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fix bounds of initial conditions for delays #474

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merged 4 commits into from Oct 19, 2023
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fix bounds of initial conditions for delays #474

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d11e851
fix bounds of initial conditions for delays
sbfnk Sep 22, 2023
b051673
Automatic readme update
actions-user Oct 12, 2023
8a85f23
remove obsolete line
sbfnk Oct 16, 2023
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add news item
sbfnk Oct 19, 2023
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1 change: 1 addition & 0 deletions NEWS.md
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Expand Up @@ -10,6 +10,7 @@

* Reduced the number of long-running examples. By @sbfnk in #459 and reviewed by @seabbs.
* Changed all instances of arguments that refer to the maximum of a distribution to reflect the maximum. Previously this did, in some instance, refer to the length of the PMF. By @sbfnk in #468.
* Fixed a bug in the bounds of delays when setting initial conditions. By @sbfnk in #474.

# EpiNow2 1.4.0

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5 changes: 4 additions & 1 deletion R/create.R
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Expand Up @@ -513,8 +513,11 @@ create_initial_conditions <- function(data) {
init_fun <- function() {
out <- list()
if (data$delay_n_p > 0) {
lower_bounds <- rep(-Inf, data$delay_n_p)
## gamma
lower_bounds[data$dist == 1] <- 0
out$delay_mean <- array(truncnorm::rtruncnorm(
n = data$delay_n_p, a = 0,
n = data$delay_n_p, a = lower_bounds,
mean = data$delay_mean_mean, sd = data$delay_mean_sd * 0.1
))
out$delay_sd <- array(truncnorm::rtruncnorm(
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96 changes: 48 additions & 48 deletions README.md
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Expand Up @@ -260,33 +260,33 @@ parameters at the latest date partially supported by data.
knitr::kable(summary(estimates))
```

| measure | estimate |
|:--------------------------------------|:----------------------|
| New confirmed cases by infection date | 2297 (1134 – 4496) |
| Expected change in daily cases | Likely decreasing |
| Effective reproduction no. | 0.89 (0.62 – 1.2) |
| Rate of growth | -0.027 (-0.1 – 0.039) |
| Doubling/halving time (days) | -26 (18 – -6.8) |
| measure | estimate |
|:--------------------------------------|:-----------------------|
| New confirmed cases by infection date | 2250 (1129 – 4224) |
| Expected change in daily cases | Likely decreasing |
| Effective reproduction no. | 0.88 (0.61 – 1.2) |
| Rate of growth | -0.028 (-0.11 – 0.036) |
| Doubling/halving time (days) | -25 (19 – -6.6) |

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 2.155254 2.161351 0.14517723 1.937754
#> 2: 2020-02-23 R NA estimate 2.121975 2.127980 0.12100600 1.935764
#> 3: 2020-02-24 R NA estimate 2.088968 2.092729 0.10097692 1.928174
#> 4: 2020-02-25 R NA estimate 2.054719 2.055714 0.08483110 1.920837
#> 5: 2020-02-26 R NA estimate 2.016873 2.017134 0.07230558 1.901956
#> 6: 2020-02-27 R NA estimate 1.977156 1.977250 0.06313689 1.875373
#> 1: 2020-02-22 R NA estimate 2.165168 2.172162 0.14593854 1.941092
#> 2: 2020-02-23 R NA estimate 2.131549 2.136040 0.11998939 1.941084
#> 3: 2020-02-24 R NA estimate 2.097955 2.098431 0.09900182 1.935873
#> 4: 2020-02-25 R NA estimate 2.060349 2.059484 0.08271136 1.925641
#> 5: 2020-02-26 R NA estimate 2.020232 2.019406 0.07061650 1.907712
#> 6: 2020-02-27 R NA estimate 1.978571 1.978434 0.06200852 1.876838
#> lower_50 lower_20 upper_20 upper_50 upper_90
#> 1: 2.065064 2.121331 2.191464 2.249999 2.402681
#> 2: 2.046891 2.096318 2.154105 2.204012 2.331598
#> 3: 2.024262 2.065044 2.116088 2.157788 2.260738
#> 4: 1.997118 2.033391 2.076033 2.111222 2.193523
#> 5: 1.967295 1.998732 2.035722 2.064998 2.133431
#> 6: 1.932713 1.961310 1.993938 2.019524 2.079810
#> 1: 2.072901 2.130679 2.202326 2.268532 2.422487
#> 2: 2.053218 2.102913 2.163595 2.215637 2.339445
#> 3: 2.030270 2.072284 2.121847 2.164987 2.260809
#> 4: 2.003278 2.036221 2.081113 2.114809 2.195010
#> 5: 1.971672 2.001096 2.038018 2.067643 2.136014
#> 6: 1.935102 1.961685 1.995176 2.019346 2.079872
```

