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Update epinow vignette #882

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Dec 10, 2024
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Update epinow vignette #882

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93 changes: 49 additions & 44 deletions vignettes/epinow.Rmd
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Original file line number Diff line number Diff line change
Expand Up @@ -37,7 +37,7 @@ options(mc.cores = 4)
reported_cases <- example_confirmed[1:60]
reporting_delay <- LogNormal(mean = 2, sd = 1, max = 10)
delay <- example_incubation_period + reporting_delay
rt_prior <- list(mean = 2, sd = 0.1)
rt_prior <- LogNormal(mean = 2, sd = 0.1)
```

We can then run the `epinow()` function with the same arguments as `estimate_infections()`.
Expand All @@ -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/RtmpdViclN/regional-epinow/2020-04-21.log'.
#> '/tmp/RtmpM4AQFy/regional-epinow/2020-04-21.log'.
#> Logging threshold set at INFO for the name logger
#> Writing EpiNow2.epinow logs to the console and:
#> '/tmp/RtmpdViclN/epinow/2020-04-21.log'.
#> '/tmp/RtmpM4AQFy/epinow/2020-04-21.log'.
#> WARN [2024-12-06 15:12:56] epinow: There were 2 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 [2024-12-06 15:12:56] 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 [2024-12-01 00:33:34] Producing following optional outputs: regions, summary, samples, plots, latest
#> INFO [2024-12-06 15:12:59] 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/RtmpdViclN/regional-epinow/2020-04-21.log'.
#> '/tmp/RtmpM4AQFy/regional-epinow/2020-04-21.log'.
#> Logging threshold set at INFO for the name logger
#> Writing EpiNow2.epinow logs to: '/tmp/RtmpdViclN/epinow/2020-04-21.log'.
#> INFO [2024-12-01 00:33:34] Reporting estimates using data up to: 2020-04-21
#> INFO [2024-12-01 00:33:34] No target directory specified so returning output
#> INFO [2024-12-01 00:33:34] Producing estimates for: testland, realland
#> INFO [2024-12-01 00:33:34] Regions excluded: none
#> INFO [2024-12-01 00:34:44] Completed estimates for: testland
#> INFO [2024-12-01 00:35:48] Completed estimates for: realland
#> INFO [2024-12-01 00:35:48] Completed regional estimates
#> INFO [2024-12-01 00:35:48] Regions with estimates: 2
#> INFO [2024-12-01 00:35:48] Regions with runtime errors: 0
#> INFO [2024-12-01 00:35:48] Producing summary
#> INFO [2024-12-01 00:35:48] No summary directory specified so returning summary output
#> INFO [2024-12-01 00:35:49] No target directory specified so returning timings
#> Writing EpiNow2.epinow logs to: '/tmp/RtmpM4AQFy/epinow/2020-04-21.log'.
#> INFO [2024-12-06 15:12:59] Reporting estimates using data up to: 2020-04-21
#> INFO [2024-12-06 15:12:59] No target directory specified so returning output
#> INFO [2024-12-06 15:12:59] Producing estimates for: testland, realland
#> INFO [2024-12-06 15:12:59] Regions excluded: none
#> INFO [2024-12-06 15:14:04] Completed estimates for: testland
#> INFO [2024-12-06 15:15:08] Completed estimates for: realland
#> INFO [2024-12-06 15:15:08] Completed regional estimates
#> INFO [2024-12-06 15:15:08] Regions with estimates: 2
#> INFO [2024-12-06 15:15:08] Regions with runtime errors: 0
#> INFO [2024-12-06 15:15:08] Producing summary
#> INFO [2024-12-06 15:15:08] No summary directory specified so returning summary output
#> INFO [2024-12-06 15:15:08] No target directory specified so returning timings
## summary
region_rt$summary$summarised_results$table
#> Region New infections per day Expected change in daily reports
#> <char> <char> <fctr>
#> 1: realland 2254 (1318 -- 4059) Likely decreasing
#> 2: testland 2217 (1328 -- 4054) Likely decreasing
#> 1: realland 2203 (1259 -- 3956) Likely decreasing
#> 2: testland 2237 (1281 -- 4185) Likely decreasing
#> Effective reproduction no. Rate of growth
#> <char> <char>
#> 1: 0.9 (0.71 -- 1.1) -0.028 (-0.097 -- 0.047)
#> 2: 0.89 (0.72 -- 1.1) -0.031 (-0.095 -- 0.049)
#> 1: 0.89 (0.71 -- 1.1) -0.031 (-0.096 -- 0.041)
#> 2: 0.9 (0.71 -- 1.1) -0.027 (-0.097 -- 0.051)
#> Doubling/halving time (days)
#> <char>
#> 1: -25 (15 -- -7.2)
#> 2: -22 (14 -- -7.3)
#> 1: -22 (17 -- -7.2)
#> 2: -26 (14 -- -7.2)
## plot
region_rt$summary$plots$R
```
Expand All @@ -140,38 +145,38 @@ region_separate_rt <- regional_epinow(
delays = delay_opts(delay),
rt = rt, gp = gp,
)
#> INFO [2024-12-01 00:35:49] Producing following optional outputs: regions, summary, samples, plots, latest
#> INFO [2024-12-06 15:15:09] 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/RtmpdViclN/regional-epinow/2020-04-21.log'.
