lme models, Thorn Thaler found a bug in some models where the calculaiton of model degrees of freedon could not be determined and proposed a fix.
If the sandwich estimate failed, the traditional covariance estimator is used instead.
Moved to a real NEWS file format.
A bug was fixed (spotted by Thorn Thaler) where normal (not t) distributions were being used with
gls models to calculate confidence intervals.
A bug was fixed for generalized linear models with no degrees of freedom, such as log-linear models.
The vignette was slightly reformatted.
An error check was added for
lme models that will fail if the covariance
matrix of the variance-covariance coefficients has issues (since
counts the number of random effects when calculating degrees of freedom).
lme, this problem is signaled by
lmeObject$apVar being a character
string (eg. "Non-positive definite approximate variance-covariance")
Fixed typo in manual
Added log fold-change transformation
Cleaned up the package vignette a little