Calculates movement matrices from user specified distribution among other areas

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

T. Carruthers and Q. Huynh

Examples

if (FALSE) {
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")

}