Package: Nematode 0.3.0

Nematode: Ecological Indices Calculator for Nematode Communities

Provides a computational toolkit for analyzing nematode communities in ecological studies. Includes methods to quantify nematode-based ecological indicators such as metabolic footprints, energy flow metrics, and community structure. These tools support assessments of soil health, ecosystem functioning, and trophic interactions, standardizing the use of nematodes as bioindicators.

Authors:Yuxuan He [aut, cre], Dong Wang [ths], Yuan Miao [ths]

Nematode_0.3.0.tar.gz
Nematode_0.3.0.zip(r-4.7)Nematode_0.3.0.zip(r-4.6)Nematode_0.3.0.zip(r-4.5)
Nematode_0.3.0.tgz(r-4.6-any)Nematode_0.3.0.tgz(r-4.5-any)
Nematode_0.3.0.tar.gz(r-4.7-any)Nematode_0.3.0.tar.gz(r-4.6-any)
Nematode_0.3.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
Nematode/json (API)
NEWS

# Install 'Nematode' in R:
install.packages('Nematode', repos = c('https://h-xuanjiu.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/h-xuanjiu/nematode/issues

Datasets:

On CRAN:

Conda:

nematode

3.30 score 2 stars 490 downloads 25 exports 25 dependencies

Last updated from:0aca509cb4. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK135
source / vignettesOK171
linux-release-x86_64OK115
macos-release-arm64OK176
macos-oldrel-arm64OK192
windows-develOK88
windows-releaseOK94
windows-oldrelOK91
wasm-releaseOK97

Exports:cal.BIcal.CIcal.EIcal.Hcal.Jcal.MIcal.NCRcal.PPIcal.SIcal.Simpsoncal.SRIcal.TDcal.WIcheck_nematode_genuscp_rel_abundancediet_rel_abundanceEcological.Indicesfuzzy_genus_matchNEFNMFnum_speciesrel_abundancerunNMDSrunPCoArunSimper

Dependencies:cliclusterdplyrgenericsgluelatticelifecyclemagrittrMASSMatrixmgcvnlmepermutepillarpkgconfigpurrrR6rlangstringdisttibbletidyselectutf8vctrsveganwithr

Readme and manuals

Help Manual

Help pageTopics
Calculate Basic Index (BI)cal.BI cal.BI.data.frame cal.BI.default cal.BI.matrix
Calculate Channel Index (CI)cal.CI cal.CI.data.frame cal.CI.default cal.CI.matrix
Calculate Enrichment Index (EI)cal.EI cal.EI.data.frame cal.EI.default cal.EI.matrix
Calculate Shannon-Wiener Index (H)cal.H cal.H.data.frame cal.H.default cal.H.matrix
Calculate Pielou's Evenness Index (J)cal.J cal.J.data.frame cal.J.default cal.J.matrix
Calculate Maturity Index (MI)cal.MI cal.MI.data.frame cal.MI.default cal.MI.matrix
Calculate Nematode Channel Ratio (NCR)cal.NCR cal.NCR.data.frame cal.NCR.default cal.NCR.matrix
Calculate Plant Parasite Index (PPI)cal.PPI cal.PPI.data.frame cal.PPI.default cal.PPI.matrix
Calculate Structure Index (SI)cal.SI cal.SI.data.frame cal.SI.default cal.SI.matrix
Calculate Simpson Indexcal.Simpson cal.Simpson.data.frame cal.Simpson.default cal.Simpson.matrix
Calculate Species Richness Index (SRI)cal.SRI cal.SRI.data.frame cal.SRI.default cal.SRI.matrix
Calculate Trophic Diversity (TD) Indexcal.TD cal.TD.data.frame cal.TD.default cal.TD.matrix
Calculate Wasilewska Index (WI)cal.WI cal.WI.data.frame cal.WI.default cal.WI.matrix
Check validity of nematode genus names against reference databasecheck_nematode_genus check_nematode_genus.character check_nematode_genus.data.frame check_nematode_genus.default
Calculate CP Relative or Absolute Abundancecp_rel_abundance cp_rel_abundance.data.frame cp_rel_abundance.default cp_rel_abundance.matrix
Calculate Diet Relative or Absolute Abundancediet_rel_abundance diet_rel_abundance.data.frame diet_rel_abundance.default diet_rel_abundance.matrix
Calculate Ecological Indices of NematodesEcological.Indices Ecological.Indices.data.frame Ecological.Indices.default Ecological.Indices.matrix
Fuzzy Matching of Nematode Genus Namesfuzzy_genus_match
Nematode Energy Footprints (NEF) CalculationNEF NEF.data.frame NEF.default NEF.matrix
Nematode Genus and Family Average Body Massnematode.ave.mass
Nematode Taxonomic and Functional Traitsnematode.info
Nematode Metabolic Footprints (NMF) CalculationNMF NMF.data.frame NMF.default NMF.matrix
Calculate Number of Speciesnum_species num_species.data.frame num_species.default num_species.matrix
Calculate the Relative Abundance of Nematodesrel_abundance rel_abundance.data.frame rel_abundance.default rel_abundance.matrix
Non-Metric Multidimensional Scaling (NMDS) AnalysisrunNMDS runNMDS.data.frame runNMDS.default runNMDS.matrix
Principal Coordinates Analysis (PCoA) AnalysisrunPCoA runPCoA.data.frame runPCoA.default runPCoA.matrix
Similarity Percentages AnalysisrunSimper runSimper.default runSimper.Ordination
Summarize NMDS Resultssummary.NMDS summary.PCoA