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.
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:
A \(q \times n\) 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.
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).
A difference e0 matrix of size \((q-1) \times n\). 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.
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.
Number of countries included in the e0 matrices.
Number of countries included in the MCMC estimation. It must be smaller or equal to nr.countries.
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.
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.
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.
Directory for storing simulation output.
List of various options used in the estimation. See e0mcmc.options.
List of country-specific bounds of the various parameter priors, as constructed from the country.overwrites option (see e0mcmc.options).
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$country_code.
Hana Sevcikova
The object is in standard cases not to be manipulated by itself, but rather as part of a bayesLife.mcmc.set object.
run.e0.mcmc, get.e0.mcmc, e0mcmc.options
sim.dir <- file.path(find.package("bayesLife"), "ex-data", "bayesLife.output")
m <- get.e0.mcmc(sim.dir)
summary(m, meta.only = TRUE)
names(m$meta)
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