popdynCPP: Population dynamics model in CPP
In Blue-Matter/MSEtool: Management Strategy Evaluation Toolkit

popdynCPP

R Documentation

Population dynamics model in CPP

Description

Project population forward pyears given current numbers-at-age and total mortality, etc for the future years

Usage

popdynCPP(
  nareas,
  maxage,
  Ncurr,
  pyears,
  M_age,
  Asize_c,
  MatAge,
  WtAge,
  FecAge,
  Vuln,
  Retc,
  Prec,
  movc,
  SRrelc,
  Effind,
  Spat_targc,
  hc,
  R0c,
  SSBpRc,
  aRc,
  bRc,
  Qc,
  Fapic,
  maxF,
  MPA,
  control,
  SSB0c,
  SRRfun,
  SRRpars,
  plusgroup = 0L,
  spawn_time_frac = 0
)

Arguments

`nareas`	The number of spatial areas
`maxage`	The maximum age
`Ncurr`	A numeric matrix (maxage+1, nareas) with current numbers-at-age in each area
`pyears`	The number of years to project the population forward
`M_age`	Numeric matrix (maxage+1, pyears) with natural mortality by age and year
`Asize_c`	Numeric vector (length nareas) with size of each area
`MatAge`	Numeric vector with proportion mature by age
`WtAge`	Numeric matrix (maxage+1, pyears) with weight by age and year
`FecAge`	Numeric matrix (maxage+1, pyears) with mature female weight by age and year
`Vuln`	Numeric matrix (maxage+1, pyears) with vulnerability by age and year
`Retc`	Numeric matrix (maxage+1, pyears) with retention by age and year
`Prec`	Numeric vector (pyears) with recruitment error
`movc`	Numeric array (nareas by nareas) with the movement matrix
`SRrelc`	Integer indicating the stock-recruitment relationship to use (1 for Beverton-Holt, 2 for Ricker)
`Effind`	Numeric vector (length pyears) with the fishing effort by year
`Spat_targc`	Integer. Spatial targeting
`hc`	Numeric. Steepness of stock-recruit relationship
`R0c`	Numeric vector of length nareas with unfished recruitment by area
`SSBpRc`	Numeric vector of length nareas with unfished spawning per recruit by area
`aRc`	Numeric. Ricker SRR a value by area
`bRc`	Numeric. Ricker SRR b value by area
`Qc`	Numeric. Catchability coefficient
`Fapic`	Numeric. Apical F value
`maxF`	A numeric value specifying the maximum fishing mortality for any single age class
`MPA`	Spatial closure by year and area
`control`	Integer. 1 to use q and effort to calculate F, 2 to use Fapic (apical F) and vulnerability to calculate F.
`SRRfun`	Optional. A stock-recruit function used if `SRrelc =3`
`SRRpars`	Optional. A named list of arguments for `SRRfun`
`plusgroup`	Integer. Include a plus-group (1) or not (0)?
`spawn_time_frac`	Numeric. Fraction of the year when spawning occurs. Default = 0.