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LIM (version 1.4.7.1)

Setup: Creates linear inverse matrices

Description

Creates the linear problem with equality and inequality equations.

Takes as input either a liminput list, as generated by Read or a filename with the linear inverse model specifications. Creates:

  • inverse matrices and vectors A, b, G, h of the equalities/inequalities: $$Ax=b$$ $$Gx>=h$$

  • if present, also generates the cost/profit function which is used as: $$\min(cost)$$ or $$\max(profit)$$

  • if the input was a flow network, Setup will also create the flow matrix (see details).

Usage

Setup(...)
# S3 method for limfile
Setup(file, verbose = TRUE, ...)
# S3 method for character
Setup(...)
# S3 method for liminput
Setup(liminput,...)

Value

a list containing:

file

name of the inverse input file.

NUnknowns

number of unknowns.

NEquations

number of equations.

NConstraints

number of constraints.

NComponents

number of components.

NExternal

number of externals.

NVariables

number of variables.

A

matrix A of equalities Ax=B.

B

vector B of equalities Ax=B.

G

matrix G of inequalities Gx>h.

H

vector H of inequalities Gx=h.

Cost

cost vector (to minimise), the weight of each unknown; if not specified; 1 for all unknowns.

Profit

profit vector (to maximise).

Flowmatrix

matrix where element ij denotes flow from compartment i to j.

VarA

matrix VarA of variable equation VarA*x=VarB.

VarB

vector VarB of variable equation VarA*x=VarB.

Flows

a vector with flow names.

Parameters

a data.frame with parameter names and values.

Components

a data.frame with state names and values.

Externals

a data.frame with external names and values.

rates

a data.frame with rate names and values.

markers

a data.frame with marker names and values.

Variables

a vector with variable names.

Unknowns

a vector with names of unknowns (either states or flows).

Weight

a vector with the weights of unknowns- default is 1.

Arguments

file

name of the inverse input file.

verbose

if TRUE: prints warnings and messages to the screen.

liminput

list of elements, as returned by Read.

...

extra parameters allowing this to be a generic function.

Author

Karline Soetaert <karline.soetaert@nioz.nl>

See Also

Read function that reads inverse input files and produces the input list used by Setup

Lsei, Ldei, Linp functions to solve inverse problem, based on output generated by setup.limfile

Examples

Run this code
   LIMinputBlending
   Setup(LIMinputBlending )

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