mixstock: functions for mixed stock analysis

mixed stock analysis functions

AuthorBen Bolker <bolker@mcmaster.ca>
Date of publication2014-09-01 20:31:28
MaintainerBen Bolker <bolker@mcmaster.ca>
LicenseGPL
Version0.9.8

View on R-Forge

Man pages

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...

calc.mult.GR: Calculate Gelman and Rubin diagnostic multiple times for...

calc.RL: Use Raftery and Lewis diagnostics to calculate MCMC chain...

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...

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 (or JAGS)

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...

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...

simmixstock2: Simulate multiple mixed stocks

sourcesize.wbugs: Run hierarchical model with via WinBUGS

startvec0: Produce (raw) starting vector of parameters for mixed stock...

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

Files in this package

mixstock/DESCRIPTION
mixstock/INDEX
mixstock/NAMESPACE
mixstock/R
mixstock/R/mixstock.R
mixstock/TODO
mixstock/build
mixstock/build/vignette.rds
mixstock/data
mixstock/data/bolten98.RData
mixstock/data/bolten98raw.txt.gz
mixstock/data/lahanas98.RData
mixstock/data/lahanas98raw.txt.gz
mixstock/data/simex.RData
mixstock/inst
mixstock/inst/CITATION
mixstock/inst/NEWS.Rd
mixstock/inst/bugs
mixstock/inst/bugs/manymany.bug
mixstock/inst/bugs/manymany.txt
mixstock/inst/bugs/pellamasuda.bug
mixstock/inst/bugs/pellamasuda.txt
mixstock/inst/bugs/rooksize.bug
mixstock/inst/doc
mixstock/inst/doc/mixstock.R
mixstock/inst/doc/mixstock.Rnw
mixstock/inst/doc/mixstock.pdf
mixstock/man
mixstock/man/AIC.mixstock.est.Rd mixstock/man/BUGS.out.Rd mixstock/man/addlabels.barplot.Rd mixstock/man/as.mcmc.bugs.Rd mixstock/man/as.mixstock.data.Rd mixstock/man/as.mixstock.est.bugs.Rd mixstock/man/blockdiag.Rd mixstock/man/bolten98.Rd mixstock/man/calc.GR.Rd mixstock/man/calc.RL.Rd mixstock/man/calc.mult.GR.Rd mixstock/man/cml.Rd mixstock/man/coef.toptim.Rd mixstock/man/expand.bugs.data.Rd mixstock/man/genboot.Rd mixstock/man/get.bot.Rd mixstock/man/gibbsC.Rd mixstock/man/gibbsmat.Rd mixstock/man/hwdiag.check.Rd mixstock/man/lahanas98.Rd mixstock/man/loglik2.C.Rd mixstock/man/markfreq.condense.Rd mixstock/man/marknames.Rd mixstock/man/mcmc.chainlength.est.Rd mixstock/man/mixstock.boot.Rd mixstock/man/mixstock.est.Rd mixstock/man/mm.wbugs.Rd mixstock/man/mysum.Rd mixstock/man/nmark.Rd mixstock/man/normcols.Rd mixstock/man/numderiv.Rd mixstock/man/p.bayes.Rd mixstock/man/packval.Rd mixstock/man/plot.mixstock.est.Rd mixstock/man/pm.wbugs.Rd mixstock/man/q.to.p.Rd mixstock/man/rdirichlet.Rd mixstock/man/runsims.Rd mixstock/man/simex.Rd mixstock/man/simmixstock0.Rd mixstock/man/simmixstock1.Rd mixstock/man/simmixstock2.Rd mixstock/man/sourcesize.wbugs.Rd mixstock/man/startvec0.Rd mixstock/man/tmcmc.Rd mixstock/man/uml.Rd mixstock/man/uml.lik.Rd
mixstock/src
mixstock/src/Makevars.gcc
mixstock/src/machdefs.h
mixstock/src/newrand.c
mixstock/src/turtle-funs.c
mixstock/src/turtle-gibbs.c
mixstock/src/utils.c
mixstock/src/utils.h
mixstock/tests
mixstock/tests/mprior.R
mixstock/vignettes
mixstock/vignettes/GR.RData
mixstock/vignettes/RL.RData
mixstock/vignettes/mcmc.RData
mixstock/vignettes/mixstock.Rnw
mixstock/vignettes/mixstock.bib
mixstock/vignettes/turtle.bib
mixstock/vignettes/umlboot.RData
mixstock/vignettes/wbugs_cache.RData

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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