R: Linear inverse model specification for the herpetological...

LIMEverglades

R Documentation

Linear inverse model specification for the herpetological food web
of the Everglades

Description

Linear inverse model specification for the herpetological wet prairie
example from the everglades.

as described in Diffendorfer et al., 2001

The everglades are a freshwater wetland in Florida, USA.

The model contains 9 functional compartments and 3 external compartments,
connected with 402 flows.

Units of the flows are gram wet weight / Ha / year

The linear inverse model LIMEverglades is generated from the file
Everglades.input which can be found in subdirectory /examples/FoodWeb
of the package directory

In this subdirectory you will find many foodweb example input files

These files can be read using Read and their output
processed by Setup which will produce a linear inverse
problem specification similar to LIMEverglades

Usage

data(LIMEverglades)

Format

a list of matrices, vectors, names and values that specify the linear
inverse model problem.

see the return value of Setup for more information about
this list

A more complete description of this structures is in vignette("LIM")

Author(s)

Karline Soetaert <karline.soetaert@nioz.nl>
Dick van Oevelen <dick.vanoevelen@nioz.nl>

References

Diffendorfer, J.E., Richards, P.M., Dalrymple, G.H., DeAngelis, D.L., 2001.
Applying Linear Programming to estimate fluxes in ecosystems or food webs:
an example from the herpetological assemblage of the freshwater Everglades.
Ecol. Model. 144, 99-120.

contains "Everglades.input", the input file; read this with Setup

LIMTakapoto, LIMRigaSummer and many others

Examples

# Cannot be solved, but the least squares solution is found
Flows <- Lsei(LIMEverglades, parsimonious = TRUE)
Everglades <- Flowmatrix(LIMEverglades)
plotweb(Everglades, main = "Everglades Herpetological Wet Prairie model",
sub = "g WW/Ha/Yr", lab.size = 0.8)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(LIM)
Loading required package: limSolve
Loading required package: diagram
Loading required package: shape
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/LIM/LIMEverglades.Rd_%03d_medium.png", width=480, height=480)
> ### Name: LIMEverglades
> ### Title: Linear inverse model specification for the herpetological food
> ### web of the Everglades
> ### Aliases: LIMEverglades
> ### Keywords: datasets
>
> ### ** Examples
>
>
> # Cannot be solved, but the least squares solution is found
> Flows <- Lsei(LIMEverglades, parsimonious = TRUE)
Warning message:
In Lsei.lim(LIMEverglades, parsimonious = TRUE) :
Problem could not be solved - least squares solution returned
> Everglades <- Flowmatrix(LIMEverglades)
Warning message:
In Lsei.lim(lim, parsimonious = TRUE) :
Problem could not be solved - least squares solution returned
> plotweb(Everglades, main = "Everglades Herpetological Wet Prairie model",
+ sub = "g WW/Ha/Yr", lab.size = 0.8)
>
>
>
>
>
> dev.off()
null device
1
>