bayesLife.mcmc.meta {bayesLife}R Documentation

MCMC Simulation Meta Object

Description

Simulation meta object bayesLife.mcmc.meta used by all chains of the same MCMC simulation. It contains information that is common to all chains. It is a part of a bayesLife.mcmc.set object.

Details

The object is in standard cases not to be manipulated by itself, but rather as part of a bayesLife.mcmc.set object.

Value

A bayesLife.mcmc.meta object stores values of the various input arguments of the run.e0.mcmc function. These are sex, nr.chains, start.year, present.year, wpp.year, my.e0.file, compression.type.
Furthermore, it contains components:

e0.matrix.all

A q x n matrix with the United Nations life expectancy estimates. q is number of years, n is number of countries (see nr.countries below). The first n_e columns correspond to countries included in the MCMC estimation (see nr.countries.estimation below), where n_e <= n. The order of the countries corresponds to the order of countries in the element regions and regionsDT, see below.

e0.matrix

Like e0.matrix.all, but it has NA values for years that were excluded from the estimation due to setting the start.year and present.year argument, and the ‘last.observed’ column (see Details in run.e0.mcmc).

d.ct

A difference e0 matrix of size (q-1) x n. Each element x_{t,i} is a difference y_{t+1,i}-y_{t,i} where y denotes elements of the e0.matrix. Outliers are set to NA.

loessSD

Matrix of the same dimension as d.ct. It contains values of the loess_sd dataset at the e0 levels of e0.matrix. See also compute.loess.

nr.countries

Number of countries included in the e0 matrices.

nr.countries.estimation

Number of countries included in the MCMC estimation. It must be smaller or equal to nr.countries.

Tc.index

A list with one element per country. For each country, it contains the index within e0.matrix where the observed historical data are not NA, i.e. it points to the data used in the estimation.

regions

List of arrays of length nr.countries. These are:
name - Region name for each country.
code - Region code for each country.
area_name - Area name for each country.
area_code - Area code for each country.
country_name - Array of country names.
country_code - Array of country codes.
Any country indices in the bayesLife.mcmc.meta object are derived from this component.

regionsDT

Like regions but for convenience it is a data.table object. A country in i-th row of this table has e0 data stored in the i-th column of e0.matrix.

output.dir

Directory for storing simulation output.

mcmc.options

List of various options used in the estimation. See e0mcmc.options.

country.bounds

List of country-specific bounds of the various parameter priors, as constructed from the country.overwrites option (see e0mcmc.options).

suppl.data

If supplemental data were used in the simulation (i.e. start year was set prior to 1950), this is a list containing information about the additional data. It has the following components of the same form as described above, but related only to the additional data: e0.matrix, regions, regionsDT, Tc.index, nr.countries, d.ct, loessSD. In addition, it has the vectors
index.from.all.countries - a vector of size nr.countries (all countries) where each element is an index to the supplemental data, i.e. a match from regions$country_code to suppl.data$regions$country_code.
index.to.all.countries - a vector of size suppl.data$nr.countries (additional countries) where each element is an index to all data, i.e. a match from suppl.data$regions$country_code to regions$country_code.

Author(s)

Hana Sevcikova

See Also

run.e0.mcmc, get.e0.mcmc, e0mcmc.options

Examples

sim.dir <- file.path(find.package("bayesLife"), "ex-data", "bayesLife.output")
m <- get.e0.mcmc(sim.dir)
summary(m, meta.only = TRUE)
names(m$meta)

[Package bayesLife version 5.0-1 Index]