2.8. Mortality

Within each time step, the total mortality of a given school is comprised of predation mortality caused by other schools, starvation mortality, fishing mortality, and diverse other natural mortality rate. The four different mortalities are computed so as to represent quasi simultaneous processes, and we consider that there is competition and stochasticity in the predation process.

Within each time step, OSMOSE considers each pair of school/source of mortality in turn in a random order. To ensure that the random order of the mortality sources and of the schools does not bias the resulting instantaneous mortality rates applied and effectively correspond to the mortality rates specified in input (for fishing and diverse natural mortality), all the mortality events are iterated within a time step over a fixed number of sub-time step.

Table 2.25 Mortality parameters

stochastic.mortality.seed	Integer to fix the random number generator.
mortality.subdt	Number of mortality sub time-steps.
mortality.algorithm	Mortality algorithm (iterative or stochastic) (Osmose <= 4.2.0)

Note

In Osmose >= 4.3.0, the mortality.algorithm parameter is no more used. Stochastic mortality algorithm is used.

Mortality processes are detailed below.

• 2.8.1. Predation mortality
  • 2.8.1.1. Size predation
  • 2.8.1.2. Accessibility
  • 2.8.1.3. Predation rate
• 2.8.2. Starvation mortality
• 2.8.3. Migration mortality
• 2.8.4. Fishing parameters (Osmose <= 4.0.0)
  • 2.8.4.1. By rate
  • 2.8.4.2. By catches
  • 2.8.4.3. Marine Protected Areas (MPAs)
• 2.8.5. Fishing parameters (Osmose >= 4.2.0 & <= 4.2.0)
  • 2.8.5.1. New algorithm
  • 2.8.5.2. Size/Age selectivity
    • 2.8.5.2.1. Step selectivity
    • 2.8.5.2.2. Sigmoid selectivity
    • 2.8.5.2.3. Gaussian selectivity
    • 2.8.5.2.4. Examples
  • 2.8.5.3. Time-variability
    • 2.8.5.3.1. Constant
    • 2.8.5.3.2. By year
    • 2.8.5.3.3. Linear
    • 2.8.5.3.4. Regime shifts
    • 2.8.5.3.5. By Dt
  • 2.8.5.4. Spatial variablity
• 2.8.6. Fishing parameters (Osmose >= 4.3)
  • 2.8.6.1. Fishing mortality rates
    • 2.8.6.1.1. Fishing period (\(F_{period}\))
    • 2.8.6.1.2. Fishing seasonality
    • 2.8.6.1.3. Case studies
  • 2.8.6.2. Size selectivities
    • 2.8.6.2.1. Knife-edge selectivity
    • 2.8.6.2.2. Sigmoid selectivity
    • 2.8.6.2.3. Gaussian selectivity
  • 2.8.6.3. Catchability
  • 2.8.6.4. Discards