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Create geofacet plot of population trajectories by province/state

Source: R/plot-geofacet.R
plot_geofacet.Rd

Generate a faceted plot of population trajectories for each strata by province/state. Given a model stratified by "state", "bbs_cws", or "bbs_usgs" and indices generated by generate_indices() this function will generate a faceted plot showing the population trajectories. All geofacet plots have one facet per state/province, so if strata-level indices from the "bbs_cws" or "bbs_usgs" are given, the function plots multiple trajectories (one for each of the relevant strata) within each facet.

Usage

plot_geofacet(
  indices,
  ci_width = 0.95,
  multiple = FALSE,
  trends = NULL,
  slope = FALSE,
  add_observed_means = FALSE,
  col_viridis = FALSE,
  indices_list,
  stratify_by,
  species,
  select
)

Arguments

indices

List. Indices generated by generate_indices().

ci_width

quantile to define the width of the plotted credible interval. Defaults to 0.95, lower = 0.025 and upper = 0.975

multiple

Logical, if TRUE, multiple strata-level trajectories are plotted within each prov/state facet

trends

List. (Optional) Output generated by generate_trends(). If included trajectories are coloured based on the same colour scale used in plot_map

slope

Logical. If dataframe of trends is included, whether colours in the plot should be based on slope trends. Default = FALSE

add_observed_means

Should the facet plots include points indicating the observed mean counts. Defaults to FALSE. Note: scale of observed means and annual indices may not match due to imbalanced sampling among strata

col_viridis

Logical flag to use "viridis" colour-blind friendly palette. Default is FALSE

indices_list

Deprecated. Use indices instead

stratify_by

Defunct.

species

Defunct.

select

Defunct.

Value

ggplot object

Examples


# Using the example model for Pacific Wrens...

# Generate indices
i <- generate_indices(pacific_wren_model,
                      regions = c("stratum", "prov_state"))
#> Processing region stratum
#> Processing region prov_state
# Generate trends
t <- generate_trends(i)

# Now make the geofacet plot.
plot_geofacet(i, trends = t, multiple = TRUE)

plot_geofacet(i, trends = t, multiple = TRUE, col_viridis = TRUE)

plot_geofacet(i, multiple = TRUE)

plot_geofacet(i, trends = t, multiple = FALSE)

plot_geofacet(i, multiple = FALSE)


# With different ci_width, specify desired quantiles in indices
i <- generate_indices(pacific_wren_model,
                      regions = c("stratum", "prov_state"),
                      quantiles = c(0.005, 0.995))
#> Processing region stratum
#> Processing region prov_state

plot_geofacet(i, multiple = FALSE, ci_width = 0.99)