Network function

Network Class Definition

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

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)