Comments (4)
@Rekyt You're welcome. I ended up modifying fd_fdis()
with my first suggestion.
Thank you (and all of your coauthors) for making this package! It has been a huge help in reducing my code run times! I have 9 regions with 10,000 simulated/randomized matrices each, so 90,000 matrices were taking days to run with the FD
package! With fd_fdis()
, it took an hour or two, at most.
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One issue I'm realizing is that when the user provides only a trait dataset and no site-species dataset, the site is automatically named s1 (see below). We could use site names like s N-row for the use case described above.
library("fundiversity")
fd_fdis(traits_birds)
#> site FDis
#> 1 s1 133.3902
Created on 2023-08-20 with reprex v2.0.2
Should we use this behavior to be consistent? Or rather revert to site names as indices?
Do you have an opinion @Bisaloo?
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Dear @mahonmb,
First of all thank you for pointing out the bug!
Second of all, thank you for suggesting a fix!
Indeed, we always thought that the input would be matrix objects but didn't realize other objects would also work with slight modifications.
I'll be fixing this behavior for all functions and include additional tests to cover it.
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Should we use this behavior to be consistent?
This approach makes the most sense to me.
We just need to make sure that the meaning of s1
, s2
, etc. is clearly documented. Something like "If the sp_com
argument is not provided or if it doesn't have rownames, arbitrary rownames s1
, s2
, s3
will be used. The @return
section of the docs seems like a good place for this. We already document it in the intro vignette but it's always good to document everything in multiple places.
We might also add a message()
but I'm more on the fence here. Having too many messages can be overwhelming for users.
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Related Issues (20)
- Hex logo
- Managing error from qhull transferred to geometry::convhulln() in fd_chull()
- Error when site contains no species in fd_fdiv() and fd_feve() HOT 2
- Errors when using non-quantitative traits in fd_fric()
- Release fundiversity 0.2.1
- Specific error obtained with Qhull HOT 3
- Investigate RCGAL as a replacement of geometry HOT 4
- Simplify CI matrix by using `_R_CHECK_DEPENDS_ONLY_TESTS_` HOT 2
- fd_fdiv() returns `NaN` on datasets without rownames
- FRic returns NA without warnings nor messages HOT 1
- Add tip in error message because of non-continuous traits HOT 1
- Renaming the vignettes to order them logically? HOT 2
- Change title of package in DESCRIPTION as it doesn't only computes "Alpha functional diversity indices"
- fd_fdis() bugs when site-species object is a data.frame() expects a matrix. HOT 2
- Using future and memoise together HOT 2
- Add link to published paper
- Should we write a vignette for non-continuous trait data? HOT 1
- Be more specific in the help with memoization HOT 2
- Have a worked through example with individual level dataset
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