Getting started with EpiNow2

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 supply 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:
#>     0.47

For 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:
#>         0.069

Users can also pass a non-parametric delay distribution vector using the NonParametric option for both the generation interval and reporting delays. It is important to note that if doing so, both delay distributions are 0-indexed, meaning the first element corresponds to the probability mass at day 0 of an individual’s infection. Because the discretised renewal equation doesn’t support mass on day 0, the generation interval should be passed in as a 0-indexed vector with a mass of zero on day 0.

example_non_parametric_gi <-  NonParametric(pmf = c(0, 0.3, 0.5, 0.2))

example_non_parametric_delay <- NonParametric(pmf = c(0.01, 0.1, 0.5, 0.3, 0.09))

These distributions are passed to downstream functions in the same way that the parametric distributions are.

Now, 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      78

Estimate 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 = gt_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	2235 (1258 – 4079)
Expected change in daily reports	Likely decreasing
Effective reproduction no.	0.89 (0.69 – 1.1)
Rate of growth	-0.029 (-0.1 – 0.049)
Doubling/halving time (days)	-24 (14 – -6.9)

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 2.295630 2.300011 0.14226384 2.072498
#> 2: 2020-02-23        R   <NA> estimate 2.254414 2.260309 0.12775375 2.058350
#> 3: 2020-02-24        R   <NA> estimate 2.213859 2.218421 0.11582310 2.039173
#> 4: 2020-02-25        R   <NA> estimate 2.167609 2.174463 0.10645004 2.011138
#> 5: 2020-02-26        R   <NA> estimate 2.119388 2.128587 0.09939624 1.977938
#> 6: 2020-02-27        R   <NA> estimate 2.072939 2.080978 0.09424020 1.942162
#>    lower_50 lower_20 upper_20 upper_50 upper_90
#>       <num>    <num>    <num>    <num>    <num>
#> 1: 2.199171 2.257930 2.331979 2.393862 2.536167
#> 2: 2.170840 2.220883 2.287825 2.346032 2.475402
#> 3: 2.137291 2.182338 2.242451 2.297515 2.410503
#> 4: 2.099378 2.138842 2.196990 2.246167 2.354895
#> 5: 2.058774 2.094525 2.147410 2.192443 2.298576
#> 6: 2.014358 2.047728 2.098028 2.142222 2.244473

Reported 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     75  77.7545 22.45421       46    62.00       70
#> 2: 2020-02-23  gp_rt     87  89.3255 24.15807       53    73.00       82
#> 3: 2020-02-24  gp_rt     86  88.5850 23.75963       54    72.00       81
#> 4: 2020-02-25  gp_rt     80  82.0745 22.36889       49    66.00       75
#> 5: 2020-02-26  gp_rt     81  82.8155 22.64243       50    67.75       76
#> 6: 2020-02-27  gp_rt    107 110.9325 29.73030       66    90.00      101
#>    upper_20 upper_50 upper_90
#>       <num>    <num>    <num>
#> 1:       81       91      118
#> 2:       93      104      132
#> 3:       92      103      132
#> 4:       86       96      120
#> 5:       86       96      124
#> 6:      115      129      163

A 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 plot_estimates

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 testland

Calling 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 = gt_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 [2024-10-15 17:53:24] Producing following optional outputs: regions, summary, samples, plots, latest
#> INFO [2024-10-15 17:53:24] Reporting estimates using data up to: 2020-04-21
#> INFO [2024-10-15 17:53:24] No target directory specified so returning output
#> INFO [2024-10-15 17:53:24] Producing estimates for: testland, realland
#> INFO [2024-10-15 17:53:24] Regions excluded: none
#> INFO [2024-10-15 17:53:46] Completed estimates for: testland
#> INFO [2024-10-15 17:54:09] Completed estimates for: realland
#> INFO [2024-10-15 17:54:09] Completed regional estimates
#> INFO [2024-10-15 17:54:09] Regions with estimates: 2
#> INFO [2024-10-15 17:54:09] Regions with runtime errors: 0
#> INFO [2024-10-15 17:54:09] Producing summary
#> INFO [2024-10-15 17:54:09] No summary directory specified so returning summary output
#> INFO [2024-10-15 17:54:10] No target directory specified so returning timings

Results 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	2107 (1035 – 4584)	Likely decreasing	0.87 (0.62 – 1.2)	-0.037 (-0.11 – 0.049)	-19 (14 – -6.2)
testland	2084 (1062 – 4392)	Likely decreasing	0.85 (0.61 – 1.2)	-0.04 (-0.11 – 0.048)	-18 (15 – -6.4)

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

estimates$summary$summary_plot

plot of chunk plot_regional_epinow_summary