Formatting: Formatting

In ELAplus: Energy Landscape Analysis for Ecological Communities

Formatting

Description

Generate occurrence(binary)/abundance/factor matrices and labels from input abundance/metadata tables.

Usage

Formatting(
  baseabtable,
  basemetadata = NULL,
  normalize = 1,
  parameters = c(0.05, 0.05, 0.95),
  grouping = 0,
  grouping_th = 0,
  reporting = TRUE
)

Arguments

baseabtable	Abundance table (samples x species) as data.frame/matrix.
basemetadata	Optional environmental metadata table (samples x factors); NULL/empty for none.
normalize	Integer 0 or 1. If 1, normalize within each sample to sum to 1.
parameters	Numeric vector/list of thresholds (following 3 parameters). 1. "0/1 threshold" 2. "min occurrence threshold" 3. "max occurrence threshold" (e.g., c(0.05, 0.05, 0.95) : species abundance > 0.05 is regarded as present, and species occurring in more than 0.05 and less than 0.95 in the all samples are kept.)
grouping	Integer 0 or 1. If 1, group similar occurrence patterns.
grouping_th	Numeric threshold for grouping (relative Hamming distance).
reporting	Logical. If TRUE, print processing summary.

Value

A list: (ocmatrix, abmatrix, fctmatrix, samplelabel, specieslabel, factorlabel).

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