Class containing outputs from model run

This is an S4 object that extends the list base type. It returns an object containing outputs from a sefraModel model run and suitable for plotting.

Usage

sefraOutputs(object, model, ...)

# S4 method for class 'sefraData,sefraModel'
sefraOutputs(object, model, ...)

Arguments

object

sefraData object.

model

stanfit object containing MCMC samples.

...

additional function arguments (not used).

Slots

.Data

list containing input data

names

names for each list item

identifier

Definition of data used for model run.

species

Ordered character vector of species codes.

species_names

Data frame of species names.

Capture data:

captures

Empirical (*_emp), expected (*_hat) and posterior predicted (*_sim) captures.

captures_live

Empirical (*_emp), expected (*_hat) and posterior predicted (*_sim) live captures.

Observation probabilities:

p_obs_logit

Estimated observation probability parameter.

p_obs

Empirical observation probabilities p_obs_cde and cumulative sum p_obs_sum, per fishery group, species and capture code.

Predicted fishery interactions:

predicted_overlap

Model predicted density overlap per species and fishery group.

predicted_deaths

Model predicted deaths per species and fishery group.

predicted_cryptic_deaths

Model predicted cryptic deaths per species and fishery group.

map_overlap

Model predicted overlap per species, cell and fishery group.

map_deaths

Model predicted deaths per species, cell and fishery group.

Risk metrics per species:

r

Maximum intrinsic growth.

PST

PST reference point.

risk_ratio

Risk ratio.

rel_mort

Relative mortality ratio.

pop_status

Population status at equilibrium.

See also

Use summary to extract summary statistics.