Entry: AIC.mixstock.est
Aliases: AIC.mixstock.est boxplot.mixstock.est as.mixstock.est coef.mixstock.est logLik.mixstock.est hist.mixstock.est confint.mixstock.est summary.mixstock.est
Keywords: misc
Description: commands for mixed stock analysis estimates
URL: ../../../library/mixstock/html/AIC.mixstock.est.html

Entry: BUGS.out
Aliases: BUGS.out
Keywords: misc
Description: generate MCMC output in BUGS format
URL: ../../../library/mixstock/html/BUGS.out.html

Entry: addlabels.barplot
Aliases: addlabels.barplot
Keywords: aplot
Description: add labels to a barplot
URL: ../../../library/mixstock/html/addlabels.barplot.html

Entry: as.mcmc.bugs
Aliases: as.mcmc.bugs
Keywords: misc
Description: convert from R2WinBUGS to CODA format
URL: ../../../library/mixstock/html/as.mcmc.bugs.html

Entry: as.mixstock.data
Aliases: as.mixstock.data mixstock.data plot.mixstock.data print.mixstock.data
Keywords: misc
Description: class for marker data from sources and mixed stocks
URL: ../../../library/mixstock/html/as.mixstock.data.html

Entry: as.mixstock.est.bugs
Aliases: as.mixstock.est.bugs as.mixstock.est.mcmc
Keywords: misc
Description: Convert BUGS or CODA objects to mixstock estimate object
URL: ../../../library/mixstock/html/as.mixstock.est.bugs.html

Entry: blockdiag
Aliases: blockdiag
Keywords: array
Description: Block diagonal matrices
URL: ../../../library/mixstock/html/blockdiag.html

Entry: bolten98
Aliases: bolten98 bolten98raw
Keywords: datasets
Description: Loggerhead turtle data from Bolten 1998
URL: ../../../library/mixstock/html/bolten98.html

Entry: calc.GR
Aliases: calc.GR
Keywords: misc
Description: Run chains and calculate Gelman and Rubin diagnostics for mixed stock analyses
URL: ../../../library/mixstock/html/calc.GR.html

Entry: calc.RL.0
Aliases: calc.RL.0 calc.mult.RL RL.max RL.burn
Keywords: misc
Description: Use Raftery and Lewis diagnostics to calculate MCMC chain lengths
URL: ../../../library/mixstock/html/calc.RL.html

Entry: calc.mult.GR
Aliases: calc.mult.GR
Keywords: misc
Description: Calculate Gelman and Rubin diagnostic multiple times for mixed stock analyses
URL: ../../../library/mixstock/html/calc.mult.GR.html

Entry: cml
Aliases: cml
Keywords: misc
Description: Mixed stock analysis by conditional maximum likelihood
URL: ../../../library/mixstock/html/cml.html

Entry: coef.toptim
Aliases: coef.toptim logLik.toptim
Keywords: misc
Description: minimal structure for optim fits
URL: ../../../library/mixstock/html/coef.toptim.html

Entry: expand.bugs.data
Aliases: expand.bugs.data
Keywords: misc
Description: convert data to BUGS input format
URL: ../../../library/mixstock/html/expand.bugs.data.html

Entry: genboot
Aliases: genboot
Keywords: misc
Description: Generate bootstrap estimates of mixed stock analyses
URL: ../../../library/mixstock/html/genboot.html

Entry: get.bot
Aliases: get.bot get.frq get.ctl get.bse get.mix put.ctl put.bse put.mix put.mp get.mp.input
Keywords: misc
Description: Masuda-Pella interchange functions
URL: ../../../library/mixstock/html/get.bot.html

Entry: gibbsC
Aliases: gibbsC
Keywords: misc
Description: Run mixed stock analysis Gibbs sampler, in C
URL: ../../../library/mixstock/html/gibbsC.html

Entry: gibbsmat
Aliases: gibbsmat gibbsrpt plotvar
Keywords: misc
Description: Plot Gibbs sampler output
URL: ../../../library/mixstock/html/gibbsmat.html

Entry: hwdiag.check
Aliases: hwdiag.check
Keywords: misc
Description: check Heidelberger and Welch diagnostic results
URL: ../../../library/mixstock/html/hwdiag.check.html

Entry: lahanas98
Aliases: lahanas98 lahanas98raw
Keywords: datasets
Description: Green turtle data from Lahanas et al. 1998
URL: ../../../library/mixstock/html/lahanas98.html

Entry: loglik2.C
Aliases: loglik2.C
Keywords: misc
Description: likelihood calculation, in C
URL: ../../../library/mixstock/html/loglik2.C.html

Entry: markfreq.condense
Aliases: markfreq.condense
Keywords: misc
Description: condense marker frequency list
URL: ../../../library/mixstock/html/markfreq.condense.html

