Skip to content

Commit

Permalink
Automatic Vignette update (#849)
Browse files Browse the repository at this point in the history
  • Loading branch information
github-actions[bot] authored Nov 1, 2024
1 parent 99be5bf commit f63e2a7
Show file tree
Hide file tree
Showing 4 changed files with 51 additions and 46 deletions.
Binary file modified vignettes/epinow-epinow-1.png
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-1.png
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
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
97 changes: 51 additions & 46 deletions vignettes/epinow.Rmd
Original file line number Diff line number Diff line change
Expand Up @@ -51,10 +51,15 @@ res <- epinow(reported_cases,
)
#> Logging threshold set at INFO for the name logger
#> Writing EpiNow2 logs to the console and:
#> '/tmp/RtmpscgdQ0/regional-epinow/2020-04-21.log'.
#> '/tmp/RtmpLVW5Qb/regional-epinow/2020-04-21.log'.
#> Logging threshold set at INFO for the name logger
#> Writing EpiNow2.epinow logs to the console and:
#> '/tmp/RtmpscgdQ0/epinow/2020-04-21.log'.
#> '/tmp/RtmpLVW5Qb/epinow/2020-04-21.log'.
#> WARN [2024-11-01 00:31:23] epinow: There were 10 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 [2024-11-01 00:31:23] epinow: Examine the pairs() plot to diagnose sampling problems
#> -
res$plots$R
```

Expand Down Expand Up @@ -89,38 +94,38 @@ region_rt <- regional_epinow(
delays = delay_opts(delay),
rt = rt_opts(prior = rt_prior),
)
#> INFO [2024-10-02 09:21:23] Producing following optional outputs: regions, summary, samples, plots, latest
#> INFO [2024-11-01 00:31:26] Producing following optional outputs: regions, summary, samples, plots, latest
#> Logging threshold set at INFO for the name logger
#> Writing EpiNow2 logs to the console and:
#> '/tmp/RtmpscgdQ0/regional-epinow/2020-04-21.log'.
#> '/tmp/RtmpLVW5Qb/regional-epinow/2020-04-21.log'.
#> Logging threshold set at INFO for the name logger
#> Writing EpiNow2.epinow logs to: '/tmp/RtmpscgdQ0/epinow/2020-04-21.log'.
#> INFO [2024-10-02 09:21:23] Reporting estimates using data up to: 2020-04-21
#> INFO [2024-10-02 09:21:23] No target directory specified so returning output
#> INFO [2024-10-02 09:21:23] Producing estimates for: testland, realland
#> INFO [2024-10-02 09:21:23] Regions excluded: none
#> INFO [2024-10-02 09:22:26] Completed estimates for: testland
#> INFO [2024-10-02 09:24:04] Completed estimates for: realland
#> INFO [2024-10-02 09:24:04] Completed regional estimates
#> INFO [2024-10-02 09:24:04] Regions with estimates: 2
#> INFO [2024-10-02 09:24:04] Regions with runtime errors: 0
#> INFO [2024-10-02 09:24:04] Producing summary
#> INFO [2024-10-02 09:24:04] No summary directory specified so returning summary output
#> INFO [2024-10-02 09:24:04] No target directory specified so returning timings
#> Writing EpiNow2.epinow logs to: '/tmp/RtmpLVW5Qb/epinow/2020-04-21.log'.
#> INFO [2024-11-01 00:31:26] Reporting estimates using data up to: 2020-04-21
#> INFO [2024-11-01 00:31:26] No target directory specified so returning output
#> INFO [2024-11-01 00:31:26] Producing estimates for: testland, realland
#> INFO [2024-11-01 00:31:26] Regions excluded: none
#> INFO [2024-11-01 00:32:52] Completed estimates for: testland
#> INFO [2024-11-01 00:36:49] Completed estimates for: realland
#> INFO [2024-11-01 00:36:49] Completed regional estimates
#> INFO [2024-11-01 00:36:49] Regions with estimates: 2
#> INFO [2024-11-01 00:36:49] Regions with runtime errors: 0
#> INFO [2024-11-01 00:36:49] Producing summary
#> INFO [2024-11-01 00:36:49] No summary directory specified so returning summary output
#> INFO [2024-11-01 00:36:50] No target directory specified so returning timings
## summary
region_rt$summary$summarised_results$table
#> Region New infections per day Expected change in daily reports
#> <char> <char> <fctr>
#> 1: realland 2251 (1309 -- 4051) Likely decreasing
#> 2: testland 2251 (1269 -- 4008) Likely decreasing
#> Effective reproduction no. Rate of growth
#> <char> <char>
#> 1: 0.9 (0.72 -- 1.1) -0.028 (-0.093 -- 0.044)
#> 2: 0.9 (0.7 -- 1.1) -0.027 (-0.099 -- 0.047)
#> 1: realland 2201 (1055 -- 4557) Likely decreasing
#> 2: testland 2302 (1117 -- 4754) Likely decreasing
#> Effective reproduction no. Rate of growth
#> <char> <char>
#> 1: 0.88 (0.61 -- 1.2) -0.033 (-0.14 -- 0.066)
#> 2: 0.9 (0.63 -- 1.2) -0.028 (-0.13 -- 0.076)
#> Doubling/halving time (days)
#> <char>
#> 1: -25 (16 -- -7.4)
#> 2: -25 (15 -- -7)
#> 1: -21 (11 -- -4.9)
#> 2: -25 (9.1 -- -5.3)
## plot
region_rt$summary$plots$R
```
Expand All @@ -140,38 +145,38 @@ region_separate_rt <- regional_epinow(
delays = delay_opts(delay),
rt = rt, gp = gp,
)
#> INFO [2024-10-02 09:24:05] Producing following optional outputs: regions, summary, samples, plots, latest
#> INFO [2024-11-01 00:36:50] Producing following optional outputs: regions, summary, samples, plots, latest
#> Logging threshold set at INFO for the name logger
#> Writing EpiNow2 logs to the console and:
#> '/tmp/RtmpscgdQ0/regional-epinow/2020-04-21.log'.
