document_model: Function to create LaTeX documentation of a model

In JFeldbauer/rodeoFABM: Create FABM fortran90 code from data.frames.

Function to create LaTeX documentation of a model

Description

This function creates LaTeX tables from the tables used to generate the FABM source code. It will generate a table with the statevariables, a table with the model parameter, a table with tzhe process names and descriptions, a table with the process expressions, and a table with the stoichiometry table.

Usage

document_model(
  vars,
  pars,
  pros,
  funs,
  stoi,
  landscape = TRUE,
  tex = "tex",
  ad_col = list(),
  name = "",
  nosplit = FALSE
)

Arguments

vars	data.frame containing the state variables
pars	data.frame containing the parameters
pros	data.frame containing the processes
funs	data.frame containing the functions
stoi	data.frame containing the stoichiometry
landscape	boolean, should the process expression table be in landscape?
tex	name of the column containing the LaTeX expressions to use as symbols
ad_col	named list of additional columns to add to the tables for vars, pars, funs, pros, and stoi. The elements of this list must be the corresponding name (e.g. vars) and the list elements should give the name of the additional column (col_name), an alternative name for the column in the created table (name_out), and a logical value if the column should be created in math mode (math).
name	additional string to paste to the created tex files
nosplit	do not split equations automatically. Sometimes LaTeX will throw an error due to splitting equations over several lines, this option can prevent this.

Author(s)

Johannes Feldbauer

Examples

## Not run: 
library(readODS)
library(rodeoFABM)

# copy example ods file
example_model <- system.file("extdata/simple_model.ods", package= 'rodeoFABM')
dir.create('example') # Create example folder
file.copy(from = example_model, to = 'example',recursive = TRUE)
setwd('example') # Change working directory to example folder

# read in example ods file
odf_file <- "simple_model.ods"
vars <- read_ods(odf_file,1)
pars <- read_ods(odf_file,2)
funs <- read_ods(odf_file,3)
pros <- read_ods(odf_file,4)
stoi <- read_ods(odf_file,5)

# generate documentation
document_model(vars,pars,pros,funs,stoi)

## example with additional columns
document_model(vars, pars, pros, funs, stoi, landscape = FALSE,
               ad_col = list(vars = list(col_name = "default",
                                         name_out = "init. value",
                                         math = FALSE),
                             pars = list(col_name = "default",
                                         name_out = "value",
                                         math = FALSE)))

## End(Not run)

JFeldbauer/rodeoFABM documentation built on Jan. 27, 2024, 11:41 a.m.