BioCro (version 3.3.0)

get_all: Get lists of modules, quantities, and solvers

Description

get_all_modules returns the fully-qualified names (of the form library_name:local_module_name) for all modules available in a BioCro module library package.

get_all_quantities returns information about all quantities used as inputs or outputs by modules available in a BioCro module library package.

get_all_ode_solvers returns the names of all ordinary differential equation (ODE) solvers available in the BioCro framework.

Usage

get_all_modules(library_name)
  get_all_quantities(library_name)
  get_all_ode_solvers()

Value

get_all_modules

A character vector of fully-qualified module names

get_all_quantities

A data frame with three columns: quantity_type (input or output), quantity_name, and module_name. A quantity will appear multiple times if it is use as both an input and an output, or if it is used by multiple modules.

get_all_ode_solvers

A character vector of ODE solver names

Arguments

library_name

The name of a BioCro module library

Details

These "get_all" functions return the modules, quantities, and ODE solvers available within the BioCro framework or a BioCro module library package.

Developer details: The get_all_modules and get_all_quantities expect a module library package to include unexported functions called get_all_modules_internal and get_all_quantities_internal, respectively. These functions should not have any input arguments, and their return values should follow the requirements described below for get_all_modules and get_all_quantities. Any module library package created by forking from the skeleton library will automatically include these functions without any modifications to the package's R code.

See Also

• modules

• module_paste

• run_biocro

Examples

# Example 1: Getting a sorted list of distinct quantities defined by modules in
# the `BioCro` module library. Doing this can be useful when writing a new
# module that is intended to work along with pre-existing modules.
all_quantities <- get_all_quantities('BioCro')
all_quantity_names <- all_quantities$quantity_name
distinct_quantities <- sort(unique(all_quantity_names))

# Example 2: Getting a list of all modules in the `BioCro` module library that
# have "ci" as an input or output, using `tolower()` to account for any possible
# variations in capitalization.
all_quantities <- get_all_quantities('BioCro')
ci_modules <- subset(all_quantities, tolower(quantity_name) == "ci")