Description Usage Arguments Value Functions Note Author(s) Examples
View source: R/Movement_calcs.R
A wrapper function for makemov used to generate movement matrices for a DLMtool 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.
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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 ( |
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 |
mov |
A four-dimensional array of dimension |
age |
An age from 1 to maxage for the movement-at-age matrix figure when |
type |
Whether to plot a movement matrix for a single age ( |
The operating model OM
with movement parameters in slot cpars
.
The mov
array is of dimension nsim
, maxage
, nareas
, nareas
.
simmov
: Estimation function for creating movement matrix.
plot_mov
: Plotting function.
Array mov
is age-specific, but currently the movement generated by simmov
is independent of age.
T. Carruthers and Q. Huynh
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