Comments (5)
dmcglinn
commented on June 11, 2024
I think this is historical because a lot of the structure of rarefaction was inherited from vegan::rarefy if you would prefer NA's then that would be easy to implement. In what context would you like to be able to supply effort > N. Also do you think the warning is still useful in these contexts?
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rueuntal
commented on June 11, 2024
I think in our current implementation it only occurs in the rescaling — by
stretching the axis we might be making inference at abundance values
outside of the observed range. I did an ad hoc fix in rescale_rarefaction,
where the extrapolated values are removed from effort.
…On Jan 23, 2017 8:20 PM, "Dan McGlinn" ***@***.***> wrote:
I think this is historical because a lot of the structure of rarefaction
was inherited from vegan::rarefy if you would prefer NA's then that would
be easy to implement. In what context would you like to be able to supply
effort > N. Also do you think the warning is still useful in these
contexts?
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dmcglinn
commented on June 11, 2024
ok I'll take a look and let you know what seems like the best solution to me.
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rueuntal
commented on June 11, 2024
OK thanks!
…On Jan 23, 2017 8:27 PM, "Dan McGlinn" ***@***.***> wrote:
ok I'll take a look and let you know what seems like the best solution to
me.
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dmcglinn
commented on June 11, 2024
In ae0d3fa it looks like I decided to return the observed S when effort > n for individual-based rarefaction unless the argument extrapolate is set to TRUE in which case the returned value is extrapolated using Chao 1.
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Related Issues (20)
- improve make_mob_in() function when spatial coordinates not available HOT 10
- Prepare for CRAN submission
- rarefaction dens_ratio argument HOT 1
- Add formula specification method for mob stats
- readme needs updating
- Extract direction of 'effect size' (D-bar) HOT 3
- make it clearer how statistics can be accessed
- Warning needed: Computing and plotting issues when the design is unbalanced HOT 7
- kNCN method not using great circle distances
- todo: post v2.0 release HOT 6
- beta diversity calculations HOT 10
- effort = NA by default in calc_comm_div and calc_div leads to not so indicative error messages
- Negative S_PIE values when very small non integer abundances HOT 11
- Wrong result from calc_SPIE when there are only singletons HOT 2
- "mob" in the headlines HOT 2
- vignette and documentation todo HOT 4
- betaC calculation should richness be extrapolated? HOT 4
- Error in `get_delta_stats` for calculating density effects when dens_ratio < 1
- calculation of betaC fails when there are at least 1 doubleton but no singletons HOT 4
- towards more consistent computation of alpha, gamma, and beta diversity HOT 5
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