R: Ecological Indices Calculator for Nematode Communities

# Ecological Indices Calculator for Nematode Communities

## Documentation for package ‘Nematode’ version 0.3.0

- DESCRIPTION file.
- Package NEWS.

## Help Pages

cal.BI | Calculate Basic Index (BI)
cal.BI.data.frame | Calculate Basic Index (BI)
cal.BI.default | Calculate Basic Index (BI)
cal.BI.matrix | Calculate Basic Index (BI)
cal.CI | Calculate Channel Index (CI)
cal.CI.data.frame | Calculate Channel Index (CI)
cal.CI.default | Calculate Channel Index (CI)
cal.CI.matrix | Calculate Channel Index (CI)
cal.EI | Calculate Enrichment Index (EI)
cal.EI.data.frame | Calculate Enrichment Index (EI)
cal.EI.default | Calculate Enrichment Index (EI)
cal.EI.matrix | Calculate Enrichment Index (EI)
cal.H | Calculate Shannon-Wiener Index (H)
cal.H.data.frame | Calculate Shannon-Wiener Index (H)
cal.H.default | Calculate Shannon-Wiener Index (H)
cal.H.matrix | Calculate Shannon-Wiener Index (H)
cal.J | Calculate Pielou's Evenness Index (J)
cal.J.data.frame | Calculate Pielou's Evenness Index (J)
cal.J.default | Calculate Pielou's Evenness Index (J)
cal.J.matrix | Calculate Pielou's Evenness Index (J)
cal.MI | Calculate Maturity Index (MI)
cal.MI.data.frame | Calculate Maturity Index (MI)
cal.MI.default | Calculate Maturity Index (MI)
cal.MI.matrix | Calculate Maturity Index (MI)
cal.NCR | Calculate Nematode Channel Ratio (NCR)
cal.NCR.data.frame | Calculate Nematode Channel Ratio (NCR)
cal.NCR.default | Calculate Nematode Channel Ratio (NCR)
cal.NCR.matrix | Calculate Nematode Channel Ratio (NCR)
cal.PPI | Calculate Plant Parasite Index (PPI)
cal.PPI.data.frame | Calculate Plant Parasite Index (PPI)
cal.PPI.default | Calculate Plant Parasite Index (PPI)
cal.PPI.matrix | Calculate Plant Parasite Index (PPI)
cal.SI | Calculate Structure Index (SI)
cal.SI.data.frame | Calculate Structure Index (SI)
cal.SI.default | Calculate Structure Index (SI)
cal.SI.matrix | Calculate Structure Index (SI)
cal.Simpson | Calculate Simpson Index
cal.Simpson.data.frame | Calculate Simpson Index
cal.Simpson.default | Calculate Simpson Index
cal.Simpson.matrix | Calculate Simpson Index
cal.SRI | Calculate Species Richness Index (SRI)
cal.SRI.data.frame | Calculate Species Richness Index (SRI)
cal.SRI.default | Calculate Species Richness Index (SRI)
cal.SRI.matrix | Calculate Species Richness Index (SRI)
cal.TD | Calculate Trophic Diversity (TD) Index
cal.TD.data.frame | Calculate Trophic Diversity (TD) Index
cal.TD.default | Calculate Trophic Diversity (TD) Index
cal.TD.matrix | Calculate Trophic Diversity (TD) Index
cal.WI | Calculate Wasilewska Index (WI)
cal.WI.data.frame | Calculate Wasilewska Index (WI)
cal.WI.default | Calculate Wasilewska Index (WI)
cal.WI.matrix | Calculate Wasilewska Index (WI)
check_nematode_genus | Check validity of nematode genus names against reference database
check_nematode_genus.character | Check validity of nematode genus names against reference database
check_nematode_genus.data.frame | Check validity of nematode genus names against reference database
check_nematode_genus.default | Check validity of nematode genus names against reference database
cp_rel_abundance | Calculate CP Relative or Absolute Abundance
cp_rel_abundance.data.frame | Calculate CP Relative or Absolute Abundance
cp_rel_abundance.default | Calculate CP Relative or Absolute Abundance
cp_rel_abundance.matrix | Calculate CP Relative or Absolute Abundance
diet_rel_abundance | Calculate Diet Relative or Absolute Abundance
diet_rel_abundance.data.frame | Calculate Diet Relative or Absolute Abundance
diet_rel_abundance.default | Calculate Diet Relative or Absolute Abundance
diet_rel_abundance.matrix | Calculate Diet Relative or Absolute Abundance
Ecological.Indices | Calculate Ecological Indices of Nematodes
Ecological.Indices.data.frame | Calculate Ecological Indices of Nematodes
Ecological.Indices.default | Calculate Ecological Indices of Nematodes
Ecological.Indices.matrix | Calculate Ecological Indices of Nematodes
fuzzy_genus_match | Fuzzy Matching of Nematode Genus Names
NEF | Nematode Energy Footprints (NEF) Calculation
NEF.data.frame | Nematode Energy Footprints (NEF) Calculation
NEF.default | Nematode Energy Footprints (NEF) Calculation
NEF.matrix | Nematode Energy Footprints (NEF) Calculation
nematode.ave.mass | Nematode Genus and Family Average Body Mass
nematode.info | Nematode Taxonomic and Functional Traits
NMF | Nematode Metabolic Footprints (NMF) Calculation
NMF.data.frame | Nematode Metabolic Footprints (NMF) Calculation
NMF.default | Nematode Metabolic Footprints (NMF) Calculation
NMF.matrix | Nematode Metabolic Footprints (NMF) Calculation
num_species | Calculate Number of Species
num_species.data.frame | Calculate Number of Species
num_species.default | Calculate Number of Species
num_species.matrix | Calculate Number of Species
rel_abundance | Calculate the Relative Abundance of Nematodes
rel_abundance.data.frame | Calculate the Relative Abundance of Nematodes
rel_abundance.default | Calculate the Relative Abundance of Nematodes
rel_abundance.matrix | Calculate the Relative Abundance of Nematodes
runNMDS | Non-Metric Multidimensional Scaling (NMDS) Analysis
runNMDS.data.frame | Non-Metric Multidimensional Scaling (NMDS) Analysis
runNMDS.default | Non-Metric Multidimensional Scaling (NMDS) Analysis
runNMDS.matrix | Non-Metric Multidimensional Scaling (NMDS) Analysis
runPCoA | Principal Coordinates Analysis (PCoA) Analysis
runPCoA.data.frame | Principal Coordinates Analysis (PCoA) Analysis
runPCoA.default | Principal Coordinates Analysis (PCoA) Analysis
runPCoA.matrix | Principal Coordinates Analysis (PCoA) Analysis
runSimper | Similarity Percentages Analysis
runSimper.default | Similarity Percentages Analysis
runSimper.Ordination | Similarity Percentages Analysis
summary.NMDS | Summarize NMDS Results
summary.PCoA | Summarize NMDS Results