#> '/tmp/RtmpM4AQFy/regional-epinow/2020-04-21.log'.
#> Logging threshold set at INFO for the name logger
#> Writing EpiNow2.epinow logs to: '/tmp/RtmpdViclN/epinow/2020-04-21.log'.
#> INFO [2024-12-01 00:35:49] Reporting estimates using data up to: 2020-04-21
#> INFO [2024-12-01 00:35:49] No target directory specified so returning output
#> INFO [2024-12-01 00:35:49] Producing estimates for: testland, realland
#> INFO [2024-12-01 00:35:49] Regions excluded: none
#> INFO [2024-12-01 00:37:03] Completed estimates for: testland
#> INFO [2024-12-01 00:37:37] Completed estimates for: realland
#> INFO [2024-12-01 00:37:37] Completed regional estimates
#> INFO [2024-12-01 00:37:38] Regions with estimates: 2
#> INFO [2024-12-01 00:37:38] Regions with runtime errors: 0
#> INFO [2024-12-01 00:37:38] Producing summary
#> INFO [2024-12-01 00:37:38] No summary directory specified so returning summary output
#> INFO [2024-12-01 00:37:38] No target directory specified so returning timings
#> Writing EpiNow2.epinow logs to: '/tmp/RtmpM4AQFy/epinow/2020-04-21.log'.
#> INFO [2024-12-06 15:15:09] Reporting estimates using data up to: 2020-04-21
#> INFO [2024-12-06 15:15:09] No target directory specified so returning output
#> INFO [2024-12-06 15:15:09] Producing estimates for: testland, realland
#> INFO [2024-12-06 15:15:09] Regions excluded: none
#> INFO [2024-12-06 15:16:23] Completed estimates for: testland
#> INFO [2024-12-06 15:17:02] Completed estimates for: realland
#> INFO [2024-12-06 15:17:02] Completed regional estimates
#> INFO [2024-12-06 15:17:02] Regions with estimates: 2
#> INFO [2024-12-06 15:17:02] Regions with runtime errors: 0
#> INFO [2024-12-06 15:17:02] Producing summary
#> INFO [2024-12-06 15:17:02] No summary directory specified so returning summary output
#> INFO [2024-12-06 15:17:02] No target directory specified so returning timings
## summary
region_separate_rt$summary$summarised_results$table
#> Region New infections per day Expected change in daily reports
#> <char> <char> <fctr>
#> 1: realland 2094 (1035 -- 4404) Likely decreasing
#> 2: testland 2225 (1305 -- 3875) Likely decreasing
#> 1: realland 2072 (1008 -- 4386) Likely decreasing
#> 2: testland 2264 (1344 -- 3892) Likely decreasing
#> Effective reproduction no. Rate of growth
#> <char> <char>
#> 1: 0.86 (0.6 -- 1.2) -0.038 (-0.11 -- 0.049)
#> 2: 0.89 (0.7 -- 1.1) -0.029 (-0.093 -- 0.041)
#> 1: 0.85 (0.6 -- 1.2) -0.039 (-0.11 -- 0.049)
#> 2: 0.9 (0.71 -- 1.1) -0.026 (-0.091 -- 0.041)
#> Doubling/halving time (days)
#> <char>
#> 1: -18 (14 -- -6.2)
#> 2: -24 (17 -- -7.4)
#> 2: -26 (17 -- -7.6)
## plot
region_separate_rt$summary$plots$R
```
Expand Down
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