Plots fitted index series: observed points with 95% observation intervals and
the model-predicted index, faceted by fleet. Every fleet holding
index_data is drawn, a fishery with a CPUE series as much as a survey.
Usage
plot_index(
Rceattle,
file = NULL,
model_names = NULL,
species = NULL,
incl_proj = FALSE,
width = 7,
height = 6.5,
error = TRUE,
log = FALSE,
line_col = NULL,
right_adj = 0,
top_adj = 0.05,
single.plots = FALSE
)Arguments
- Rceattle
A single
fit_mod()object or a list of them (overlaid).- file
Optional file stem; if given the figure is written to
<file>_survey_indices.png.- model_names
Legend labels for the models.
- species
Species (indices) to include. Default all.
- incl_proj
Include projection years.
- width, height
Saved figure size (inches).
- error
Draw observed points and error bars.
- log
Plot the index on the log scale.
- line_col, right_adj, top_adj, single.plots
Deprecated base-graphics arguments, retained for back-compatibility and ignored.
Details
The interval follows the fleet's Index_distribution: lognormal quantiles on
a "Lognormal" fleet, and observed +/- 1.96 sd truncated at zero on a
natural-scale one ("MVN", "MVNORM", "Normal", "TruncatedNormal"),
whose sd is absolute and in the units of the index.
The predicted line is the MEDIAN of the fitted observation distribution,
index_hat * exp(-bias_adjust_obs * sd^2 / 2), which is where the lognormal
likelihood is centred, so about half the observations should fall below it.
It equals the reported index_hat where bias_adjust_obs = FALSE. A
natural-scale fleet has no such offset and is drawn unchanged.