Adjusting Simulated Biomass Using Observed Yield Data: A Guide for Dealing with Deprecated Functions and Mizer's matchYield()

[XW112112]

I want to use observed biomass data to adjust the model-simulated biomass. However, I only have observed yield data for different species (12 species) for each year, and no SSB (Spawning Stock Biomass) data. Could you please advise on how to use observed yield data to adjust model-simulated yield data?

I'm aware that two related functions in mizer, calibrateYield() and matchYields(), were previously used for data matching. However, I now see they have been deprecated. The help documentation for matchYields() indicates that the matchYield() function from the mizerExperimental package can be used for matching.

The problem is, I don't know how to incorporate my observed yield data frame into the matchYield() function. My data frame contains the observed yield for each fish species for each year from 1980-2020, and the gear is always 'trawl'. The data frame has four columns: species, gear, year, and yield_observed.

Please provide me with guidance and instructions. Thank you very much!"

[gustavdelius]

Hi. Thank you for asking.

You can still use calibrateYield() and matchYields() in case you have already set up fishing (see setFishing() and gear_params() for details about setting up fishing). The only reason the functions are deprecated is that it is rare for people to know the fishing parameters unless they have done some stock assessment, in which case it is better to first calibrate to the biomass instead of the yield.

Are you in a situation where you have knowledge of the fishing mortality for your species? If not, then there is no way to deduce the biomasses from the yield. If you do have information about fishing mortality then I'll be happy to help you set things up.

Best,
Gustav

[XW112112]

Hi, Thank you very much for your prompt and helpful reply! I appreciate you reminding me about the role of fishing mortality (F) in the calibration process.

I do have information on fishing mortality (F) for my species. My F information comes from two primary sources:

1. Directly estimated fishing mortality coefficients (F): I am collecting published F estimates from various literature sources for my target pecies, I have this information available for all target species.

2. Parameters for calculating fishing mortality: I also have calculated the fishing mortality coefficients (F) for each species using Gear selectivity (SS), Catchability (Q), and Fishing effort (E).
   Gear selectivity (SS): For this data source, I am using a Sigmoid length-based selection equation. I have gathered literature data on the l25​ and l50 values for different species, which allows me to estimate the species-specific gear selectivity (SS) curves.
   Catchability (Q): For this source, I intend to use the fishing mortality coefficients (F) found in the literature as the catchability (Q).
   Fishing effort (E): I have data on annual fishing effort corresponding to the annual observed catch for each year from 1986-2023. This effort data includes details such as the number of fishing vessels of different horsepower, their total kilowatt power, and the total tonnage of fish caught by all vessels.

My ultimate goal is to use the observed yield data to calibrate the model-simulated biomass. Given that I have these two types of information related to fishing mortality, I am hoping you can provide further guidance on how to best set up the model and perform this calibration.

I am particularly interested in understanding how to effectively incorporate these different F information sources, especially the detailed gear and effort data in the second category, into MIZER to adjust the model-simulated biomass.

Thank you again for your invaluable support. I look forward to your further advice!

Best regards,
Xue wei