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Plot temporal detection rates

plot_surveys.Rd

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

Usage

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

Arguments

fit

A fitted model object from fit_model().

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").

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.

restricted

logical. If TRUE (default), when include_predictors is FALSE and the model was fit with project_kappa = TRUE, plots random survey effects with orthogonal projection, i.e., \(\boldsymbol{\kappa}(\boldsymbol{I} - \boldsymbol{P_{X_3}})\), where \(\boldsymbol{I} - \boldsymbol{P_{X_3}}\) is the orthogonal complement of the column space of the site-averaged survey design matrix. If FALSE, plots random effects without orthogonal projection, i.e., \(\boldsymbol{\kappa}\) only. Has no effect when include_predictors is TRUE as the linear predictor is unaffected by orthogonal projection.

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.

See also

fit_model(), plot_intercepts(), plot_coefficients(), plot_sites(), plot_correlations(), plot_partitions(), plot_realised()