#> '/tmp/RtmpLVW5Qb/regional-epinow/2020-04-21.log'.
#> Logging threshold set at INFO for the name logger
#> Writing EpiNow2.epinow logs to: '/tmp/RtmpscgdQ0/epinow/2020-04-21.log'.
#> INFO [2024-10-02 09:24:05] Reporting estimates using data up to: 2020-04-21
#> INFO [2024-10-02 09:24:05] No target directory specified so returning output
#> INFO [2024-10-02 09:24:05] Producing estimates for: testland, realland
#> INFO [2024-10-02 09:24:05] Regions excluded: none
#> INFO [2024-10-02 09:25:18] Completed estimates for: testland
#> INFO [2024-10-02 09:25:50] Completed estimates for: realland
#> INFO [2024-10-02 09:25:50] Completed regional estimates
#> INFO [2024-10-02 09:25:50] Regions with estimates: 2
#> INFO [2024-10-02 09:25:50] Regions with runtime errors: 0
#> INFO [2024-10-02 09:25:50] Producing summary
#> INFO [2024-10-02 09:25:50] No summary directory specified so returning summary output
#> INFO [2024-10-02 09:25:51] No target directory specified so returning timings
#> Writing EpiNow2.epinow logs to: '/tmp/RtmpLVW5Qb/epinow/2020-04-21.log'.
#> INFO [2024-11-01 00:36:50] Reporting estimates using data up to: 2020-04-21
#> INFO [2024-11-01 00:36:50] No target directory specified so returning output
#> INFO [2024-11-01 00:36:50] Producing estimates for: testland, realland
#> INFO [2024-11-01 00:36:50] Regions excluded: none
#> INFO [2024-11-01 00:38:30] Completed estimates for: testland
#> INFO [2024-11-01 00:39:02] Completed estimates for: realland
#> INFO [2024-11-01 00:39:02] Completed regional estimates
#> INFO [2024-11-01 00:39:02] Regions with estimates: 2
#> INFO [2024-11-01 00:39:02] Regions with runtime errors: 0
#> INFO [2024-11-01 00:39:02] Producing summary
#> INFO [2024-11-01 00:39:02] No summary directory specified so returning summary output
#> INFO [2024-11-01 00:39:03] No target directory specified so returning timings
## summary
region_separate_rt$summary$summarised_results$table
#> Region New infections per day Expected change in daily reports
#> <char> <char> <fctr>
#> 1: realland 2077 (1045 -- 4285) Likely decreasing
#> 2: testland 2246 (1324 -- 3909) Likely decreasing
#> Effective reproduction no. Rate of growth
#> <char> <char>
#> 1: 0.85 (0.61 -- 1.2) -0.039 (-0.11 -- 0.044)
#> 2: 0.89 (0.7 -- 1.1) -0.027 (-0.094 -- 0.046)
#> 2: testland 2217 (1007 -- 4591) Likely decreasing
#> Effective reproduction no. Rate of growth
#> <char> <char>
#> 1: 0.85 (0.61 -- 1.2) -0.039 (-0.11 -- 0.044)
#> 2: 0.88 (0.58 -- 1.2) -0.03 (-0.15 -- 0.072)
#> Doubling/halving time (days)
#> <char>
#> 1: -18 (16 -- -6.5)
#> 2: -25 (15 -- -7.3)
#> 2: -23 (9.7 -- -4.8)
## plot
region_separate_rt$summary$plots$R
```
Expand Down

0 comments on commit f63e2a7

Please sign in to comment.