generate_map: Generate a map of trends by strata.

In BrandonEdwards/bbsBayes: Hierarchical Bayesian Analysis of North American BBS Data

Generate a map of trends by strata.

Description

generate_map allows you to generate a colour-coded map of species trends for each strata. Given trends generated by generate_strata_trends, this function will shade in each stratum based on the percent change in that stratum.

Usage

generate_map(
  trend = NULL,
  select = FALSE,
  stratify_by = NULL,
  slope = FALSE,
  species = "",
  col_viridis = FALSE
)

Arguments

trend	Dataframe of strata trends produced by generate_strata_trends or generate_regional_trends(..., regions = "stratum")
select	logical flag to indicate if the stratum data need to be selected out of an trends object that includes continental, national, or other region-types. Default is FALSE
stratify_by	How were the data stratified?
slope	Logical, if TRUE, maps values of the alternative trend metric if slope = TRUE was used in generate_strata_trends, the slope of a log-linear regression through the annual indices. Default FALSE.
species	Text, optional species name to add plot title. if left blank "" no title is added
col_viridis	Logical flag to use "viridis" colour-blind friendly palette. Default is FALSE

Value

spplot object

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 continental and stratum indices
indices <- generate_indices(jags_mod = jags_mod,
                            jags_data = jags_data)

# Now, generate the trends
trends <- generate_trends(indices = indices)

# Generate the map. Set select = TRUE because we are passing a
#    dataframe of trends of more than just the stratum regions
map <- generate_map(trend = trends,
                    stratify_by = "bbs_cws",
                    select = TRUE,
                    species = "Pacific Wren")

BrandonEdwards/bbsBayes documentation built on March 3, 2023, 9:55 a.m.