extractLIMdata: Extract data from formatted LIM.

In dswdejonge/fwstability: Infer Food-Web Stability

Extract data from formatted LIM.

Description

This function automatically extracts (physiological) data from a LIM that is formatted with tags.

Usage

extractLIMdata(model, verbose = TRUE)

Arguments

model

(required) A named list containing elements with food web model data. LIM (required) should contain a read-in LIM. Achieved through Read(<path-to-input-file>) web (optional) can contain a named numeric vector with flow solutions. If the LIM is not resolved, the function will use the parsimonious (least distance) solution. aTag (optional) Tag assigned to the variables representing the assimilated amount of material. Default is set to "ass". Not case sensitive. gTag (optional) Tag assigned to the variables representing growth. Default is set to "growth". Not case sensitive. mTag (optional) Tag assigned to the flows or variables containing the natural, i.e. non-predatory, mortality. Default is set to "mort". Not case sensitive. deadTag (optional) Tag assigned to the dead compartments (e.g. detritus, carrion, nutrients). Default is set to "dead". Not case sensitive. defTag (optional) Tag assigned to the flows representing defecation. Default is set to "def". Not case sensitive. setup (optional) Setup(Read(lim.input)). By inclusion the function won't setup the model, thereby potentially saving time.

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 and variables representing assimilation, growth, defecation, and mortality of an organism must be named as: "compartmentTag" or "tagCompartment" (not case sensitive). The dead compartments must include the deadTag. For more information on setting up the LIM, please review the vignette.

Value

Returns a list with flowmatrix FM, biomasses BM, conversion efficiencies CE$AE and CE$GE, names of external compartments externals, information on dead compartments dead, and mortality rates MR.

References

LIM package, Soetaert & van Oevelen 2015.

See Also

getJacobian

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