Ecological Indices Calculator for Nematode Communities
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Documentation for package ‘Nematode’ version 0.2.0
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 |
| 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 |