A simulation program for the marking, tagging, sampling, and estimation of hatchery salmon

CFM Sim, short for Constant Fractional Marking Simulation, is a PC compatible computer program that simulates the following processes for multiple stocks of chinook salmon over multiple years:

1. the initial marking and tagging of fish, followed by natural mortality, fishing mortality, and maturation processes, each repeated for ages 2, 3, 4, and 5;
2. the sampling of marine and freshwater catches and escapements, where the catches and escapements generally include a mixture of stocks;
3. the statistical estimation of catches and escapements for each stock separately, based on the catch and escapement sample data.

The program was designed to simulate these processes for hatchery-raised and naturally-spawned fall-run chinook salmon from California's Central Valley. The user can model hatchery and natural stocks in 14 different watersheds in the Central Valley simultaneously.

The primary reason for developing CFM Sim was to provide a tool for fisheries biologists and biometricians that could be used to study the effects of different constant fractional marking (CFM) rates on the quality of estimates of production. CFM Sim can be used to compare the accuracy of production estimates when a CFM rate of 20% or a CFM rate of 40% is applied to releases from a Central Valley artificial production facility.

Many other factors besides the CFM rate affect the quality of production estimates. Some of the factors that the user of CFM Sim can manipulate include the following:

• marine survival rates;
• age-specific ocean, freshwater, and terminal fishing harvest rates;
• sampling rate of catches in the marine fisheries;
• sampling rate of catches in the freshwater fisheries;
• sampling rate of spawning escapement;
• sampling rate of the hatchery return;
• maturation rates.

For example, the user can evaluate changes in the accuracy of production estimates for the watersheds in the Central Valley due to changes in age 4 marine harvest rates while holding the CFM rate and other rates constant.

CFM Sim can also be used to analyze the effect of selective fisheries on the spawning escapement of natural and hatchery bound Central Valley chinook salmon stocks. Selective fisheries, as used in this model, are fisheries which target on externally marked hatchery fish. However, selective fisheries will unintentionally kill unmarked fish (possibly unmarked hatchery origin fish, progeny of naturally spawning hatchery fish, and wild fish). This unintentional mortality, collectively labeled latent hooking mortality here, includes drop off mortality (a fish is hooked, but not landed and then subsequently dies because of hook injury) and shaker or hook-and-release mortality (the fish is hooked, landed, released, and then subsequently dies from hook and/or handling injury) (Lawson and Sampson 1996). One option of CFM Sim is to simulate the presence of a selective marine fishery with a specific shaker mortality rate, which is defined as a fraction of the harvest rate. The user can vary harvest and shaker mortality rates to study the effects on both escapement and total shaker mortality.

• Hicks AC. 2003. A discussion and analysis of four constant fractional marking alternatives for California's Central Valley salmon hatcheries. Unpublished Master's Thesis, University of Idaho.

  Hicks' thesis

• Newman KB, Hicks AC, Hankin DG. 2004. A marking, tagging, and recovery program for Central Valley hatchery chinook salmon. Unpublished report for California Department of Fish and Game and the CALFED Ecosystem Restoration Program.

  MTR program simulations for Central Valley hatchery salmon (2004)

• Hicks AC. 2005. A second analysis of a marking, tagging, and recovery program for Central Valley hatchery chinook salmon. Unpublished report for California Department of Fish and Game and the CALFED Ecosystem Restoration Program.

  MTR program simulations for Central Valley hatchery salmon (2005)

Download the user guide

CFMsim user guide

Download the program with a working example

CFMsim program and example