Nematode (version 0.2.0)

NEF: Nematode Energy Footprints (NEF) Calculation

Description

Nematode Energy Footprints (NEF) Calculation

Usage

NEF(data, abundance, AE = list(Ba = 0.6, Fu = 0.38, Pp = 0.25, Op = 0.5), ...)
# S3 method for data.frame
NEF(data, abundance, AE = list(Ba = 0.6, Fu = 0.38, Pp = 0.25, Op = 0.5), ...)
# S3 method for matrix
NEF(data, abundance, AE = list(Ba = 0.6, Fu = 0.38, Pp = 0.25, Op = 0.5), ...)
# S3 method for default
NEF(data, abundance, AE = list(Ba = 0.6, Fu = 0.38, Pp = 0.25, Op = 0.5), ...)

Value

A list object of class "NEF" containing the following components:

data

A list with original input data:

• data - Original genus abundance data.frame or matrix of nematode genera

• Abundance - Total abundance data used for calculations

Energy.flux

A list containing energy flow calculations:

• Energy.flux: Data frame of energy flows (\(\mu g~C~100g^{-1}~dry~soil\)) per feeding group. Columns:

  • Sample.ID - Sample identifier

  • BaEF - Bacterial feeders energy flows

  • FuEF - Fungal feeders energy flows

  • PpEF - Plant feeders energy flows

  • OpEF - Omnivores/Predators energy flows

  • TNEF - Total energy flows of nematodes

• C.flux.node: Data frame of Biomass (\(\mu g~C~100g^{-1}~dry~soil\)) per feeding group. Columns:

  • Sample.ID - Sample identifier

  • Ba - Bacterial feeders biomass

  • Fu - Fungal feeders biomass

  • Pp - Plant feeders biomass

  • Op - Omnivores/Predators biomass

• C.flux.path: Data frame of energy flows (\(\mu g~C~100g^{-1}~dry~soil~day^{-1}\)). Columns:

  • Sample.ID - Sample identifier

  • R.to.Ba - Carbon flux from Resources to bacterial feeders

  • R.to.Fu - Carbon flux from Resources to fungal feeders

  • R.to.Pp - Carbon flux from Resources to plant feeders

  • Ba.to.Op - Carbon flux from bacterial to omnivorous channels

  • Fu.to.Op - Carbon flux from fungal to omnivorous channels

  • Pp.to.Op - Carbon flux from plant to omnivorous channels

• U: Data frame of ecosystem stability indices. Columns:

  • Sample.ID - Sample identifier

  • U - Energy flow uniformity index

Arguments

data

A data.frame or matrix containing nematode genus abundance data. Rows represent samples, and columns represent genera.

abundance

A data.frame containing abundance information for the samples. It must match the row names of the input data.

AE

A named list specifying the assimilation efficiencies for nematode feeding groups. Must contain the following elements:

• Ba - Assimilation efficiency for bacterial feeders (default: 0.6)

• Fu - Assimilation efficiency for fungal feeders (default: 0.38)

• Pp - Assimilation efficiency for plant feeders (default: 0.25)

• Op - Assimilation efficiency for omnivores/predators (default: 0.5)

...

Additional arguments (currently unused).

Examples

data <- data.frame(
  Cephalobus = c(10, 20, 30),
  Eucephalobus = c(5, 10, 12),
  Acrobeloides = c(1, 2, 3),
  Caenorhabditis = c(5, 8, 15),
  Aphelenchus = c(5, 13, 11),
  Leptonchus = c(3, 10, 15),
  Pratylenchus = c(9, 2, 15),
  Tylenchus = c(5, 0, 15),
  Mesodorylaimus = c(7, 10, 18),
  Discolaimus = c(1, 10, 25),
  row.names = c("Sample1", "Sample2", "Sample3")
)
abundance <- data.frame(
  Abundance = c(100, 200, 300),
  row.names = c("Sample1", "Sample2", "Sample3")
)
result <- NEF(data, abundance)
print(result)