plot_all_phi_trace {BEDASSLE} | R Documentation |

## Plots all the trace plots for the phi parameters for all populations

### Description

Plots all trace plots for the phi parameters in all populations. For convenience,
the `F_{k}`

statistic is presented in place of the phi parameter, as this is the
statistic users care about. `F_{k}`

is defined as `\frac{1}{1+phi_{k}}`

.

### Usage

```
plot_all_phi_trace(phi_mat, percent.burnin = 0, thinning = 1, population.names = NULL)
```

### Arguments

`phi_mat` |
The |

`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 |

### Details

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.

### Author(s)

Gideon Bradburd

*BEDASSLE*version 1.6.1 Index]