Plot temporal detection rates

Plots species-level temporal detection rates combining survey predictors averaged over sites (if included via make_data()) and survey random effects (kappa).

Usage

plot_surveys(
  fit,
  species = NULL,
  surveys = NULL,
  seasons = NULL,
  intercepts = TRUE,
  back_transform = TRUE,
  include_predictors = TRUE,
  ndraws = NULL,
  seed = NULL,
  palette = "YlGn",
  ...
)

Arguments

fit: A fitted model object from occARU().
species: character. Vector of species to plot. If NULL (default), all species are plotted. Must be one of attr(occARU_data, "species").
surveys: character. Vector of survey dates to plot. If NULL (default), all surveys are plotted. Must be one of attr(occARU_data, "surveys").
seasons: character. Vector of seasons to plot. If NULL (default), all seasons are plotted. Must be one of attr(occARU_data, "seasons").
intercepts: logical. If TRUE (default), species-level baseline log detection rates are added to the survey effects. If FALSE, only the temporal deviations are plotted on the log scale.
back_transform: logical. Only used when intercepts = TRUE. If TRUE (default), log detection rates are back-transformed to the natural scale via exp(). If FALSE, values are left on the log scale.
include_predictors: logical. If TRUE (default), includes predictors in the survey effects, if included. If FALSE, only plots the random effects.
ndraws: Positive integer. Number of draws to use for plotting, passed to tidybayes::spread_rvars(). Default: NULL (uses all draws).
seed: Positive numeric. Seed to use when subsampling draws when ndraws is not NULL. Default: random integer.
palette: character. Colour palette to be passed to ggplot2::scale_fill_brewer(). Default: "YlGn".
...: Additional arguments passed to ggdist::stat_lineribbon() such as .width and point_interval.

Value

A ggplot object with occARU-specific attributes attached:

plot_data: The tibble used to produce the plot.

Usage

Arguments

Value

See also