Description Usage Arguments Value

`Summarize`

is intended to help document results, by providing explanation for outputs from `obj$report()`

1 |

`obj` |
the TMB object after it has been previously optimized |

`species_names` |
an optional character-vector giving species names |

`rotation_method` |
what rotation method is used when visualizing results (default |

Tagged list of useful output

- parhat
a list of fixed-effect estimates, with same format as starting values

- L_pj
the loadings matrix, where e.g.

`L_pj[1,2]`

gives the association of species 1 with factor 2- Psi
the array of factors, where e.g.

`Psi[1,2,3]`

gives the value at site 1 of factor 2 in time 3- L_pj_rot
the loadings matrix after rotation, useful for ease of interpretation

- Psi_rot
the value of factors, useful for ease of interpretation

- range_jz
Decorrelation distance for factor j (1st column: spatial; 2nd column: spatio-temporal

- theta_npt
Empirical Bayes prediction of log-density, where e.g.,

`theta_npt[1,2,3]`

gives the log-density for site 1 and species 2 in time 3- eta_npt
Empirical Bayes prediction of log-detectability, where e.g.,

`eta_npt[1,2,3]`

gives the log-detectability for site 1 and species 2 in time 3- logchat_i
Empirical Bayes prediction of log-expectation for observation i

- nll_i
Empirical Bayes prediction of one-half of the deviance residual for observation i

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