1 Overview


Here we give a high-level overview of the workflow required for defining and fitting a model with epidemia. The primary model fitting function is epim(). This takes a model description and additional arguments relating to the fitting algorithm, and proceeds to fit the model using a precompiled Stan program. This allows model fitting to begin immediately as opposed to requiring compilation each time epim() is called.

This is similar to the workflow for fitting Bayesian regression models with rstanarm. A key difference, however, is that the models fit by epidemia are much more complex, and are therefore inherently more difficult to specify. epidemia aims to simplify this process by modularizing the model definition into three distinct parts: transmission, infections and observations. These components of the model are defined with the functions epirt(), epiinf() and epiobs() respectively.

epidemia contains an example dataset EuropeCovid which contains data on daily death counts from Covid-19 in 11 European Countries from February through May 2020, and a set of binary indicators of non-pharmaceutical interventions. This is used as an example throughout.

library(dplyr)
library(epidemia)
library(rstanarm)
data("EuropeCovid")

We begin by describing epim() in more detail, and then proceed to discuss the three modeling functions.

2 Model Fitting


epim() is the only model fitting function in epidemia. It has arguments rt, inf, and obs which expect a description of the transmission model, infection model and all observational models respectively. Together, these fully define the joint distribution of data and parameters. Each of these model components are described in terms of variables that are expected to live in a single dataframe, data. This dataframe must be compatible with the model components, in the sense that it holds all variables defined in these models. For our example, these variables are the following.

data <- EuropeCovid$data
colnames(data)
## [1] "country"                      "date"                        
## [3] "schools_universities"         "self_isolating_if_ill"       
## [5] "public_events"                "lockdown"                    
## [7] "social_distancing_encouraged" "deaths"                      
## [9] "pop"

The data argument is described in more detail in Section 6.

In addition to taking a model description and a dataframe, epim() has various additional arguments which specify how the model should be fit. If algorithm = "sampling" then the model will be fit using Stan’s adaptive Hamiltonian Monte Carlo sampler. This is done internally by calling rstan::sampling. If algorithm = "meanfield" or algorithm = "fullrank", then Stan’s variational Bayes algorithms are used instead, by calling rstan::vb. Any unnamed arguments in the call to epim() are passed directly onto the rstan sampling function. epim() returns a fitted model object of class "epimodel", which contains posterior samples from the model along with other useful objects.

In general, the adaptive Hamiltonian Monte Carlo sampler should be used for final inference. Nonetheless, fitting these models using HMC is often computationally demanding, and variational Bayes can often be fruitful for quickly iterating models. All arguments for epim() are described in Table 2.1.

Table 2.1: Formal arguments for epim()
Argument Description
rt An object of class "epirt", resulting from a call to epirt(). This defines the model for reproduction numbers \(R\).
inf An object of class "epiinf", resulting from a call to epiinf(). This entirely defines the model for infections \(i_t\).)
obs Either an object of class "epiobs", or a list of such objects. Each element of the list defines a model for an observed variable.
data A dataframe with all data required for fitting the model. This includes all observation variables and covariates specified in the models for the reproduction number and ascertainment rates.
algorithm One of "sampling", "meanfield" or "fullrank". This determines the rstan sampling function to use for fitting the model. "sampling" corresponds to an adaptive HMC sampler, while "meanfield" and "fullrank" are both variational Bayes algorithms.
group_subset If specified, a character vector naming a subset of regions to include in the model.
prior_PD Same as in rstan::stan_glm. If TRUE, samples all parameters from their prior distributions. This is useful for prior predictive checks. Defaults to FALSE.
Additional arguments to pass to the rstan function used to fit the model. If algorithm = "sampling", then this function is rstan::sampling. Otherwise rstan::vb is used.Please see the documentation for these functions.

We now describe the three modeling functions in more detail, starting with epirt().

3 Transmission


epirt() defines the model for time-varying reproduction numbers, which was described in Section 4 of the model description article. It has a formula argument which defines the linear predictor \(\eta\), an argument link defining the link function g, and additional arguments to specify priors on parameters making up \(\eta\).

A general R formula gives a symbolic description of a model. It takes the form y ~ model, where y is the response and model is a collection of terms separated by the + operator. model fully defines a linear predictor used to predict y. In this case, the “response” being modeled are reproduction numbers which are unobserved. epirt therefore requires that the left hand side of the formula takes the form R(group, date), where group and date refer to variables representing the region and date respectively. The right hand side can consist of fixed effects, random effects, and autocorrelation terms. For our example, a viable call to epirt() is the following.

rt <- epirt(
  R(country, date) ~ 1 + lockdown + public_events,
  link = scaled_logit(7)
)

In the above example, two fixed effects are included which represent the effects of lockdown and public events. These effects are assumed constant across countries. They could alternatively be partially pooled by using the term (lockdown + public_events | country). For information on how to interpret such terms, please read the partial-pooling article. Using link = scaled_logit(7) lets the link function be the scaled logit link described in the model description article (Equation 4.2), where \(K = 7\) is maximum possible value for reproduction numbers. For simplicity, we have omitted any prior arguments, however these should generally be specified explicitly. Please see here for detailed information on how to use priors. All arguments for epirt() are listed in Table 3.1.

