ecoStep: Ecosystem Step

In cboettig/bs-tipping: Bifurcation or State Tipping in a Trophic Cascade Experiment

Description

Compute the rate of change of the five ecosystem state variables given initial conditions and parameters

Usage

ecoStep(X, pars = c(qE = 0.01), fA = 2, cJA = 0.1, cJF = 0.5,
  cFA = 0.3, vuln = 80, hide = 80, surv = 0.6, Fo = 200, DF = 0.09,
  Zmix = 4, nZ = 10, rP = 3, Load = 0.6, mP = 0.1, Ho = 4,
  DH = 0.5, cHF = 0.1, alf = 0.3, cPH = 0.25, I0 = 300,
  k_sat = 0.012, k_inh = 0.004, DOC = 5, eps0 = 0.0213 + 0.0514 * DOC,
  epsP = 0.0177)

Arguments

X	vector of length 3 with names P0 (initial phytoplankton), H0 (initial herbivore [zooplankton]), A0 (adult piscivorous fish), F0 (planktivorous fish), and J0 (juvenile piscivores). Indicates starting value of state variables
pars	a length 1 vector with name qE, indicating harvesting rate of adults
fA	Fecundity of adult piscivore (2 in OLD)
cJA	Density dependent mortality rate of juveniles
cJF	Consumption of juveniles by planktivores
cFA	Consumption of planktivores by adult piscivores
vuln	Vulnerability coefficient (this is "v" in eco lett table/ equations)
hide	Hiding coefficient (this is "h" in eco lett table/ equations)
surv	Overwinter survivorship of adults
Fo	Refuge density of planktivores
DF	Diffusion parameter for planktivores
Zmix	depth of mixed layer in meters
nZ	number of steps for vertical integration
rP	phytoplankton growth parameter
Load	daily phosphorus load
mP	phytoplankton daily mortality
Ho	refuge biomass
DH	diffusion parameter for zooplankton (herbivore)
cHF	consumption rate by planktivore (of zooplankton)
alf	conversion efficiency of consumed phytoplankton to zooplankton
cPH	consumption rate of phytoplankton by zooplankton
I0	surface irradiance, microEinsteins m-1 s-1
k_sat, k_inh	photosynthesis-irradiance parameters
k_inh	per microEinsteins
DOC, eps0, epsP	Light extinction parameters from Carpenter et al. L&O 1998; DOC is dissolved organic carbon; eps are in units per m
eps0, epsP	extinction coefficient, per m
I0	surface irradiance
k_sat	per microEinsteins m-1 s-1
DOC	dissolved organic carbon, g m-3

Value

named vector of length 5, with names corresponding to juvenile bass (J0), adult bass (A0), and sunfish (F0) abundances.

Note

F are referred to as planktivorous fish, but they do feed on the juvenile piscivores (J).

Examples

ecoStep(X=c(A0=1.5,F0=25,J0=2, H0=1, P0=1), pars=c(qE=0.01))

cboettig/bs-tipping documentation built on May 5, 2019, 7:08 a.m.