I have made some changes to the lmer. It works as it should but I could not get rid of the warning message that pops when I run the program. I have added the following options which allows the program run without stopping but with the warning message. I believe it is the check.nobs.vs.rankZ = "warningSmall" part. How could I get rid of this, any suggestions? Thank you.
lmerControl(check.nobs.vs.nlev = "ignore",check.nobs.vs.rankZ =
"warningSmall",check.nlev.gtreq.5 = "ignore",check.nobs.vs.nRE="ignore",
check.rankX = c("ignore"),check.scaleX = "ignore",check.formula.LHS="ignore",
## convergence checking options
check.conv.grad = .makeCC("warning", tol = 1e-3, relTol = NULL),
check.conv.singular = .makeCC(action = "ignore", tol = 1e-4),
check.conv.hess = .makeCC(action = "warning", tol = 1e-6)
Warning Message from R:
Warning message:
In checkZrank(reTrms$Zt, n = n, control, nonSmall = 1e+06) :
number of observations (=300) <= rank(Z) (=300); the random-effects parameters and the
residual variance (or scale parameter) are probably unidentifiable
You should try check.nobs.vs.rankZ="ignore".
lmerControl doesn't need to specify anything other than the non-default options: at a quick glance, these are your non-default values:
lmerControl(check.nobs.vs.nlev = "ignore",check.nobs.vs.rankZ =
"ignore",check.nlev.gtreq.5 = "ignore",check.nobs.vs.nRE="ignore",
check.rankX = c("ignore"),
check.scaleX = "ignore",
check.formula.LHS="ignore",
check.conv.grad = .makeCC("warning", tol = 1e-3, relTol = NULL))
In general I would suggest it's wise to turn off only the specific warnings and errors you know you want to override -- the settings above look like they could get you in trouble.
I haven't checked this since you didn't give a reproducible example ...