make_config: Set and check parameter settings of estimate_R

Description Usage Arguments Details Value Examples

View source: R/make_config.R

Description

This function defines settings for estimate_R It takes a list of named items as input, set defaults where arguments are missing, and return a list of settings.

Usage

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make_config(
  ...,
  incid = NULL,
  method = c("non_parametric_si", "parametric_si", "uncertain_si", "si_from_data",
    "si_from_sample")
)

Arguments

...

Acceptable arguments for ... are:

t_start

Vector of positive integers giving the starting times of each window over which the reproduction number will be estimated. These must be in ascending order, and so that for all i, t_start[i]<=t_end[i]. t_start[1] should be strictly after the first day with non null incidence.

t_end

Vector of positive integers giving the ending times of each window over which the reproduction number will be estimated. These must be in ascending order, and so that for all i, t_start[i]<=t_end[i].

n1

For method "uncertain_si" and "si_from_data"; positive integer giving the size of the sample of SI distributions to be drawn (see details).

n2

For methods "uncertain_si", "si_from_data" and "si_from_sample"; positive integer giving the size of the sample drawn from the posterior distribution of R for each serial interval distribution considered (see details).

mean_si

For method "parametric_si" and "uncertain_si" ; positive real giving the mean serial interval (method "parametric_si") or the average mean serial interval (method "uncertain_si", see details).

std_si

For method "parametric_si" and "uncertain_si" ; non negative real giving the standard deviation of the serial interval (method "parametric_si") or the average standard deviation of the serial interval (method "uncertain_si", see details).

std_mean_si

For method "uncertain_si" ; standard deviation of the distribution from which mean serial intervals are drawn (see details).

min_mean_si

For method "uncertain_si" ; lower bound of the distribution from which mean serial intervals are drawn (see details).

max_mean_si

For method "uncertain_si" ; upper bound of the distribution from which mean serial intervals are drawn (see details).

std_std_si

For method "uncertain_si" ; standard deviation of the distribution from which standard deviations of the serial interval are drawn (see details).

min_std_si

For method "uncertain_si" ; lower bound of the distribution from which standard deviations of the serial interval are drawn (see details).

max_std_si

For method "uncertain_si" ; upper bound of the distribution from which standard deviations of the serial interval are drawn (see details).

si_distr

For method "non_parametric_si" ; vector of probabilities giving the discrete distribution of the serial interval, starting with si_distr[1] (probability that the serial interval is zero), which should be zero.

si_parametric_distr

For method "si_from_data" ; the parametric distribution to use when estimating the serial interval from data on dates of symptoms of pairs of infector/infected individuals (see details). Should be one of "G" (Gamma), "W" (Weibull), "L" (Lognormal), "off1G" (Gamma shifted by 1), "off1W" (Weibull shifted by 1), or "off1L" (Lognormal shifted by 1).

mcmc_control

An object of class estimate_R_mcmc_control, as returned by function make_mcmc_control.

seed

An optional integer used as the seed for the random number generator at the start of the function (then potentially reset within the MCMC for method si_from_data); useful to get reproducible results.

mean_prior

A positive number giving the mean of the common prior distribution for all reproduction numbers (see details).

std_prior

A positive number giving the standard deviation of the common prior distribution for all reproduction numbers (see details).

cv_posterior

A positive number giving the aimed posterior coefficient of variation (see details).

incid

As in functionestimate_R.

method

As in functionestimate_R.

Details

Analytical estimates of the reproduction number for an epidemic over predefined time windows can be obtained using function estimate_R, for a given discrete distribution of the serial interval. make_config allows to generate a configuration specifying the way the estimation will be performed.

The more incident cases are observed over a time window, the smallest the posterior coefficient of variation (CV, ratio of standard deviation over mean) of the reproduction number. An aimed CV can be specified in the argument cv_posterior (default is 0.3), and a warning will be produced if the incidence within one of the time windows considered is too low to get this CV.

The methods vary in the way the serial interval distribution is specified.

In short there are five methods to specify the serial interval distribution (see below for details on each method). In the first two methods, a unique serial interval distribution is considered, whereas in the last three, a range of serial interval distributions are integrated over:

———————– method "non_parametric_si" ——————-

The discrete distribution of the serial interval is directly specified in the argument si_distr.

———————– method "parametric_si" ———————–

The mean and standard deviation of the continuous distribution of the serial interval are given in the arguments mean_si and std_si. The discrete distribution of the serial interval is derived automatically using discr_si.

