rescale_posterior: Rescale species values for indicator

In BiologicalRecordsCentre/BRCindicators: Creating multispecies biodiversity indicators

Rescale species values for indicator

Description

This function takes in the output from a sparta occupancy model and rescales the posteriers so that the gemean for each species is the same in the first year. This function accounts for species that have no data at the beginning of the period, by bringing them in at the geomean, and those that have no data at the end of the period, by applying a multiplier to the result of the species data.

Usage

rescale_posterior(
  input_dir,
  subset_table = NULL,
  index = 100,
  max = 10000,
  min = 1,
  year_limit = 10,
  upperQuantile = 0.975,
  lowerQuantile = 0.025,
  verbose = TRUE
)

Arguments

input_dir	the location of occupancy model output files
subset_table	dataframe with columns for years and rows for species. Column names must be character years and row names must match the file names in input_dir
index	The index value for the first year, defaults to 100.
max	The upper limit allowed for scaled values. Values greater than this will be set equal to max.
min	The upper limit allowed for scaled values. Values greater than this will be set equal to min.
year_limit	The minimum length of 'good years' for a species to be included
upperQuantile	The upper confidence interval to use (as a probability)
lowerQuantile	The lower confidence interval to use (as a probability)
verbose	If TRUE progress is written to console

Details

There are two options for calculating confidence intervals; the first is to use the 95 is to calculate the indicator line for each iteration (given in the posterior data) and then to present the 97.5 and 2.5 quantiles of these lines. Both are returned in the summary table.

Value

A list with two elements, a summary (data.frame) and the rescaled data (list)

BiologicalRecordsCentre/BRCindicators documentation built on April 22, 2024, 2:32 p.m.