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

Functions

addlabels.barplot Man page
AIC.mixstock.est Man page
as.mcmc.bugs Man page
as.mixstock.data Man page
as.mixstock.est Man page
as.mixstock.est.bugs Man page
as.mixstock.est.mcmc Man page
blockdiag Man page
bolten98 Man page
bolten98raw Man page
boxplot.mixstock.est Man page
BUGS.out Man page
calc.GR Man page
calc.mult.GR Man page
calc.mult.RL Man page
calc.RL.0 Man page
cml Man page
cml.grad Man page
cml.lik Man page
coef.mixstock.est Man page
coeftab.mixstock.est Man page
coef.toptim Man page
confint.mixstock.est Man page
dcmat.a Man page
expand.bugs.data Man page
genboot Man page
get.bot Man page
get.bse Man page
get.ctl Man page
get.frq Man page
get.mix Man page
get.mp.input Man page
gibbs Man page
gibbsC Man page
gibbsmat Man page
gibbsrpt Man page
hist.mixstock.est Man page
hwdiag.check Man page
label.mixstock.data Man page
lahanas98 Man page
lahanas98raw Man page
locnames Man page
loglik2.C Man page
logLik.mixstock.est Man page
logLik.toptim Man page
lsolve Man page
markfreq.condense Man page
marknames Man page
MAXMARK Man page
MAXSRC Man page
mcmc.chainlength.est Man page
mixnames Man page
mixstock.boot Man page
mixstock.data Man page
mixstock.dimnames Man page
mixstock.est Man page
mm.wbugs Man page
mysum Man page
mysumvec Man page
nmark Man page
nmark<- Man page
nmix Man page
nmix<- Man page
normcols Man page
nsource Man page
nsource<- Man page
numderiv Man page
packval Man page
packval2 Man page
p.bayes Man page
plot.mixstock.data Man page
plot.mixstock.est Man page
plotvar Man page
pm.wbugs Man page
print.mixstock.data Man page
print.mixstock.est Man page
p.to.q Man page
put.bse Man page
put.ctl Man page
put.mix Man page
put.mp Man page
q.to.p Man page
rdirichlet Man page
RL.burn Man page
RL.max Man page
runsims Man page
simex Man page
sim.mark.freq Man page
simmixstock0 Man page
simmixstock1 Man page
simmixstock2 Man page
sourcenames Man page
sourcesize.wbugs Man page
startvec Man page
startvec0 Man page
summary.mixstock.est Man page
tmcmc Man page
uml Man page
uml.ds Man page
uml.em Man page
uml.grad Man page
uml.lik Man page
unpackval Man page
unpackval2 Man page
write.TO.bugscode Man page
xyplot.mixstock.est Man page

Files

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

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

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.