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Initial set up for Rsim dynamic simulation

Source: R/ecosim.R
rsim.params.Rd

Converts the outputs from Rpath into rates for use in Rsim.

Usage

rsim.params(
  Rpath,
  mscramble = 2,
  mhandle = 1000,
  preyswitch = 1,
  scrambleselfwt = 0,
  handleselfwt = 0,
  steps_yr = 12,
  steps_m = 1
)

Arguments

Rpath

R object containing a static Rpath model.

mscramble

Base value for vulnerability in functional response; default = 2 (mixed response).

mhandle

Base value for handling time in functional response; default = 1000 (off).

preyswitch

Exponent for prey switching in functional response; default = 1 (off).

scrambleselfwt

Value of 1 indicates all predators overlap in the foraging arena while 0 treats predators individually.

handleselfwt

Value of 1 indicates all prey overlap in the arena and contribute to saturation while 0 treats prey individually.

steps_yr

Number of time steps per year; default = 12.

steps_m

Number of time steps per month; default = 1.

Value

Returns an object of class Rsim.params, a list of 39 objects that is passed to the rsim.run function via the rsim.scenario function.

  • NUM_GROUPS, number of total model groups

  • NUM_LIVING, number of living model groups

  • NUM_DEAD, number of detritus model groups

  • NUM_GEARS, number of fishery model groups

  • NUM_BIO, number of living + detritus model groups

  • spname, named NUM_GROUPS+1 length character vector beginning with "Outside" containing names of all model groups

  • spnum, named NUM_GROUPS+1 length character vector beginning with "Outside" numbered 0, containing numbers of all model groups

  • B_BaseRef, named NUM_GROUPS+1 length character vector beginning with "Outside" containing Rpath base biomass of all model groups

  • MzeroMort, named NUM_GROUPS+1 length character vector beginning with "Outside" containing unaccounted mortality, calculated as PB * (1.0 - EE), of all model groups

  • UnassimRespFrac, named NUM_GROUPS+1 length character vector beginning with "Outside" containing the proportion of consumption that goes to detritus of all model groups

  • ActiveRespFrac, named NUM_GROUPS+1 length character vector beginning with "Outside" containing the proportion of consumption that is "lost to heat" for all model groups

  • FtimeAdj, named NUM_GROUPS+1 length character vector beginning with "Outside" containing rate of change of feeding time, currently set to 0 for all model groups

  • FtimeQBOpt, named NUM_GROUPS+1 length character vector beginning with "Outside" containing base QB for all consumer model groups, or base PB for primary producers

  • PBopt, named NUM_GROUPS+1 length character vector beginning with "Outside" containing base PB for all model groups

  • NoIntegrate, named NUM_GROUPS+1 length character vector beginning with "Outside" containing flag set to 0 for high turnover model groups and set to spnum for all others

  • Handleself, named NUM_GROUPS+1 length character vector beginning with "Outside" containing flag for handling time influence, set for all model groups with function argument handleselfwt, default 0 for individual prey handling time

  • Scrambleself, named NUM_GROUPS+1 length character vector beginning with "Outside" containing flag for predator density influence, set for all model groups with function argument scrambleselfwt, default 0 for individual predator density dependent predation

  • PreyFrom, numeric vector length NumPredPreyLinks+1, spnum of prey for each predator prey interaction pair in the model

  • PreyTo, numeric vector length NumPredPreyLinks+1, spnum of predator for each predator prey interaction pair in the model

  • QQ, numeric vector length NumPredPreyLinks+1, base consumption rate for each predator prey interaction pair in the model

  • DD, numeric vector length NumPredPreyLinks+1, handling time effect on functional response for each predator prey pair, set for all model groups with function argument mhandle, default = 1000

  • VV, numeric vector length NumPredPreyLinks+1, vulnerability effect on functional response for each predator prey pair, set for all model groups with function argument mscramble, default = 2

  • HandleSwitch, numeric vector length NumPredPreyLinks+1, prey density dependence effect on functional response for each predator prey pair, set for all model groups with function argument preyswitch, default = 1

  • PredPreyWeight, numeric vector length NumPredPreyLinks+1, relative weight of individual predator to total predators for each predator prey pair, used if scrambleselfwt>0

  • PreyPreyWeight, numeric vector length NumPredPreyLinks+1, relative weight of individual prey to total prey for each predator prey pair, used if handleselfwt>0

  • NumPredPreyLinks, number of predator to prey linkages over all groups in the model

  • FishFrom, numeric vector length NumFishingLinks+1, spnum of landing and discard for each fishery interaction in the model

  • FishThrough, numeric vector length NumFishingLinks+1, spnum of gear type for each fishery interaction in the model

  • FishQ, numeric vector length NumFishingLinks+1, landings or discards relative to base fished group biomass for each fishery interaction in the model

  • FishTo, numeric vector length NumFishingLinks+1, spnum of sink for each fishery interaction in the model ("Outside" for landings or detritus group for discards)

  • NumFishingLinks, number of model group landings and discards to fishery links over all groups in the model

  • DetFrac, numeric vector length NumDetLinks+1, fraction of detritus going to DetTo for each living and detritus group in the model

  • DetFrom, numeric vector length NumDetLinks+1, spnum flowing to detritus for each living and detritus group in the model

  • DetTo, numeric vector length NumDetLinks+1, spnum of detritus sink for each living and detritus group in the model

  • NumDetLinks, number of model group links to detritus over all groups in the model

  • BURN_YEARS, number of model run burn-in (spin up) years, default value -1

  • COUPLED, number to control species interactions, value of 0 allows density dependent non-interacting species, default value 1

  • RK4_STEPS, number of RK4 integration steps per month, default value 4

  • SENSE_LIMIT, numeric vector of multipliers on biomass determining acceptable range for continuing a model run within BURN_YEARS

See also

Other Rsim functions: extract.node(), rsim.plot(), rsim.run(), rsim.scenario(), rsim.step(), write.Rsim()

Examples

# Read in Rpath parameter file and generate model object
Rpath <- rpath(AB.params)
# Create default dynamic parameters from Rpath model
Rsim.params <- rsim.params(Rpath)