MLZ: Mean Length-based Z Estimators

2.1 Data preparation

MLZ uses the S4 class system. Data and life history parameters, i.e., von Bertalanffy Linf and K, are stored in a single object of class MLZ_data with pre-defined slots. Slots in the S4 class can be accessed with @.

library(MLZ)
class?MLZ_data
data(Goosefish)
Goosefish@vbLinf

Length data are imported as either a data frame of individual records or as a matrix (years x length bins):

data(SilkSnapper)
new.dataset <- new("MLZ_data", Year = 1983:2013, Len_df = SilkSnapper, length.units = "mm")

The bin_length function can be used to convert individual lengths into a length frequency matrix with specified length bins.

bin_length(SilkSnapper)

The plot function can be used to visualize the data to aid in the selection of \(L_c\).

plot(new.dataset, type = "comp")

## Warning: The dot-dot notation (`..ncount..`) was deprecated in ggplot2 3.4.0.
## ℹ Please use `after_stat(ncount)` instead.
## ℹ The deprecated feature was likely used in the MLZ package.
##   Please report the issue to the authors.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.

Once Lc is identified, calc_ML() can be used to mean lengths from records larger than Lc.

new.dataset@Lc <- 310
new.dataset <- calc_ML(new.dataset)

new.dataset@MeanLength
new.dataset@ss

A summary method function is also available for class MLZ_data.

summary(new.dataset)

2.2 Mortality estimation

Once mean lengths > Lc are calculated, mortality can be estimated using the ML function:

est <- ML(Goosefish, ncp = 2)

The function returns an object of class MLZ_model which includes predicted values of the data, parameter estimates with correlation matrix and gradient vector. summary and plot method functions are also available for MLZ_model objects.

plot(est)

summary(est)

## $Stock
## [1] "Goosefish: Northern Management Region"
## 
## $Model
## [1] "ML"
## 
## $Estimates
##          Estimate Std. Error
## Z[1]        0.141      0.005
## Z[2]        0.310      0.037
## Z[3]        0.551      0.046
## yearZ[1] 1978.316      0.832
## yearZ[2] 1987.767      1.222
## sigma      24.342      0.000

With i = 1, 2, ... I change points, Z[i] is the estimated mortality rate in successive time periods. yearZ[i] indicates the time when mortality changed from Z[i] to Z[i+1].

The analysis can be repeated by considering alternative numbers of change points (years in which mortality changes, estimated in continuous time).

model1 <- ML(Goosefish, ncp = 0)
model2 <- ML(Goosefish, ncp = 1)
model3 <- ML(Goosefish, ncp = 2)

2.3 Model selection

Model runs with different change points can be compared using AIC. The compare_models function facilitates this feature and produces a plot of the predicted data.

compare_models(model1, model2, model3)

##                   negLL npar      AIC delta.AIC
## 2-change point 111.1122    6 234.2244  0.000000
## 1-change point 116.5551    4 241.1103  6.885858
## 0-change point 157.9197    2 319.8394 85.615006

compare_models can also be used with MLCR and MLmulti (See section 4).

3.1 Data preparation

To explore changes in the length distribution over time, the modal_length function plots the modal length from each annual length distribution. The modal length can change for several reasons, including changes in mortality, selectivity, and recruitment.

modal_length(new.dataset, breaks = seq(80, 830, 10))

3.2 Mortality estimation

profile_ML(Goosefish, ncp = 1)

profile_ML(Goosefish, ncp = 2)

4.1 MLCR (Mean Length with Catch Rate)

To use the MLCR estimator (Huynh et al. 2017b), a time series of CPUE is needed:

data(MuttonSnapper)
MuttonSnapper@CPUE

If the CPUE is biomass-based, e.g., pounds of fish per gear haul, then length-weight exponent b is also needed.

MuttonSnapper@lwb <- 3.05

The corresponding estimation function and grid search function are MLCR and profile_MLCR, respectively:

MLCR(MuttonSnapper, ncp = 2, "WPUE")

4.2 MLmulti (Multispecies Mean Length estimator)

For a multispecies analysis (Huynh et al. 2017a), seperate MLZ_data objects are created for seperate stocks/species and should be stored in a list:

data(PRSnapper)
typeof(PRSnapper)

## [1] "list"

The corresponding estimation function and grid search function are MLmulti and profile_MLmulti, respectively. For both functions, the Single Species Model or Multispecies 1, 2, or 3 must also be identified in the model argument:

MLmulti(PRSnapper, ncp = 1, model = "MSM1")

In component estimates of the output object, the mortality estimates Z[i,n] are indexed by time period i and species n, change points yearZ[i] are indexed by time period i, and sigma[n] is indexed by species n. For models MSM2 and MSM3, Z[i,n] are estimated for i = 1 and derived for i > 1. Esimated parameters can be viewed by checking component opt from the output:

res <- MLmulti(PRSnapper, ncp = 1, model = "MSM1")
names(res@opt$par)

The compare_models function will correctly count the number of estimated parameters for AIC calculation.

4.3 MLeffort (Mean Length with Effort)

MLeffort uses a time series of mean length and effort to estimate a catchability coefficient q and natural mortality M (Then et al.). Parameter \(t_0\) from the von Bertalanffy equation is needed as well:

data(Nephrops)
Nephrops@Effort
Nephrops@vbt0 <- 0
MLeffort(Nephrops, start = list(q = 0.1, M = 0.2), n_age = 24)

Unlike other models in the package, starting values are required in MLeffort.

Instead of using an analytic model for the mean length, MLeffort uses an age-structured population model. The youngest age in the age-structured model is \(t_c\) which is obtained from von Bertalanffy parameters and \(L_c\): \(t_c = \frac{-1}{K}log(1 - \frac{L_c}{L_{\infty}}) + t_0\)

In the MLeffort function call, the number of ages above \(t_c\) to be modeled is specified in argument n_age. Time steps smaller than one year can be used by indicating the number of seasons in the model with argument n_season. The season is matched to the season in which mean lengths are observed with argument obs_season. Currently only one observation per year is supported. The timing within the observed season that lengths are observed is set with argument timing, i.e. timing = 0, 0.5 is the beginning and middle of the season, respectively. The equilibrium effort prior to the first year of the model is indicated with argument eff_init, i.e. eff_init = 0 for virgin equilibrium conditions.

MLeffort(Nephrops, start = list(q = 0.1, M = 0.3), n_age = 24, n_season = 1, obs_season = 1, timing = 0.5)

Finally, the model can be run with a fixed M with the argument estimate.M = FALSE, in which case, the value of M for the model is obtained from slot @M in the MLZ_data object.

Nephrops@M <- 0.3
MLeffort(Nephrops, start = list(q = 0.1), n_age = 24, estimate.M = FALSE)