Append and created a testthat unit test of the fix

[Peacesandy]

1. Appended * 1e6 to line 28 and made some modifications to the code base
2. create a testthat unit test of the fix on the file testthat.R

Console output after running the code

Warning (test-lefser.R:14:3): lefser and lefserPlot work Convert counts to relative abundances with 'relativeAb()' Backtrace: ▆

1. ├─testthat::expect_error(lefser(zellersub, groupCol = NULL, blockCol = NULL)) at test-lefser.R:14:3
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. └─lefser::lefser(zellersub, groupCol = NULL, blockCol = NULL)

Warning (test-lefser.R:15:3): lefser and lefserPlot work Convert counts to relative abundances with 'relativeAb()' Backtrace: ▆

1. ├─withr::with_seed(...) at test-lefser.R:15:3
2. │ └─withr::with_preserve_seed(...)
3. └─lefser::lefser(zellersub, groupCol = "study_condition", blockCol = NULL)

Warning (test-lefser.R:26:3): lefser and lefserPlot work Convert counts to relative abundances with 'relativeAb()' Backtrace: ▆

1. ├─withr::with_seed(...) at test-lefser.R:26:3
2. │ └─withr::with_preserve_seed(...)
3. └─lefser::lefser(zellersub, groupCol = "study_condition", blockCol = "age_category") ───────────────────────────────────────────────────────────────────────────────────

══ Results ════════════════════════════════════════════════════════════════════════ Duration: 5.9 s

[ FAIL 0 | WARN 3 | SKIP 0 | PASS 15 ]

1.For the append task

• The counts are divided by column sums and then multiplied by 1e6 to obtain relative abundances.

I'm open to corrections and feedbacks and possibility to restructure the code if it's not correct

[lwaldron]

(note I just updated my comments)

[Peacesandy]

Okay, I'll make the changes and get back

[Peacesandy]

• I used the .gitignore file, to ignore the R.history and R.data
• I refactrored the codebase and made the changes
• I'm not sure if I did great in documenting that relativeAb returns counts per million, I'm open to learning more and making changes

[Peacesandy]

Resolved all comments - I just pushed a commit

[lwaldron]

Great! Are test and check passing?

[Peacesandy]

Great! Are test and check passing?

Yes they are

The output on the console

``` [ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ][ FAIL 0 | WARN 0 | SKIP 1 | PASS 0 ]

══ Skipped tests (1) ══════════════════════════════════════════════════════════════════ • identical(Sys.getlocale("LC_COLLATE"), "en_US.UTF-8") is not TRUE (1): test-lefser.R:6:3

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 0 ] [ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]> ```

[lwaldron]

I made 2 final changes:

1. deleted again the documentation of assay that I told you to add! It was actually covered by @inheritParams
2. fixed the unit tests that were only done on US locale, since results change now that we use CPM instead of fraction. The numeric tests should ideally be changed to be done on any locale.

[lwaldron]

Great work @Peacesandy !!!

[Peacesandy]

Thank you so much @lwaldron I really learnt a lot