TimeStratPetersenNonDiagErrorNP_fit {BTSPAS}

Wrapper (*_fit) to fit the Time Stratified Petersen Estimator with NON Diagonal Entries function and a non-parametric travel time estimator..

Description

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.

Usage

TimeStratPetersenNonDiagErrorNP_fit(
  title = "TSPNDENP",
  prefix = "TSPNDENP-",
  time,
  n1,
  m2,
  u2,
  sampfrac = rep(1, length(u2)),
  jump.after = NULL,
  bad.n1 = c(),
  bad.m2 = c(),
  bad.u2 = c(),
  logitP.cov = rep(1, length(u2)),
  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(2, rep(10, ncol(as.matrix(logitP.cov)) - 1)),
  tauP.alpha = 0.001,
  tauP.beta = 0.001,
  Delta.max = NULL,
  prior.muTT = NULL,
  tauTT.alpha = 0.1,
  tauTT.beta = 0.1,
  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
)

Arguments

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 matrix of the number of fish released in stratum [i] and recovered in [j-1] strata later. For example m2[3,5] is the number of marked fish released in stratum 3 and recovered 4 strata later in stratum 7. The first column is the number of marked fish recovered in the stratum of release, i.e. 0 strata later. Use the TimeStratPetersenDiagError_fit function for cases where recaptures take place ONLY in the stratum of release, i.e. the diagonal case.

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. The length of u2 should be between the length of n1 and length n1 + number of columns in m2 -1

sampfrac

Deprecated because it really doesn't work as intended. You must remove all references to sampfrac from your code. Contact [e-mail] for more information.

jump.after

A numeric vector with elements belonging to time. In some cases, the spline fitting the population numbers should be allowed to jump. For example, the population size could take a jump when hatchery released fish suddenly arrive at the trap. The jumps occur AFTER the strata listed in this argument.

bad.n1

A numeric vector with elements belonging to time. In some cases, something goes wrong in the stratum, and the number of marked fish releases should be discarded. The values of n1 and m2 will be set to 0 for these strata.

bad.m2

A numeric vector with elements belonging to time. In some cases, something goes wrong in the stratum, and the number of recovered marked fish should be ignored. For example, poor handling is suspected to induce handling induced mortality in the marked fish and so only very few are recovered. The values of n1 and m2 will be set to 0 for these strata.

bad.u2

A numeric vector with elements belonging to time. In some cases, something goes wrong in the stratum, and the number of unmarked fish captured should be ignored. The values of u2 in the entire row will be set to NA for these strata. DO NOT SET the value of u2 to 0 because this indicates that the trap was operating and captured no fish.

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

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 for the prior for the variance of the random noise for the smoothing spline.

tauU.beta

One of the parameters along with tauU.alpha for the prior for the variance of the random noise for the smoothing spline.

taueU.alpha

One of the parameters along with taueU.beta for the prior for the variance of noise around the spline.

taueU.beta

One of the parameters along with taueU.alpha for the prior for the variance of noise around the spline.

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

Delta.max

Maximum transition time for marked fish, i.e. all fish assumed to have moved by Delta.max unit of time

prior.muTT

- prior for movement rates. These are like a Dirchelet type prior where x are values representing belief in the travel times. For example, x=c(1,4,3,2) represents a system where the maximum travel time is 3 strata after release with 1/10=.1 of the animals moving in the stratum of release 4/10=.4 of the animals taking 1 stratum to move etc So if x=c(10,40,30,20), this represent the same movement pattern but a strong degree of belief

tauTT.alpha

One of the parameters along with tauTT.beta for the prior on 1/var of logit continuation ratio for travel times

tauTT.beta

One of the parameters along with tauTT.alpha for the prior on 1/var of logit continuation ratio for travel times

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 browser() calls to allow the user to peek into the internal variables. Not useful except to package developers.

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.

Details

Normally the user makes a call to the *_fit function which then calls the fitting function.

Use the TimeStratPetersenDiagError_fit function for cases where recaptures take place ONLY in the stratum of release, i.e. the diagonal case.

The *NP functions fit a non-parametric distribution for the travel times.

Value

An MCMC object with samples from the posterior distribution. A series of graphs and text file are also created in the working directory.

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.trrp.net/library/document/?id=369

Examples

 
##---- See the vignette  for examples of how to use this package
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