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Automatic Vignette update (#872)
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Co-authored-by: github-merge-queue <[email protected]>
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152 changes: 74 additions & 78 deletions vignettes/estimate_infections_options.Rmd
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Original file line number Diff line number Diff line change
Expand Up @@ -184,20 +184,20 @@ def <- estimate_infections(reported_cases,
)
# summarise results
summary(def)
#> measure estimate
#> <char> <char>
#> 1: New infections per day 2248 (1257 -- 4197)
#> 2: Expected change in daily reports Likely decreasing
#> 3: Effective reproduction no. 0.89 (0.7 -- 1.1)
#> 4: Rate of growth -0.029 (-0.1 -- 0.05)
#> 5: Doubling/halving time (days) -24 (14 -- -6.9)
#> measure estimate
#> <char> <char>
#> 1: New infections per day 2252 (1263 -- 4114)
#> 2: Expected change in daily reports Likely decreasing
#> 3: Effective reproduction no. 0.91 (0.71 -- 1.1)
#> 4: Rate of growth -0.025 (-0.099 -- 0.05)
#> 5: Doubling/halving time (days) -28 (14 -- -7)
# elapsed time (in seconds)
get_elapsed_time(def$fit)
#> warmup sample
#> chain:1 39.295 14.837
#> chain:2 30.967 17.867
#> chain:3 19.880 20.187
#> chain:4 30.845 17.029
#> chain:1 38.369 14.121
#> chain:2 21.395 19.918
#> chain:3 19.866 20.072
#> chain:4 33.197 15.001
# summary plot
plot(def)
```
Expand All @@ -218,20 +218,20 @@ agp <- estimate_infections(reported_cases,
)
# summarise results
summary(agp)
#> measure estimate
#> <char> <char>
#> 1: New infections per day 2237 (1219 -- 4117)
#> 2: Expected change in daily reports Likely decreasing
#> 3: Effective reproduction no. 0.9 (0.7 -- 1.1)
#> 4: Rate of growth -0.027 (-0.1 -- 0.05)
#> 5: Doubling/halving time (days) -25 (14 -- -6.7)
#> measure estimate
#> <char> <char>
#> 1: New infections per day 2269 (1271 -- 4110)
#> 2: Expected change in daily reports Likely decreasing
#> 3: Effective reproduction no. 0.9 (0.71 -- 1.1)
#> 4: Rate of growth -0.028 (-0.098 -- 0.048)
#> 5: Doubling/halving time (days) -25 (14 -- -7.1)
# elapsed time (in seconds)
get_elapsed_time(agp$fit)
#> warmup sample
#> chain:1 29.162 17.576
#> chain:2 25.503 16.575
#> chain:3 30.866 20.561
#> chain:4 16.315 19.859
#> chain:1 27.935 16.850
#> chain:2 25.793 19.368
#> chain:3 24.928 20.662
#> chain:4 20.156 20.117
# summary plot
plot(agp)
```
Expand Down Expand Up @@ -262,18 +262,18 @@ dep <- estimate_infections(reported_cases,
summary(dep)
#> measure estimate
#> <char> <char>
#> 1: New infections per day 2281 (1272 -- 4202)
#> 1: New infections per day 2252 (1277 -- 3986)
#> 2: Expected change in daily reports Likely decreasing
#> 3: Effective reproduction no. 0.9 (0.7 -- 1.2)
#> 4: Rate of growth -0.027 (-0.099 -- 0.053)
#> 5: Doubling/halving time (days) -26 (13 -- -7)
#> 3: Effective reproduction no. 0.9 (0.71 -- 1.1)
#> 4: Rate of growth -0.027 (-0.096 -- 0.045)
#> 5: Doubling/halving time (days) -26 (15 -- -7.2)
# elapsed time (in seconds)
get_elapsed_time(dep$fit)
#> warmup sample
#> chain:1 38.446 17.392
#> chain:2 35.284 25.287
#> chain:3 37.985 14.862
#> chain:4 19.169 21.754
#> chain:1 39.785 21.487
#> chain:2 38.549 24.341
#> chain:3 40.301 20.255
#> chain:4 38.609 22.631
# summary plot
plot(dep)
```
Expand Down Expand Up @@ -352,26 +352,22 @@ project_rt <- estimate_infections(reported_cases,
prior = rt_prior, future = "project"
)
)
#> Warning: There were 1 divergent transitions after warmup. See
#> https://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: Examine the pairs() plot to diagnose sampling problems
# summarise results
summary(project_rt)
#> measure estimate
#> <char> <char>
#> 1: New infections per day 2259 (1269 -- 4270)
#> 1: New infections per day 2286 (1251 -- 4245)
#> 2: Expected change in daily reports Likely decreasing
#> 3: Effective reproduction no. 0.9 (0.7 -- 1.2)
#> 4: Rate of growth -0.028 (-0.1 -- 0.053)
#> 5: Doubling/halving time (days) -25 (13 -- -6.9)
#> 3: Effective reproduction no. 0.91 (0.69 -- 1.2)
#> 4: Rate of growth -0.025 (-0.1 -- 0.057)
#> 5: Doubling/halving time (days) -27 (12 -- -6.6)
