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 |
coeftab.mixstock.est |
construct (or print) a mixed stock analysis estimate object |
confint.mixstock.est |
commands for mixed stock analysis estimates |
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 |
markfreq.condense |
condense marker frequency list |
marknames |
Extract/assign names from mixed stock data |
MAXMARK |
Mixed stock analysis by conditional maximum likelihood |
MAXSRC |
Mixed stock analysis by conditional maximum likelihood |
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 |
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 |
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 |