R/default_parms.R

In noamross/sodi: Individual-Based Modeling of Sudden Oak Death

#' Default sodi parameters
#' @export
default_parms <- list(
  K=500,                 #Carrying capacity
  bbox = c(0,sqrt(500),0,sqrt(500)),   #Area dimensions
  n0 = 500,               #Initial population
  infect0=1,             #Number of infected individuals at start
  stages0=rep(1,500),     #Distribution of size classes
  dispersalfn = 3,        #disease dispersal: 1-exp, 2-fattail, 3-normal,0 for no spatial component
  seedshadow = 0,          #dispersal kernel for reproduction, if 0, random location
  sp_names = c("Tanoak"),  #vector of species names
  sp_stages = c(2),        #vector of the number of size classes for each species
  m = c(1, 1),           #dispersal parameter
  seedm = c(1,1),          #dispersal parameter for reproduction
  times = seq(0,100,1), #Times to report.  If a single number, the max time, and all events will be recorded
  f = c(0.01, 0.01),     #Fecundity parameter
  g = c(0.1, 0),         #Growth rates
  d = c(0.005, 0.005),   #Death rates
  r = c(0.5, 0.5),       #Resprout probability at death from disease
  alpha = c(0.005, 0.005),  #Increase in death rate per infection
  lamda = c(0.3, 0.3),   #Per-stage contact rate.
  beta = c(1, 1),        #Probability of acquiring disease when contacted
  mu = c(0.05, 0.05),   #Per-infection recovery rate
  xi = c(1, 1),     #Fecundity reduction minus one per infection
  omega = c(1, 1),  #Competitive coefficient
  max_inf = c(1, 1),  #Maximum number of infections per plant.  Set to 1 for S/I model.
  beta_meth = 0 #Maximum infection method.  Zero for none, 1 for step function, 2 for decreasing probability
)