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Nematode (version 0.2.0)

Ecological Indices Calculator for Nematode Communities

Description

Nematode communities serve as crucial bioindicators in ecological studies, reflecting soil health, ecosystem functioning, and trophic interactions. To standardize these assessments, we developed a computational toolkit for quantifying nematode-based ecological indicators, including metabolic footprints, energy flow metrics, and community structure analysis.

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Version

Install

install.packages('Nematode')

Version

0.2.0

License

GPL (>= 3)

Maintainer

Yuxuan He

Last Published

August 20th, 2025

Functions in Nematode (0.2.0)

cal.TD

Calculate Trophic Diversity (TD) Index
cal.Simpson

Calculate Simpson Index
cal.SI

Calculate Structure Index (SI)
cal.WI

Calculate Wasilewska Index (WI)
runPCoA

Principal Coordinates Analysis (PCoA) Analysis
runSimper

Similarity Percentages Analysis
summary.NMDS

Summarize NMDS Results
num_species

Calculate Number of Species
cal.H

Calculate Shannon-Wiener Index (H)
cal.J

Calculate Pielou's Evenness Index (J)
NMF

Nematode Metabolic Footprints (NMF) Calculation
Ecological.Indices

Calculate Ecological Indices of Nematodes
cal.MI

Calculate Maturity Index (MI)
NEF

Nematode Energy Footprints (NEF) Calculation
cal.NCR

Calculate Nematode Channel Ratio (NCR)
cal.CI

Calculate Channel Index (CI)
cal.EI

Calculate Enrichment Index (EI)
cal.BI

Calculate Basic Index (BI)
fuzzy_genus_match

Fuzzy Matching of Nematode Genus Names
cal.SRI

Calculate Species Richness Index (SRI)
cal.PPI

Calculate Plant Parasite Index (PPI)
check_nematode_genus

Check validity of nematode genus names against reference database
nematode.ave.mass

Nematode Genus and Family Average Body Mass
nematode.info

Nematode Taxonomic and Functional Traits
diet_rel_abundance

Calculate Diet Relative or Absolute Abundance
runNMDS

Non-Metric Multidimensional Scaling (NMDS) Analysis
rel_abundance

Calculate the Relative Abundance of Nematodes