to: /var/folders/n9/h_419gjj2mg3d208nplgvbg40000gp/T//RtmpV4gG8k/epinow/2020-04-21.log
#> INFO [2024-05-08 10:28:27] Reporting estimates using data up to: 2020-04-21
#> INFO [2024-05-08 10:28:27] No target directory specified so returning output
#> INFO [2024-05-08 10:28:27] Producing estimates for: testland, realland
#> INFO [2024-05-08 10:28:27] Regions excluded: none
#> INFO [2024-05-08 10:29:12] Completed estimates for: testland
#> INFO [2024-05-08 10:29:22] Completed estimates for: realland
#> INFO [2024-05-08 10:29:22] Completed regional estimates
#> INFO [2024-05-08 10:29:22] Regions with estimates: 2
#> INFO [2024-05-08 10:29:22] Regions with runtime errors: 0
#> INFO [2024-05-08 10:29:22] Producing summary
#> INFO [2024-05-08 10:29:22] No summary directory specified so returning summary output
#> INFO [2024-05-08 10:29:22] No target directory specified so returning timings
#> Writing EpiNow2.epinow logs to: /tmp/RtmpJDlhZu/epinow/2020-04-21.log
#> INFO [2024-05-10 07:54:30] Reporting estimates using data up to: 2020-04-21
#> INFO [2024-05-10 07:54:30] No target directory specified so returning output
#> INFO [2024-05-10 07:54:30] Producing estimates for: testland, realland
#> INFO [2024-05-10 07:54:30] Regions excluded: none
#> INFO [2024-05-10 07:56:06] Completed estimates for: testland
#> INFO [2024-05-10 07:56:24] Completed estimates for: realland
#> INFO [2024-05-10 07:56:24] Completed regional estimates
#> INFO [2024-05-10 07:56:24] Regions with estimates: 2
#> INFO [2024-05-10 07:56:24] Regions with runtime errors: 0
#> INFO [2024-05-10 07:56:24] Producing summary
#> INFO [2024-05-10 07:56:24] No summary directory specified so returning summary output
#> INFO [2024-05-10 07:56:24] No target directory specified so returning timings
## summary
region_separate_rt$summary$summarised_results$table
#> Region New infections per day Expected change in daily reports
#> <char> <char> <fctr>
#> 1: realland 2052 (1055 -- 4175) Likely decreasing
#> 2: testland 2150 (802 -- 4889) Likely decreasing
#> 1: realland 2106 (1042 -- 4307) Likely decreasing
#> 2: testland 2128 (843 -- 4774) Likely decreasing
#> Effective reproduction no. Rate of growth
#> <char> <char>
#> 1: 0.85 (0.61 -- 1.2) -0.041 (-0.11 -- 0.043)
#> 2: 0.86 (0.5 -- 1.3) -0.037 (-0.19 -- 0.084)
#> 1: 0.86 (0.6 -- 1.2) -0.038 (-0.11 -- 0.046)
#> 2: 0.86 (0.52 -- 1.3) -0.038 (-0.18 -- 0.081)
#> Doubling/halving time (days)
#> <char>
#> 1: -17 (16 -- -6.3)
#> 2: -19 (8.2 -- -3.7)
#> 1: -18 (15 -- -6.3)
#> 2: -18 (8.6 -- -3.8)
## plot
region_separate_rt$summary$plots$R
```
Expand Down
1 change: 1 addition & 0 deletions vignettes/epinow.Rmd.orig
View file
Original file line number Diff line number Diff line change
Expand Up @@ -20,6 +20,7 @@ knitr::opts_chunk$set(
fig.height = 6.5,
fig.path = "epinow-"
)
set.seed(9876)
```

The _EpiNow2_ package contains functionality to run `estimate_infections()` in production mode, i.e. with full logging and saving all relevant outputs and plots to dedicated folders in the hard drive.
Expand Down
Binary file modified vignettes/estimate_infections_options-bp-1.png
View file
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file modified vignettes/estimate_infections_options-data-1.png
View file
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file modified vignettes/estimate_infections_options-default-1.png
View file
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file modified vignettes/estimate_infections_options-fixed-1.png
View file
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file modified vignettes/estimate_infections_options-gp_projection-1.png
View file
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file modified vignettes/estimate_infections_options-lower_accuracy-1.png
View file
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file modified vignettes/estimate_infections_options-no_delays-1.png
View file
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file modified vignettes/estimate_infections_options-nonparametric-1.png
View file
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file modified vignettes/estimate_infections_options-susceptible_depletion-1.png
View file
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file modified vignettes/estimate_infections_options-truncation-1.png
View file
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file modified vignettes/estimate_infections_options-weekly_rw-1.png
View file
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading

0 comments on commit 45d290a

Please sign in to comment.