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).
Setup(...)
# S3 method for limfile
Setup(file, verbose = TRUE, ...)
# S3 method for character
Setup(...)
# S3 method for liminput
Setup(liminput,...)a list containing:
name of the inverse input file.
number of unknowns.
number of equations.
number of constraints.
number of components.
number of externals.
number of variables.
matrix A of equalities Ax=B.
vector B of equalities Ax=B.
matrix G of inequalities Gx>h.
vector H of inequalities Gx=h.
cost vector (to minimise), the weight of each unknown; if not specified; 1 for all unknowns.
profit vector (to maximise).
matrix where element ij denotes flow from compartment i to j.
matrix VarA of variable equation VarA*x=VarB.
vector VarB of variable equation VarA*x=VarB.
a vector with flow names.
a data.frame with parameter names and values.
a data.frame with state names and values.
a data.frame with external names and values.
a data.frame with rate names and values.
a data.frame with marker names and values.
a vector with variable names.
a vector with names of unknowns (either states or flows).
a vector with the weights of unknowns- default is 1.
name of the inverse input file.
if TRUE: prints warnings and messages to the screen.
list of elements, as returned by Read.
extra parameters allowing this to be a generic function.
Karline Soetaert <karline.soetaert@nioz.nl>
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
LIMinputBlending
Setup(LIMinputBlending )
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