bdm-class: Class definition for 'bdm' object

In cttedwards/bdm: Bayesian biomass dynamics model

Class definition for bdm object

Description

This is the primary object class for the bdm package. It inherits from the stanmodel superclass.

Usage

bdm(path, model.code, model.name = "")

Arguments

path	path to stan code
model.code	model code as a character string
model.name	optional model name

Slots

data

a list of input data

inits

a list of initial values

chains

the number of chains

iter

the number of samples for each chain

warmup

the 'burnin' period for each chain

thin

the period of sampling from each chain

nsamples

the resultant number of samples retained from the sample run

trace

list holding the processed samples from extract(..., permuted = TRUE, inc_warmup = FALSE).

trace_array

array holding the processed samples from extract(..., permuted = FALSE, inc_warmup = TRUE). This should rarely be needed for direct access but is used for diagnostic plots.

map

list containing the maxium a posterior model fit

model_name

character string giving the model name.

model_code

the model code in the Stan modelling language.

model_cpp

translation of Stan code into C++.

dso

object of class cxxdso holding the compiled C++ code as a dynamic shared object.

Examples

# initialise default model object
mdl <- bdm()

# inspect Stan model code

cttedwards/bdm documentation built on Oct. 11, 2022, 7:52 p.m.