importFrom("graphics", "abline", "lines", "par", "plot", "points",
importFrom("stats", "dnorm", "lm", "pchisq", "pnorm", "qchisq",
"quantile", "rcauchy", "rexp", "rnorm", "runif", "var")

# This file no longer generated by roxygen as that cannot handle the S3 methods properly

importFrom("graphics", "axis", "box", "legend", "lines", "locator",
"mtext", "par", "plot", "points", "polygon", "segments",

importFrom("graphics", "abline", "legend", "lines", "par", "points",
importFrom("stats", "dbeta", "dnorm", "dwilcox", "fitted", "lm",
"loess", "model.matrix", "optim", "pf", "predict", "pt",

importFrom("graphics", "abline", "axis", "barplot", "frame",
"grconvertX", "grconvertY", "layout", "legend", "mtext",
importFrom("stats", "as.dendrogram", "as.dist", "cor", "cutree",
"dist", "hclust", "heatmap", "kmeans", "order.dendrogram",
"pchisq", "reorder", "rnorm", "sd", "var")

importFrom("graphics", "box", "lines", "par", "plot", "polygon", "text")

importFrom("stats", "lm", "mad", "median", "sd")

importFrom("stats", "pnorm", "qnorm", "rnorm", "runif", "sd")

importFrom("graphics", "abline", "arrows", "legend", "plot", "points")

### convert base functions or S3 methods into S4 methods
#exportMethods("plot", "hist") # come from 'graphics'
#exportMethods("summary")      # comes from 'base'
importFrom("quantmod", "findPeaks")  # used in "seqSeg" in '03-utilities.R'
importFrom("gtools", "rdirichlet", "ddirichlet") # used in '04-algorithms.R'
importFrom("graphics", "par", "segments")  # used in "plotTumorData",
"rbeta", "dbeta", "rbinom", "dbinom", "rnorm", "dnorm",
importFrom(combinat, "combn")    # used for combinations of psi-values
importFrom(combinat, "xsimplex") # used for generateSimplex
export("tumorGen", "dataGen", "runAlg") # deprecated
### needed for simulations; currently internal

importFrom("mc2d", "rdirichlet", "ddirichlet") # used in '04-algorithms.R'

import(dplyr, except = c(last, first, between))

importFrom(graphics, image, layout, legend, par, plot, rect, text)
importFrom(stats, as.dendrogram, as.dist, complete.cases, cor, dist, hclust, kruskal.test, median, na.omit, pchisq, quantile)