# rest of dplyr.R exported via hack in src_monetdb

export(AssessMonophyly, GetSummaryMonophyly, GetResultMonophyly, GetIntruderTaxa, GetIntruderTips, GetOutlierTaxa, GetOutlierTips, GetAncNodes, PlotMonophyly)

export(AssessMonophyly, CollapseMonophyletics, GetSummaryMonophyly, GetResultMonophyly, GetIntruderTaxa, GetIntruderTips, GetOutlierTaxa, GetOutlierTips, GetAncNodes, PlotMonophyly)

useDynLib(MonoPoly, .registration = TRUE, .fixes = ".MP_")
importFrom("stats", ".checkMFClasses", "coef", "convolve", "cor",

import(annotate, clusterProfiler, org.Hs.eg.db, pheatmap, RColorBrewer)

importFrom(Matrix, sparseMatrix, diag, crossprod, solve)
## addo ang calcGamma CreateL2D eigenPCA export.meshDist gdif meshDist.matrix meshDist.mesh3d meshres.mesh3d orp pcaplot3d.nosymproc pcaplot3d.symproc projBack read.obj render.matrixDist render.meshDist RGB2Grey rotaxis3d.matrix rotaxis3d.mesh3d rot.proc scaleproc Semislide warpmovie3d.matrix warpmovie3d.mesh3d write.obj place.patch
## private functions in Morpho beginning with dot:
## .bindArr2 .calcTang_U_s .calcTang_U .covPCApermut .CVAcrova .CVAdists .difplotLM2D .difplotLM .fx. groupPCAcrova

importFrom("utils", "hasName", "combn", "setTxtProgressBar", "txtProgressBar")

importFrom("graphics", "abline", "plot", "points", "polygon",
importFrom("stats", "aggregate", "approx", "ave", "cov", "diffinv", "dist",
"hclust", "median", "qf", "quantile", "rnorm", "runif",

export(runModels, runModels_Interactive, createTable, parseModels, getSavedata_Data, getSavedata_Fileinfo)

export(runModels, runModels_Interactive, createTable, extractModelSummaries, extractModelParameters, getSavedata_Data, getSavedata_Fileinfo)

importFrom("grDevices", "as.raster", "dev.cur", "dev.new", "dev.set",
importFrom("graphics", "abline", "axis", "layout", "lines", "locator",
"mtext", "par", "plot", "points", "rasterImage", "segments",

AICc, beta.weights, coeffs, coeffs.default, coeffs.glmer, coeffs.gls, coeffs.lme, coeffs.lmer, coeffs.mer, coeffs.spautolm,  dredge, get.models, getAllTerms, getAllTerms.default, getAllTerms.formula, getAllTerms.glmer, getAllTerms.lme, getAllTerms.lmer, getAllTerms.mer, model.avg, par.avg, print.averaging, print.model.selection,
#tTable.gam, tTable.glmer, tTable.gls, tTable.lme, tTable.lmer, tTable.mer, tTable.spautolm,