e0.diagnose {bayesLife} | R Documentation |
Function e0.diagnose
runs convergence diagnostics of existing MCMCs, using the raftery.diag
function from the coda package.
e0.diagnose(sim.dir, thin = 225, burnin = 10000, express = FALSE, country.sampling.prop = NULL, keep.thin.mcmc = FALSE, verbose = TRUE)
sim.dir |
Directory with the MCMC simulation results. |
thin |
Thinning interval. |
burnin |
Number of iterations to be discarded from the beginning of the parameter traces. |
express |
Logical. If |
country.sampling.prop |
Proportion of countries that are included in the diagnostics. If it is |
keep.thin.mcmc |
Logical. If |
verbose |
Logical switching log messages on and off. |
The function invokes the e0.raftery.diag
function separately for country-independent parameters and for country-specific parameters. It results in two possible states: red, i.e. it did not converge, and green, i.e. it converged.
The resulting object is stored in
‘{sim.dir}/diagnostics/bayesLife.convergence_{thin}_{burnin}.rda’ and can be accessed using the function get.e0.convergence
.
Function has.mcmc.converged
from the bayesTFR package can be used to check if the existing diagnostics converged.
e0.diagnose
returns an object of class bayesLife.convergence
with components:
result |
Table containing all not-converged parameters. Its columns include ‘Total iterations needed’ and ‘Remaining iterations’. |
lresult.country.independent |
Number of rows in |
country.independent |
Result of |
country.specific |
Result of |
iter.needed |
Number of additional iterations suggested in order to achieve convergence. |
iter.total |
Total number of iterations of the original unthinned set of chains. |
use.nr.traj |
Suggestion for number of trajectories in generating predictions. |
burnin |
Burnin used. |
thin |
Thinning interval used. |
status |
Vector of character strings containing the result status. Possible values: ‘green’, ‘red’. |
mcmc.set |
Object of class |
thin.mcmc |
If |
express |
Value of the input argument |
nr.countries |
Vector with elements |
Hana Sevcikova, Adrian Raftery
e0.raftery.diag
, raftery.diag
, summary.bayesLife.convergence
, get.e0.convergence
, create.thinned.e0.mcmc