initModel: Create model object and generate code
In dkneis/rodeoApp: Interfaces for Rodeo-Based Models

Description Usage Arguments Value Note Author(s)

Creates a model object from user inputs and builds a shared library from generated Fortran code.

initModel(dir = ".", xlFile = "model.xlsx", funsR = "functions.r",
  funsF = list.files(path = dir, pattern = ".+[.]f95$"), tables = c(vars =
  "vars", pars = "pars", funs = "funs", pros = "pros", stoi = "stoi"),
  colsep = ",", stoiAsMatrix = FALSE, dllname = NULL)

`dir`	Directory where input files are located. This is assumed to apply to any input files (i.e. `xlFile`, `funsR`, `funsF`, and possibly the values of `tables`).
`xlFile`	Either the base name of file in MS Excel format holding the model definition or `NULL`. In the latter case, the model definition is read from delimited text files using `read.table(header=TRUE, sep=colsep)` where the last argument is under user control (see `colsep` below).
`funsR`	Base name of file with function definitions in R.
`funsF`	Base name of file with function definitions in Fortran 95.
`tables`	Named vector with required elements 'vars', 'pars', 'funs', 'pros', and 'stoi'. If a file name was supplied in `xlFile`, the values are interpreted as the names of worksheets holding the declaration of variables, parameters, functions, process rates, and stoichiometry factors, respectively. If `xlFile` is an empty string, the values are interpreted as the names of delimited text files holding the respective information.
`colsep`	Specifies the column separator in text files. Only used if `xlFile` is `NULL`.
`stoiAsMatrix`	Logical. Allows the stoichiometry matrix to be supplied as a 3-column table or as a matrix.
`dllname`	Character string used as the name for the built library. This is the base name without file extension (must not contain path separators, white space, etc.). If set to `NULL` (the default), an automatic name is assigned. The library is created in the folder returned by `tempdir()` and it carries the system-specific extension for shared libraries according to `.Platform$dynlib.ext`.

A list with the following components.

model : Object of class rodeo representing the model.
dllfile : File path of library with compiled Fortran code.
funsR : Full name of the file with R functions.
vars : Data frame with variable declarations.
pars : Data frame with parameter declarations.

Files in MS Excel format can also be created/edited with free software such as, e.g., LibreOffice Calc.

Spreadsheets are typically more convenient to edit as compared to delimited text files. However, with text files it is easier to track the history of a model using version control software and/or diff tools.

David Kneis david.kneis@tu-dresden.de

dkneis/rodeoApp documentation built on May 15, 2019, 9:12 a.m.