Rename identity() to seq.identity()

[Barry Grant]

Lets get rid of the annoying startup message about the identity() function by reluctantly re-naming to seq.ide() or seq.identity(). I guess the later would be best...

> library(bio3d)

Attaching package: ‘bio3d’

The following object is masked from ‘package:base’:

    identity

Also need to track down all calls to identity() in the example sections of Rd files and vignettes/tutorials.

[Barry Grant]

Xinqiu has renamed identity() to seq.identity() and edited various Rd and R files accordingly.

[Barry Grant]

Sorry, need to rename to "seqidentity()"

• checking Rd \usage sections ... NOTE S3 methods shown with full name in documentation object 'seq.identity': ‘seq.identity’

[Xinqiu Yao]

I've done it