
import("OpenMx")
import("bitops")
import("rpart")
importFrom("grDevices", "heat.colors", "rainbow")
importFrom("graphics", "barplot", "legend", "lines", "pairs", "par",
             "plot", "strwidth", "text")
importFrom("stats", "as.dist", "cmdscale", "coef", "cor", "cov",
             "logLik", "median", "pchisq", "qnorm", "runif", "var")
importFrom("stats", "dist", "rnorm")
importFrom("utils", "flush.console", "getS3method", "sessionInfo","str")
importFrom("utils", "setTxtProgressBar")
importFrom("parallel","parLapply","clusterMap")
importFrom("sets","as.set")
importFrom("graphics", "hist")


export("evaluate")
S3method("evaluate","semforest")


export("semtree")
export("semforest")
export("semtree.control")
export("semforest.control")

export("semtree.constraints")

S3method("merge","semforest")

export("subtree")

export("biodiversity")
export("diversityMatrix")
export("hellinger")
export("klsym")
S3method("plot","diversityMatrix")

export("prune")

S3method("summary","semtree")
S3method("summary","semforest")
S3method("print","semtree.control")
S3method("print","semforest.control")
S3method("print","semtree")
S3method("print","summary.semtree")
S3method("print","semforest.varimp")
S3method("print","semforest")

S3method("prune","semtree")
S3method("prune","semforest")

export("parameters")
export("se")
#S3method("parameters","semtree")
#S3method("se","semtree")

export("nodeFunSemtree")

export("varimp")

S3method("plot","semtree")

S3method("plot","semforest.proximity")
S3method("plot","semforest.varimp")

export("varimpConvergencePlot")


#export("toLatex")
S3method("toLatex","semtree")
importFrom("utils","toLatex")



export("toTable")
export("getTerminalNodes")

export("proximity")
export("outliers")
#export("availableCpus")
export("evaluateTree")
export("getNodeById")
#export("get.children.map")
export("subforest")

# only for debugging
#export("semtree.apply.wrapper")
#export("semtreeApplyWrapper")
#export("bootstrap")
#export("traverse")
#export("getOCParameterNames")
#export("evalForestOob")
#export("aggregateVarimp")
#export("fitSubmodels")
#export("modelEstimates")
#export("getHeight")

export("partialDependencePlot")
export("partialDependence")
S3method("plot","partialDependence")

# only temporary export; remove for shipping
#export("crossvalidatedSplit")
#export("cvLikelihood")
#export("evaluateDataLikelihood")
#export("evaluateTreePrediction")
#export("setData")
#export("safeRunAndEvaluate")
#export("getCovariatesFromTree")
#export("plot.predictions")


#importFrom("utils","toLatex")