Roxygen documentation rewrite

[jayqi]

Overhaul of our Roxygen documentation to resolve #192.

Changes to Reporter Documentation

• New articles PackageReporters and NetworkReporters contain sections defining their respective public interfaces.
  • These are hidden from documentation indices (in RStudio or pkgdown) by using @keywords internal. They are still findable if you do ?PackageReporters, so there is still a meaningful description written for people who bother looking for them.
  • Sections for various public interfaces are defined using rsixygen-generated doc skeletons.
  • The articles for all user-facing reporters inherit these sections. This way, each one is standalone (contains full documentation for public interface), but underlying roxygen content is not duplicated for ease of maintenance.
• User-facing reporter articles document NULL objects rather than the class constructors themselves. This way, we can leave out the completely useless @Usage and @Format sections.
• Standardizing around the general language of "network reporters" in the documentation. I don't think we really had any term here before, and I've personally used "graph reporters" when it came up. Since this is user facing and refers to networks in a package, I think the word "network" is the right thing here. (See discussion in Major Refactor to GraphReporters #181.) (Also relevant to Update Style Guide in CONTRIBUTING.md with Function Naming Conventions #183)

Summary of Other Changes:

• AbstractPackageReporter and AbstractGraphReporter are no longer exported. Resolves Exporting of Abstract Classes #190.
• Removed docs_shared. This was only getting used in one place (CreatePackageReport) so I just copied them in and got rid of it.
• Created package documentation in pkgnet.R. This will show up with you do ?pkgnet or ?pkgnet-package. Resolves Write roxygen article for package #193.

[codecov-io]

Codecov Report

Merging #198 into master will not change coverage.
The diff coverage is 100%.

@@           Coverage Diff           @@
##           master     #198   +/-   ##
=======================================
  Coverage   91.52%   91.52%           
=======================================
  Files          11       11           
  Lines         920      920           
=======================================
  Hits          842      842           
  Misses         78       78

Impacted Files	Coverage Δ
R/PackageDependencyReporter.R	81.65% <ø> (ø)	⬆️
R/CreatePackageReport.R	98.24% <ø> (ø)	⬆️
R/PackageFunctionReporter.R	93.33% <ø> (ø)	⬆️
R/DefaultReporters.R	100% <ø> (ø)	⬆️
R/PackageInheritanceReporter.R	100% <ø> (ø)	⬆️
R/GraphClasses.R	93.82% <ø> (ø)	⬆️
R/AbstractGraphReporter.R	86.28% <ø> (ø)	⬆️
R/AbstractPackageReporter.R	100% <ø> (ø)	⬆️
R/PackageSummaryReporter.R	100% <100%> (ø)	⬆️

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[bburns632]

Just one function to add back to the roxygen docs, so it gets NAMESPACE'd: knitr::opts_chunk. Also, can you comment on the dual families for functions.