bbsBayes (version 2.5.3)

geofacet_plot: Generate a geofacet plot of population trajectories by province/state

Description

geofacet_plot allows you to 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_strata_indices or generate_regional_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

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

Value

ggplot object

Arguments

indices_list

Dataframe of strata or state/province indices produced by generate_strata_indices or generate_regional_indices

select

logical flag to indicate if the strata_level data need to be selected out of an indices_list object that includes stratum, national, or other region-types. Default is FALSE

stratify_by

How were the data stratified?

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

Optional dataframe of matching strata or state/province trends produced by generate_strata_trends or generate_regional_trends. If included trajectories are coloured based on the same colour scale used in generate_map

slope

Optional Logical, if dataframe of trends is included, colours in the plot are 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

species

Species name to be added onto the plot

col_viridis

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

Examples

# Toy example with Pacific Wren sample data
# First, stratify the sample data

strat_data <- stratify(by = "bbs_cws", sample_data = TRUE)

# Prepare the stratified data for use in a JAGS model.
jags_data <- prepare_jags_data(strat_data = strat_data,
                               species_to_run = "Pacific Wren",
                               model = "firstdiff",
                               min_year = 2009,
                               max_year = 2018)

# Now run a JAGS model.
jags_mod <- run_model(jags_data = jags_data,
                      n_adapt = 0,
                      n_burnin = 0,
                      n_iter = 10,
                      n_thin = 1)

# Generate the  stratum indices
indices <- generate_indices(jags_mod = jags_mod,
                            jags_data = jags_data,
                            regions = c("stratum"))

# Now make the geofacet plot.
gp <- geofacet_plot(indices_list = indices,
                    stratify_by = "bbs_cws",
                    species = "Pacific Wren",
                    multiple = TRUE)

# There is an unfortunate conflict between geofacet function in the geofacet package
# and the S3 +.gg method in other ggplot-extension-packages like ggmcmc
# The geofacet_plot function may fail with the following error message:
#  Error: Don't know how to add e2 to a plot
# If this happens, you can fix the problem by following these steps
#   1 - save your model output
#   2 - restart your R-session
#   3 - reload the bbsBayes package (do not re-load the other conflicting package, e.g., ggmcmc)