Table 3.1: Formal arguments for epirt()
Argument Description
formula An object of class "formula" which determines the linear predictor \(\eta\) for \(R\). The left hand side must take the form R(group, date), where group and date variables. group must be a factor vector indicating group membership (i.e. country, state, age cohort), and date must be a vector of class "Date". This is syntactic sugar for the reproduction number in the given group at the give date.
link The link function \(g\). Can be "log", "identity" or a call to scaled_logit(). Defaults to log.
center If TRUE, covariates in formula are centered to have mean zero. All priors should then be interpreted as priors on the centered covariates.
prior Same as in rstanarm::stan_glm. Defines the prior on \(\beta\). rstanarm provided priors, a shifted_gamma can be used. Note if autoscale=TRUE in the call to the prior function, then automatic rescaling takes place.
prior_intercept Same as in rstanarm::stan_glm. Prior for the regression intercept \(\beta_0\) (if it exists).
prior_covariance Same as in rstanarm::stan_glmer. Defines the prior on the covariance matrix \(\Sigma\). Only use if the formula has one or more terms of the form (x | y), in which case there are parameters to partially pool, i.e. \(b\) has positive length.

4 Infections


The model for infections is represented by epiinf(). For the basic version of the model, this defines the generation distribution of the disease, the number of days for which to seed infections, and the prior distribution on the parameter \(\tau\) (Equation 3.2). Recall that \(\tau\) is the prior mean on daily seeded infections. These three parameters are controlled by the arguments gen, seed_days and prior_tau respectively. For our example, a possible model is the following.

inf <- epiinf(
  gen = EuropeCovid$si,
  seed_days = 6L,
  prior_tau = rstanarm::exponential(0.02)
)

EuropeCovid$si is a numeric vector representing the probability mass function for the serial interval of Covid-19. Here, we are implicitly assuming that the generation distribution can be approximated well by the serial interval. In this example, \(\tau\) is given an exponential prior with a mean of 50. These seeds occur over a period of 6 days.

epiinf() has additional arguments which allow the user to extend the basic model. Using latent=TRUE replaces the renewal process (Equation 1.3) with Equation 5.1. Daily infections are then treated as latent parameters that are sampled along with other parameters. The family argument then gives the distribution for \(p(i'_t, d)\), while prior_aux defines the prior on the coefficient of dispersion \(d\).

Recall that one can adjust the infection process to explicitly model changes in infection rates as the remaining susceptible population is depleted. In particular, the adjustment ensures that cumulative infections never breaches the initial susceptible population. The adjustment was described in Section 5.3 of the model description article. It can be employed by setting pop_adjust = TRUE and using the susceptibles argument to point towards a variable in the dataframe which gives the susceptible population at each point in time. All argument to epiinf() are described in Table 4.1.

Table 4.1: Formal arguments for epiinf()
Argument Description
gen A numeric vector giving the probability mass function \(g_k\) of the generation distribution. Must be a simplex vector, i.e. nonnegative and summing to 1.
seed_days An integer giving the number of seed days \(v + 1\). Defaults to 6L.
latent If TRUE, treat infections as latent parameters using the extensions described in Section 5.2.
family Specifies the family for \(p(i'_t, d)\). Only used if latent = TRUE, and currently restricted to log-normal.
prior_aux Prior on the coefficient of variation \(d\).
prior_tau Prior distribution for the hyperparameter \(\tau\), which is the mean of the prior distribution for infection seeding. Defaults to rstanarm::exponential(0.03).
pop_adjust If TRUE, applies a population adjustment to the infection process \(i_t\). Defaults to FALSE.
susceptibles A character vector giving the name of the variable corresponding to the susceptible population over time. Only used if pop_adjust=TRUE.

5 Observations


Each observational model is given by a call to epiobs(). In particular, this must define the model for ascertainment rates \(\alpha\) and the time distribution from infection to observation \(\pi\). epiobs() has a formula argument. The left hand side must define the observation vector \(Y\) which is to be modeled, while the right hand side defines a linear predictor for the ascertainment rate \(\alpha\). The argument i2o plays a similar role to the gen argument in epiinf(), however it instead defines the vector \(\pi\) in Equation (1.2).

Suppose we wish to model daily deaths, which as we saw is a variable in data. One could use the following.

deaths <- epiobs(
  deaths ~ 1,
  i2o = EuropeCovid$inf2death,
  link = scaled_logit(0.02)
)

The above models the infection fatality rate, \(\alpha\), as an intercept transformed by the scaled logit link. This implies that it is constant over time, can achieve a maximum value of 2%, and a minimum value of 0%. If prior_intercept is chosen to be symmetric around zero, then the prior mean of \(\alpha\) is 1%. EuropeCovid$inf2death is a numeric simplex vector that gives the same delay distribution as used in Flaxman et al. (2020), which is a discretized p.d.f. of a mixture of Gamma random variables.

