plot_coef,commOccu-method: Plot effect sizes of covariates in community occupancy model

Description

Plot effect sizes for all species in a community (multi-species) occupancy model. Currently only supports continuous covariates, not categorical covariates.

Usage

# S4 method for commOccu
plot_coef(
  object,
  mcmc.list,
  submodel = "state",
  ordered = TRUE,
  combine = FALSE,
  outdir,
  level = c(outer = 0.95, inner = 0.75),
  colorby = "significance",
  scales = "free_y",
  community_lines = FALSE,
  ...
)

Value

A list of ggplot objects (one list item per covariate).

Arguments

object: commOccu object
mcmc.list: mcmc.list. Output of fit called on a commOccu object
submodel: character. Submodel to get plots for. Can be "det" or "state"
ordered: logical. Order species in plot by median effect (TRUE) or by species name (FALSE)
combine: logical. Combine multiple plots into one plot (via facets)?
outdir: character. Directory to save plots to (optional)
level: numeric. Probability mass to include in the uncertainty interval (two values named "outer" and "inner", in that order). Second value (= inner interval) will be plotted thicker.
colorby: character. Whether to color estimates by "significance" (of the effect estimates), or "Bayesian p-value" (of the species). Currently allows only "significance".
scales: character. Passed to facet_grid. Can be "free" to scale x axes of effect estimates independently, or "free_y" to scale all x axes identically.
community_lines: logical. Add faint vertical lines to the plot indicating median community effect (solid line) and its confidence interval (first value from level).
...: additional arguments for ggsave - only relevant if outdir is defined.

Details

Users who wish to create their own visualizations can use the data stored in the ggplot output. It is accessed via e.g. output$covariate_name$data