Review PaRe reports of HADES packages, and identify points for improvement

[schuemie]

@mvankessel-EMC generated PaRe reports for all HADES packages and added links to the reports to the package status page. We should review these reports and identify places where refactoring is needed.

[mvankessel-EMC]

It's too late for the HADES Hack-a-thon, but I thought it would be useful to show how I go through the PaRe reports. So here are some things I picked up for Achilles.

Achilles

Function diagram

Function diagram of Achilles

There are two functions that interact with a lot of other (internal) functions: achilles() and exportToJson(). These are the functions that carry out most of the work, and should probably be prioritized for unit-testing.

Function Definitions

Function	Number of arguments	Lines of code	Cyclomatic complexity	Location
achilles	24	505	96	Achilles.R (from line: 127)

achilles() could probably do with some refactoring. It has a lot of logic behind it, which theoretically requires 96 different unit tests to test all of the 505 lines of code. It also has bunch of arguments (24), which is not ideal, but provides an all-in-one way to interact with the package.

According to Codecov 2% of the code is covered. To meaningfully refactor anything unit-tests need to be made to to safeguard the current behavior.

Lintr

There are quite some code-style messages and warnings. Most of which boil down to:

• local variable 'x' assigned but may not be used
• 1:nrow(...) is likely to be wrong in the empty edge case. Use seq_len(nrow(...)) instead.
• Lines should not be more than 80 characters.
• Commas should always have a space after.
• Trailing whitespace is superfluous.

Dependencies

• tseries is not whitelisted, but saw its last CRAN update on 2023-05-02. But is only used for one function: tseries::adf.test(). And is called once in isStationary()
• data.table is used for one function: data.table::fwrite(), which is widely used in various functions in exportToAres.R.
• readr is used for one function: readr::write_csv(). And is called once in exportResultsToCSV()
• tidyr is used for one function: tidyr::crossing. And is called once in generateDomainOverlapSql()