Coherence: Calculate stability metrics

Description Usage Arguments Value

View source: R/Coherence.R

Description

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

Usage

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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

OPTIONAL, 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 Dec. 17, 2017, 11:35 p.m.