est.GT: no visible global function definition for 'hist'
est.GT: no visible global function definition for 'density'
est.GT: no visible global function definition for 'curve'
est.GT: no visible global function definition for 'dgamma'
est.GT: no visible global function definition for 'dweibull'
est.GT: no visible global function definition for 'dlnorm'
est.R0.EG: no visible global function definition for 'lm'
est.R0.EG: no visible global function definition for 'coefficients'
est.R0.EG: no visible global function definition for 'predict'
est.R0.EG: no visible global function definition for 'glm'
est.R0.EG: no visible global function definition for 'poisson'
est.R0.ML: no visible global function definition for 'optim'
est.R0.ML: no visible global function definition for 'optimize'
est.R0.ML: no visible global function definition for 'uniroot'
est.R0.ML: no visible global function definition for 'qchisq'
est.R0.ML: no visible global function definition for 'glm'
est.R0.ML: no visible global function definition for 'poisson'
est.R0.SB: no visible global function definition for 'na.omit'
est.R0.TD: no visible global function definition for 'rmultinom'
est.R0.TD: no visible global function definition for 'quantile'
est.R0.TD: no visible global function definition for 'na.omit'
fit.epid: no visible global function definition for 'dpois'
generation.time: no visible global function definition for 'pgamma'
generation.time: no visible global function definition for 'plnorm'
generation.time: no visible global function definition for 'pweibull'
impute.incid: no visible global function definition for 'optim'
plot.R0.GT: no visible global function definition for 'plot'
plot.R0.S: no visible global function definition for 'filled.contour'
plot.R0.S : <anonymous>: no visible global function definition for
  'heat.colors'
plot.R0.S: no visible global function definition for 'title'
plot.R0.S: no visible global function definition for 'contour'
plot.R0.S: no visible global function definition for 'axis'
plot.R0.S: no visible global function definition for 'points'
plot.R0.S: no visible global function definition for 'text'
plot.R0.S: no visible global function definition for 'dev.new'
plot.R0.S: no visible global function definition for 'plot'
plot.R0.sR: no visible global function definition for 'plot'
plot.R0.sR: no visible global function definition for 'dev.new'
plotRAR: no visible global function definition for 'plot'
plotRAR: no visible global function definition for 'arrows'
plotREG: no visible global function definition for 'plot'
plotREG: no visible global function definition for 'lines'
plotREG: no visible global function definition for 'points'
plotREG: no visible global function definition for 'arrows'
plotREG: no visible global function definition for 'legend'
plotRML: no visible global function definition for 'plot'
plotRML: no visible global function definition for 'arrows'
plotRSB: no visible global function definition for 'plot'
plotRSB: no visible global function definition for 'polygon'
plotRSB: no visible global function definition for 'lines'
plotRSB: no visible global function definition for 'abline'
plotRSB: no visible global function definition for 'axis'
plotRTD: no visible global function definition for 'split.screen'
plotRTD: no visible global function definition for 'screen'
plotRTD: no visible global function definition for 'plot'
plotRTD: no visible global function definition for 'axis'
plotRTD: no visible global function definition for 'polygon'
plotRTD: no visible global function definition for 'lines'
plotRTD: no visible global function definition for 'abline'
plotRTD: no visible global function definition for 'close.screen'
plotfit.R0.sR: no visible global function definition for 'dev.new'
plotfitRAR: no visible global function definition for 'plot'
plotfitRAR: no visible global function definition for 'points'
plotfitRAR: no visible global function definition for 'axis'
plotfitRSB: no visible global function definition for 'plot'
plotfitRSB: no visible global function definition for 'lines'
plotfitRSB: no visible global function definition for 'points'
plotfitRSB: no visible global function definition for 'axis'
plotfitRSB: no visible global function definition for 'dev.new'
plotfitRSB: no visible global function definition for 'split.screen'
plotfitRSB: no visible global function definition for 'screen'
plotfitRSB: no visible global function definition for 'abline'
plotfitRSB: no visible global function definition for 'close.screen'
plotfitRxx: no visible global function definition for 'plot'
plotfitRxx: no visible global function definition for 'lines'
plotfitRxx: no visible global function definition for 'points'
plotfitRxx: no visible global function definition for 'axis'
sim.epid: no visible global function definition for 'rpois'
sim.epid: no visible global function definition for 'rnbinom'
sim.epid: no visible global function definition for 'rmultinom'
sim.epid.indiv: no visible global function definition for 'rgamma'
sim.epid.indiv: no visible global function definition for 'runif'
sim.epid.indiv: no visible global function definition for 'rpois'
sim.epid.indiv: no visible global function definition for 'rnbinom'
smooth.Rt: no visible global function definition for 'na.omit'
Undefined global functions or variables:
  abline arrows axis close.screen coefficients contour curve density
  dev.new dgamma dlnorm dpois dweibull filled.contour glm heat.colors
  hist legend lines lm na.omit optim optimize pgamma plnorm plot points
  poisson polygon predict pweibull qchisq quantile rgamma rmultinom
  rnbinom rpois runif screen split.screen text title uniroot
Consider adding
  importFrom("grDevices", "dev.new", "heat.colors")
  importFrom("graphics", "abline", "arrows", "axis", "close.screen",
             "contour", "curve", "filled.contour", "hist", "legend",
             "lines", "plot", "points", "polygon", "screen",
             "split.screen", "text", "title")
  importFrom("stats", "coefficients", "density", "dgamma", "dlnorm",
             "dpois", "dweibull", "glm", "lm", "na.omit", "optim",
             "optimize", "pgamma", "plnorm", "poisson", "predict",
             "pweibull", "qchisq", "quantile", "rgamma", "rmultinom",
             "rnbinom", "rpois", "runif", "uniroot")
to your NAMESPACE file.