Read {LIM}R Documentation

Reads an inverse input file

Description

Reads an inverse input file and creates the inverse problem as a list, of type "liminput"

Usage

Read(file, verbose=FALSE, checkLinear=TRUE, remtabs=TRUE)

Arguments

file name of inverse input file
verbose if TRUE: prints warnings and messages to the screen
checkLinear if FALSE: does not check for linearity
remtabs remove tabs

Details

The structure of an inverse input file is explained in vignette("LIM") which should be consulted.

In short the inverse input file contains the declaration sections enclosed inbetween two lines starting with a ##.
For instance, the following section declares two components
# COMP
State1
State2
# END COMP

Only the first 4 characters of the section names are read
The following sections are allowed:

Any (part of a) line starting with a "!" is considered a comment.

Input is NOT case sensitive

The output of this function is used as input in function Setup which creates the inverse matrices

By default, only linear problems can be solved, and the function checks whether the input is linear. To toggle off this check, set checkLinear to FALSE.

Some input files contain tabs, which are converted to spaces, unless this logical is set to FALSE.

Value

a list containing :

file name of inverse input file
pars a data.frame with parameter declarations
comp a data.frame with compartments (or states, stocks)
rate a data.frame with rate declarations
extern a data.frame with external declarations
flows a data.frame with flow declarations
vars a data.frame with variable declarations
cost a data.frame with cost declarations
profit a data.frame with profit declarations
equations a data.frame with equality declarations
constraints a data.frame with constraint declarations
reactions a data.frame with reaction declarations
posreac a vector with TRUE if reaction or flow is unidirectional (and is thus positive), FALSE if two-way reaction or flow
marker a data.frame with marker declarations - see vignette("LIM")
parnames a vector with parameter names
varnames a vector with variable names
compnames a vector with compartment names
externnames a vector with names of externals
Type a string; one of "web" (flows are unknowns), "reaction" (reaction rates unknown) and "simple" (compartments are unknowns

Author(s)

Karline Soetaert <k.soetaert@nioo.knaw.nl>

See Also

Setup the function to create inverse matrices, based on output of Read

Examples

  # this input has been created with function Read:
  LIMinputBlending
  ## Not run: 
  wd <- getwd()
  setwd(paste(system.file(package="LIM"), "/examples/Foodweb", sep=""))
  Read("RigaAutumn.input")
  setwd(wd)
  
## End(Not run)
  

[Package LIM version 1.2 Index]