Computes the negative log-likelihood for tag-recapture data using a seasonal, age-based model.
Usage
get_tag_like(
tag_switch,
minK,
n_K,
n_T,
n_I,
n_J,
first_yr,
M_a,
hrate_ysa,
tag_release_cta,
tag_recap_ctaa,
minI,
maxI,
maxJ,
shed1,
shed2,
tag_rep_rates_ya,
tag_H_factor,
tag_var_factor
)Arguments
- tag_switch
Integer flag to turn the likelihood on (>0) or off (0).
- minK
Integer, starting cohort index.
- n_K
Number of cohorts.
- n_T
Number of tagging time periods.
- n_I
Number of release ages.
- n_J
Number of recapture ages.
- first_yr
First model year.
- M_a
Vector of natural mortality at age.
- hrate_ysa
3D array year, season, age of harvest rates.
- tag_release_cta
3D array cohort, time, age of numbers of tags released.
- tag_recap_ctaa
4D array cohort, time, rel_age, recap_age of numbers of tags recaptured.
- minI, maxI, maxJ
Vectors giving the min and max release and recapture ages for each cohort.
- shed1, shed2
Vectors of shedding rates per time period.
- tag_rep_rates_ya
Matrix of tag reporting rates by year and age.
- tag_H_factor
Numeric scaling factor for incomplete mixing.
- tag_var_factor
Overdispersion factor.