Following MASH's modularity principles the repository is divided into sub-folders for each one of the components of the simulation.

Archive

Mostly depreceated code.

Documents

Some helpfull documents that explain the basics of MASH.

HUMAN

Routines related to human characteristics and behaviour.

ACTIVITY.SPACE

MICRO

BEHAVIOR

PROTECTIVE.CLOTHING

SWATTING

MASS.TREAT

VACCINES

LANDSCAPE

Defines the setup of the environment in which the simulation will run. In the case of mosquito-borne diseases the sugar sources, feeding sites, oviposition spots and mating landmarks are defined here.

MACRO

Not implemented yet.

MICRO

High resolution environments for detailed analysis of interactions.

Micro2Macro

PDG

Not implemented yet.

PLACES

Not implemented yet.

Lessons

MOSQUITO

AQUATIC.ECOLOGY

Variations of the routines needed for aquatic mosquito stages.

  • emerge: mosquitos emerge at a constant rate from oviposition spots (with seasonality variance)
  • EL4P: mosquitos eggs are laid and develop as they would expect in reality through four larval instars and pupa stage (needs to be fixed)

CHOOSE.HOST

Routines that define which host will be bitten by each mosquito.

FEEDING.CYCLE

DHM

Contains all the main routines for the full mosquito life-cycle

  • setup.DHM.R: contains the parameters necessary to change mosquito’s behaviours in the simulation
  • test.DHM.R: temporarily the main routine to test DHM functions

DHM-Basic

RM

Routines that deal with the movement of mosquitos through the landscape.

VECTOR.CONTROL

Implementation of several vector control interventions. setup.VectorControl.R contains the main functions and switches for the interventions to be activated. Each folder contains the implementation of the routines for the control measure.

#Basic random uniform coverage example
setup.Random_Uniform_LANDSCAPE_BasedInterventions(IRS_Coverage = .5, LARVICIDING_Coverage = .5)

PATHOGEN

Generic

Plasmodium.falciparum

Simulations

Stores the main MASH simulations routines.

Default

MosquitoDefault

Utilities

Assortment of various routines for auxiliary tasks.

AnalysisRoutines

Contains some preliminary analysis routines for experiments performed in MASH. They are currently implemented in Mathematica but most of them can easily be translated to R.

Some of the notebooks require “PajaroLoco” (networks). HMSC coded that package and it is publicly available so it is not a problem using or maintaining it.

Open the individual notebooks for a description on what they were created for and please remember to Cell/Delete All Output to avoid repository bloating.

sinHaz