TrophInd {NetIndices}

The trophic level and omnivory index

Description

Calculates the trophic level and omnivory index of each component of a food web.

Usage

TrophInd(Flow = NULL, Tij = t(Flow), 
         Import = NULL, Export = NULL, Dead = NULL)

Arguments

Flow

network matrix with Flow[i,j] the flow from i (row) to j (column); component positions in rows and columns must be the same; if present, rownames or columnnames denote the compartment names.

Tij

network matrix where connectance is from column j to row i; component positions in rows and columns must be the same ; if present, rownames or columnnames denote the compartment names.

Import

vector with either the *indices* or the *names* of external compartmens from where flow enters the network; the indices point to the column positions in Tij (and the row positions in Flow).

Export

vector with either the *indices* or the *names* of external compartmens to where flow leaves the network; the indices point to the row positions in Tij (and the column positions in Flow).

Dead

vector with either the *indices* or the *names* of dead matter; the indices point to row positions in Tij; the trophic level of these components is assumed to be 1.

Details

Primary producers, defined as those compartments that do not receive matter from another internal compartment, will be assigned a trophic level of 1.

In many trophic level calculations, it is also assumed that TL of detritus, dissolved organic matter and other inert material (i.e. that does not feed) is also = 1.

If this is desired, these compartments have to be designated as "Dead" (i.e. Dead should contain an index to row positions in Tij of these compartments.

If not specified as "Dead", these compartments will have a TL > 1 and consequently the TL of other compartments will be higher too.

The mathematical formulation of these indices can be found in the package vignette - vignette("NetIndices").

The PDF can be found in the subdirectory ‘doc’ of the NetIndices package.

Value

a 2-columned data.frame with, for each compartment of the network the following:

TL

the trophic level of a compartment, defined as 1 + the weighted average of the trophic levels of its food items.

OI

the omnivory index, the variety in the trophic levels of a consumer's food.

Note

Up to version 1.4.1, the estimation of TL produced strange results in case compartments feed on themselves. Then it was possible to produce negative Trophic levels. From version 1.4.2, it is implemented that self-feeding does not affect the TL of the compartment. Because of that, results may be different from the initial versions in such cases.

Author(s)

Karline Soetaert <[e-mail]>, Julius Kipyegon Kones<[e-mail]>

References

Christensen V, Pauly D. 1992. ECOPATH II - a software for balancing steady-state ecosystem models and calculating network characteristics. Ecological Modelling 61: 169-185.

Lindeman RL. 1942. The trophic dynamic aspect of ecology. Ecology 23: 399-418.

Kones, J.K., Soetaert, K., van Oevelen, D. and J.Owino (2009). Are network indices robust indicators of food web functioning? a Monte Carlo approach. Ecological Modelling, 220, 370-382.

Examples

# The takapoto atoll network
# First trophic level without assuming that TL of detritus and DOC is 1
TrophInd(Takapoto, Import = "CO2",
        Export = c("CO2", "Sedimentation", "Grazing"))

# Now imposing TL=1 for detritus and DOC 
TrophInd(Takapoto, Import = "CO2",
        Export = c("CO2", "Sedimentation", "Grazing"),
        Dead = c("Detritus", "DOC"))