Network: Network Class Definition

In MGDrivE: Mosquito Gene Drive Explorer

Description

A Network class object stores all the information for a simulation on a defined landscape.

Format

An R6Class generator object

Constructor

• params: see parameterizeMGDrivE

• driveCube: an inheritance cube

• patchReleases: see basicRepeatedReleases for examples on how to set up release schedules

• migrationMale: a stochastic matrix whose dimensions conform to the number of patches

• migrationFemale: a stochastic matrix whose dimensions conform to the number of patches

• migrationBatch: a list of batch migration parameters. SeebasicBatchMigration

• directory: character string of output directory

• verbose: Chatty? Default is TRUE

Methods

• get_timeAq: see get_timeAq_Network

• get_beta: see get_beta_Network

• get_muAd: see get_muAd_Network

• get_muAq: see get_muAq_Network

• get_alpha: see get_alpha_Network

• get_drivecubeindex: see get_drivecubeindex_Network

• get_tau: see get_tau_Network

• get_genotypesID: see get_genotypesID_Network

• get_genotypesN: see get_genotypesN_Network

• get_eta: see get_eta_Network

• get_phi: see get_phi_Network

• get_omega: see get_omega_Network

• get_xiF: see get_xiF_Network

• get_xiM: see get_xiM_Network

• get_s: see get_s_Network

• get_nPatch: see get_nPatch_Network

• get_conADM: see get_conM_Network

• get_conADF: see get_conF_Network

• get_tNow: see get_tNow_Network

• get_patchReleases: see get_patchReleases_Network

• oneDay_Migration: see oneDay_Migration_Deterministic_Network or see oneDay_Migration_Stochastic_Network

• reset: see reset_Network

• oneDay: see oneDay_Network

• oneRun: see oneRun_Network

• multRun: see multRun_Network

Fields

• parameters: see parameterizeMGDrivE

• patches: a list of Patch objects

• nPatch: number of patches

• simTime: maximum time of simulation

• sampTime: how often to write output, tNow %% sampTime

• driveCube: an inheritance cube

• tNow: current time of simulation (time starts at 2 because time 1 is the initial equilibrium state)

• runID: an identifier for the current simulation run, useful for Monte Carlo simulation

• directory: a character string of where to store output

• conADM: a connection to write male population dynamics out to

• conADF: a connection to write female population dynamics out to

• migrationMale: a stochastic matrix whose dimensions conform to the number of patches

• migrationFemale: a stochastic matrix whose dimensions conform to the number of patches

• migrationBatch: list of items for batch migration in stochastic sim.

• mMoveMat: holder object for male migration

• fMoveArray: holder object for female migration

• patchReleases: a list of release schedules for each patch

Examples

 ## Not run: 
 # There are no simple examples for this, so looking at the vignettes would be
 #  most useful.

 # Complete manual with examples, but none explored in depth.
 vignette("MGDrivE-Examples", package = "MGDrivE")

 # One example, explored in great detail. This is probably more helpful.
 vignette("MGDrivE-Run", package = "MGDrivE")

 
## End(Not run)

MGDrivE documentation built on Oct. 23, 2020, 7:28 p.m.