Improve package interface for `Specimen` superclass methods

[jasonratcliff]

Interface

To improve the interface of the Specimen class public methods, add a shared filter_* prefix to methods for filtering operations:

• filter_limit() replaces limit()
• filter_taxa() replaces taxa()
• filter_collections() replaces collections()

Provide new common arguments for setting the behavior of the Specimen class methods:

• .return

  • By default, .return = FALSE allows chaining methods for subsequent filtering
    • When TRUE, return a tibble object containing filtered records

• .identifier

  • By default, .identifier = NULL utilizes the column set by the public field identifier
    • Enables flexible specification for methods dealing with taxonomic annotation columns

Development

Update package development infrastructure:

• Implement modular test_that() local environments
• Ensure test coverage for new parameters
• Revise roxygen2 docstrings and update man/*.Rd files