RBdata-class: Class-'RBdata'

In quang-huynh/RBassess: An Age- And Length-Based Assessment Model for Rainbow Trout in British Columbia, Canada

Description

An S4 class for setting up inputs for the rainbow trout assessment.

Slots

Lake

Name of lake.

Year

Year of survey.

Length_bin

A vector of midpoints of the length bins. Width of all length bins assumed to be equal. Typically in centimeters.

Age

A vector of integer ages. Should be consecutive from 1 to the maximum age.

Age_adjust

A vector of accumulated growing degree days (converted to years) corresponding to the integer ages.

Length

A vector (single year sample) for the length composition data. The vector should be of length equal to length(Length_bins).

Age_length

A matrix (single year sample) for the age-length sammples. The matrix should have length(Age) rows and length(Length_bins) columns.

L_stock

A vector of mean lengths at stocking, in order of the corresponding ages.

stock_density

A vector of stocking density, in order of the corresponding ages. In units of numbers per hectacre.

bag_limit

The daily bag limit (number of fish per angler day) used to calculated the probability of harvesting.

release_mortality

Release mortality, i.e., the proportion of fish that die due to catch and release. Default is 0.1.

p_vrel

The proportion of fish caught by anglers that are subsequently voluntarily released. Default is zero.

prior_Linf

Von Bertalanffy asymptotic length. Vector of length two for mean and standard deviation, respectively.

prior_K

Von Bertalanffy growth coefficient. Vector of length two for mean and standard deviation, respectively.

prior_CV_Len

Coefficient in variation in length-at-age. Vector of length two for mean and standard deviation, respectively.

prior_M

Instantaneous natural mortality (per year). Vector of length two for mean and standard deviation, respectively.

prior_Effort

Fishing effort. Vector of length two for mean and standard deviation, respectively. In units of angler days per hectacre.

prior_q

Catchability coefficient for scaling effort. Vector of length two for mean and standard deviation, respectively.

prior_GN_SL50

Gillnet length at 50% selectivity for the survey. Vector of length two for mean and standard deviation, respectively. Default priors are based on values from Askey et al. (2007).

prior_GN_gamma

Steepness of selectivity for gillnet (positive values). Vector of length two for mean and standard deviation, respectively. Default priors are based on values from Askey et al. (2007).

prior_angler_gamma

Angler length at 50% selectivity. Vector of length two for mean and standard deviation, respectively.

prior_angler_SL50

Steepness of selectivity for angler (positive values). Vector of length two for mean and standard deviation, respectively.

References

Asky, P.J. Post, J.R., Parkinson, E.A., Rivot, E., Paul, A.J., and Biro, P.A. 2007. Estimation of gillnet efficiency and selectivity across multiple sampling units: A hierarchical Bayesian analysis using mark-recapture data. Fisheries Research 83: 162-174.

See Also

fit_model run_mcmc BC_lakes plot.RBdata

Examples

new_data <- new("RBdata")

quang-huynh/RBassess documentation built on May 8, 2019, 7:30 a.m.