Network.Rd
A Network
class object stores all the information for a simulation on
a defined landscape.
An R6Class
generator object
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
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
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
# 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") # }