MLmulti {MLZ} | R Documentation |
Multispecies mean length mortality estimator
Description
Estimator of instantaneous total mortality (Z) from a time series of mean length data for a suite of stocks that are fished together.
Usage
MLmulti(MLZ.list, ncp, model = c("SSM", "MSM1", "MSM2", "MSM3"),
start = NULL, grid.search = TRUE, parallel = ifelse(ncp > 2, TRUE,
FALSE), min.time = 3, Z.max = 5, figure = TRUE)
Arguments
MLZ.list |
A list containing objects of class |
ncp |
The number of change points in total mortality in the time series. |
model |
The multispecies model to be used. |
start |
An optional list of starting values. See details. |
grid.search |
If |
parallel |
Whether grid search is performed in parallel. Ignored if |
min.time |
The minimum number of years between each change point for the grid search, passed
to |
Z.max |
The upper boundary for Z estimates. |
figure |
If |
Details
For a model with I
change points and N
species, the starting values in
start
is a list with the following entries:
Single Species Model (SSM, independent trends in mortality among species):
Z | a matrix with nrow = I+1 and ncol = N . |
yearZ | a matrix with nrow = I and ncol = N . |
Multispecies Model 1 (MSM1, common mortality change points but changes in Z are independent):
Z | a matrix with nrow = I+1 and ncol = N . |
yearZ | a vector with length = I . |
Multispecies Model 2 (MSM2, common mortality change points. Changes in F vary by estimated relative catchabilities among species):
Z1 | a vector with length = N . |
yearZ | a vector with length = I . |
delta | a vector with length = I . |
epsilon | a vector with length = N-1 . |
Multispecies Model 3 (MSM3, common mortality change points and common proportional changes in F):
Z1 | a vector with length = N . |
yearZ | a vector with length = I . |
delta | a vector with length = I . |
If ncp = 0
change points is specified, then the method simplifies to the Single Species Model.
The start
list should contain a single entry:
Z | a vector with length = N . |
start
can be NULL
, in which case, the supplied starting values depend on
the value of grid.search
. If grid.search = TRUE
, starting values will use the
values for yearZ
which minimize the negative log-likelihood from the grid search.
Otherwise, the starting values for yearZ
evenly divide the time series.
Value
An object of class MLZ_model
.
References
Huynh, Q.C, Gedamke, T., Hoenig, J.M, and Porch C. 2017. Multispecies Extensions to a Nonequilibrium Length-Based Mortality Estimator. Marine and Coastal Fisheries 9:68-78.
See Also
Examples
## Not run:
data(PRSnapper)
res_eq <- MLmulti(PRSnapper, ncp = 0, start = list(Z = matrix(0.5, nrow = 1, ncol = 3)))
res_SSM <- MLmulti(PRSnapper, ncp = 1, model = "SSM")
MSM1.start.Z <- matrix(0.5, nrow = 2, ncol = 3)
MSM1.start.yearZ <- 1990
start.list <- list(Z = MSM1.start.Z, yearZ = MSM1.start.yearZ)
res_MSM1 <- MLmulti(PRSnapper, ncp = 1, model = "MSM1", start = start.list, grid.search = FALSE)
res_MSM2 <- MLmulti(PRSnapper, ncp = 1, model = "MSM2")
st.Z1 <- rep(0.5, 3)
st.yearZ <- 1990
st.delta <- 1
start.list <- list(Z1 = st.Z1, yearZ = st.yearZ, delta = st.delta)
resMSM3 <- MLmulti(PRSnapper, ncp = 1, model = "MSM3", start = start.list)
## End(Not run)