View source: R/TimeStratPetersenNonDiagErrorNP_fit.R
TimeStratPetersenNonDiagErrorNP_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.
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
)
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
|
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 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 |
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 |
One of the parameters along with |
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. |
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.
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
##---- See the vignette for examples of how to use this package
##
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