TimeStratPetersenDiagErrorWHSteel_fit {BTSPAS} | R Documentation |
Takes the number of marked fish released, the number of recaptures, and the number of unmarked fish and uses Bayesian methods to fit a fit a spline through the population numbers and a hierarchical model for the trap efficiencies over time. The output is written to files and an MCMC object is also created with samples from the posterior.
TimeStratPetersenDiagErrorWHSteel_fit( title = "TSPDE-WHSteel", prefix = "TSPDE-WHSteel-", time, n1, m2, u2.W.YoY, u2.W.1, u2.H.1, sampfrac = rep(1, length(u2.W.YoY)), hatch.after = NULL, bad.n1 = c(), bad.m2 = c(), bad.u2.W.YoY = c(), bad.u2.W.1 = c(), bad.u2.H.1 = c(), logitP.cov = as.matrix(rep(1, length(n1))), n.chains = 3, n.iter = 2e+05, n.burnin = 1e+05, n.sims = 2000, tauU.alpha = 1, tauU.beta = 0.05, taueU.alpha = 1, taueU.beta = 0.05, prior.beta.logitP.mean = c(logit(sum(m2, na.rm = TRUE)/sum(n1, na.rm = TRUE)), rep(0, ncol(as.matrix(logitP.cov)) - 1)), prior.beta.logitP.sd = c(stats::sd(logit((m2 + 0.5)/(n1 + 1)), na.rm = TRUE), rep(10, ncol(as.matrix(logitP.cov)) - 1)), tauP.alpha = 0.001, tauP.beta = 0.001, run.prob = seq(0, 1, 0.1), debug = FALSE, debug2 = FALSE, InitialSeed = ceiling(stats::runif(1, min = 0, 1e+06)), save.output.to.files = TRUE )
title |
A character string used for a title on reports and graphs |
prefix |
A character string used as the prefix for created files. All created graph files are of the form prefix-xxxxx.pdf. |
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. |
n1 |
A numeric vector of the number of marked fish released in each time stratum. |
m2 |
A numeric vector of the number of marked fish from n1 that are
recaptured in each time stratum. All recaptures take place within the
stratum of release. Use the |
u2.W.YoY |
A numeric vector of the number of unmarked wild Young-of-Year fish captured in each stratum. |
u2.W.1 |
A numeric vector of the number of unmarked wild age 1+ fish captured in each stratum. |
u2.H.1 |
A numeric vector of the number of unmarked hatchery age 1+ fish (i.e. adipose fin clipped) captured in each stratum. |
sampfrac |
Deprecated because it really doesn't work as intended. You must remove all references to sampfrac from your code. Contact cschwarz.stat.sfu.ca@gmail.com for more information. |
hatch.after |
A numeric vector with elements belonging to |
bad.n1 |
A numeric vector with elements belonging to |
bad.m2 |
A numeric vector with elements belonging to |
bad.u2.W.YoY |
A numeric vector with elements belonging to |
bad.u2.W.1 |
A numeric vector with elements belonging to |
bad.u2.H.1 |
A numeric vector with elements belonging to |
logitP.cov |
A numeric matrix for covariates to fit the logit(catchability). Default is a single intercept, i.e. all strata have the same mean logit(catchability). |
n.chains |
Number of parallel MCMC chains to fit. |
n.iter |
Total number of MCMC iterations in each chain. |
n.burnin |
Number of burn-in iterations. |
n.sims |
Number of simulated values to keeps for posterior distribution. |
tauU.alpha |
One of the parameters along with |
tauU.beta |
One of the parameters along with |
taueU.alpha |
One of the parameters along with |
taueU.beta |
One of the parameters along with |
prior.beta.logitP.mean |
Mean of the prior normal distribution for logit(catchability) across strata |
prior.beta.logitP.sd |
SD of the prior normal distribution for logit(catchability) across strata |
tauP.alpha |
One of the parameters for the prior for the variance in logit(catchability) among strata |
tauP.beta |
One of the parameters for the prior for the variance in logit(catchability) among strata |
run.prob |
Numeric vector indicating percentiles of run timing should be computed. |
debug |
Logical flag indicating if a debugging run should be made. In the debugging run, the number of samples in the posterior is reduced considerably for a quick turn around. |
debug2 |
Logical flag indicated if additional debugging information is
produced. Normally the functions will halt at |
InitialSeed |
Numeric value used to initialize the random numbers used in the MCMC iterations. |
save.output.to.files |
Should the plots and text output be save to the files in addition to being stored in the MCMC object? |
Normally, data is passed to the wrapper which then calls the fitting function.
An MCMC object with samples from the posterior distribution. A series of graphs and text file are also created in the working directory.
Bonner, S.J. sbonner6@uwo.ca and Schwarz, C. J. cschwarz.stat.sfu.ca@gmail.com.
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
##---- See the vignettes for example on how to use this package.