#############
## EXPORTS
#############
export(adiag1, A.mat, AI, AI2, AI3, atcg1234, D.mat, design.score, E.mat, EM, EMMA, fdr, hdm, map.plot2, mmer, mmer2, poe, score.calc, transp)

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

# S3 METHODS
#S3method(ranef, mmer)
#S3method(print, ranef.mmer)
S3method(summary, mmer)
S3method(print, summary.mmer)
S3method(residuals, mmer)
S3method(print, residuals.mmer)
S3method(fitted, mmer)
S3method(print, fitted.mmer)
S3method(coef, mmer)
S3method(print, coef.mmer)
S3method(anova, mmer)
S3method(plot, mmer)

############
# IMPORTS
############
  importFrom("graphics", "abline", "axis", "image", "layout", "legend",
             "lines", "plot", "points", "rect", "text", "locator",
             "par", "grid", "plot.new", "polygon")
  importFrom("utils", "combn", "setTxtProgressBar", "txtProgressBar")
  importFrom("RColorBrewer", "brewer.pal")
  importFrom("matrixcalc", "matrix.trace")
  importFrom("plotrix","draw.arc")
## FULL IMPORTS
  import("methods")
  import("Matrix")
  
### extra suggested by CRAN
  importFrom("grDevices", "col2rgb", "colorRampPalette", "gray.colors",
             "rgb")
  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")

  
  

