# Multispecies mean length mortality estimator Estimator of instantaneous total mortality (Z) from a time series of mean length data for a suite of stocks that are fished together. ```r 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 `MLZ_data`. - `ncp`: The number of change points in total mortality in the time series. `ncp + 1` total mortality rates will be estimated. - `model`: The multispecies model to be used. - `start`: An optional list of starting values. See details. - `grid.search`: If `TRUE`, a grid search will be performed using the `profile_MLmulti` function to find the best starting values for the change points (the years when mortality changes). Ignored if `start` is provided. - `parallel`: Whether grid search is performed in parallel. Ignored if `grid.search = FALSE`. - `min.time`: The minimum number of years between each change point for the grid search, passed to `profile_MLmulti`. Not used if `grid.search = FALSE`. - `Z.max`: The upper boundary for Z estimates. - `figure`: If `TRUE`, a call to `plot` of observed and predicted mean lengths will be produced. ## Returns An object of class `MLZ_model`. ## 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. ## Examples ```r ## 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) ``` ## 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 `profile_MLmulti`

MLmulti function