parTabSetup_aux: MCMC parameter setup

Description Usage Arguments Value

View source: R/par_setup.R

Description

Sets up the parameter table for use in MCMC

Usage

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parTabSetup_aux(locationInfo, version = 1, sharedProb = FALSE,
  parFile = "", locationParFile = "", locationNormLik = FALSE,
  locationWeights = FALSE, forecast = FALSE)

Arguments

locationInfo

data frame of location info, see data(locationInfo). Needs columns for L_H, N_H and rawName

version

which model version is being run (see print_version_names)

sharedProb

boolean indicating if all locations share the same risk curve

parFile

if already specified, where to find the parameter table file without location parameters

locationParFile

as parFile, but with location specific parameters added

locationNormLik

boolean deciding whether or not a normal likelihood function is used (otherwise binomial). If NULL, uses the binomial. If not NULL, true or false indicates whether the likelihood standard deviations are location specific or not.

locationWeights

bool deciding if location weightings should be used (otherwise all locations have equal weighting)

forecast

if TRUE, sets up the parameter table for the forecasting analysis

Value

a matrix of needed settings for the MCMC algorithm. For each parameter, gives a name, lower and upper bounds, boolean for log scale, initial step sizes, log proposal and whether or not the parameter should be fixed.


jameshay218/zikaProj documentation built on Jan. 9, 2020, 7:26 p.m.