functions for mixed stock analysis

[Up] [Top]

Documentation for package ‘mixstock’ version 0.9.5.1

Help Pages

A B C D E G H L M N P Q R S T U W X

-- A --

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

-- B --

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

-- C --

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

-- D --

dcmat.a Likelihoods and gradients of stock analysis models

-- E --

expand.bugs.data convert data to BUGS input format

-- G --

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

-- H --

hist.mixstock.est commands for mixed stock analysis estimates
hwdiag.check check Heidelberger and Welch diagnostic results

-- L --

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

-- M --

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

-- N --

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 --

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 --

q.to.p Real-to-multifrequency transformation

-- R --

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

-- S --

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

-- T --

tmcmc Mixed stock analysis by Markov Chain Monte Carlo

-- U --

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

-- W --

write.TO.bugscode Run many-to-many model via WinBUGS (or JAGS)

-- X --

xyplot.mixstock.est construct (or print) a mixed stock analysis estimate object