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Last data update: 2014.03.03

R: Creates linear inverse matrices

Setup

R Documentation

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

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.

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.

Author(s)

Karline Soetaert <karline.soetaert@nioz.nl>

Examples

   LIMinputBlending
   Setup(LIMinputBlending )

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/Setup.Rd_%03d_medium.png", width=480, height=480)
> ### Name: Setup
> ### Title: Creates linear inverse matrices
> ### Aliases: Setup Setup.limfile Setup.liminput Setup.character
> ### Keywords: IO utilities
> 
> ### ** Examples
> 
>    LIMinputBlending
$file
[1] "blending.input"

$pars
          name nr val par1 par2 par3 par4 var flow comp external reaction
1 MinNutrientA  1  80   NA   NA   NA   NA  NA   NA   NA       NA       NA
2 MinNutrientB  2  50   NA   NA   NA   NA  NA   NA   NA       NA       NA
3 MinNutrientC  3  25   NA   NA   NA   NA  NA   NA   NA       NA       NA
4 MinNutrientD  4   5   NA   NA   NA   NA  NA   NA   NA       NA       NA

$comp
          name nr val par1 par2 par3 par4 var flow comp external reaction
1 pIngredient1  1  NA   NA   NA   NA   NA  NA   NA   NA       NA       NA
2 pIngredient2  2  NA   NA   NA   NA   NA  NA   NA   NA       NA       NA
3      pFiller  3  NA   NA   NA   NA   NA  NA   NA   NA       NA       NA

$rate
NULL

$extern
NULL

$flows
NULL

$vars
NULL

$cost
   name nr val par1 par2 par3 par4 var flow comp external reaction
1 cost1  1  40   NA   NA   NA   NA  NA   NA    1       NA       NA
2 cost1  1  60   NA   NA   NA   NA  NA   NA    2       NA       NA

$profit
NULL

$equations
         name nr val par1 par2 par3 par4 var flow comp external reaction
left  Balance  1  -1   NA   NA   NA   NA  NA   NA    1       NA       NA
left1 Balance  1  -1   NA   NA   NA   NA  NA   NA    2       NA       NA
left2 Balance  1  -1   NA   NA   NA   NA  NA   NA    3       NA       NA
left3 Balance  1   1   NA   NA   NA   NA  NA   NA   NA       NA       NA

$constraints
        name nr val par1 par2 par3 par4 var flow comp external reaction
1  NutrientA  1 100   NA   NA   NA   NA  NA   NA    1       NA       NA
2  NutrientA  1 200   NA   NA   NA   NA  NA   NA    2       NA       NA
3  NutrientA  1  -1    1   NA   NA   NA  NA   NA   NA       NA       NA
4  NutrientB  2  50   NA   NA   NA   NA  NA   NA    1       NA       NA
5  NutrientB  2 150   NA   NA   NA   NA  NA   NA    2       NA       NA
6  NutrientB  2  -1    2   NA   NA   NA  NA   NA   NA       NA       NA
7  NutrientC  3  40   NA   NA   NA   NA  NA   NA    1       NA       NA
8  NutrientC  3  10   NA   NA   NA   NA  NA   NA    2       NA       NA
9  NutrientC  3  -1    3   NA   NA   NA  NA   NA   NA       NA       NA
10 NutrientD  4  10   NA   NA   NA   NA  NA   NA    1       NA       NA
11 NutrientD  4  -1    4   NA   NA   NA  NA   NA   NA       NA       NA

$reactions
NULL

$posreac
NULL

$marker
NULL

$parnames
[1] "MinNutrientA" "MinNutrientB" "MinNutrientC" "MinNutrientD"

$varnames
NULL

$compnames
[1] "PINGREDIENT1" "PINGREDIENT2" "PFILLER"     

$externnames
NULL

$Type
[1] "simple"

attr(,"class")
[1] "liminput"
>    Setup(LIMinputBlending )
$file
[1] "blending.input"

$NUnknowns
[1] 3

$NEquations
[1] 1

$NConstraints
[1] 4

$NComponents
[1] 3

$NExternal
NULL

$NVariables
[1] 0

$A
     [,1] [,2] [,3]
[1,]   -1   -1   -1

$B
[1] -1

$G
     [,1] [,2] [,3]
[1,]  100  200    0
[2,]   50  150    0
[3,]   40   10    0
[4,]   10    0    0

$H
[1] 80 50 25  5

$Cost
[1] 40 60  0

$Profit
NULL

$Flowmatrix
NULL

$VarA
NULL

$VarB
NULL

$Parameters
          name val
1 MinNutrientA  80
2 MinNutrientB  50
3 MinNutrientC  25
4 MinNutrientD   5

$Components
          name val
1 PINGREDIENT1   1
2 PINGREDIENT2   1
3      PFILLER   1

$Externals
data frame with 0 columns and 0 rows

$rates
          name val
1 PINGREDIENT1   0
2 PINGREDIENT2   0
3      PFILLER   0

$markers
NULL

$Variables
NULL

$costnames
[1] cost1
Levels: cost1

$profitnames
NULL

$eqnames
[1] Balance
Levels: Balance

$ineqnames
[1] NutrientA NutrientB NutrientC NutrientD
Levels: NutrientA NutrientB NutrientC NutrientD

$Unknowns
[1] "PINGREDIENT1" "PINGREDIENT2" "PFILLER"     

$ispos
[1] TRUE

attr(,"class")
[1] "lim"
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>