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.bugs    Convert BUGS or CODA objects to mixstock
                        estimate object
blockdiag               Block diagonal matrices
bolten98                Loggerhead turtle data from Bolten 1998
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.RL.0               Use Raftery and Lewis diagnostics to calculate
                        MCMC chain lengths
cml                     Mixed stock analysis by conditional maximum
                        likelihood
coef.toptim             minimal structure for optim fits
expand.bugs.data        convert data to BUGS input format
genboot                 Generate bootstrap estimates of mixed stock
                        analyses
get.bot                 Masuda-Pella interchange functions
gibbsC                  Run mixed stock analysis Gibbs sampler, in C
gibbsmat                Plot Gibbs sampler output
hwdiag.check            check Heidelberger and Welch diagnostic results
lahanas98               Green turtle data from Lahanas et al. 1998
loglik2.C               likelihood calculation, in C
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
mixstock.boot           Bootstrap samples of mixed stock analysis data
mixstock.est            construct (or print) a mixed stock analysis
                        estimate object
mm.wbugs                Run many-to-many model via WinBUGS
mysum                   summaries of MCMC output
nmark                   Set and query mixed stock parameters
normcols                scale columns to frequencies
numderiv                take the numeric derivative of a function
packval                 Pack and unpack contribution and marker
                        frequencies
p.bayes                 Empirical Bayes estimate of prior strength for
                        source marker frequencies
plot.mixstock.est       plot mixed stock analysis estimates
pm.wbugs                Run Pella-Masuda model via WinBUGS
q.to.p                  Real-to-multifrequency transformation
rdirichlet              Dirichlet deviates
runsims                 Run mixed stock simulations
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
sourcesize.wbugs        Run hierarchical model with via WinBUGS
startvec0               Produce (raw) starting vector of parameters for
                        mixed stock analysis
tmcmc                   Mixed stock analysis by Markov Chain Monte
                        Carlo
uml                     Mixed stock analysis by unconditional maximum
                        likelihood
uml.lik                 Likelihoods and gradients of stock analysis
                        models