Entry: marknames
Aliases: marknames sourcenames mixnames locnames mixstock.dimnames label.mixstock.data
Keywords: misc
Description: Extract/assign names from mixed stock data
URL: ../../../library/mixstock/html/marknames.html

Entry: mcmc.chainlength.est
Aliases: mcmc.chainlength.est
Keywords: misc
Description: Estimate appropriate chain length for mixed stock analysis by MCMC
URL: ../../../library/mixstock/html/mcmc.chainlength.est.html

Entry: mixstock.boot
Aliases: mixstock.boot
Keywords: misc
Description: Bootstrap samples of mixed stock analysis data
URL: ../../../library/mixstock/html/mixstock.boot.html

Entry: mixstock.est
Aliases: mixstock.est print.mixstock.est
Keywords: misc
Description: construct (or print) a mixed stock analysis estimate object
URL: ../../../library/mixstock/html/mixstock.est.html

Entry: mm.wbugs
Aliases: mm.wbugs write.TO.bugscode
Keywords: misc
Description: Run many-to-many model via WinBUGS (or JAGS)
URL: ../../../library/mixstock/html/mm.wbugs.html

Entry: mysum
Aliases: mysum mysumvec
Keywords: misc
Description: summaries of MCMC output
URL: ../../../library/mixstock/html/mysum.html

Entry: nmark
Aliases: nmark nmark<- nmix nmix<- nsource nsource<-
Keywords: misc
Description: Set and query mixed stock parameters
URL: ../../../library/mixstock/html/nmark.html

Entry: normcols
Aliases: normcols
Keywords: misc
Description: scale columns to frequencies
URL: ../../../library/mixstock/html/normcols.html

Entry: numderiv
Aliases: numderiv
Keywords: misc
Description: take the numeric derivative of a function
URL: ../../../library/mixstock/html/numderiv.html

Entry: p.bayes
Aliases: p.bayes
Keywords: misc
Description: Empirical Bayes estimate of prior strength for source marker frequencies
URL: ../../../library/mixstock/html/p.bayes.html

Entry: packval
Aliases: packval packval2 unpackval unpackval2
Keywords: misc
Description: Pack and unpack contribution and marker frequencies
URL: ../../../library/mixstock/html/packval.html

Entry: plot.mixstock.est
Aliases: plot.mixstock.est
Keywords: misc
Description: plot mixed stock analysis estimates
URL: ../../../library/mixstock/html/plot.mixstock.est.html

Entry: pm.wbugs
Aliases: pm.wbugs
Keywords: misc
Description: Run Pella-Masuda model via WinBUGS
URL: ../../../library/mixstock/html/pm.wbugs.html

Entry: q.to.p
Aliases: q.to.p p.to.q
Keywords: misc
Description: Real-to-multifrequency transformation
URL: ../../../library/mixstock/html/q.to.p.html

Entry: rdirichlet
Aliases: rdirichlet
Keywords: distribution
Description: Dirichlet deviates
URL: ../../../library/mixstock/html/rdirichlet.html

Entry: runsims
Aliases: runsims
Keywords: misc
Description: Run mixed stock simulations
URL: ../../../library/mixstock/html/runsims.html

Entry: simex
Aliases: simex
Keywords: datasets
Description: A small sample mixed stock analysis data set
URL: ../../../library/mixstock/html/simex.html

Entry: simmixstock0
Aliases: simmixstock0
Keywords: misc
Description: Simulate a sample from sources and mixed stock
URL: ../../../library/mixstock/html/simmixstock0.html

Entry: simmixstock1
Aliases: simmixstock1 sim.mark.freq
Keywords: misc
Description: Simulate marker frequencies and distributions in a mixed stock
URL: ../../../library/mixstock/html/simmixstock1.html

Entry: simmixstock2
Aliases: simmixstock2
Keywords: misc
Description: Simulate multiple mixed stocks
URL: ../../../library/mixstock/html/simmixstock2.html

Entry: sourcesize.wbugs
Aliases: sourcesize.wbugs
Keywords: misc
Description: Run hierarchical model with via WinBUGS
URL: ../../../library/mixstock/html/sourcesize.wbugs.html

Entry: startvec0
Aliases: startvec0 startvec lsolve
Keywords: misc
Description: Produce (raw) starting vector of parameters for mixed stock analysis
URL: ../../../library/mixstock/html/startvec0.html

Entry: tmcmc
Aliases: tmcmc gibbs
Keywords: misc
Description: Mixed stock analysis by Markov Chain Monte Carlo
URL: ../../../library/mixstock/html/tmcmc.html

Entry: uml
Aliases: uml uml.ds uml.em
Keywords: misc
Description: Mixed stock analysis by unconditional maximum likelihood
URL: ../../../library/mixstock/html/uml.html

Entry: uml.lik
Aliases: uml.lik uml.grad cml.lik cml.grad dcmat.a
Keywords: misc
Description: Likelihoods and gradients of stock analysis models
URL: ../../../library/mixstock/html/uml.lik.html
