useDynLib(OncoSimulR, .registration=TRUE)

export("oncoSimulPop", "oncoSimulIndiv", "samplePop",
       "plotPoset", "oncoSimulSample", "allFitnessEffects",
       "evalGenotype", "evalAllGenotypes", "simOGraph"
     , "plotClonePhylog", "OncoSimulWide2Long"
       )

S3method(plot, oncosimul)
S3method(print, oncosimul)
S3method(summary, oncosimul)
S3method(plot, oncosimulpop)
S3method(summary, oncosimulpop)
S3method(print, oncosimulpop)
S3method(plot, fitnessEffects)


importFrom("data.table", rbindlist, .rbind.data.table) 
importFrom(Rcpp, evalCpp)
importFrom("igraph", igraph.to.graphNEL, graph.data.frame, V, E,
           "V<-", "E<-", plot.igraph, layout.reingold.tilford,
           delete.vertices, neighborhood, get.adjacency)
import(graph)
import(Rgraphviz)
importFrom("parallel", mclapply, detectCores, mcMap)
importFrom("gtools", combinations, permutations)

importFrom("graphics", "axis", "box", "legend", "matplot", "par", "polygon")
importFrom("methods", "as")
importFrom("stats", "na.omit", "runif", "smooth.spline")
importFrom("utils", "type.convert")
importFrom("RColorBrewer", "brewer.pal")
importFrom("grDevices", "colorRampPalette", "hsv", "rainbow")