ELPruning: ELPruning

In ELAplus: Energy Landscape Analysis for Ecological Communities

ELPruning

Description

Pruning shallow stable states of energy landscape.

Iteratively prunes stable states (merges basins). If type="relative", stable state whose energy depth is smaller than th times the deepest basin depth are pruned and merged to the deeper basins. If type="bootstrap", stable state whose bootstrap confidence interval (default: 95 cross zero is pruned. The function updates stable states and corresponding tipping structures, and returns both the pruned ELA object and a mapping table from stable states before pruning to those after pruning.

Usage

ELPruning(
  ela,
  type = "relative",
  th = 0.05,
  lower_qr = 0.05,
  bootstrap_ene = NULL,
  threads = 1,
  reporting = TRUE,
  fork = TRUE
)

Arguments

ela	output of ELA function.
type	the type of pruning "relative"(use with th) or "bootstrap" (use with lower_qr and bootstrap_ene)
th	ratio of the depth of the basin to be pruned with respect to the deepest basin.
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.
bootstrap_ene	a data frame of bootstrap energies generated by bootstrap_ELA. Necessary when type="quantile".
threads	number of cores (threads) used for calculation.
reporting	enable/disable the reporting function.
fork	logical; if TRUE and threads > 1, a cluster is created internally for parallel execution.

Value

A list of two elements: (1) pruned ELA tuple (same format as ELA output), and (2) a data frame with columns ss.before.pruning and ss.after.pruning.

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