setup.fit.mcmc: Setup parameters for MCMC Procedure - Fit Data

In predsci/DICE: DICE: Dynamics of Interacting Community Epidemics

Description

Setup all the required parameters for the MCMC procedure on the fit data. These include: The min/max and step size values for all the parameters, the initial values for all the parameters, a vector with the list of parameters that will be optimized, the total number of parameters and the number of parameters that will be optimized. The code also allocates an array, tab, where the history of the MCMC chain is recorded.

Usage

setup.fit.mcmc(mydata = NULL, run.list = NULL, opt.list = NULL,
  tps = NULL, par_names = par_names)

Arguments

mydata	- dataframe with all the data for this DICE run
run.list	A list with parameters needed for the MCMC procedure
opt.list	A Logical list with TRUE or FALSE values for all the parameters and find the proper values needed for this prior. supported by DICE. These values are based on the model used for the basic reproduction number.
tps	A numeric array of days for the disease season - the day numbers are consistent with the weeks/months
par_names	- - An array with the all parameters ordered as required by DICE

Value

A list with the following arguments:

par_min

Minimum values for all the parameters supported by DICE for each region

par_max

Maximum values for all the parameters supported by DICE for each region

pardx

Step-size for MCMC for all the parameters supported by DICE for each region

par

Initial values for all the parameters for each region

logbase

Base for log values - currently code assumes base 10

nopt

Integer-the number of parameters that will be optimized

tab

A 2D numeric array with nlines and (nparam+1) columns used to store the MCMC history of all the parameters and the likelihood

Examples

setup.fit.mcmc{mydata = mydata,
run.list = run.list, opt.list = opt.list, tps = tps, par_names = par_names}

predsci/DICE documentation built on Aug. 9, 2019, 9:41 a.m.