Reported cases are returned in a separate data frame in order to
Expand All @@ -295,19 +295,19 @@ 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 64 65.9345 18.66876 40.00 53 60
#> 2: 2020-02-23 gp_rt 77 79.2645 21.46606 48.00 64 72
#> 3: 2020-02-24 gp_rt 76 78.7490 21.98367 48.00 64 71
#> 4: 2020-02-25 gp_rt 74 76.7340 21.21429 45.95 62 69
#> 5: 2020-02-26 gp_rt 79 81.5060 22.30854 50.00 65 74
#> 6: 2020-02-27 gp_rt 113 115.6395 30.70588 70.00 94 105
#> 1: 2020-02-22 gp_rt 64 65.8305 17.79986 41 53 60
#> 2: 2020-02-23 gp_rt 77 78.5915 21.24272 47 64 72
#> 3: 2020-02-24 gp_rt 76 77.9760 21.13539 47 63 71
#> 4: 2020-02-25 gp_rt 74 75.8540 20.46272 47 61 69
#> 5: 2020-02-26 gp_rt 79 80.8435 20.94625 50 66 74
#> 6: 2020-02-27 gp_rt 113 115.5645 29.60269 72 96 105
#> upper_20 upper_50 upper_90
#> 1: 68 76 100.00
#> 2: 83 92 117.05
#> 3: 82 91 120.00
#> 4: 80 89 115.00
#> 5: 85 95 120.00
#> 6: 120 134 171.00
#> 1: 68 76 98.00
#> 2: 82 91 115.00
#> 3: 82 91 116.00
#> 4: 79 89 112.00
#> 5: 84 94 118.00
#> 6: 120 134 167.05
```

A range of plots are returned (with the single summary plot shown
Expand Down Expand Up @@ -356,19 +356,19 @@ estimates <- regional_epinow(
gp = NULL,
stan = stan_opts(cores = 4, warmup = 250, samples = 1000)
)
#> INFO [2023-10-11 14:51:31] Producing following optional outputs: regions, summary, samples, plots, latest
#> INFO [2023-10-11 14:51:31] Reporting estimates using data up to: 2020-04-21
#> INFO [2023-10-11 14:51:31] No target directory specified so returning output
#> INFO [2023-10-11 14:51:31] Producing estimates for: testland, realland
#> INFO [2023-10-11 14:51:31] Regions excluded: none
#> INFO [2023-10-11 14:51:54] Completed estimates for: testland
#> INFO [2023-10-11 14:52:19] Completed estimates for: realland
#> INFO [2023-10-11 14:52:19] Completed regional estimates
#> INFO [2023-10-11 14:52:19] Regions with estimates: 2
#> INFO [2023-10-11 14:52:19] Regions with runtime errors: 0
#> INFO [2023-10-11 14:52:19] Producing summary
#> INFO [2023-10-11 14:52:19] No summary directory specified so returning summary output
#> INFO [2023-10-11 14:52:19] No target directory specified so returning timings
#> INFO [2023-10-12 13:04:43] Producing following optional outputs: regions, summary, samples, plots, latest
#> INFO [2023-10-12 13:04:43] Reporting estimates using data up to: 2020-04-21
#> INFO [2023-10-12 13:04:43] No target directory specified so returning output
#> INFO [2023-10-12 13:04:43] Producing estimates for: testland, realland
#> INFO [2023-10-12 13:04:43] Regions excluded: none
#> INFO [2023-10-12 13:05:08] Completed estimates for: testland
#> INFO [2023-10-12 13:05:31] Completed estimates for: realland
#> INFO [2023-10-12 13:05:31] Completed regional estimates
#> INFO [2023-10-12 13:05:31] Regions with estimates: 2
#> INFO [2023-10-12 13:05:31] Regions with runtime errors: 0
#> INFO [2023-10-12 13:05:31] Producing summary
#> INFO [2023-10-12 13:05:31] No summary directory specified so returning summary output
#> INFO [2023-10-12 13:05:32] No target directory specified so returning timings
```

Results from each region are stored in a `regional` list with across
Expand All @@ -391,10 +391,10 @@ output.
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 | 2199 (1118 – 4254) | Likely decreasing | 0.87 (0.63 – 1.2) | -0.03 (-0.098 – 0.038) | -23 (18 – -7.1) |
| testland | 2132 (1079 – 4492) | Likely decreasing | 0.86 (0.61 – 1.2) | -0.032 (-0.1 – 0.038) | -21 (18 – -6.6) |
| Region | New confirmed cases by infection date | Expected change in daily cases | Effective reproduction no. | Rate of growth | Doubling/halving time (days) |
|:---------|:--------------------------------------|:-------------------------------|:---------------------------|:------------------------|:-----------------------------|
| realland | 2128 (1143 – 4078) | Likely decreasing | 0.87 (0.64 – 1.2) | -0.032 (-0.095 – 0.033) | -22 (21 – -7.3) |
| testland | 2155 (1133 – 4435) | Likely decreasing | 0.87 (0.64 – 1.2) | -0.032 (-0.097 – 0.038) | -22 (18 – -7.2) |

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