APL.KF.individualloop: no visible global function definition for
  'optim'
PSM.estimate: no visible global function definition for 'optim'
PSM.plot : smoothplot: no visible global function definition for 'plot'
PSM.plot : smoothplot: no visible global function definition for
  'na.omit'
PSM.plot : smoothplot: no visible global function definition for
  'points'
PSM.plot : smoothplot: no visible global function definition for 'rug'
PSM.plot : smoothplot: no visible global function definition for
  'mtext'
PSM.plot : smoothplot: no visible global function definition for
  'title'
PSM.plot : dataXplot: no visible global function definition for 'plot'
PSM.plot : dataXplot: no visible global function definition for 'mtext'
PSM.plot : dataXplot: no visible global function definition for 'title'
PSM.plot : dataplot: no visible global function definition for 'plot'
PSM.plot : dataplot: no visible global function definition for 'mtext'
PSM.plot : dataplot: no visible global function definition for 'title'
PSM.plot : resplot: no visible global function definition for 'plot'
PSM.plot : resplot: no visible global function definition for 'abline'
PSM.plot : resplot: no visible global function definition for 'mtext'
PSM.plot : resplot: no visible global function definition for 'title'
PSM.plot : acfplot: no visible global function definition for 'acf'
PSM.plot : acfplot: no visible global function definition for 'title'
PSM.plot : etaplot: no visible global function definition for
  'plot.new'
PSM.plot : etaplot: no visible global function definition for
  'plot.window'
PSM.plot : etaplot: no visible global function definition for 'mtext'
PSM.plot: no visible global function definition for 'par'
PSM.simulate: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  abline acf mtext na.omit optim par plot plot.new plot.window points
  rnorm rug title
Consider adding
  importFrom("graphics", "abline", "mtext", "par", "plot", "plot.new",
             "plot.window", "points", "rug", "title")
  importFrom("stats", "acf", "na.omit", "optim", "rnorm")
to your NAMESPACE file.