# NAMESPACE for package 'wiqid'

importFrom("utils", "packageVersion", "head", "tail", "flush.console", "modifyList")
importFrom("stats", "AIC", "acf", "as.dist", "as.formula",
  "density", "bw.nrd0", "bw.SJ", "bw.bcv", "bw.nrd", "bw.ucv",
  "dbinom", "dpois", "median", "model.matrix",
  "na.omit", "nlm", "optim", "optimize", "pchisq", "plogis",
  "pnorm", "predict", "qlogis", "qnorm", "rbeta", "rbinom",
  "rgamma", "rnorm", "runif", "sd", "terms", "var",
  "nobs", "logLik", "update", "window",
  "dt", "pt", "qt", "rt",
  "dbeta", "pbeta", "qbeta",
  "dgamma", "pgamma", "qgamma",
  "coef", "model.frame", "dnorm", "quantile", "cor")
importFrom("parallel", "detectCores", "makeCluster", "stopCluster",
  "clusterExport", "clusterEvalQ", "clusterSetRNGStream", "parLapply")
importFrom("MASS", "mvrnorm", "eqscplot")
importFrom("grDevices", "devAskNewPage", "dev.interactive", "adjustcolor", "palette",
  "topo.colors", "colorRampPalette")
importFrom("graphics", "abline", "hist", "lines", "matplot", "par",
  "plot", "plot.default", "polygon", "rect", "segments", "points",
  "text", "box", "layout", "title")

importFrom("truncnorm", "rtruncnorm")
importFrom("coda", "mcmc", "mcmc.list", "as.mcmc.list", "effectiveSize")
importFrom("HDInterval", "hdi")
importFrom("mcmcOutput", "mcmcOutput")


export(
  survCJS, survCJSaj,
  survRD, survRDah,
  closedCapM0, closedCapMb, closedCapMh2, closedCapMhJK, closedCapMt, closedCapMtcov,
  occSS, occSStime, occSS0, occSScovSite,
  occSSrn, occSSrn0, occSSrnSite,
  occ2sps,
  occMS0, occMStime, occMScovSite, occMS,
  Bnormal, Bnormal2, Bbinom, Bbinomial, Bpoisson,
  BoccSS0, BoccSS, BsurvCJS, Bsecr0,
  richRarefy,
  richACE, richICE, richChao1, richChao2, richJack1, richJack2, richBoot, richMM,
  richJackA1, richJackA2, richRenLau,
  richCurve, richSobs, richSingle, richDouble, richUnique, richDuplicate,
  biodSimpson, biodShannon, biodBerger, biodBrillouin,
  distShell, distBrayCurtis,
  distChaoJaccCorr, distChaoJaccNaive, distChaoSorCorr, distChaoSorNaive,
  distChord, distJaccard, distMatching, distMorisitaHorn, distOchiai, distPreston,
  distRogersTanimoto, distSimRatio, distSorensen, distWhittaker,
  AICc, allCombinations, AICtable, WAIC, predictAvg,
  plotComb,
  plotPost, # postPriorOverlap, # moved to mcmcOutput
  plotACs,
  # densityFolded, # moved to mcmcOutput
  as.Bwiqid,
  # diagPlot, tracePlot, densityPlot, acfPlot, crosscorrPlot, # moved to mcmcOutput
  simpleRhat, getMCerror,
  showShinyApp,
  dt2, pt2, qt2, rt2,
  dt3, pt3, qt3, rt3,
  dbeta2, pbeta2, qbeta2, rbeta2, getBeta2Par,
  dbeta3, pbeta3, qbeta3, rbeta3, getBeta3Par,
  dgamma2, pgamma2, qgamma2, rgamma2, getGammaPar,
  "standardize", "standardize2match",
  "secrFit")

S3method("print", "wiqid")
S3method("logLik", "wiqid")
S3method("nobs", "wiqid")
S3method("coef", "wiqid")
S3method("vcov", "wiqid")
S3method("predict", "wiqid")
S3method("AICc", "default")

S3method("print", "Bwiqid")
S3method("summary", "Bwiqid")
S3method("plot", "Bwiqid")
# S3method("window", "Bwiqid")
S3method("head", "Bwiqid")
S3method("tail", "Bwiqid")

S3method("as.Bwiqid", "default")
# S3method("as.Bwiqid", "Bwiqid")
# S3method("as.Bwiqid", "data.frame")
# S3method("as.Bwiqid", "mcmc.list")
# S3method("as.Bwiqid", "mcmc")
# S3method("as.Bwiqid", "bugs")
# S3method("as.Bwiqid", "rjags")
# S3method("as.Bwiqid", "runjags")
# S3method("as.Bwiqid", "jagsUI")

