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A B C D E G H L M N P Q R S T U W
| addlabels.barplot | add labels to a barplot |
| AIC.mixstock.est | commands for mixed stock analysis estimates |
| as.mcmc.bugs | convert from R2WinBUGS to CODA format |
| as.mixstock.data | class for marker data from sources and mixed stocks |
| as.mixstock.est | commands for mixed stock analysis estimates |
| as.mixstock.est.bugs | Convert BUGS or CODA objects to mixstock estimate object |
| as.mixstock.est.mcmc | Convert BUGS or CODA objects to mixstock estimate object |
| blockdiag | Block diagonal matrices |
| bolten98 | Loggerhead turtle data from Bolten 1998 |
| bolten98raw | Loggerhead turtle data from Bolten 1998 |
| boxplot.mixstock.est | commands for mixed stock analysis estimates |
| BUGS.out | generate MCMC output in BUGS format |
| calc.GR | Run chains and calculate Gelman and Rubin diagnostics for mixed stock analyses |
| calc.mult.GR | Calculate Gelman and Rubin diagnostic multiple times for mixed stock analyses |
| calc.mult.RL | Use Raftery and Lewis diagnostics to calculate MCMC chain lengths |
| calc.RL.0 | Use Raftery and Lewis diagnostics to calculate MCMC chain lengths |
| cml | Mixed stock analysis by conditional maximum likelihood |
| cml.grad | Likelihoods and gradients of stock analysis models |
| cml.lik | Likelihoods and gradients of stock analysis models |
| coef.mixstock.est | commands for mixed stock analysis estimates |
| coef.toptim | minimal structure for optim fits |
| confint.mixstock.est | commands for mixed stock analysis estimates |
| dcmat.a | Likelihoods and gradients of stock analysis models |
| expand.bugs.data | convert data to BUGS input format |
| genboot | Generate bootstrap estimates of mixed stock analyses |
| get.bot | Masuda-Pella interchange functions |
| get.bse | Masuda-Pella interchange functions |
| get.ctl | Masuda-Pella interchange functions |
| get.frq | Masuda-Pella interchange functions |
| get.mix | Masuda-Pella interchange functions |
| get.mp.input | Masuda-Pella interchange functions |
| gibbs | Mixed stock analysis by Markov Chain Monte Carlo |
| gibbsC | Run mixed stock analysis Gibbs sampler, in C |
| gibbsmat | Plot Gibbs sampler output |
| gibbsrpt | Plot Gibbs sampler output |
| hist.mixstock.est | commands for mixed stock analysis estimates |
| hwdiag.check | check Heidelberger and Welch diagnostic results |
| label.mixstock.data | Extract/assign names from mixed stock data |
| lahanas98 | Green turtle data from Lahanas et al. 1998 |
| lahanas98raw | Green turtle data from Lahanas et al. 1998 |
| locnames | Extract/assign names from mixed stock data |
| logLik.mixstock.est | commands for mixed stock analysis estimates |
| logLik.toptim | minimal structure for optim fits |
| loglik2.C | likelihood calculation, in C |
| lsolve | Produce (raw) starting vector of parameters for mixed stock analysis |
| markfreq.condense | condense marker frequency list |
| marknames | Extract/assign names from mixed stock data |
| mcmc.chainlength.est | Estimate appropriate chain length for mixed stock analysis by MCMC |
| mixnames | Extract/assign names from mixed stock data |
| mixstock.boot | Bootstrap samples of mixed stock analysis data |
| mixstock.data | class for marker data from sources and mixed stocks |
| mixstock.dimnames | Extract/assign names from mixed stock data |
| mixstock.est | construct (or print) a mixed stock analysis estimate object |
| mm.wbugs | Run many-to-many model via WinBUGS (or JAGS) |
| mysum | summaries of MCMC output |
| mysumvec | summaries of MCMC output |
| nmark | Set and query mixed stock parameters |
| nmark<- | Set and query mixed stock parameters |
| nmix | Set and query mixed stock parameters |
| nmix<- | Set and query mixed stock parameters |
| normcols | scale columns to frequencies |
| nsource | Set and query mixed stock parameters |
| nsource<- | Set and query mixed stock parameters |
| numderiv | take the numeric derivative of a function |
| p.bayes | Empirical Bayes estimate of prior strength for source marker frequencies |
| p.to.q | Real-to-multifrequency transformation |
| packval | Pack and unpack contribution and marker frequencies |
| packval2 | Pack and unpack contribution and marker frequencies |
| plot.mixstock.data | class for marker data from sources and mixed stocks |
| plot.mixstock.est | plot mixed stock analysis estimates |
| plotvar | Plot Gibbs sampler output |
| pm.wbugs | Run Pella-Masuda model via WinBUGS |
| print.mixstock.data | class for marker data from sources and mixed stocks |
| print.mixstock.est | construct (or print) a mixed stock analysis estimate object |
| put.bse | Masuda-Pella interchange functions |
| put.ctl | Masuda-Pella interchange functions |
| put.mix | Masuda-Pella interchange functions |
| put.mp | Masuda-Pella interchange functions |
| q.to.p | Real-to-multifrequency transformation |
| rdirichlet | Dirichlet deviates |
| RL.burn | Use Raftery and Lewis diagnostics to calculate MCMC chain lengths |
| RL.max | Use Raftery and Lewis diagnostics to calculate MCMC chain lengths |
| runsims | Run mixed stock simulations |
| sim.mark.freq | Simulate marker frequencies and distributions in a mixed stock |
| simex | A small sample mixed stock analysis data set |
| simmixstock0 | Simulate a sample from sources and mixed stock |
| simmixstock1 | Simulate marker frequencies and distributions in a mixed stock |
| simmixstock2 | Simulate multiple mixed stocks |
| sourcenames | Extract/assign names from mixed stock data |
| sourcesize.wbugs | Run hierarchical model with via WinBUGS |
| startvec | Produce (raw) starting vector of parameters for mixed stock analysis |
| startvec0 | Produce (raw) starting vector of parameters for mixed stock analysis |
| summary.mixstock.est | commands for mixed stock analysis estimates |
| tmcmc | Mixed stock analysis by Markov Chain Monte Carlo |
| uml | Mixed stock analysis by unconditional maximum likelihood |
| uml.ds | Mixed stock analysis by unconditional maximum likelihood |
| uml.em | Mixed stock analysis by unconditional maximum likelihood |
| uml.grad | Likelihoods and gradients of stock analysis models |
| uml.lik | Likelihoods and gradients of stock analysis models |
| unpackval | Pack and unpack contribution and marker frequencies |
| unpackval2 | Pack and unpack contribution and marker frequencies |
| write.TO.bugscode | Run many-to-many model via WinBUGS (or JAGS) |