Community_Indices: Calculate nematode community indices

In amynang/marcel: Calculates nematode community indices

Calculate nematode community indices

Usage

all.indices(x, nemaplex, ...)

Enrichment(x, nemaplex)
Structure(x, nemaplex)
Channel(x, nemaplex)
C_P(x, nemaplex)
Maturity(x, nemaplex, exclude.plant.feeders = TRUE, exclude.cp1 = TRUE)
Plant.Parasite(x, nemaplex, exclude.cp1 = TRUE)

Arguments

x	A dataframe with locations/samples as rows and nematode taxa (families or genera) as columns. Values can be raw counts, densities or frequencies of the taxa in each sample
nemaplex	The output of query_nemaplex(), containing information about the c-p scores and the feeding habits of the taxa in x
exclude.plant.feeders	Logical. Not excluding plant feeding nematodes corresponds to \SigmaMI in Ferris & Bongers (2009). Defaults to TRUE
exclude.cp1	Logical. Excluding the cp1 class corresponds to (\Sigma)MI2-5 in Ferris & Bongers (2009). Defaults to TRUE

Details

b = (Ba2 + Fu2) * W2, where W2 = 0.8,

e = (Ba1 * W1) + (Fu2 * W2), where W1 = 3.2 and W2 = 0.8

s = (Ban*Wn + Can*Wn + Fun*Wn + Omn*Wn)

where n=3-5, W3.= 1.8, W4.= 3.2, W5.= 5.0

The Enrichment index is calculated as EI = 100 * e / (e + b)

The Structure index is calculated as SI = 100 * s / (s + b)

The Channel index is calculated as CI = 100 * (0.8*Fu2 / (3.2*Ba1 + 0.8*Fu2))

The Coloniser_Persister classes are given as percentages of the total abundance

The Maturity index is calculated as \Sigma([i]*cp[i]) / \Sigmacp[i] with i in [1-5] and cp[i] is the (relative) abundance of that class. Note that the index can be calculated with or without herbivores and with or without the cp1 class.

Value

Either a single column dataframe (in the case of individual index functions), or a dataframe with samples as rows and all the indices calculated by maRcel as columns

Author(s)

Angelos Amyntas

References

Ferris, H., Bongers, T. and Goede, R.G.M. de (2001) A framework for soil food web diagnostics: extension of the nematode faunal analysis concept. Applied Soil Ecology 18, 13-29.

Ferris, H., & Bongers, A. M. T. (2009). Indices Developed Specifically for analysis of Nematode Assemblages. In M. J. Wilson, & T. Kakouli-Duarte (Eds.), Nematodes as Environmental Indicators (pp. 124-145). CAB International.

See Also

query_nemaplex

Examples

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

## The function is currently defined as
function (x) 
{
  }

amynang/marcel documentation built on June 24, 2024, 10 p.m.