gStability: gstability

In ELAplus: Energy Landscape Analysis for Ecological Communities

gstability

Description

Calculate energy gap, energy barrier and stable state entropy.

This function evaluates stability indices for both (i) the pruned and (ii) the non-pruned energy landscape. For each sample, it assigns the basin by Bi and computes: - energy gap (sample energy minus basin energy), - energy barrier (minimum tipping energy connected to the basin minus basin energy), - stable state entropy (SSentropy).

For basin connectivity: when only one stable state exists, tipping energy is treated as Inf and therefore energy barrier is returned as Inf.

Usage

gStability(
  sa,
  ocmat,
  enmat = NULL,
  seitr = 1000,
  seconvTime = 10000,
  pruning_type = "relative",
  th = 0.1,
  lower_qr = 0.05,
  threads = 1,
  reporting = TRUE,
  bs_params = NULL
)

Arguments

sa	: output of runSA function.
ocmat	: matrix of presence/absence status for each sample.
enmat	: matrix of environmental factors for each sample. Normalization required.
seitr	: Number of stochastic search iterations.
seconvTime	: Maximum number of iterations for each search.
pruning_type	the type of pruning "relative"(use with th) or "bootstrap" (use with lower_qr and bootstrap_ene)
th	: Numerical (0~1). Ratio of the depth of the basin to be pruned with respect to the deepest basin in each pair.
lower_qr	Numeric value. Quantile used for constructing confidence intervals from bootstrap samples to check whether the estimated energy gaps include zero. Default is lower_qr = 0.05,necessary when type="bootstrap".
threads	number of cores (threads) used for calculation.#' @param threads : number of cores (threads) used for calculation.
reporting	: enable/disable the reporting function.
bs_params	output of bootstrap_SA. list of estimated parameters using bootstrap resampled data set, necessary when type="bootstrap".

Value

A list of four elements: (1) pruned stability data frame, (2) non-pruned stability data frame, (3) auxiliary object for pruned landscape (parameters + stable states table), and (4) auxiliary object for sample-wise evaluation (inputs and ELA objects).

ELAplus documentation built on May 28, 2026, 5:09 p.m.