A wrapper function for makemov used to generate movement matrices for the operating model. Calculates a movement matrix from user-specified unfished stock biomass fraction in each area and probability of staying in the area in each time step.
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.- prob
Mean probability of staying across all areas (single value) or a vector of the probability of individuals staying in each area (same length as dist).
- distE
Logit (normal) St.Dev error for sampling stock fractions from the fracs vector
- probE
Logit (normal) St.Dev error for sampling desired probability of staying either by area (prob is same length as dist) or the mean probability of staying (prob is a single number).
- prob2
Optional vector as long as prob and dist. Upper bounds on uniform sampling of probability of staying, lower bound is prob.
- figure
Logical to indicate if the movement matrix will be plotted (mean values and range across
OM@nsim
simulations.)- mov
A four-dimensional array of dimension
c(nsim, maxage, nareas, nareas)
or a five-dimensional array of dimensionc(nsim, maxage, nareas, nareas, nyears + proyears)
specifying movement in the operating model.- age
An age from 0 to maxage for the movement-at-age matrix figure when
type = "matrix"
.- type
Whether to plot a movement matrix for a single age (
"matrix"
) or the full movement versus age figure ("all"
)- year
If
mov
is a 5-dimensional array, the year (from 1 to nyears + proyears) for which to plot movement.- qval
The quantile to plot or report the range of values among simulations.
Value
The operating model OM
with movement parameters in slot cpars
.
The mov
array is of dimension nsim
, maxage
, nareas
, nareas
.
Functions
simmov()
: Estimation function for creating movement matrix.plot_mov()
: Plotting function.
Note
Array mov
is age-specific, but currently the movement generated by simmov
is
independent of age.
Examples
if (FALSE) { # \dontrun{
movOM_5areas <- simmov(testOM, dist = c(0.01,0.1,0.2,0.3,0.39), prob = c(0.1,0.6,0.6,0.7,0.9))
movOM_5areas@cpars$mov[1, 1, , ] # sim 1, age 1, movement from areas in column i to areas in row j
plot_mov(movOM_5areas@cpars$mov)
plot_mov(movOM_5areas@cpars$mov, type = "all")
} # }