getDeadInfo: Gets list with information on dead compartments.

In dswdejonge/fwstability: Infer Food-Web Stability

Gets list with information on dead compartments.

Description

This function determines for each dead compartment whether or not defecation occurs into it, and, if parallel flows occur, what fraction of each flow is defecation.

Usage

getDeadInfo(dead, readLIM, web, FM = NULL, defTag = NULL, verbose = TRUE)

Arguments

dead	(required) A list with the element "names" that contains a character vector with names of all dead compartments.
readLIM	(required) A linear inverse model read into the R environment with the R-package LIM. Can be achieved with readLIM <- Read("path_to_input_file")
web	(required) A named numeric vector with the flow solutions.
FM	(optional) A flow matrix with flows from source in rows to sink in columns.
defTag	(optional) Tag assigned to the flows representing defecation. Default is set to "def". Not case sensitive.
verbose	(optional) Should the function provide messages?

Details

In order for this function to work, the LIM must be set-up in a specific way. The flows representing defecation of an organism must be named as: "compartmentTag" or "tagCompartment" (not case sensitive). For more information on setting up the LIM, please review the vignette.

Value

Returns a list with two elements:

• names: a character vector with names of dead compartments

• frac: a matrix the same size as FM containing the fraction of each flow that is defecation

References

LIM package, Soetaert & van Oevelen 2015.

See Also

getFlowMatrix

dswdejonge/fwstability documentation built on Dec. 7, 2022, 7:24 p.m.