SppTrendSummary: SppTrendSummary - Species trend summary

In GPowney/TrendSummaries: TrendSummaries - summarising occupancy model outputs

Description

This function extracts trends for individual species from occupancy model outputs. Data describing the uncertainty and value of the trend estimates are also extracted. Trends are estimated as the annual growth rate between two given years, for example for a long-term trend, the function estiamtes annual growth rate between the first and last year of the time series. This function will be updated to allow the user to specify the exact years for which the trend is calculated.

Usage

SppTrendSummary(
  indata = "../data/sampled_posterior_1000/",
  output_path = "../trend_summary/",
  short_term_length = 10,
  a_17 = "no",
  include_rhat_check = "yes",
  include_prec_check = "yes",
  REGION_IN_Q = "psi.fs",
  model_useable_columns = "yes"
)

Arguments

indata	The file path to an selection of .csv files (one per species) containing sampled annual occupancy estiamtes from the posterior distribution. These data can be extract using the "SampPost" function.
output_path	The location where the outputs should be saved.
short_term_length	The number of years used for the short-term trend.
a_17	Are these species "article 17 species? This has specific relevence to UK biodiversity indicators and will eventually be removed from this package.
include_rhat_check	Loads in the RhatSummary output data to test if occupancy estiamtes for the years of interest converged, if not this test is failed.
include_prec_check	A simple test of whether the precision of the trend estimate is less than 0.2, if so the fail criterion is true.
REGION_IN_Q	The region for which the trends will be extracted. UK based occupancy model examples include, 'psi.fs', 'psi.fs.r_GB', 'psi.fs.r_ENLGAND'.
model_useable_columns	Include a simple column that identifies if the species failed either the precision or Rhat tests.

Value

A summary file (.csv) containing the individual trends for each species. Each row is a species. There are trends for the long-term (LT) and short-term trend (ST). As the function summarises the trends across a given number of iterations (based on the SampPost, sample number), the mean and median are used to produce the best guess of the true trend. Uncertainty is represented by the 95 of the trend estimate. Finally the number of samples used to produce the trend are displayed.

GPowney/TrendSummaries documentation built on Nov. 15, 2021, 6:14 p.m.