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

In jniedballa/camtrapR: Camera Trap Data Management and Preparation of Occupancy and Spatial Capture-Recapture Analyses

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 signature '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,
  ...
)

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

Value

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

jniedballa/camtrapR documentation built on April 7, 2024, 9:08 p.m.