dev: Update to roxygen2 v4
set UseAlpha=FALSE by default
lodsby2dhist must be passed scoring matrix

* only nblast function should be checking options
Additional details for scoring matrix documentation
Add basic package documentation
rename smat(_alpha) to smat(_alpha).fcwb

* want to emphasise that these were trained for a specific template space
* and having a matric called smat and a lot of function arguments and local
  variables called smat is confusing
Make smat.fcwb not smat_alpha the default
Only set the default scoring matrix if unset on load
Document package options
Don't set default smat option, but use appropriate smat when argument is null
doc: we no longer set nat.nblast.defaultsmat on package load
Merge branch 'feature/alpha-defaults'

* feature/alpha-defaults:
  doc: we no longer set nat.nblast.defaultsmat on package load
  Don't set default smat option, but use appropriate smat when argument is null
  Document package options
  Only set the default scoring matrix if unset on load
  Make smat.fcwb not smat_alpha the default
  rename smat(_alpha) to smat(_alpha).fcwb
  Add basic package documentation
  Additional details for scoring matrix documentation
  lodsby2dhist must be passed scoring matrix
  set UseAlpha=FALSE by default
make sd an explicit parameter of blast

* it is the key (only) parameter for nblast v1