get_prepared_data: Get the prepared species dataset used for JAGS

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

Get the prepared species dataset used for JAGS

Description

get_prepared_data returns a data frame of the data that was used for JAGS. This is the subsetted data based on the selected species to model, with zero counts filled in and any other route/strata filter applied.

Usage

get_prepared_data(jags_data = NULL)

Arguments

jags_data

List of JAGS input data produced by prepare_jags_data

Value

Data frame of 9 variables:

count	Number of species observed for this route run
strat	Numerical factors of the stratum
obser	Numerical factor of the observer
year	Numerical factor of the year
firstyr	1 if this was the observer's first year, 0 otherwise
strat_name	Name of the stratum
route	Route that this count was taken on
rYear	Year this count was conducted
yearscale	Scaled year

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. In this
#   toy example, we will set the minimum year as 2009 and
#   maximum year as 2018, effectively only setting up to
#   model 10 years of data. We will use the "first difference
#   model.
jags_data <- prepare_jags_data(strat_data = strat_data,
                               species_to_run = "Pacific Wren",
                               model = "firstdiff",
                               min_year = 2009,
                               max_year = 2018)

# Obtain the reassembled data frame for the data sent to JAGS
prepped_data <- get_prepared_data(jags_data = jags_data)

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