Quick start
In the following section we give an overview of the simple use case for epinow() and regional_epinow().
The first step to using the package is to load it as follows.
library(EpiNow2)Reporting delays, incubation period and generation time
Distributions can be supplied in two ways. First, one can supplying delay data to estimate_delay(), where a subsampled bootstrapped lognormal will be fit to account for uncertainty in the observed data without being biased by changes in incidence (see ?EpiNow2::estimate_delay()).
Second, one can specify predetermined delays with uncertainty using the distribution functions such as Gamma or Lognormal. An arbitrary number of delay distributions are supported in dist_spec() with a common use case being an incubation period followed by a reporting delay. For more information on specifying distributions see (see ?EpiNow2::Distributions).
For example if data on the delay between onset and infection was available we could fit a distribution to it, using estimate_delay(), with appropriate uncertainty as follows (note this is a synthetic example),
reporting_delay <- estimate_delay(
rlnorm(1000, log(2), 1),
max_value = 14, bootstraps = 1
)If data was not available we could instead specify an informed estimate of the likely delay using the distribution functions Gamma or LogNormal. To demonstrate, we choose a lognormal distribution with mean 2, standard deviation 1 and a maximum of 10. This is just an example and unlikely to apply in any particular use case.
reporting_delay <- LogNormal(mean = 2, sd = 1, max = 10)
reporting_delay
#> - lognormal distribution (max: 10):
#> meanlog:
#> 0.58
#> sdlog:
#> 0.47For the rest of this vignette, we will use inbuilt example literature estimates for the incubation period and generation time of Covid-19 (see here for the code that generates these estimates). These distributions are unlikely to be applicable for your use case. We strongly recommend investigating what might be the best distributions to use in any given use case.
example_generation_time
#> - gamma distribution (max: 14):
#> shape:
#> - normal distribution:
#> mean:
#> 1.4
#> sd:
#> 0.48
#> rate:
#> - normal distribution:
#> mean:
#> 0.38
#> sd:
#> 0.25
example_incubation_period
#> - lognormal distribution (max: 14):
#> meanlog:
#> - normal distribution:
#> mean:
#> 1.6
#> sd:
#> 0.064
#> sdlog:
#> - normal distribution:
#> mean:
#> 0.42
#> sd:
#> 0.069Now, to the functions.
epinow()
This function represents the core functionality of the package and includes results reporting, plotting, and optional saving. It requires a data frame of cases by date of report and the distributions defined above.
Load example case data from {EpiNow2}.
reported_cases <- example_confirmed[1:60]
head(reported_cases)
#> date confirm
#> <Date> <num>
#> 1: 2020-02-22 14
#> 2: 2020-02-23 62
#> 3: 2020-02-24 53
#> 4: 2020-02-25 97
#> 5: 2020-02-26 93
#> 6: 2020-02-27 78Estimate cases by date of infection, the time-varying reproduction number, the rate of growth, and forecast these estimates into the future by 7 days. Summarise the posterior and return a summary table and plots for reporting purposes. If a target_folder is supplied results can be internally saved (with the option to also turn off explicit returning of results). Here we use the default model parameterisation that prioritises real-time performance over run-time or other considerations. For other formulations see the documentation for estimate_infections().
estimates <- epinow(
data = reported_cases,
generation_time = generation_time_opts(example_generation_time),
delays = delay_opts(example_incubation_period + reporting_delay),
rt = rt_opts(prior = list(mean = 2, sd = 0.2)),
stan = stan_opts(cores = 4, control = list(adapt_delta = 0.99)),
verbose = interactive()
)
names(estimates)
#> [1] "estimates" "estimated_reported_cases"
#> [3] "summary" "plots"
#> [5] "timing"Both summary measures and posterior samples are returned for all parameters in an easily explored format which can be accessed using summary. The default is to return a summary table of estimates for key parameters at the latest date partially supported by data.
knitr::kable(summary(estimates))| measure | estimate |
|---|---|
| New infections per day | 2199 (962 – 4757) |
| Expected change in daily reports | Likely decreasing |
| Effective reproduction no. | 0.88 (0.58 – 1.2) |
| Rate of growth | -0.034 (-0.15 – 0.076) |
| Doubling/halving time (days) | -20 (9.1 – -4.6) |
Summarised parameter estimates can also easily be returned, either filtered for a single parameter or for all parameters.
head(summary(estimates, type = "parameters", params = "R"))
#> date variable strat type median mean sd lower_90
#> <Date> <char> <char> <char> <num> <num> <num> <num>
#> 1: 2020-02-22 R <NA> estimate 2.288484 2.293707 0.1613209 2.044132
#> 2: 2020-02-23 R <NA> estimate 2.254878 2.259642 0.1403568 2.040359
#> 3: 2020-02-24 R <NA> estimate 2.217611 2.222709 0.1251234 2.026980
#> 4: 2020-02-25 R <NA> estimate 2.174854 2.182984 0.1150322 2.002758
#> 5: 2020-02-26 R <NA> estimate 2.132196 2.140643 0.1089983 1.974475
#> 6: 2020-02-27 R <NA> estimate 2.088958 2.095945 0.1056741 1.933753
#> lower_50 lower_20 upper_20 upper_50 upper_90
#> <num> <num> <num> <num> <num>
#> 1: 2.181696 2.246458 2.328439 2.398968 2.574407
#> 2: 2.162459 2.217716 2.289158 2.349965 2.508728
#> 3: 2.136181 2.184912 2.247679 2.303535 2.440930
#> 4: 2.101307 2.148035 2.204825 2.256175 2.381675
#> 5: 2.064946 2.108764 2.160005 2.207901 2.331636
#> 6: 2.023783 2.062603 2.114298 2.159626 2.285821Reported cases are returned in a separate data frame in order to streamline the reporting of forecasts and for model evaluation.
