Refactor specimen distribution map functions

[jasonratcliff]

To limit the number of exported functions, define a new subclass inheriting the Specimens R6 superclass (#62). Relevant for the following public functions:

• layer_borders()
• layer_specimens()
• layer_themes()
• layer_ggmap()
• layer_elevation()
• spl_states()
• spl_order()
• spl_bbox()
• spl_legend()
• spl_id()
• build_map()

Refactoring presents an opportunity for encapsulation of specimen records into an S4 object (#42).

See also: #45

[jasonratcliff]

Updating from R version 4.0.2 to ~4.1.2 introduced some breaking changes for figure generation. Generally, consolidation of mapping functions and review of related scripts (inst/scripts/ for introduction, results, and discussion chapters) is needed. After refactoring, implementing CI/CD with a stable version image should be pursued for reproducibility best practices.

Short Term

• Updates to ggplot2 (v3.3.2->3.3.5) cause retention of extra scale values

  • Depends on spp_color / spp_shape data vectors
  • Possibly related to ggplot2 PR 3685
    • [x] Set manual scale limits

• Improve organization to cleanup cluttered namespace

  • May involve renaming / deprecation of currently public functions
    • [x] Reduce number of exported functions (e.g., layer_*, spl_)

[jasonratcliff]

Encountered the following error when updated renv.lock:

configure: error: gdal-config not found or not executable.
ERROR: configuration failed for package ‘rgdal’
* removing ‘/Users/jasonratcliff/Thesis/renv/staging/2/rgdal’

Error: install of package 'rgdal' failed ["~/Thesis/renv/staging/2/rgdal" does not exist]
Show stack trace

Possible fix (4/10/22):

• https://stackoverflow.com/a/26836125
  • [x] Update gdal via homebrew