Closed PeetoomHeida closed 10 months ago
PeetoomHeida
commented
2 years ago Oops, I started writing an example for the Metacommunity constructor, but I realized after making the PR that I didn't finish it. This is related to #43, but I currently don't understand the package well enough to finish the example.
richardreeve
commented
2 years ago Thanks @PeetoomHeida! Could you reference Pielou's evenness in the docs, and ideally link to another implementation so I can check the code?
PeetoomHeida
commented
2 years ago I have grabbed the implementation from R vegan, and made a MWE here. I made the function for this package consistent with the others in there, where cols are sites are rows are spp, so be sure to make that switch in matrix structure when checking it in the Julia version. I also fixed the docstrings and added it to the ecology.md docs
coveralls
commented
2 years ago This pull request's base commit is no longer the HEAD commit of its target branch. This means it includes changes from outside the original pull request, including, potentially, unrelated coverage changes.
| Changes Missing Coverage | Covered Lines | Changed/Added Lines | % | ||
|---|---|---|---|---|---|
| src/Ecology.jl | 0 | 16 | 0.0% | ||
| <!-- | Total: | 0 | 16 | 0.0% | --> |
| Totals | |
|---|---|
| Change from base Build 1090744121: | 4.0% |
| Covered Lines: | 538 |
| Relevant Lines: | 626 |
codecov[bot]
commented
2 years ago Merging #45 (9711d54) into dev (41992a6) will decrease coverage by
1.27%. The diff coverage is0.00%.
@@ Coverage Diff @@
## dev #45 +/- ##
==========================================
- Coverage 82.05% 80.78% -1.28%
==========================================
Files 15 15
Lines 613 666 +53
==========================================
+ Hits 503 538 +35
- Misses 110 128 +18 | Impacted Files | Coverage Δ | |
|---|---|---|
| src/Diversity.jl | 87.50% <ø> (ø) |
|
| src/Ecology.jl | 78.04% <0.00%> (-21.96%) |
:arrow_down: |
| src/Metacommunity.jl | 77.27% <ø> (+1.66%) |
:arrow_up: |
| src/Partition.jl | 100.00% <0.00%> (ø) |
|
| src/DiversityMeasure.jl | 88.32% <0.00%> (+0.53%) |
:arrow_up: |
| src/Phylogenetics.jl | 81.13% <0.00%> (+0.73%) |
:arrow_up: |
| src/API.jl | 93.75% <0.00%> (+1.15%) |
:arrow_up: |
| src/Types.jl | 94.23% <0.00%> (+1.20%) |
:arrow_up: |
| src/Iterators.jl | 60.86% <0.00%> (+1.77%) |
:arrow_up: |
| ... and 1 more |
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PeetoomHeida
commented
2 years ago Thanks for this. Sorry for the delay in spotting you'd made the changes. I've made some comments on your edits - I understand why you've switched rows and columns, but I think it just makes things more confusing given we always use them the other way round - in fact you confused yourself at one point! I'll probably have more to say after you've made these changes, but I'm onto it now. Apologies again for the delay.
It looks like a bunch of files that I didn't mean to stage commits to got mixed into the PR. I'll sort this out and take a look at the row/column issues as well.
richardreeve
commented
2 years ago Great. However, before I review it you need to restore Project.toml in the root of the package - that defines the package, so you can't delete that! Then we can run the tests and I'll review it again.
PeetoomHeida
commented
2 years ago Oh man, thanks for your patience as I get better at making PRs. Hopefully everything is good now, and hopefully the next PR goes smoother! The Project.toml file should be added now
44 addressed, fixed a typo in the documentation