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Calculate transition probabilities for sex-age classes

Source: R/core_model_demographic_herd.R
calc_transition_probabilities.Rd

Calculates hazard rates and daily transition probabilities (death, offtake, survival, and growth) across different sex-age cohorts. Converts annual inputs to daily hazards, then derives daily probabilities from those hazards.

Usage

calc_transition_probabilities(cohort_duration_days, offtake_rate, death_rate)

Arguments

cohort_duration_days

Numeric vector of length 6. Amount of time that each animal spends in a specific cohort (days).

offtake_rate

Numeric vector of length 6. Annual proportion of animals removed from the herd for each sex-age cohort (fraction).

death_rate

Numeric vector of length 6. Fraction of deaths in a herd over a year for each sex-age cohort (fraction)

Value

A named list with:

hazard_death

Numeric vector of length 6. Instantaneous mortality hazard rate for the 6 sex–age cohorts. Represents the risk of death per unit time (day) (cohorts= FJ, FS, FA, MJ, MS, MA)

hazard_offtake

Numeric vector of length 6. Instantaneous offtake hazard rate for the 6 sex-age cohorts. Represents the risk to leave the herd through planned removals per unit of time (day-1) (cohorts= FJ, FS, FA, MJ, MS, MA)

probability_death

Named numeric vector of length 10. Probability of animal dying within the model time interval for 10 cohorts (fraction). (cohorts= FB: Female Birth, FJ: Female Juvenile, FS: Female Sub-adult, FA: Female Adult, FC: Female Culling, MB: Male Birth, MJ: Male Juvenile, MS: Male Sub-adult, MA: Male Adult, MC: Male Culling)

probability_offtake

Named numeric vector of length 10. Probability that an animal will be removed from the herd within the model time interval for 10 cohorts (fraction). (cohorts= FB: Female Birth, FJ: Female Juvenile, FS: Female Sub-adult, FA: Female Adult, FC: Female Culling, MB: Male Birth, MJ: Male Juvenile, MS: Male Sub-adult, MA: Male Adult, MC: Male Culling)

probability_survival

Named numeric vector of length 10. Probability that an animal remains alive in the herd within the model time interval for 10 cohorts (fraction). (cohorts= FB: Female Birth, FJ: Female Juvenile, FS: Female Sub-adult, FA: Female Adult, FC: Female Culling, MB: Male Birth, MJ: Male Juvenile, MS: Male Sub-adult, MA: Male Adult, MC: Male Culling)

probability_growth

Named numeric vector of length 10. Probability of growing into the next age class for 10 cohorts (fraction) (cohorts= FB: Female Birth, FJ: Female Juvenile, FS: Female Sub-adult, FA: Female Adult, FC: Female Culling, MB: Male Birth, MJ: Male Juvenile, MS: Male Sub-adult, MA: Male Adult, MC: Male Culling)

This function is part of the run_demographic_herd_module().

See also

run_demographic_herd_module()