NAMESPACE

# C++ stuff:
useDynLib(qgraph, .registration=TRUE)
importFrom(Rcpp, evalCpp)

# Rest:
export(mutualInformation) 
# export(vein)
export(flow)
importFrom("utils", "capture.output")
importFrom("grDevices", "hcl")
S3method(print, ggmFit)
S3method(plot, ggmFit)
export(ggmFit)
export(pathways)
export(smallworldIndex)
export(clusteringTable)
export(clusteringPlot)
export(centralityTable)
export(centralityPlot)
export(qgraph)
export(qgraph.layout.fruchtermanreingold)
export(qgraph.loadings)
#export(qgraph.efa)
#export(qgraph.svg)
#export(qgraph.pca)
#export(qgraph.sem)
#export(qgraph.panel)
#export(qgraph.semModel)
#export(qgraph.cfa)
#export(qgraph.lavaan)
#export(qgraph.gui)
export(centrality)
S3method(print, qgraph)
export(qgraph.animate)
S3method(plot, qgraph)
S3method(summary, qgraph)
#importFrom(sem,"sem","standardizedCoefficients")
#importFrom(psych,"principal")
#importFrom(lavaan,"lavaan","cfa","standardizedSolution", "standardizedsolution", "parameterEstimates", "parameterestimates","inspect")
importClassesFrom(lavaan,"lavaan")
importFrom(stats,"factanal")
# importFrom(ellipse,"ellipse")
importFrom(corpcor,"cor2pcor")
importFrom(graphics,"plot","points","lines","polygon")
importFrom(png,"readPNG")
importFrom(jpeg,"readJPEG")
import(plyr)
importFrom(Hmisc,"subplot")
import(igraph)
S3method(as.igraph, qgraph)
importFrom(colorspace,rainbow_hcl)
importFrom(Matrix,sparseMatrix)
export(averageLayout)

export(getWmat)
S3method(getWmat, matrix)
S3method(getWmat, data.frame)
S3method(getWmat, igraph)
S3method(getWmat, qgraph)
S3method(getWmat, list)
S3method(getWmat, bootnetResult)


importFrom(reshape2, "melt")
import(ggplot2)
# importFrom(glasso, glasso)
# importFrom(sna, component.largest)

import(fdrtool)

importFrom(psych,corr.p)

# export(smoothAnimationList)
# export(mixGraphs)

# Functions Giulio:
export(smallworldness)
export(clustOnnela)
export(clustZhang)
export(clustWS)
export(clustcoef_auto)
export(centrality_auto)
export(mat2vec)

# LASSO STUFF:
export(wi2net)
export(EBICglasso)
export(ggmModSelect)
#export(EBICglasso2)
#export(EBICglassoCluster)
importFrom(Matrix, forceSymmetric)
import(glasso)

## corauto stuff:
#importFrom(huge, huge.npn)
#importFrom(psych, tetrachoric)
#importFrom(psych, polychoric)
export(cor_auto)
importFrom(lavaan, lavCor)

export(VARglm)

export(FDRnetwork)



# importFrom(sendplot, "xy.send")
# export(qgraphAnnotate)

#importFrom(d3Network, "d3ForceNetwork")

importFrom(gtools, mixedorder)
importFrom(gtools, mixedsort)

export(qgraphMixed)


# exports for the BW function
export(makeBW)

# Extra:

# Extra:
importFrom("grDevices", "col2rgb", "dev.cur", "dev.list", "dev.new",
             "dev.off", "dev.size", "jpeg", "pdf", "png", "postscript",
             "rainbow", "rgb", "tiff")
importFrom("graphics", "par", "rect", "strheight", "strwidth", "text",
             "title", "xspline")
importFrom("methods", "is")
importFrom("stats", "BIC", "ave", "coef", "cor", "cov", "cov2cor",
             "glm", "loess", "pchisq", "predict", "qt", "quantile",
             "rnorm", "sd", "weighted.mean")
importFrom("utils", "browseURL", "combn", "menu", "setTxtProgressBar",
             "txtProgressBar")
importFrom("graphics", "plot.new", "plot.window")
importFrom("stats", "uniroot")


# Parallel:
import(parallel)
importFrom("pbapply","pblapply")
importFrom("abind","abind")


#export(as.ggraph)