Description Usage Arguments Details Value Author(s) See Also

Function `e0.diagnose`

runs convergence diagnostics of existing MCMCs, using the `raftery.diag`

function from the coda package.

1 2 | ```
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`

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