export("Dim", "Header", "Mode", "Numerify", "Rfile.index",
"get.ext", "getRepositories", "has.method", "head2", "headl",
"nearest.to", "out.of", "p.to.Z", "packages.loaded", "pad.left",
"pctile", "ppa", "preview", "prv", "prv.large",
"se.na", "search.cran", "sim.cor", "simple.date", "spc",

importFrom("stats", "cor", "dist", "kmeans", "predict", "quantile",

importFrom("stats", "qnorm", "sd", "pt", "t.test", "var.test")

importFrom("stats", "binomial", "coef", "glm", "rgamma", "rnorm",
"runif", "vcov", "dgamma", "rbeta", "model.matrix")

"runif", "vcov", "dgamma", "rbeta", "model.matrix", "uniroot")

importFrom("graphics", "axis", "contour", "legend", "lines", "par",
importFrom("stats", "aggregate", "median", "optim", "plot.ts", "qnorm",
"quantile", "rgamma", "rnorm", "rpois", "rweibull","dbeta","dnorm","pnorm","dgamma","na.omit")

#useDynLib("NHMM", .registration = TRUE, .fixes = "C_")
export(HMM,NHMM,NHMM_MVN, OBIC, Oz, OQQ, OXcoef, OWcoef, Oemparams)
importFrom("graphics", "abline", "hist", "par", "plot")
importFrom("stats", "cutree", "dgamma", "dist", "hclust", "na.omit",

importFrom("graphics", "abline", "grid", "lines", "plot", "polygon","title")
importFrom("stats", "acf", "cor", "kmeans", "lm", "optim", "pnorm","predict", "qqplot", "quantile", "rmultinom", "rnorm","runif", "sd", "var")

importFrom("graphics", "abline", "legend", "lines", "mtext", "par",
importFrom("stats", "Box.test", "acf", "complete.cases", "cor.test",
"ks.test", "lm", "lowess", "na.exclude", "nlminb", "optim",
"pchisq", "predict", "qchisq", "qnorm", "quantile", "rexp")

export("generatePerturbations", "findPathF1", "findPathF2", "findPathF3", "L2")

# conditional import of class ExpressionSet from package Biobase
if( "Biobase" %in% rownames(utils::installed.packages()) ){

importFrom(utils, capture.output, .DollarNames, file_test, flush.console, getS3method, packageDescription, setTxtProgressBar, str)

, divergence_update_H, divergence_update_W # divergence based updates
, euclidean_update_H, euclidean_update_W # euclidean based updates
, offset_euclidean_update_H, offset_euclidean_update_W # nmf with offset (euclidean based)
, Euclidean_rss # compute residual sum of squares (without memory duplication)
, KL_divergence # compute the KL divergence (with no memory duplication)
importFrom(stats, coefficients, coef, fitted, offset, predict, residuals)