Read {LIM} | R Documentation |
Reads an inverse input file and creates the inverse problem as a list, of type "liminput"
Read(file, verbose=FALSE, checkLinear=TRUE, remtabs=TRUE)
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 |
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.
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 |
Karline Soetaert <k.soetaert@nioo.knaw.nl>
Setup
the function to create inverse matrices, based on output of Read
# 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)