streamline deprecation warnings

[sbfnk]

Before releasing 1.5.0 we should check that

• all deprecation warnings point to the correct version
• no functions remain which have their deprecation cycle completed
• all deprecation warnings state that functionality will be removed completely with version 2.0.0
• all deprecated functions have been moved to deprecated.R
• deprecated functions have been moved to a dedicated section in _pkgdown.yml Group deprecated functions together in pkgdown Reference Page #583

[jamesmbaazam]

We should probably also add a "Deprecations" section in the NEWS file to gather everything in one place.