GradELA: GradELA

In ELAplus: Energy Landscape Analysis for Ecological Communities

GradELA

Description

Estimate energy landscape across environmental gradients.

Runs ELA and ELPruning comprehensively across specified environmental parameters. One environmental parameter can be changed by specifying eid over steps within range. If env is not given, the mean vector of enmat is used as the reference environmental condition.

Usage

GradELA(
  sa = sa,
  pruning_type = "relative",
  eid = NULL,
  enmat = enmat,
  env = NULL,
  range = NULL,
  steps = 16,
  th = 0.05,
  threads = 1,
  SS.itr = 20000,
  FindingTip.itr = 10000,
  lower_qr = 0.05,
  bs_params = NULL,
  ocmat = NULL
)

Arguments

sa	output of runSA function.
pruning_type	the type of pruning "relative"(use with th) or "bootstrap" (use with lower_qr,ocmat and bs_params)
eid	target environmental factor: the specified environmental factor to be changed.
enmat	array/matrix of environmental factors for each sample (normalization required).
env	array of environmental factor values. For the environmental parameters that are not specified for eid, these values are used as references. If not specified, then the mean of values in enmat are used as references.
range	range over which the environmental factor specified by eid is changed.
steps	number of steps in the range.
th	ratio of the depth of the basin to be pruned with respect to the deepest basin.
threads	number of cores (threads) used for calculation.
SS.itr	number of iterations to identify stable states.
FindingTip.itr	number of iterations to identify tipping points.
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".
bs_params	output of bootstrap_SA. list of estimated parameters using bootstrap resampled data set. necessary when type="bootstrap".
ocmat	community composition matrix.

Value

A list of three elements: (1) ELA results for each step (pruned), (2) the sequence of environmental values, and (3) the reference env vector.

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