The content presented in this repository offers a detailed analysis of marine stock levels in the Timor region. While focused on Timor, the code methodologies and are adaptable for similar assessments in other countries. This resource is intended to guide sustainable fisheries management and policy development, applicable beyond its primary regional focus.

Stock status indicators for each species in each area were calculated using the LBB method proposed in Froese et al., 2018, a technique for estimating stock status based on length-frequency data. This method is applicable to species that continue to grow throughout their lives, such as most commercially exploited fish and invertebrates. These species require no additional input other than the length-frequency (LF) data. The LBB estimates various parameters for one or multiple LF samples that represent the population, including asymptotic length (Linf), mean length at first capture (Lc), relative natural mortality (M/K), and relative fishing mortality (F/M).

Below the main indicators of the assessment, useful for interpretation in the results section:

• Linf**: a**symptotic length

• Lc: mean length at first capture, or length at which 50% of the individuals are retained by the gear

• Lopt: length class with the highest biomass in an unfished population. A fishery would obtain the maximum possible yield if it were to catch only fish of this size.

• M/K: relative natural mortality

• F/M: relative fishing mortality (fishing pressure)

• B/B0: current biomass relative to unfished biomass

• B/Bmsy: ratio between the observed biomass and the biomass that would provide the maximum sustainable yield (equal or higher than 1 in case of sustainable fishery)

We can plot the F/Fmsy ratio against the B/Bmsy ratio to get a sense of the sustainability of a fishery. From https://sustainablefisheries-uw.org/seafood-101/overfished-overfishing-rebuilding-stocks/:

Overfishing refers to fishing mortality (F), or the rate of fish killed by catching them (just think of this as the proportion of fish caught). There is an ideal proportion of fish to catch that will produce MSY—this is called FMSY. If the proportion of fish caught (F) is greater than FMSY, overfishing is happening. If F is less than FMSY, underfishing is happening. Fishing mortality is usually given as a ratio of F/FMSY; a ratio over 1 means overfishing.

Overfished refers to the biomass (B) of a population, or stock, of fish. This is the amount of fish in the water. There is some amount of biomass, B, that will produce MSY—this is BMSY. If the biomass of fish in the water is well below BMSY, the stock is overfished, or depleted. If the amount of fish in the water is more than would produce MSY it is underfished. The ratio of B/BMSY is commonly used, though the number of demarcation varies by governing body (B may represent spawning biomass, vulnerable biomass, or total stock biomass).

Analyses were performed on the lLF data of 3 fish groups (Snappers, Jacks/trevally and mackerel scad) over the period 2018-2022. For each fish group (FG), 3 stocks were defined on a geographical basis: north coast, south coast and Atauro.

Since that the goal is to obtain the stock assessment in each area, the analysis was conducted by combining data from all the years of in order to gain a comprehensive understanding of the overall situation. This means that the LF curves of each FG refer to a period of 4 years.

The population parameters for each FG wet set as follows:

In order to obtain a higher resolution in the length intervals, the LF curves were spline interpolated. Below is an example of interpolation performed on the snapper stock at Atauro. The comparison is between the original data (left) and the interpolated data (right).

Below is the Atauro’ mackerel LF data used for the analyses and shown for representation purposes. Length unit is millimeters, and CatchNo represents the number of individuals.

The plot below shows the length-frequency data for each FG in each stock-area used for the analyses:

## Running Jags model to fit SL and N distributions
## Running Jags model to fit SL and N distributions
## Running Jags model to fit SL and N distributions
## Running Jags model to fit SL and N distributions
## Running Jags model to fit SL and N distributions
## Running Jags model to fit SL and N distributions

The model returned an error when running on the following stocks (due to the multimodal shape of LF curves?):

## [1] "snapper_North"        "jacks_trevally_North" "jacks_trevally_South"

According to the significance of the indicators described in the methods section, all stocks are in in excellent condition and have the potential to produce more.