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Automatic readme update
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94 changes: 47 additions & 47 deletions README.md
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Expand Up @@ -183,17 +183,17 @@ case*.
``` r
reporting_delay <- dist_spec(
mean = convert_to_logmean(2, 1),
mean_sd = 1,
mean_sd = 0.1,
sd = convert_to_logsd(2, 1),
sd_sd = 1,
sd_sd = 0.1,
max = 10,
dist = "lognormal"
)
#> Warning: The meaning of the 'max' argument has changed compared to previous versions. It now indicates the maximum of a distribution rather than the length of the probability mass function (including 0) that it represented previously. To replicate previous behaviour reduce max by 1.
#> This warning is displayed once every 8 hours.
reporting_delay
#>
#> Uncertain lognormal distribution with (untruncated) logmean 0.58 (SD 1) and logSD 0.47 (SD 1)
#> Uncertain lognormal distribution with (untruncated) logmean 0.58 (SD 0.1) and logSD 0.47 (SD 0.1)
```

We use example literature estimates for the incubation period and
Expand Down Expand Up @@ -253,10 +253,10 @@ estimates <- epinow(
stan = stan_opts(cores = 4, control = list(adapt_delta = 0.99)),
verbose = interactive()
)
#> WARN [2023-10-23 15:25:44] epinow: There were 94 divergent transitions after warmup. See
#> WARN [2023-10-23 15:48:57] epinow: There were 4 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 [2023-10-23 15:25:44] epinow: Examine the pairs() plot to diagnose sampling problems
#> WARN [2023-10-23 15:48:57] epinow: Examine the pairs() plot to diagnose sampling problems
#> -
names(estimates)
#> [1] "estimates" "estimated_reported_cases"
Expand All @@ -275,31 +275,31 @@ knitr::kable(summary(estimates))

| measure | estimate |
|:--------------------------------------|:------------------------|
| New confirmed cases by infection date | 2280 (1133 – 4426) |
| New confirmed cases by infection date | 2252 (1149 – 4344) |
| Expected change in daily cases | Likely decreasing |
| Effective reproduction no. | 0.88 (0.61 – 1.2) |
| Rate of growth | -0.026 (-0.099 – 0.037) |
| Doubling/halving time (days) | -26 (19 – -7) |
| Rate of growth | -0.028 (-0.097 – 0.037) |
| Doubling/halving time (days) | -25 (19 – -7.2) |

Summarised parameter estimates can also easily be returned, either
filtered for a single parameter or for all parameters.

``` r
head(summary(estimates, type = "parameters", params = "R"))
#> date variable strat type median mean sd lower_90
#> 1: 2020-02-22 R <NA> estimate 2.210129 2.211761 0.14910486 1.979834
#> 2: 2020-02-23 R <NA> estimate 2.176867 2.180979 0.12396389 1.985529
#> 3: 2020-02-24 R <NA> estimate 2.145840 2.147910 0.10346629 1.985943
#> 4: 2020-02-25 R <NA> estimate 2.111952 2.112633 0.08746531 1.973143
#> 5: 2020-02-26 R <NA> estimate 2.074024 2.075317 0.07560421 1.951849
#> 6: 2020-02-27 R <NA> estimate 2.035373 2.036200 0.06731181 1.927648
#> 1: 2020-02-22 R <NA> estimate 2.211701 2.217243 0.14597709 1.988324
#> 2: 2020-02-23 R <NA> estimate 2.181901 2.184682 0.12107578 1.993033
#> 3: 2020-02-24 R <NA> estimate 2.149836 2.150013 0.10092850 1.992176
#> 4: 2020-02-25 R <NA> estimate 2.113283 2.113323 0.08533249 1.976792
#> 5: 2020-02-26 R <NA> estimate 2.074752 2.074784 0.07390672 1.958135
#> 6: 2020-02-27 R <NA> estimate 2.033230 2.034629 0.06602990 1.929502
#> lower_50 lower_20 upper_20 upper_50 upper_90
#> 1: 2.108234 2.173689 2.245269 2.307258 2.460105
#> 2: 2.096213 2.150163 2.208539 2.261730 2.390554
#> 3: 2.076440 2.118961 2.171197 2.217385 2.321605
#> 4: 2.050793 2.090603 2.134651 2.171913 2.259926
#> 5: 2.023419 2.056433 2.094532 2.126930 2.203052
#> 6: 1.993168 2.019440 2.052276 2.081485 2.148915
#> 1: 2.117796 2.172195 2.253123 2.310431 2.467065
#> 2: 2.104521 2.148204 2.212394 2.262825 2.392313
#> 3: 2.082463 2.121549 2.174472 2.216943 2.316859
#> 4: 2.054536 2.091270 2.134167 2.171521 2.254397
#> 5: 2.023523 2.056483 2.093294 2.124909 2.194132
#> 6: 1.988627 2.017829 2.051124 2.079665 2.140766
```

