Description Usage Arguments Details Value Author(s) References Examples
View source: R/TimeStratPetersenDiagErrorWHChinook_fit.R
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.
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title = "TSPDE-WHChinook2",
prefix = "TSPDE-WHChinook2-",
time,
n1,
m2,
u2.A.YoY,
u2.N.YoY,
u2.A.1,
u2.N.1,
clip.frac.H.YoY,
clip.frac.H.1,
sampfrac = rep(1, length(u2.A.YoY)),
hatch.after.YoY = NULL,
bad.m2 = c(),
bad.u2.A.YoY = c(),
bad.u2.N.YoY = c(),
bad.u2.A.1 = c(),
bad.u2.N.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,
trunc.logitP = 15
)
TimeStratPetersenDiagErrorWHChinook_fit(
title = "TSPDE-WHChinook",
prefix = "TSPDE-WHChinook-",
time,
n1,
m2,
u2.A,
u2.N,
clip.frac.H,
sampfrac = rep(1, length(u2.A)),
hatch.after = NULL,
bad.n1 = c(),
bad.m2 = c(),
bad.u2.A = c(),
bad.u2.N = 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, max = 1e+06)),
save.output.to.files = TRUE,
trunc.logitP = 15
)
|
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.A.YoY, u2.N.YoY |
Number of YoY unmarked fish with/without adipose fin clips All YoY wild fish have NO adipose fin clips; however, hatchery fish are a mixture of fish with adipose fin clips (a known percentage are marked) and unmarked fish. So u2.A.YoY MUST be hatchery fish. u2.N.YoY is a mixture of wild and hatchery fish. |
u2.A.1, u2.N.1 |
Number of Age1 unmarked fish with/with out adipose fin clips All Age1 wild fish have NO adipose fin clips; however, hatchery fish are a mixture of fish with adipose fin clips (a known percentage are marked) and unmarked fish. So u2.A.1 MUST be hatchery fish. u2.N.1 is a mixture of wild and hatchery fish. |
clip.frac.H.YoY, clip.frac.H.1 |
Fraction of the YoY hatchery/Age1 (from last year's releases) hatchery fish are clipped?\ (between 0 and 1) |
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.YoY |
A numeric vector with elements belonging to
|
bad.m2 |
A numeric vector with elements belonging to |
bad.u2.A.YoY, bad.u2.N.YoY |
List of julian weeks where the value of u2.A.YoY/u2.N.YoY is suspect. These are set to NA prior to the fit. |
bad.u2.A.1, bad.u2.N.1 |
List of julian weeks where the value of u2.A.1/u2.N.1 is suspect. These are set to NA prior to the fit. |
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? |
trunc.logitP |
Truncate logit(P) between c(=trunc.logitP, trunc.logitP) when plotting the logitP over time. Actual values of logit(P) are not affected. |
u2.A |
A numeric vector of the number of unmarked fish with adipose clips captured in each stratum. |
u2.N |
A numeric vector of the number of unmarked fish with NO-adipose clips captured in each stratum. |
clip.frac.H |
A numeric value for the fraction of the hatchery fish that have the adipose fin clipped (between 0 and 1). |
hatch.after |
A numeric vector with elements belonging to |
bad.n1 |
A numeric vector with elements belonging to |
bad.u2.A |
A numeric vector with elements belonging to |
bad.u2.N |
A numeric vector with elements belonging to |
Normally use the *_fit to pass the data to 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
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##---- See the vignettes for examples on how to run this analysis.
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