calc_coherence: Calculate stability metrics

In James-Thorson/VAST: Vector-Autoregressive Spatio-Temporal (VAST) Model

Calculate stability metrics

Description

Coherence calculates buffering ('phi') and coherence ('psi')

Usage

calc_coherence(
  Report,
  Data,
  covhat = NULL,
  yearbounds_zz = matrix(c(1, Data$n_t), nrow = 1)
)

Arguments

Report	output report, e.g., from Report <- obj$report()
Data	tagged list of input data
covhat	estimated covariance used for calculating coherence
yearbounds_zz	matrix with two columns, giving first and last years for defining one or more periods (rows) used to calculate changes in synchrony over time (only used if Options['Calculate_Synchrony']=1)

Value

Tagged list containing measures of synchrony

phi_xz

Synchrony index for each site (x) and each period (row of yearbounds_zz)

phi_z

weighted-average of phi_xz for each period, weighted by average community-abundance at each site in that period

psi

Measure of proportion of variance explained by leading eigen-vectors

L_c

Cholesky decomposition of covhat

James-Thorson/VAST documentation built on Feb. 9, 2025, 9:05 a.m.