glossa_analysis: Main Analysis Function for GLOSSA Package

In glossa: User-Friendly 'shiny' App for Bayesian Species Distribution Models

Main Analysis Function for GLOSSA Package

Description

This function wraps all the analysis that the GLOSSA package performs. It processes presence-absence data, environmental covariates, and performs species distribution modeling and projections under past and future scenarios.

Usage

glossa_analysis(
  pa_data = NULL,
  fit_layers = NULL,
  proj_files = NULL,
  study_area_poly = NULL,
  predictor_variables = NULL,
  decimal_digits = NULL,
  scale_layers = FALSE,
  buffer = NULL,
  native_range = NULL,
  suitable_habitat = NULL,
  other_analysis = NULL,
  seed = NA,
  waiter = NULL
)

Arguments

pa_data	A list of data frames containing presence-absence data.
fit_layers	A SpatRaster stack containing model fitting environmental layers.
proj_files	A list of file paths containing environmental layers for projection scenarios.
study_area_poly	A spatial polygon defining the study area.
predictor_variables	A list of predictor variables to be used in the analysis.
decimal_digits	An integer specifying the number of decimal places to which coordinates should be rounded.
scale_layers	Logical; if TRUE, covariate layers will be scaled based on fit layers.
buffer	Buffer value or distance in decimal degrees (arc_degrees).
native_range	A vector of scenarios ('fit_layers', 'projections') where native range modeling should be performed.
suitable_habitat	A vector of scenarios ('fit_layers', 'projections') where habitat suitability modeling should be performed.
other_analysis	A vector of additional analyses to perform (e.g., 'variable_importance', 'functional_responses', 'cross_validation').
seed	Optional; an integer seed for reproducibility of results.
waiter	Optional; a waiter instance to update progress in a Shiny application.

Value

A list containing structured outputs from each major section of the analysis, including model data, projections, variable importance scores, and habitat suitability assessments.

glossa documentation built on Oct. 15, 2024, 5:08 p.m.