simmov2: Calculates movement matrices from user specified distribution...

In Blue-Matter/MSEtool: Management Strategy Evaluation Toolkit

Calculates movement matrices from user specified distribution among other areas

Description

A wrapper function for makemov2 used to generate movement matrices for the operating model. Calculates a movement matrix from user-specified relative movement to other areas and probability of staying in the area in each time step.

Usage

simmov2(
  OM,
  dist = c(0.05, 0.6, 0.35),
  distE = 0.01,
  frac_other = matrix(c(NA, 2, 1, 3, NA, 1, 1, 4, NA), nrow = 3, byrow = T),
  frac_otherE = 0.01,
  prob = 0.8,
  probE = 1,
  figure = TRUE
)

Arguments

OM	Operating model, an object of class OM.
dist	A vector of fractions of unfished stock in each area. The length of this vector will determine the number of areas (nareas) in the OM.
distE	Logit (normal) St.Dev error for sampling desired fraction in each area
frac_other	A matrix (nareas rows from, nareas columns to) of relative fractions moving to other areas (the positive diagonal (staying) is unspecified).
frac_otherE	Logit (normal) St.Dev error for sampling desired fraction moving to other areas.
prob	the mean probability of staying in the same area among all areas
probE	Logit (normal) St.Dev error for sampling desired probability of staying in each area
figure	Logical to indicate if the movement matrix will be plotted (mean values and range across OM@nsim simulations.)

Value

The operating model OM with movement parameters in slot cpars. The mov array is of dimension nsim, maxage, nareas, nareas.

Functions

• simmov2(): Estimation function for creating movement matrix.

Note

Array mov is age-specific, but currently the movement generated by simmov is independent of age.

Author(s)

T. Carruthers and Q. Huynh

Examples

## Not run: 
movOM_3areas <- simmov2(testOM, frac_other = matrix(c(NA,2,1, 2,NA,1, 1,2,NA),
nrow=3, byrow=T), frac_otherE = 0.01, prob = 0.8, probE = 0.3)
# sim 1, age 1, movement from areas in column i to areas in row j
movOM_3areas@cpars$mov[1, 1, , ] 
plot_mov(movOM_3areas@cpars$mov)
plot_mov(movOM_3areas@cpars$mov, type = "all")


## End(Not run)

Blue-Matter/MSEtool documentation built on Dec. 23, 2024, 7:23 a.m.