export("dif", "dis", "kmeans.run", "mat.dif", "mat.dis", "mmds","mmds.project", "mmds.plot", "mmds.2D.plot","mmds.2D.multi", "mmds.3D.plot","scree.plot", "random.msa", "import.fasta", "import.msf", "sil.score", "write.mmds.pdb","col.group","extract.cluster","export.fasta")

importFrom("grDevices", "col2rgb", "dev.new", "dev.off", "pdf", "png",
importFrom("graphics", "abline", "barplot", "box", "layout", "lines",

importFrom("stats", "quantile", "sd", "qnorm", "rnorm")

importFrom("stats", "pbinom", "cov", "quantile", "sd", "qnorm", "rnorm", "filter")

import(devtools, grplasso, MASS, Matrix, mboost, parallel, plsRcox, pROC, survival, pkgconfig)
axis, close.screen, frame, legend, lines, mtext, par,
aggregate, anova, as.formula, coef, model.weights, na.exclude,
na.omit, p.adjust, predict, quantile, rbinom, rnorm, runif, rweibull)

exportPattern("^[[:alpha:]]+") # export names that start with a letter
importFrom(graphics, lines, plot, matlines, matplot, plot.default,
importFrom(stats, model.extract, terms, qnorm, approx,
profile, fitted, qt, spline, coef, confint,

import(utils, rpanel, tkrplot, MASS, boot)

import(utils, rpanel, tkrplot, MASS, boot, stats, graphics, grDevices, datasets)

import(utils, rpanel, tkrplot, MASS, boot, stats, graphics, grDevices, datasets, lattice, SpatialEpi)

import(utils, MASS, boot, stats, graphics, grDevices, datasets)

# Export all names
#exportPattern(".")
export(as.one.mode, as.tnet, BC, betweenness_w, CC, C.score, closeness_w, compart, computeModules, clustering_tm, czvalues, degreedistr, dfun, discrepancy, empty, endpoint, extinction, fd, frame2webs, genweb, grouplevel, H2fun, linklevel, listModuleInformation, ND, nested, nestedness, networklevel, nodespec, npartite, null.distr, null.t.test, nullmodel, PAC, PDI, plotModuleWeb, plotPAC, plotweb, plotweb2, plot.wine, printoutModuleInformation, projecting_tm, robustness, second.extinct, shuffle.web, slope.bipartite, sortweb, specieslevel, strength, swap.web, symmetrise_w, togetherness, tnet_igraph, V.ratio, vaznull, versionlog, visweb, web2edges, webs2array, wine)
# Import all packages listed as Imports or Depends
importFrom(igraph, graph.edgelist, set.edge.attribute, betweenness, V) #for tnet functions
importFrom(MASS, fitdistr)
import(methods)
#importFrom(vegan, cca, commsimulator, designdist, fisher.alpha, fisherfit, nestedchecker, nesteddisc, nestednodf, nestedtemp, treeheight, vegdist)
importFrom(permute, allPerms) # for use in vegan::nesteddisc
#importFrom(sna, betweenness, closeness, geodist, gplot)
#importFrom(tnet, betweenness_w, closeness_w, clustering_tm, projecting_tm)
importFrom(fields, image.plot)