Description Usage Arguments Details Author(s)

This function plots the parameter value estimated in each sampled generation of the MCMC against the index of that sampled generation for each parameter in the model.

1 | ```
plot_all_trace(MCMC.output, percent.burnin = 0, thinning = 1, population.names = NULL)
``` |

`MCMC.output` |
The standard MCMC output file generated from a BEDASSLE run. |

`percent.burnin` |
The percent of the sampled MCMC generations to be discarded as "burn-in." If the
MCMC is run for 1,000,000 generations, and sampled every 1,000 generations, there
will be 1,000 sampled generations. A |

`thinning` |
The multiple by which the sampled MCMC generations are thinned. A |

`population.names` |
A vector of length |

A trace plot is a basic visual tool for assessing MCMC mixing. If the chain is mixing well, the trace plot will resemble a "fuzzy caterpillar." If the trace plot has not plateaued, it is an indication that the chain has not converged on the stationary posterior distribution, and must be run longer. If the trace plot of a parameter exhibits high autocorrelation, the user may wish to either increase or decrease the scale of the tuning parameter on that parameter, to decrease or increase acceptance rates, respectively. If the chain appears to be bouncing between areas of "fuzzy caterpillar-dom," it may be an indication of a multi-modal likelihood surface.

Gideon Bradburd

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