In smitdave/MASH: MASH (Modular Analysis and Simulation for Human Health)

Guide to Writing Components and Modules for MASH

Note: XX refers to generic function or class and is purely for illustrative example.
Note: proper documentation should use roxygen2.

Classes

Methods

Conventions for Writing Public Methods (initialized in public list and accessed by self$XX()):
- get_XX() : return the thing. potentially with ix arg for lists (if ix = NULL then return the whole list)
- set_XX() : set the thing, potentially with (XX, ix) arg for setting an element of list (if ix = NULL set the entire object)
- push_XX() : push to the end of the thing; useful for growing vectors
- accumulate_XX() : add to the thing, sort of like XX += YY
- increment_XX(): increment the thing by 1; like the above but just for one
- track_XX(): add to the history of XX (ie; track_Travel records travel history...)
- extend_XX(): add empty/NULL values to end of lists for memory allocation
- add_XX(): useful for when you need to add very specific information to something with a specific structure (ie: add_riskList)
- clear_XX(): zero out multiple entries in this list object according to some logic
- zero_XX(): similar to clear_XX() but takes as an argument an integer index; only zeros out a single element.
- full_XX(): return indices of full slots (0L if none)
- empty_XX(): return indices of empty slots (0L if none)
- init_XX(): used to initalize routines (see init_MacroHuman_travel() in MACRO-Human-Travel.R)
- sim_XX(): simulate a thing (eg sim_ActivitySpace)
  - need to turn simMacro into sim_Macro()
Getters & Setters:
- set_XX(XX, ix = NULL): XX is the new replacement, if the field XX is indexed (ie; a vector or list), ix is the index to replace. If ix = NULL, the entire field is replaced.
- get_XX(ix = NULL): If the field XX is indexed (ie; a vector or list), ix is the index to get If ix = NULL, the entire field is returned.
Pointers:

Fields

Setup Functions

XX.Setup() are functions called before any R6Class objects are created in an environment, and directly add/modify methods and fields in R6ClassGenerator objects.

Init Methods

XX.Init() are methods attached to R6ClassGenerator objects that initialize certain parameters or fields of R6Class objects that already exist in an environment. They are not typically called during construction of the object and are usually called afterwards, with user input, prior to beginning a simulation.

Parameters Functions

XX.Parameters() are functions that usually return a list of parameters, and are typically called with default arguments during initialization and whose output is typically assigned to a private field of the form private$XX_PAR.