generate_trends {bbsBayes}R Documentation

Generate regional trends continent and strata and optionally for countries, states/provinces, or BCRs from analyses run on the stratifications that support these composite regions

Description

generate_trends calculates the geometric mean annual changes in population size for composite regions.

Usage

generate_trends(
  indices = NULL,
  Min_year = NULL,
  Max_year = NULL,
  quantiles = c(0.025, 0.05, 0.25, 0.75, 0.95, 0.975),
  slope = FALSE,
  prob_decrease = NULL,
  prob_increase = NULL
)

Arguments

indices

regional indices generated by generate_indices

Min_year

Minimum year to calculate trends from (e.g., 1970). Default is NULL, in which case the trend is calculated from the first year of the time-series of the supplied annual_indices file

Max_year

Maximum year to calculate trends to (e.g., 2018). Default is NULL, in which case the trend is calculated up to the last year of the time-series of the supplied annual_indices file

quantiles

vector of quantiles to be sampled from the posterior distribution Defaults to c(0.025,0.05,0.25,0.5,0.75,0.95,0.975)

slope

Logical, if TRUE, calculates an alternative trend metric, the slope of a log-linear regression through the annual indices. Default FALSE

prob_decrease

Optional vector of percent-change values to calculate the posterior probabilities that the population has decreased by at least this much (e.g., prob_decrease = c(50) would result in a calculation of the probability that the population has decreased by more than 50 percent over the period of the trend, i.e., less than half the population remains. Default is NULL, in which case no probability of decrease is calculated.

prob_increase

Optional vector of percent-change values to calculate the posterior probabilities that the population has increased by at least this much (e.g., prob_increase = c(100) would result in a calculation of the probability that the population has incrased by more than 100 percent, i.e., doubled, over the period of the trend. Default is NULL, in which case no probability of increase is calculated.

Value

Dataframe with one row for each region included in indices object, and columns including:

Start_year

first year of the trend

End_year

last year of the trend

Region

short name of the region

Region_alt

Long name for region

Region_type

Type of region including continental, national,Province_State,BCR, bcr_by_national, or stratum

Strata_included

Strata included in the trend and annual index calculations

Strata_excluded

Strata potentially excluded from the trend and annual index calculations because they have no observations of the species in the first part of the time series

Trend

Estimated mean annual percent change over the trend time-period (i.e., Start_year - End_year), according to an endpoint comparison of annual index in Start_year and the annual index in End_year

Trend_Q_quantiles

quantiles of the posterior distribution of Trend estimates, matching levels included in the quantiles argument

Percent_Change

Estimated total percent change over the trend time-period

Percent_Change_Q_quantiles

quantiles of the posterior distribution of Percent Change estimates, matching levels included in the quantiles argument

Slope_Trend

Estimated mean annual percent change over the trend time-period, according to the slope of a linear regression through the log-transformed annual indices

Slope_Trend_Q_quantiles

quantiles of the posterior distribution of Percent Change estimates, matching levels included in the quantiles argument

prob_decrease_X_percent

proportion of the posterior distribution of Percent_Change that is below the percentage values supplied in prob_decrease

prob_increase_X_percent

proportion of the posterior distribution of Percent_Change that is above the percentage values supplied in prob_increase

Relative_Abundance

Mean of the annual index values across all years. An estimate of the average relative abundance of the species in the region. Can be interepreted as the predicted average count of the species in an average year on an average route by an average observer, for the years, routes, and observers in the existing data

Observed_Relative_Abundance

Mean of the observed annual counts of birds across all routes and all years. An alternative estimate of the average relative abundance of the species in the region. For composite regions (i.e., anything other than stratum-level estimates) this average count is calculated as an area-weighted average across all strata included

Number_of_Strata

The number of strata included in the region

Width_of_X_percent_Credible_Interval

Width (in percent/year) of the credible interval on the Trend calculation. Calculated for the widest credible interval requested in quantiles argument. Default is 95 percent CI (i.e., Trend_Q0.975 - Trend_Q0.025)

Width_of_X_percent_Credible_Interval_Slope

Width (in percent/year) of the credible interval on the Trend calculation for the slope-based trend. Calculated for the widest credible interval requested in quantiles argument. Default is 95 percent CI (i.e., Slope_Trend_Q0.975 - Slope_Trend_Q0.025)

Number_of_Routes

The number of unique BBS routes included in the annual indices for this region and species, i.e., number of routes for this region and species for the years since generate_indices(startyear)

Mean_Number_of_Routes

The average number of BBS routes across years contributing data for this region and species

backcast_flag

approximate proportion of the included species range*years that are supported by data in a given region and year, e.g., 1.0 = data cover full time-series, 0.75 = data cover 75 percent of time-series. Only calculated if max_backcast != NULL

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)



[Package bbsBayes version 2.3.6.2020 Index]