Draws an MCMC sample from the joint posterior distribution of age-specific fertility rates, survival and migration proportions and baseline population counts.
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))Number of iterations to save.
Number of burn-in iterations; not saved.
Thinning parameter; save every 'thin'th iteration.
Shape parameter of the distribution of the variance of the age-specific ferility rate initial estimates.
Scale parameter of the distribution of the variance of the age-specific ferility rate initial estimates.
Shape parameter of the distribution of the variance of the age-specific survival proportion initial estimates.
Scale parameter of the distribution of the variance of the age-specific survival proportion initial estimates.
Shape parameter of the distribution of the variance of the age-specific migration proportion initial estimates.
Scale parameter of the distribution of the variance of the age-specific migration proportion initial estimates.
Shape parameter of the distribution of the variance of the age-specific population count initial estimates and census counts.
Scale parameter of the distribution of the variance of the age-specific population count initial estimates and census counts.
Matrix of initial estimates of age-specific fertility rates with age groups as rows, time periods as columns.
Matrix of initial estimates of age-specific survival proportions with age groups as rows, time periods as columns.
Matrix of initial estimates of age-specific migration proportions with age groups as rows, time periods as columns.
Matrix of initial estimates of age-specific baseline population counts with age groups as rows, time periods as columns.
Matrix of MCMC start values of age-specific fertility rates with age groups as rows, time periods as columns.
Matrix of MCMC start values of age-specific survival proportions with age groups as rows, time periods as columns.
Matrix of MCMC start values of age-specific migration proportions with age groups as rows, time periods as columns.
Matrix of MCMC start values of age-specific baseline population counts with age groups as rows, time periods as columns.
MCMC start value for variance of the age-specific fertility rate initial estimates.
MCMC start value for variance of the age-specific survival proportions initial estimates.
MCMC start value for variance of the age-specific migration proportions initial estimates.
MCMC start value for variance of the age-specific baseline count initial estimates.
Matrix fo census counts, with age groups as rows, time periods as columns.
List of matrices of variances for Gaussian Metropolis random walk proposals. Components are
Function to do cohort component projection.
Number of age.size-year periods to over which to do the reconstruction, beginning at the baseline year.
Width of the age groups and time periods in years.
Logical; should progress messages be printed.
A tolerance parameter to stop over-/under-flow when taking logits of survival proportions.
A list with components;
mcmc object containing MCMC chains for age-specific fertility rates.
mcmc object containing MCMC chains for age-specific survival proportions.
mcmc object containing MCMC chains for age-specific migration proportions.
mcmc object containing MCMC chains for age-specific baseline counts.
mcmc object containing MCMC chains for age-specific population counts at years subsequent to baseline.
mcmc object containing MCMC chains for the vital rate variance parameters.
“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.
A list containing the initial estimates and hyperparmaters of the variance distributions.
A list containing Metropolis start values for the vital rates, migration proportions, baseline counts and variance parameters.
“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.
burkina-faso-females
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.
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.