Ecological Indices Calculator for Nematode Communities


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Documentation for package ‘Nematode’ version 0.2.0

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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
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