Additional arguments include family, which specifies the sampling distribution \(p(y_t, \phi)\). There are also arguments allowing the user to control prior distributions for parameters describing \(\alpha\), and the prior on the auxiliary variable \(\phi\). All arguments to epiobs() are shown in Table 5.1.

Table 5.1: Formal arguments for epiobs()
Argument Description
formula An object of class "formula" which determines the linear predictor for the ascertainment rate for a particular observation vector. The left hand side must define the response that is being modeled (i.e. the actual observations, not the latent ascertainment rates)in a given country on a given date. obs refers to the response variable to be modeled.
i2o A numeric (simplex) vector defining the probability mass function \(\pi_k\) of the time distribution from infection to observation.
family A string representing the family of the sampling distribution \(p(y_t,\phi)\). Can be one of "poisson", "neg_binom", "quasi_poisson", "normal" or "log_normal".
link A string representing the link function used to transform the linear predictor. Can be one of "logit", "probit", "cauchit", "cloglog", "identity". Defaults to "logit".
center, prior, prior_intercept same as in epirt(), described above.
prior_aux The prior distribution for the auxiliary parameter \(\phi\), if it exists. Only used if family is "neg_binom" (reciprocal dispersion), "quasi_poisson" (dispersion), "normal" (standard deviation) or "log_normal" (sigma parameter).
... Additional arguments for model.frame.

6 Data


Recall that the data argument to epim() must contain all variables used in the transmission, infection and observational models. For our example, this looks like

data
## # A tibble: 899 x 9
## # Groups:   country [11]
##    country date       schools_universi… self_isolating_i… public_events lockdown
##    <fct>   <date>                 <int>             <int>         <int>    <int>
##  1 Austria 2020-02-22                 0                 0             0        0
##  2 Austria 2020-02-23                 0                 0             0        0
##  3 Austria 2020-02-24                 0                 0             0        0
##  4 Austria 2020-02-25                 0                 0             0        0
##  5 Austria 2020-02-26                 0                 0             0        0
##  6 Austria 2020-02-27                 0                 0             0        0
##  7 Austria 2020-02-28                 0                 0             0        0
##  8 Austria 2020-02-29                 0                 0             0        0
##  9 Austria 2020-03-01                 0                 0             0        0
## 10 Austria 2020-03-02                 0                 0             0        0
## # … with 889 more rows, and 3 more variables:
## #   social_distancing_encouraged <int>, deaths <int>, pop <int>

The columns country and date define the region and time period corresponding to each of the remaining variables. epim() assumes that the first seeding day (i.e. the start of the epidemic) in each region is the first date found in the dataframe. The last date is the final date at which the epidemic is simulated for the group. It is up to the user to appropriately choose these dates. For our example, the first and last dates for each group can be seen as follows.

summarise(data, start = min(date), end = max(date))
## # A tibble: 11 x 3
##    country        start      end       
##  * <fct>          <date>     <date>    
##  1 Austria        2020-02-22 2020-05-05
##  2 Belgium        2020-02-18 2020-05-05
##  3 Denmark        2020-02-21 2020-05-05
##  4 France         2020-02-07 2020-05-05
##  5 Germany        2020-02-15 2020-05-05
##  6 Italy          2020-01-27 2020-05-05
##  7 Norway         2020-02-24 2020-05-05
##  8 Spain          2020-02-09 2020-05-05
##  9 Sweden         2020-02-18 2020-05-05
## 10 Switzerland    2020-02-14 2020-05-05
## 11 United_Kingdom 2020-02-13 2020-05-05

These start dates are 30 days prior to observing 10 cumulative deaths in each country.

7 A First Fit

We are ready to fit out first model. This is done by returning to the model fitting function epim(). Our call is as follows. Note that we use refresh=0 to suppress the algorithm printing output in this article - however this should be disabled when you run models for yourself as this output is useful.

fm <- epim(
  rt = rt,
  inf = inf,
  obs = deaths,
  data = data,
  group_subset = "France",
  algorithm = "fullrank",
  tol_rel_obj = 1e-3,
  seed = 12345,
  refresh = 0
)
## Warning: Pareto k diagnostic value is 0.76. Resampling is unreliable. Increasing
## the number of draws or decreasing tol_rel_obj may help.
## Registered S3 methods overwritten by 'car':
##   method                          from
##   influence.merMod                lme4
##   cooks.distance.influence.merMod lme4
##   dfbeta.influence.merMod         lme4
##   dfbetas.influence.merMod        lme4

plot_obs(fm, type = "deaths")

8 References

Flaxman, Seth, Swapnil Mishra, Axel Gandy, H Juliette T Unwin, Thomas A Mellan, Helen Coupland, Charles Whittaker, et al. 2020. “Estimating the effects of non-pharmaceutical interventions on COVID-19 in Europe.” Nature. https://doi.org/10.1038/s41586-020-2405-7.