Description Usage Arguments Value Examples
View source: R/init_epimodel.R
Initializes a bookkeeping list containing the population level and subject level bookkeeping objects, measurement, and epidemic process settings. At a minimum, the epimodel object must be initialized with the states, params, rates, flow, and either the vector of observation times or a matrix with data.
1 2 3 4 5 |
states |
character vector with names of compartments corresponding
exactly to the names of compartments used in the |
params |
numeric vector of process parameters with element names
corresponding exactly to names of parameters used in the |
rates |
character vector with strings specifying the flow rates between
compartments. Each variable in a rate must correspond to the name of one of
the |
flow |
numeric matrix of dimension |
dat |
matrix of dimension |
time_var |
string indicating the name of the variable coding observation
times in |
popsize |
size of the population. |
obs_mat |
population-level bookkeeping matrix for compartment counts at observation times. |
initdist_prior |
vector of parameters for dirichlet prior for default categorical distribution over initial distribution at t0. Defaults to flat prior unless otherwise specified. |
meas_vars |
character vector specifying which compartments are measured. |
r_meas_process |
function to simulate from the measurement process, with
named arguments |
d_meas_process |
function to evaluate the density of the measurement
process with arguments and output specified as in |
covar |
optional numeric matrix of time varying covariates (currently not working). |
tcovar |
numeric vector of times for time-varying covariates (currently not working). |
sim_settings |
bookkeeping list for simulation settings. |
config_mat |
population-level bookkeeping matrix for compartment counts and the configuration of individuals at times of state transition. |
list containing bookkeeping objects and model configuration objects.
1 2 3 4 |
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.