Reported cases are returned in a separate data frame in order to
Expand All @@ -308,19 +308,19 @@ streamline the reporting of forecasts and for model evaluation.
``` r
head(summary(estimates, output = "estimated_reported_cases"))
#> date type median mean sd lower_90 lower_50 lower_20
#> 1: 2020-02-22 gp_rt 66 68.0235 18.59435 41.00 55 62
#> 2: 2020-02-23 gp_rt 77 78.7080 21.53129 48.00 63 71
#> 3: 2020-02-24 gp_rt 75 77.2745 21.88597 45.95 62 70
#> 4: 2020-02-25 gp_rt 73 74.6660 20.14501 44.00 60 69
#> 5: 2020-02-26 gp_rt 78 79.7365 20.88835 49.00 65 73
#> 6: 2020-02-27 gp_rt 111 113.8450 30.85604 71.00 93 103
#> 1: 2020-02-22 gp_rt 66 68.5465 19.07920 41 55 62
#> 2: 2020-02-23 gp_rt 77 79.5490 21.35089 48 64 72
#> 3: 2020-02-24 gp_rt 76 78.2090 21.52515 46 64 71
#> 4: 2020-02-25 gp_rt 73 75.6065 21.16763 45 61 68
#> 5: 2020-02-26 gp_rt 78 79.9800 21.56129 48 65 73
#> 6: 2020-02-27 gp_rt 110 112.3640 29.46587 68 92 103
#> upper_20 upper_50 upper_90
#> 1: 70.0 80 101.00
#> 2: 82.0 92 117.00
#> 3: 80.0 89 118.00
#> 4: 78.4 87 110.00
#> 5: 83.0 93 116.00
#> 6: 117.0 130 168.05
#> 1: 71 80 104
#> 2: 84 92 117
#> 3: 81 91 118
#> 4: 79 89 113
#> 5: 83 93 119
#> 6: 117 130 165
```

A range of plots are returned (with the single summary plot shown
Expand Down Expand Up @@ -369,19 +369,19 @@ estimates <- regional_epinow(
gp = NULL,
stan = stan_opts(cores = 4, warmup = 250, samples = 1000)
)
#> INFO [2023-10-23 15:25:50] Producing following optional outputs: regions, summary, samples, plots, latest
#> INFO [2023-10-23 15:25:50] Reporting estimates using data up to: 2020-04-21
#> INFO [2023-10-23 15:25:50] No target directory specified so returning output
#> INFO [2023-10-23 15:25:50] Producing estimates for: testland, realland
#> INFO [2023-10-23 15:25:50] Regions excluded: none
#> INFO [2023-10-23 15:26:26] Completed estimates for: testland
#> INFO [2023-10-23 15:27:04] Completed estimates for: realland
#> INFO [2023-10-23 15:27:04] Completed regional estimates
#> INFO [2023-10-23 15:27:04] Regions with estimates: 2
#> INFO [2023-10-23 15:27:04] Regions with runtime errors: 0
#> INFO [2023-10-23 15:27:04] Producing summary
#> INFO [2023-10-23 15:27:04] No summary directory specified so returning summary output
#> INFO [2023-10-23 15:27:04] No target directory specified so returning timings
#> INFO [2023-10-23 15:49:03] Producing following optional outputs: regions, summary, samples, plots, latest
#> INFO [2023-10-23 15:49:03] Reporting estimates using data up to: 2020-04-21
#> INFO [2023-10-23 15:49:03] No target directory specified so returning output
#> INFO [2023-10-23 15:49:03] Producing estimates for: testland, realland
#> INFO [2023-10-23 15:49:03] Regions excluded: none
#> INFO [2023-10-23 15:49:40] Completed estimates for: testland
#> INFO [2023-10-23 15:50:15] Completed estimates for: realland
#> INFO [2023-10-23 15:50:15] Completed regional estimates
#> INFO [2023-10-23 15:50:15] Regions with estimates: 2
#> INFO [2023-10-23 15:50:15] Regions with runtime errors: 0
#> INFO [2023-10-23 15:50:15] Producing summary
#> INFO [2023-10-23 15:50:15] No summary directory specified so returning summary output
#> INFO [2023-10-23 15:50:15] No target directory specified so returning timings
```

Results from each region are stored in a `regional` list with across
Expand All @@ -406,8 +406,8 @@ knitr::kable(estimates$summary$summarised_results$table)

| Region | New confirmed cases by infection date | Expected change in daily cases | Effective reproduction no. | Rate of growth | Doubling/halving time (days) |
|:---------|:--------------------------------------|:-------------------------------|:---------------------------|:------------------------|:-----------------------------|
| realland | 2195 (1148 – 4208) | Likely decreasing | 0.86 (0.62 – 1.2) | -0.031 (-0.096 – 0.035) | -22 (20 – -7.2) |
| testland | 2203 (1122 – 4194) | Likely decreasing | 0.86 (0.62 – 1.2) | -0.031 (-0.096 – 0.033) | -22 (21 – -7.2) |
| realland | 2070 (1106 – 4154) | Likely decreasing | 0.85 (0.62 – 1.2) | -0.033 (-0.095 – 0.033) | -21 (21 – -7.3) |
| testland | 2153 (1124 – 4194) | Likely decreasing | 0.86 (0.62 – 1.2) | -0.032 (-0.094 – 0.035) | -22 (20 – -7.4) |

A range of plots are again returned (with the single summary plot shown
below).
Expand Down
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