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Improvements
Added method references DOI to the description field of the DESCRIPTION file.
Removed redundant \dontrun{} from examples.
Replaced cat() with message() where suppression options like verbose are
not available, except for printing raw R Markdown content in vignettes,
which requires cat().
Removed setting options(warn=-1) and options(warn=0) in function.
Reset the user's options() in vignettes after changing it.