santize w_dens #86
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santize w_dens #86
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thibautjombart
requested changes
Aug 17, 2022
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Thanks for getting this started, and well done on your first PR! I would recommend:
- implementing the feature as a separate function in a dedicated file in R/
- adding a warning (already added to the code as suggestion); note we may want to check if we need to add a 'quiet' option
- the test needs to use testthat syntax
Looking forward to discussing these points :)
tests/test_w_dens.R
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There is a specific syntax for test to use in a package, using testthat. See other test files in this project for some examples. Here, the additional tests should include:
- testing that the warning is issued when it should, and that it is the exact message expected
- testing that the replacement of non-positive values is made when it should
If we go down the road of implementing satitize_pmf then ideally the test is in a file test-satitize_pmf.R.
add warning message sanitize_pmf Co-authored-by: Thibaut Jombart <[email protected]>
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@CyGei - going through other open issues now, is this still relevant? |
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Trying my first PR.
Issue: when w_dens contains 0s (not necessarily trailing 0s), the arbritary threshold 1e-15 can lead to some errors.
Solution: replace any 0s with the minimum value in w_dens.
Test : see tests/test_w_dens.R.
Questions: should we use the same procedure for f_dens?
Should we use dexp() for the starting 0s ?
Why the dexp() tail sums to 1e-4?