View source: R/TimeStratPetersenDiagError_fit.R
TimeStratPetersenDiagError_fit | 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.
TimeStratPetersenDiagError_fit(
title = "TSDPE",
prefix = "TSPDE-",
time,
n1,
m2,
u2,
sampfrac = rep(1, length(u2)),
jump.after = NULL,
bad.n1 = c(),
bad.m2 = c(),
bad.u2 = c(),
logitP.cov = as.matrix(rep(1, length(n1))),
logitP.fixed = NULL,
logitP.fixed.values = NULL,
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,
set.browser = FALSE
)
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. |
u2 |
A numeric vector of the number of unmarked fish captured in each stratum. These will be expanded by the capture efficiency to estimate the population size 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. |
jump.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 |
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). |
logitP.fixed |
A numeric vector (could be null) of the time strata
where the logit(P) would be fixed. Typically, this is used when the capture
rates for some strata are 0 and logit(P) is set to -10 for these strata. The
fixed values are given in |
logitP.fixed.values |
A numerical vector (could be null) of the fixed values for logit(P) at strata given by logitP.fixed. Typically this is used when certain strata have a 0 capture rate and the fixed value is set to -10 which on the logit scale gives p[i] essentially 0. Don't specify values such as -50 because numerical problems could occur in JAGS. |
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. |
set.browser |
Should the function enter browser model when called (useful for debugging) |
Normally, the wrapper (*_fit) function is called which then calls the fitting routine.
Use the TimeStratPetersenNonDiagError_fit
function for cases
where recaptures take place outside the stratum of release.
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. \Sexpr[results=rd]{tools:::Rd_expr_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.trrp.net/library/document/?id=369
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