# elapsed time (in seconds)
get_elapsed_time(project_rt$fit)
#> warmup sample
#> chain:1 38.457 21.569
#> chain:2 37.331 31.316
#> chain:3 41.696 20.026
#> chain:4 36.001 29.542
#> chain:1 41.976 20.312
#> chain:2 38.670 30.656
#> chain:3 45.302 24.642
#> chain:4 36.433 27.803
# summary plot
plot(project_rt)
```
Expand All @@ -393,18 +389,18 @@ fixed <- estimate_infections(reported_cases,
summary(fixed)
#> measure estimate
#> <char> <char>
#> 1: New infections per day 16388 (9713 -- 29178)
#> 1: New infections per day 15662 (9110 -- 27614)
#> 2: Expected change in daily reports Increasing
#> 3: Effective reproduction no. 1.2 (1.1 -- 1.3)
#> 4: Rate of growth 0.049 (0.035 -- 0.064)
#> 5: Doubling/halving time (days) 14 (11 -- 20)
#> 4: Rate of growth 0.048 (0.033 -- 0.062)
#> 5: Doubling/halving time (days) 14 (11 -- 21)
# elapsed time (in seconds)
get_elapsed_time(fixed$fit)
#> warmup sample
#> chain:1 2.980 1.299
#> chain:2 2.341 1.762
#> chain:3 1.905 1.488
#> chain:4 2.371 1.124
#> chain:1 2.563 1.206
#> chain:2 2.538 1.338
#> chain:3 2.858 1.677
#> chain:4 2.729 1.812
# summary plot
plot(fixed)
```
Expand Down Expand Up @@ -439,18 +435,18 @@ bkp <- estimate_infections(bp_cases,
summary(bkp)
#> measure estimate
#> <char> <char>
#> 1: New infections per day 2332 (1913 -- 2873)
#> 1: New infections per day 2361 (1935 -- 2913)
#> 2: Expected change in daily reports Decreasing
#> 3: Effective reproduction no. 0.89 (0.86 -- 0.92)
#> 4: Rate of growth -0.027 (-0.035 -- -0.02)
#> 4: Rate of growth -0.027 (-0.034 -- -0.02)
#> 5: Doubling/halving time (days) -25 (-35 -- -20)
# elapsed time (in seconds)
get_elapsed_time(bkp$fit)
#> warmup sample
#> chain:1 4.038 4.143
#> chain:2 4.717 4.175
#> chain:3 3.792 4.339
#> chain:4 4.155 4.375
#> chain:1 3.878 4.202
#> chain:2 3.700 4.273
#> chain:3 3.950 4.249
#> chain:4 4.075 5.439
# summary plot
plot(bkp)
```
Expand All @@ -474,18 +470,18 @@ rw <- estimate_infections(reported_cases,
summary(rw)
#> measure estimate
#> <char> <char>
#> 1: New infections per day 2105 (1056 -- 4290)
#> 1: New infections per day 2107 (1036 -- 4243)
#> 2: Expected change in daily reports Likely decreasing
#> 3: Effective reproduction no. 0.87 (0.63 -- 1.2)
#> 4: Rate of growth -0.038 (-0.11 -- 0.043)
#> 5: Doubling/halving time (days) -18 (16 -- -6.3)
#> 3: Effective reproduction no. 0.86 (0.62 -- 1.2)
#> 4: Rate of growth -0.039 (-0.11 -- 0.044)
#> 5: Doubling/halving time (days) -18 (16 -- -6.2)
# elapsed time (in seconds)
get_elapsed_time(rw$fit)
#> warmup sample
#> chain:1 8.861 11.035
#> chain:2 10.882 14.697
#> chain:3 10.258 14.744
#> chain:4 9.483 11.982
#> chain:1 9.317 17.282
#> chain:2 10.950 15.554
#> chain:3 11.766 16.676
#> chain:4 9.807 12.646
# summary plot
plot(rw)
```
Expand All @@ -504,20 +500,20 @@ no_delay <- estimate_infections(
)
# summarise results
summary(no_delay)
#> measure estimate
#> <char> <char>
#> 1: New infections per day 2788 (2410 -- 3253)
#> 2: Expected change in daily reports Decreasing
#> 3: Effective reproduction no. 0.89 (0.81 -- 0.97)
#> 4: Rate of growth -0.031 (-0.06 -- -0.00082)
#> 5: Doubling/halving time (days) -22 (-850 -- -11)
#> measure estimate
#> <char> <char>
#> 1: New infections per day 2800 (2394 -- 3288)
#> 2: Expected change in daily reports Decreasing
#> 3: Effective reproduction no. 0.89 (0.81 -- 0.98)
#> 4: Rate of growth -0.031 (-0.064 -- 0.0014)
#> 5: Doubling/halving time (days) -23 (490 -- -11)
# elapsed time (in seconds)
get_elapsed_time(no_delay$fit)
#> warmup sample
#> chain:1 49.555 43.752
#> chain:2 47.479 30.349
#> chain:3 45.951 42.126
#> chain:4 36.484 33.659
#> chain:1 44.262 33.583
#> chain:2 45.474 33.991
#> chain:3 39.716 40.068
#> chain:4 51.969 31.387
# summary plot
plot(no_delay)
```
Expand Down Expand Up @@ -552,10 +548,10 @@ summary(non_parametric)
# elapsed time (in seconds)
get_elapsed_time(non_parametric$fit)
#> warmup sample
#> chain:1 4.566 0.667
#> chain:2 4.359 0.797
#> chain:3 4.592 0.604
#> chain:4 4.892 0.565
#> chain:1 4.453 0.676
#> chain:2 4.365 0.788
#> chain:3 4.619 0.622
#> chain:4 4.961 0.544
# summary plot
plot(non_parametric)
```
Expand Down

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