#' Get default model parameters.
#'
#' \code{def_pars} takes returns the default values for all host and symbiont
#' parameters used in the model.
#'
#' @param nsym The number of distinct symbionts to include in the model.
#'
#' @return A list of the default values for
#' all parameters used in the model. Each list element is named as the
#' parameter name. Host parameters have length one, and symbiont parameters have length \code{nsym}
#' @examples
#' def_pars()
#' pars <- def_pars()
def_pars <- function(nsym=1) {
return(list(
jHT0=0.03, # Host specific biomass turnover rate (d^-1)
nNH=0.18, # N:C ratio in host biomass (-)
nNX=0.2, # N:C ratio in prey biomass (-)
sigmaNH=0.9, # Proportion of host nitrogen turnover recycled (-)
sigmaCH=0.1, # Proportion of host carbon turnover recycled (-)
jXm=0.13, # Maximum specific host feeding rate (molX/CmolH/d)
jNm=0.035, # Maximum specific host DIN uptake rate (molN/CmolH/d)
jHGm=1, # Maximum specific host growth rate (CmolH/CmolH/d)
kCO2=10, # Rate of host CCM's (molCO2/molC/d)
KN=1.5e-6, # Half-saturation constant for host DIN uptake (molN/L)
KX=1e-6, # Half-saturation constant for host feeding (CmolX/L)
initH=1, # Initial host biomass (CmolH)
yC=0.8,
jST0=rep(0.03, nsym), # Symbiont specific biomass turnover rate (d^-1)
nNS=rep(0.13, nsym), # N:C ratio in symbiont biomass (-)
yCL=rep(0.1, nsym), # L:C ratio in fixed carbon (=quantum yield) (molC/mol ph)
kNPQ=rep(112, nsym), # capacity of non-photochemical quenching (mol ph/CmolS/d)
# calculated as 4x max. photochemical quenching (Gorbunov et al. 2001)
kROS=rep(80, nsym), # amount of excess light beyond NPQ capacity (e.g., jeL-jNPQ) that doubles ROS production relative to baseline (mol ph/CmolS/d)
k=rep(1, nsym), # exponent on ROS production (-)
astar=rep(1.34, nsym), # Symbiont specific cross-sectional area (m^2/C-molS)
sigmaNS=rep(0.9, nsym), # Proportion of symbiont nitrogen turnover recylced (-)
sigmaCS=rep(0.9, nsym), # Proportion of symbiont carbon turnover recycled (-)
jCPm=rep(2.8, nsym), # Maximum specific photosynthate production rate (Cmol/CmolS/d)
jSGm=rep(0.25, nsym), # Maximum specific symbiont growth rate (CmolS/CmolS/d)
initS=rep(1, nsym), # Initial symbiont biomass (CmolS)
b=rep(5, nsym) # Scaling parameter for bleaching response
))
}
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