Closed paulinetrinh closed 2 years ago
Merging #105 (c833534) into master (f6cf209) will increase coverage by
10.80%
. The diff coverage is0.00%
.
@@ Coverage Diff @@
## master #105 +/- ##
===========================================
+ Coverage 65.95% 76.75% +10.80%
===========================================
Files 13 13
Lines 796 796
===========================================
+ Hits 525 611 +86
+ Misses 271 185 -86
Impacted Files | Coverage Δ | |
---|---|---|
R/phylodivnet.R | 0.00% <0.00%> (ø) |
|
R/s3functions.R | 96.26% <0.00%> (+40.18%) |
:arrow_up: |
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^^For our reference. I was trying to fix phylodivnet.R
and add testing coverage for that function, only to find out that the function does not work. I committed my changes to phylodivnet.R
and added in the test-phylodivnet.R
testing script without any real tests and am unable to hit the codecov/patch target of 66%, which is why it failed.
@paulinetrinh If I recall correctly, we abandoned phylodivnet
after deciding that it was computationally infeasible. I think the best thing to do would be to remove it from the code base -- if someone ever needs it they can search the history looking for it. What do you think of this strategy?
@adw96 That sounds good to me! I was going to bring up the options to you and see what you wanted to do but I can remove it from the code base as long as you're ok with that!
@adw96 I should mention additionally that there is another script divnet_alpha_estimates.R
that has no code coverage. I'm not sure if it's used anywhere (doesn't seem like it?) or if it's completed. Should we leave that in the code base?
Hmmmm... It looks like it might be useful. Could you please see if there are any implications of removing it by creating a branch with it removed and seeing if that branch passes checks?
(I expect that if we haven't documented it anywhere then others are probably not using it either)
Sounds good! It's actually not in the NAMESPACE so people are definitely not using it.
Hmmmm... it may be internal though... Does breakaway use it? (perhaps with DivNet:::divnet_alpha_estimates()
?)
I'm not seeing the function make_alpha_estimates()
written in divnet_alpha_estimates.R
being called anywhere in DivNet or breakaway's repositories, but I'll make a separate branch to test its removal.
Before that I will:
phylodivnet()
from the code base and add the commits to this pull request
I increased code coverage for S3 functions by covering more of the H0 options in testBetaDiversity. I updated the NAMESPACE, started fixing the
phylodivnet.R
file and created atest-phylodivnet.R
thinking that I would increase unit testing onphylodivnet()
... However, after going throughphylodivnet()
I don't think that function is completed so it can't be covered by testing.phylodivnet()
takes up about 12% (96 lines) of DivNet's code so we should consider either completing the function or something.