popRecon.sampler: MCMC Sampler for the popReconstruct Package

Description Usage Arguments Details Value Vignettes Author(s) References

View source: R/pop_reconstruction_functions.R

Description

Draws an MCMC sample from the joint posterior distribution of age-specific fertility rates, survival and migration proportions and baseline population counts.

Usage

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popRecon.sampler(n.iter, burn.in = 0, thin.by = 1, al.f = 1, be.f = 0.0109,
al.s = 1, be.s = 0.0109, al.g = 1, be.g = 0.0436, al.n = 1, be.n = 0.0109,
mean.f, mean.s, mean.g, mean.b, start.f = mean.f, start.s = mean.s,
start.g = mean.g, start.b = mean.b, start.sigmasq.f = 5, start.sigmasq.s = 5,
start.sigmasq.g = 5, start.sigmasq.n = 5, pop.data, prop.vars,
ccmp.function = popRecon.ccmp.female, proj.periods = ncol(mean.f),
age.size = 5, verb = FALSE, s.tol = 10^(-10))

Arguments

n.iter

Number of iterations to save.

burn.in

Number of burn-in iterations; not saved.

thin.by

Thinning parameter; save every 'thin'th iteration.

al.f

Shape parameter of the distribution of the variance of the age-specific ferility rate initial estimates.

be.f

Scale parameter of the distribution of the variance of the age-specific ferility rate initial estimates.

al.s

Shape parameter of the distribution of the variance of the age-specific survival proportion initial estimates.

be.s

Scale parameter of the distribution of the variance of the age-specific survival proportion initial estimates.

al.g

Shape parameter of the distribution of the variance of the age-specific migration proportion initial estimates.

be.g

Scale parameter of the distribution of the variance of the age-specific migration proportion initial estimates.

al.n

Shape parameter of the distribution of the variance of the age-specific population count initial estimates and census counts.

be.n

Scale parameter of the distribution of the variance of the age-specific population count initial estimates and census counts.

mean.f

Matrix of initial estimates of age-specific fertility rates with age groups as rows, time periods as columns.

mean.s

Matrix of initial estimates of age-specific survival proportions with age groups as rows, time periods as columns.

mean.g

Matrix of initial estimates of age-specific migration proportions with age groups as rows, time periods as columns.

mean.b

Matrix of initial estimates of age-specific baseline population counts with age groups as rows, time periods as columns.

start.f

Matrix of MCMC start values of age-specific fertility rates with age groups as rows, time periods as columns.

start.s

Matrix of MCMC start values of age-specific survival proportions with age groups as rows, time periods as columns.

start.g

Matrix of MCMC start values of age-specific migration proportions with age groups as rows, time periods as columns.

start.b

Matrix of MCMC start values of age-specific baseline population counts with age groups as rows, time periods as columns.

start.sigmasq.f

MCMC start value for variance of the age-specific fertility rate initial estimates.

start.sigmasq.s

MCMC start value for variance of the age-specific survival proportions initial estimates.

start.sigmasq.g

MCMC start value for variance of the age-specific migration proportions initial estimates.

start.sigmasq.n

MCMC start value for variance of the age-specific baseline count initial estimates.

pop.data

Matrix fo census counts, with age groups as rows, time periods as columns.

prop.vars

List of matrices of variances for Gaussian Metropolis random walk proposals. Components are

ccmp.function

Function to do cohort component projection.

proj.periods

Number of age.size-year periods to over which to do the reconstruction, beginning at the baseline year.

age.size

Width of the age groups and time periods in years.

verb

Logical; should progress messages be printed.

s.tol

A tolerance parameter to stop over-/under-flow when taking logits of survival proportions.

Details

This is the main function of the popReconstruct package. It takes initial estimates of age-specific vital rates, migration proportions and population counts in the baseline year and draws an MCMC sample from the joint posterior distribution defined in Wheldon et al. (2011). See the vignette burkina-faso-females for an extended illustration of its use.

Value

A list with components;

fert.rate.mcmc

mcmc object containing MCMC chains for age-specific fertility rates.

surv.prop.mcmc

mcmc object containing MCMC chains for age-specific survival proportions.

mig.prop.mcmc

mcmc object containing MCMC chains for age-specific migration proportions.

baseline.count.mcmc

mcmc object containing MCMC chains for age-specific baseline counts.

lx.mcmc

mcmc object containing MCMC chains for age-specific population counts at years subsequent to baseline.

variances.mcmc

mcmc object containing MCMC chains for the vital rate variance parameters.

alg.stats

“algorithm statistics”; a list with components acceptance.proportions giving Metropolis acceptance proportions for each vital rate parameter, pop.went.negative giving the number of times Metropolis proposals resulted in negative poplation counts, run.time giving the time taken to run the sampler and some other, as yet undocumented, components.

fixed.params

A list containing the initial estimates and hyperparmaters of the variance distributions.

start.vals

A list containing Metropolis start values for the vital rates, migration proportions, baseline counts and variance parameters.

alg.params

“algorithm parameters”; a list returning some of the arguments supplied for this run, saved for later reference. For example, Metropolis proposal variances (prop.vars) and the number of iterations (iters) are stored here.

Vignettes

burkina-faso-females

Author(s)

Mark C. Wheldon

References

Wheldon, M. C., Raftery, A. E., Clark, S. J. and Gerland, P. (2011) Estimating Demographic Parameters with Uncertainty. Working Paper No. 108, Center for Statistics and the Social Sciences, University of Washington, Seattle. http://www.csss.washington.edu/Papers/wp108.pdf.


popReconstruct documentation built on May 29, 2017, 10:34 p.m.