CP1.ar1: no visible global function definition for ‘integrate’
MCCP.ar1: no visible global function definition for ‘integrate’
Pmax.non: no visible global function definition for ‘dnbinom’
Pmax.non: no visible global function definition for ‘pnbinom’
Pmax1: no visible global function definition for ‘integrate’
Psum.non: no visible global function definition for ‘dnbinom’
Psum.non: no visible global function definition for ‘pnbinom’
Psum1: no visible global function definition for ‘integrate’
RElmeNB: no visible global function definition for ‘integrate’
ar1.2.mmg: no visible global function definition for ‘dgamma’
ar1.fun: no visible global function definition for ‘dnbinom’
ar1.intg: no visible global function definition for ‘dgamma’
ar1.lk: no visible global function definition for ‘integrate’
ar1.ln.intg: no visible global function definition for ‘dlnorm’
ar1.ln2.mmg: no visible global function definition for ‘dlnorm’
ar1.mm.ln: no visible global function definition for ‘dlnorm’
ar1.mmg: no visible global function definition for ‘dgamma’
ar22.fun: no visible global function definition for ‘dnbinom’
ar22.fun: no visible global function definition for ‘pnbinom’
cum.fun: no visible global function definition for ‘dgamma’
cum.fun: no visible global function definition for ‘pnbinom’
cum1.ln: no visible global function definition for ‘dlnorm’
cum1.ln: no visible global function definition for ‘pnbinom’
densYijGivenYij_1AndGY: no visible global function definition for
  ‘pnbinom’
densYijGivenYij_1AndGY: no visible global function definition for
  ‘dnbinom’
dens_Yi.gY: no visible global function definition for ‘dnbinom’
fitParaAR1: no visible global function definition for ‘optim’
fitParaIND: no visible global function definition for ‘optim’
fitSemiAR1: no visible global function definition for ‘optim’
fitSemiAR1: no visible global function definition for ‘optimize’
fitSemiIND: no visible global function definition for ‘optim’
fitSemiIND: no visible global function definition for ‘optimize’
formulaToDat: no visible global function definition for ‘model.matrix’
formulaToDat: no visible global function definition for
  ‘model.response’
formulaToDat: no visible global function definition for ‘model.frame’
formulaToDat: no visible binding for global variable ‘na.omit’
formulaToDat: no visible global function definition for ‘update’
index.batch: no visible global function definition for ‘sd’
index.batch: no visible global function definition for ‘quantile’
index.batch: no visible global function definition for ‘model.response’
index.batch: no visible global function definition for ‘model.frame’
int.denRE: no visible global function definition for ‘dlnorm’
int.denRE: no visible global function definition for ‘dgamma’
int.fun: no visible global function definition for ‘dgamma’
int1.ln: no visible global function definition for ‘dlnorm’
lk.fun: no visible global function definition for ‘integrate’
lk.ln.fun: no visible global function definition for ‘integrate’
lmeNB: no visible global function definition for ‘optim’
lmeNB.sp.ind: no visible global function definition for ‘var’
lmeNB.sp.ind: no visible binding for global variable ‘quantile’
max.fun: no visible global function definition for ‘dgamma’
max.fun: no visible global function definition for ‘pnbinom’
max.ln: no visible global function definition for ‘dlnorm’
max.ln: no visible global function definition for ‘pnbinom’
mmS.fun: no visible global function definition for ‘rnbinom’
pp.ci: no visible global function definition for ‘qnorm’
ppv.ci: no visible global function definition for ‘qnorm’
print.LinearMixedEffectNBFreq: no visible global function definition
  for ‘qnorm’
rNBME.R: no visible global function definition for ‘rgamma’
rNBME.R: no visible global function definition for ‘rlnorm’
rNBME.R: no visible global function definition for ‘runif’
rNBME.R: no visible global function definition for ‘rbinom’
rNBME.R: no visible global function definition for ‘rnorm’
rNBME.R: no visible global function definition for ‘rnbinom’
rbb: no visible global function definition for ‘rbeta’
rbb: no visible global function definition for ‘rbinom’
rnb.ar1: no visible global function definition for ‘rnbinom’
Undefined global functions or variables:
  dgamma dlnorm dnbinom integrate model.frame model.matrix
  model.response na.omit optim optimize pnbinom qnorm quantile rbeta
  rbinom rgamma rlnorm rnbinom rnorm runif sd update var
Consider adding
  importFrom("stats", "dgamma", "dlnorm", "dnbinom", "integrate",
             "model.frame", "model.matrix", "model.response", "na.omit",
             "optim", "optimize", "pnbinom", "qnorm", "quantile",
             "rbeta", "rbinom", "rgamma", "rlnorm", "rnbinom", "rnorm",
             "runif", "sd", "update", "var")
to your NAMESPACE file.