———————– method "uncertain_si" ———————–

Method "uncertain_si" allows accounting for uncertainty on the serial interval distribution as described in Cori et al. AJE 2013. We allow the mean μ and standard deviation σ of the serial interval to vary according to truncated normal distributions. We sample n1 pairs of mean and standard deviations, (μ^{(1)},σ^{(1)}),...,(μ^{(n_2)},σ^{(n_2)}), by first sampling the mean μ^{(k)} from its truncated normal distribution (with mean mean_si, standard deviation std_mean_si, minimum min_mean_si and maximum max_mean_si), and then sampling the standard deviation σ^{(k)} from its truncated normal distribution (with mean std_si, standard deviation std_std_si, minimum min_std_si and maximum max_std_si), but imposing that σ^{(k)}<μ^{(k)}. This constraint ensures that the Gamma probability density function of the serial interval is null at t=0. Warnings are produced when the truncated normal distributions are not symmetric around the mean. For each pair (μ^{(k)},σ^{(k)}), we then draw a sample of size n2 in the posterior distribution of the reproduction number over each time window, conditionally on this serial interval distribution. After pooling, a sample of size \code{n1}\times\code{n2} of the joint posterior distribution of the reproduction number over each time window is obtained. The posterior mean, standard deviation, and 0.025, 0.05, 0.25, 0.5, 0.75, 0.95, 0.975 quantiles of the reproduction number for each time window are obtained from this sample.

———————– method "si_from_data" ———————–

Method "si_from_data" allows accounting for uncertainty on the serial interval distribution. Unlike method "uncertain_si", where we arbitrarily vary the mean and std of the SI in truncated normal distributions, here, the scope of serial interval distributions considered is directly informed by data on the (potentially censored) dates of symptoms of pairs of infector/infected individuals. This data, specified in argument si_data, should be a dataframe with 5 columns:

Assuming a given parametric distribution for the serial interval distribution (specified in si_parametric_distr), the posterior distribution of the serial interval is estimated directly from these data using MCMC methods implemented in the package coarsedatatools. The argument mcmc_control is a list of characteristics which control the MCMC. The MCMC is run for a total number of iterations of mcmc_control$burnin + n1*mcmc_control$thin; but the output is only recorded after the burnin, and only 1 in every mcmc_control$thin iterations, so that the posterior sample size is n1. For each element in the posterior sample of serial interval distribution, we then draw a sample of size n2 in the posterior distribution of the reproduction number over each time window, conditionally on this serial interval distribution. After pooling, a sample of size \code{n1}\times\code{n2} of the joint posterior distribution of the reproduction number over each time window is obtained. The posterior mean, standard deviation, and 0.025, 0.05, 0.25, 0.5, 0.75, 0.95, 0.975 quantiles of the reproduction number for each time window are obtained from this sample.

———————– method "si_from_sample" ———————-

Method "si_from_sample" also allows accounting for uncertainty on the serial interval distribution. Unlike methods "uncertain_si" and "si_from_data", the user directly provides (in argument si_sample) a sample of serial interval distribution to be explored.

Value

An object of class estimate_R_config with components t_start, t_end, n1, n2, mean_si, std_si, std_mean_si, min_mean_si, max_mean_si, std_std_si, min_std_si, max_std_si, si_distr, si_parametric_distr, mcmc_control, seed, mean_prior, std_prior, cv_posterior, which can be used as an argument of function estimate_R.

Examples

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## Not run: 
## Note the following examples use an MCMC routine
## to estimate the serial interval distribution from data,
## so they may take a few minutes to run

## load data on rotavirus
data("MockRotavirus")

## estimate the reproduction number (method "si_from_data")
## we are not specifying the time windows, so by defaults this will estimate
## R on sliding weekly windows
incid <- MockRotavirus$incidence
method <- "si_from_data"
config <- make_config(incid = incid, 
                     method = method, 
                     list(si_parametric_distr = "G",
                     mcmc_control = make_mcmc_control(burnin = 1000, 
                     thin = 10, seed = 1),
                     n1 = 500, 
                     n2 = 50,
                     seed = 2))

R_si_from_data <- estimate_R(incid,
                            method = method,
                            si_data = MockRotavirus$si_data,
                            config = config)
plot(R_si_from_data)                          

## you can also create the config straight within the estimate_R call, 
## in that case incid and method are automatically used from the estimate_R
## arguments:
R_si_from_data <- estimate_R(incid,
                            method = method,
                            si_data = MockRotavirus$si_data,
                            config = make_config(
                     list(si_parametric_distr = "G",
                     mcmc_control = make_mcmc_control(burnin = 1000, 
                     thin = 10, seed = 1),
                     n1 = 500, 
                     n2 = 50,
                     seed = 2)))
plot(R_si_from_data)    

## End(Not run)

annecori/EpiEstim documentation built on May 4, 2021, 9:41 a.m.