RunTime: Compute percentiles of the run timing distribution.

In BTSPAS: Bayesian Time-Stratified Population Analysis

Description

Take the posterior sample of U[1,...nstrata] and compute the percentiles of the run timing. This uses the quantile() function from the "actuar" package which is designed to compute quantiles of grouped data. It is assumed that there are no fish in the system prior to the first point

Usage

RunTime(time, U, prob = seq(0, 1, 0.1))

Arguments

time	A numeric vector of time used to label the strata. For example, this could be julian week for data stratified at a weekly level.
U	matrix of posterior samples. Each row is a sample from the posterior.
prob	Quantiles of the run timing to estimate.

Value

An MCMC object with samples from the posterior distribution. A series of graphs and text file are also created in the working directory. This information is now added to the fit object as well and so it is unlikely that you will use this function.

Author(s)

Bonner, S.J. [e-mail] and Schwarz, C. J. [e-mail].

References

Bonner, S. J., & Schwarz, C. J. (2011). Smoothing population size estimates for Time-Stratified Mark-Recapture experiments Using Bayesian P-Splines. Biometrics, 67, 1498-1507. doi: 10.1111/j.1541-0420.2011.01599.x

Schwarz, C. J., & Dempson, J. B. (1994). Mark-recapture estimation of a salmon smolt population. Biometrics, 50, 98-108.

Schwarz, C.J., D. Pickard, K. Marine and S.J. Bonner. 2009. Juvenile Salmonid Outmigrant Monitoring Evaluation, Phase II - December 2009. Final Technical Memorandum for the Trinity River Restoration Program, Weaverville, CA. 155 pp. + appendices available at https://www.fws.gov/arcata/fisheries/reports/technical/TR_Final_Report.pdf

BTSPAS documentation built on Oct. 25, 2021, 9:07 a.m.