Fchibar2: no visible global function definition for 'pchisq'
LDMatrix: no visible global function definition for 'model.matrix'
LDMatrix: no visible global function definition for 'as.formula'
akaike: no visible global function definition for 'pchisq'
chibar: no visible global function definition for 'pchisq'
chibar.summary : Fchibar: no visible global function definition for
  'pchisq'
chibar.summary: no visible global function definition for 'matplot'
chibar.summary: no visible global function definition for 'abline'
cocamat: no visible global function definition for 'contr.treatment'
create.U: no visible global function definition for 'runif'
create.XMAT: no visible global function definition for 'contrasts<-'
create.XMAT: no visible global function definition for 'contrasts'
create.XMAT: no visible global function definition for 'model.matrix'
create.XMAT: no visible global function definition for 'as.formula'
hidden.emfit.S: no visible global function definition for 'runif'
hidden.emfit.S: no visible global function definition for 'xtabs'
hidden.emfit.S: no visible global function definition for 'quantile'
hidden.emfit.X: no visible global function definition for 'runif'
hidden.emfit.X: no visible global function definition for 'xtabs'
hidden.emfit.X: no visible global function definition for 'quantile'
hmm.hmm.anova: no visible global function definition for 'pchisq'
hmmm.hmmm.anova: no visible global function definition for 'pchisq'
hmmm.model.summary: no visible global function definition for 'pchisq'
loglin.model: no visible global function definition for 'terms'
loglin.model: no visible global function definition for
  'contr.treatment'
model.summary: no visible global function definition for 'pchisq'
model.summary: no visible global function definition for 'pnorm'
mphineq.fit: no visible global function definition for 'optimize'
pesi.sim: no visible global function definition for 'rnorm'
pw.set: no visible global function definition for 'combn'
qchibar: no visible global function definition for 'uniroot'
testDF: no visible global function definition for 'uniroot'
testDF: no visible global function definition for 'qchisq'
Undefined global functions or variables:
  abline as.formula combn contr.treatment contrasts contrasts<- matplot
  model.matrix optimize pchisq pnorm qchisq quantile rnorm runif terms
  uniroot xtabs
Consider adding
  importFrom("graphics", "abline", "matplot")
  importFrom("stats", "as.formula", "contr.treatment", "contrasts",
             "contrasts<-", "model.matrix", "optimize", "pchisq",
             "pnorm", "qchisq", "quantile", "rnorm", "runif", "terms",
             "uniroot", "xtabs")
  importFrom("utils", "combn")
to your NAMESPACE file.