# importFrom("mritc", "initOtsu", "makeMRIspatial", "mritc.bayes")

importFrom("methods",show,setClass, setClassUnion, setMethod, setOldClass, setValidity,
getClass, getClassDef, callGeneric, as, is, extends,

importFrom(graphics, axis, layout, mtext, par, plot,

export(mrs, andova, plotTree, plot1D, plot2D)

#       gibbs.msbsvar,   # Leave out until we update.

# Declare S3 methods for printing and summaries
# Summary and plot methods for objects of SS class.

importFrom("graphics", "abline", "box", "close.screen", "contour",
"layout", "lines", "mtext", "pairs", "par", "persp", "plot",
"plot.new", "points", "polygon", "screen", "split.screen",
importFrom("stats", "approx", "ar.ols", "as.formula", "as.ts",
"density", "embed", "frequency", "kmeans", "lm", "optim",
"pchisq", "pf", "qnorm", "quantile", "rchisq", "rgamma",
"rnorm", "runif", "start", "ts", "ts.plot", "tsp", "var")

useDynLib(MSCMT, .registration = TRUE, .fixes = "C_")

#exportPattern("^[[:alpha:]]+") # comment for check and CRAN submission
#importFrom(Rcpp, evalCpp)      # comment for check and CRAN submission

importFrom("stats", "predict", "sd","fitted", "frequency", "lm", "ts")

useDynLib(MSGLasso)
export(MSGLasso, MSGLasso.cv, Cal_grpWTs, FindingGRGrps, FindingPQGrps)

useDynLib(MSGLasso)
export(MSGLasso, MSGLasso.cv, Cal_grpWTs, FindingGRGrps, FindingPQGrps)

export(Compute.input.variables, MSIseq.train, MSIseq.classify, read.fasta, find.mono.repeats)

import("ggplot2", "ggpubr", "doParallel", "nleqslv", "foreach")
importFrom("stats", "dbinom", "optimize", "pbinom", "pnorm", "pt",
"qbinom", "qnorm", "qt", "rbinom", "rnorm", "sd", "sigma",

importFrom("graphics", "mtext", "par", "plot", "points","segments","rect","legend", "lines", "locator")
importFrom("stats", "cor", "cov", "mahalanobis", "pchisq", "pf", "qchisq","qnorm")
importFrom("stats","pnorm", "qbeta", "qf", "plnorm","var", "shapiro.test")

importFrom("graphics", "legend", "lines", "par", "plot", "text")
importFrom("stats", "aggregate", "coef", "complete.cases", "na.omit",
"optim", "pnorm", "quantile", "rexp", "rgamma", "rnorm",