head(summary(estimates, output = "estimated_reported_cases"))
#> date type median mean sd lower_90 lower_50 lower_20
#> <Date> <char> <num> <num> <num> <num> <num> <num>
#> 1: 2020-02-22 gp_rt 74.0 76.9430 21.47422 46 62 70.0
#> 2: 2020-02-23 gp_rt 87.0 89.5820 24.71017 54 72 82.0
#> 3: 2020-02-24 gp_rt 86.0 88.6670 24.76764 53 71 80.6
#> 4: 2020-02-25 gp_rt 81.0 82.6625 22.56520 49 66 75.0
#> 5: 2020-02-26 gp_rt 79.0 81.8240 23.31905 48 65 75.0
#> 6: 2020-02-27 gp_rt 107.5 111.2375 30.27595 69 89 101.0
#> upper_20 upper_50 upper_90
#> <num> <num> <num>
#> 1: 79 89 116.00
#> 2: 92 104 135.00
#> 3: 92 103 133.00
#> 4: 87 96 121.00
#> 5: 85 96 121.05
#> 6: 115 129 166.00A range of plots are returned (with the single summary plot shown below). These plots can also be generated using the following plot method.
plot(estimates)
plot of chunk unnamed-chunk-11
regional_epinow()
The regional_epinow() function runs the epinow() function across multiple regions in an efficient manner.
Define cases in multiple regions delineated by the region variable.
reported_cases <- data.table::rbindlist(list(
data.table::copy(reported_cases)[, region := "testland"],
reported_cases[, region := "realland"]
))
head(reported_cases)
#> date confirm region
#> <Date> <num> <char>
#> 1: 2020-02-22 14 testland
#> 2: 2020-02-23 62 testland
#> 3: 2020-02-24 53 testland
#> 4: 2020-02-25 97 testland
#> 5: 2020-02-26 93 testland
#> 6: 2020-02-27 78 testlandCalling regional_epinow() runs the epinow() on each region in turn (or in parallel depending on the settings used). Here we switch to using a weekly random walk rather than the full Gaussian process model giving us piecewise constant estimates by week.
estimates <- regional_epinow(
data = reported_cases,
generation_time = generation_time_opts(example_generation_time),
delays = delay_opts(example_incubation_period + reporting_delay),
rt = rt_opts(prior = list(mean = 2, sd = 0.2), rw = 7),
gp = NULL,
stan = stan_opts(cores = 4, warmup = 250, samples = 1000)
)
#> INFO [2024-05-10 07:58:14] Producing following optional outputs: regions, summary, samples, plots, latest
#> INFO [2024-05-10 07:58:14] Reporting estimates using data up to: 2020-04-21
#> INFO [2024-05-10 07:58:14] No target directory specified so returning output
#> INFO [2024-05-10 07:58:14] Producing estimates for: testland, realland
#> INFO [2024-05-10 07:58:14] Regions excluded: none
#> INFO [2024-05-10 07:58:29] Completed estimates for: testland
#> INFO [2024-05-10 07:58:41] Completed estimates for: realland
#> INFO [2024-05-10 07:58:41] Completed regional estimates
#> INFO [2024-05-10 07:58:41] Regions with estimates: 2
#> INFO [2024-05-10 07:58:41] Regions with runtime errors: 0
#> INFO [2024-05-10 07:58:41] Producing summary
#> INFO [2024-05-10 07:58:41] No summary directory specified so returning summary output
#> INFO [2024-05-10 07:58:41] No target directory specified so returning timingsResults from each region are stored in a regional list with across region summary measures and plots stored in a summary list. All results can be set to be internally saved by setting the target_folder and summary_dir arguments. Each region can be estimated in parallel using the {future} package (when in most scenarios cores should be set to 1). For routine use each MCMC chain can also be run in parallel (with future = TRUE) with a time out (max_execution_time) allowing for partial results to be returned if a subset of chains is running longer than expected. See the documentation for the {future} package for details on nested futures.
Summary measures that are returned include a table formatted for reporting (along with raw results for further processing). Futures updated will extend the S3 methods used above to smooth access to this output.
knitr::kable(estimates$summary$summarised_results$table)| Region | New infections per day | Expected change in daily reports | Effective reproduction no. | Rate of growth | Doubling/halving time (days) |
|---|---|---|---|---|---|
| realland | 2060 (1007 – 4579) | Likely decreasing | 0.86 (0.59 – 1.2) | -0.039 (-0.12 – 0.056) | -18 (12 – -5.9) |
| testland | 2136 (1050 – 4356) | Likely decreasing | 0.86 (0.62 – 1.2) | -0.036 (-0.11 – 0.048) | -19 (14 – -6.4) |
A range of plots are again returned (with the single summary plot shown below).
estimates$summary$summary_plot
plot of chunk unnamed-chunk-15