The lsmeans package is being deprecated and further development will take place in its successor, emmeans. Users may use emmeans in almost exactly the same way as lsmeans, but a few function names and internal details are changed.
In transitioning to emmeans, users will find that the vignettes are constructed quite differently and that, in those and in the documentation, emphasis is placed on “estimated marginal means” rather than “least-squares means”. The term “estimated marginal means” is broader and more appropriate for use with some models, e.g. ordinal regression, that don't really involve least-squares methods. That is the reason for the change.
Accordingly, emmeans users are encouraged to use the functions emmeans(),
emtrends(), emmip(), etc. in lieu of lsmeans(), etc.
The latter functions are still available in emmeans; they run
the corresponding emmxxxx function and relabel the results.
The emmeans package provides some functions that help convert scripts and R Markdown
files containing lsmeans code so they will work in emmeans.
There is also a function to convert ref.grid and lsmobj objects
to the emmGrid objects used in emmeans.
More extensive information is given in
vignette("transition-from-lsmeans", package = "emmeans").