#############
## EXPORTS
#############
export(adiag1, A.mat, atcg1234, hits, big.peaks.col, 
       bathy.colors, blocker, blockerL, blockerT, brewer.pal, build.HMM, D.mat, 
       design.score, E.mat, EM, fdr, fdr2, fill.design,
       GWAS, GWAS2, hadamard.prod, hdm, h2.fun, imputev, is.diagonal.matrix, 
       is.square.matrix, jet.colors, manhattan, matrix.trace, map.plot, 
       maxi.qtl, mmer,MEMMA, MNR, mmer2, nna, overlay, pedtoK, phase.F1, 
       pin, score.calcMV, spatPlots, transp,  
       vctable, vctable.help)

export(summary.MMERM, residuals.MMERM, fitted.MMERM, plot.MMERM, 
       variogram, variogram.MMERM, plot.variogram.MMERM,
       anova.MMERM, coef.MMERM, randef)

# fixef.mmer, fixef.mmerM, fixef.MMERM

# S3 METHODS

#S3method(fixef, mmerM)
#S3method(print, fixef.mmerM)

## for multivariate
S3method(summary, MMERM)
S3method(print, summary.MMERM)
S3method(residuals, MMERM)
S3method(print, residuals.MMERM)
S3method(fitted, MMERM)
S3method(print, fitted.MMERM)
S3method(coef, MMERM)
S3method(print, coef.MMERM)
S3method(anova, MMERM)
S3method(plot, MMERM)

S3method(variogram, MMERM)
S3method(plot, variogram.MMERM)


#S3method(fixef, MMERM)
#S3method(print, fixef.MMERM)

############
# IMPORTS
############
  importFrom("graphics", "abline", "axis", "image", "layout", "legend",
             "lines", "plot", "points", "rect", "text", "locator",
             "par", "grid", "plot.new", "polygon","segments", "title")
  importFrom("utils", "combn", "setTxtProgressBar", "txtProgressBar",
             "available.packages", "contrib.url")
  #importFrom("matrixcalc", "matrix.trace","is.diagonal.matrix", "is.square.matrix")
  #importFrom("lme4","lmer","VarCorr")
  #importFrom("parallel", "detectCores","mclapply") #"detectCores","makeCluster","stopCluster",
  #importFrom("doParallel","registerDoParallel")
  #importFrom("foreach", "%dopar%")
  
  
#  importFrom("beepr", "beep")
## FULL IMPORTS
  import("methods")
  import("Matrix")
  import("MASS")
  import("lattice")
  import("data.table")
  #import("foreach")
  #import("doParallel")


#  import("audio","play")
  
### extra suggested by CRAN
  importFrom("grDevices", "col2rgb", "colorRampPalette", "gray.colors",
             "rgb","dev.cur", "dev.size", "xy.coords", "topo.colors")
  importFrom("stats", "as.formula", "cov", "density", "gaussian", "glm",
             "lm", "median", "optimize", "pbeta", "pchisq", "predict",
             "printCoefmat", "qqnorm", "smooth.spline", "var", "rnorm", 
             "model.matrix","na.omit", "p.adjust","kmeans","dist", "runif",
             "nobs", "ppoints", "sd", "model.frame", "model.response", "na.pass",
             "cor", "optim", "rchisq","quantile","deriv","terms.formula")


  
  

