mixstock: functions for mixed stock analysis

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mixed stock analysis functions

Author
Ben Bolker <bolker@mcmaster.ca>
Date of publication
2014-09-01 20:31:28
Maintainer
Ben Bolker <bolker@mcmaster.ca>
License
GPL
Version
0.9.8

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