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Use of other diversity indices #113
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Not currently, but I could look into adding this functionality for you? Do you have a specific paper or blog post that outlines the exact objective function you need? AFAIK, phylogenetic endemism is a static/pre-computed quantity that pertains to each planning unit. If so, you could manually compute this metric for each planning unit and use phylogenetic endemism as a feature in your spatial prioritisation? What do you think? |
Dear Dr. Jeff,
Thank you very much for your reply. I'm using the function provided by Greg
Guerin <
https://github.com/GregGuerin/biomap/blob/master/phylogenetic.endemism.R>
that was published in this paper
<https://www.sciencedirect.com/science/article/pii/S2352711015000126> (also
this one
<https://onlinelibrary.wiley.com/doi/full/10.1111/j.1365-294X.2009.04311.x>).
Your suggestion makes complete sense. I was just wondering if we might add
a function add_max_phyloEnd_objective similar with the current
add_max_phylo_objective, so I can use the phylogenetic endemism to
prioritize phylogenetic endemism instead of PD. By doing so, I could
understand whether some regions have a unique phylogenetic history instead
of more or less diversity.
Thank you again for helping me.
Best,
Paulo
Em qua, 7 de ago de 2019 às 10:41, Jeff Hanson <notifications@github.com>
escreveu:
… Not currently, but I could look into adding this functionality for you? Do
you have a specific paper or blog post that outlines the exact objective
function you need? AFAIK, phylogenetic endemism is a static/pre-computed
quantity that pertains to each planning unit. If so, you could manually
compute this metric for each planning unit and use phylogenetic endemism as
a feature in your spatial prioritisation? What do you think?
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*Paulo Sérgio Monteiro Ferreira*
Professor da Escola Estadual de Ensino Fundamental Professor Rangel - Ingá
Doutorando em Ecologia e Recursos Naturais pela Universidade Federal do
Ceará
Mestre em Ecologia e Conservação pela Universidade Estadual da Paraíba
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Great - thank you very much for the links - that helps a lot! I think we could implement some phylogenetic endemism stuff but I want to make sure that I understand exactly what you want to achieve with the prioritisation. Please correct me if anything I've said isn't right. I can think of two approaches that phylogenetic endemism could be used to generate a prioritisation:
Do either of these approaches match up with what you're trying to do? I would generally caution against the first approach though, because it doesn't follow the principle of complementarity. Please let me know if what I've written doesn't make sense, and I can try explaining it more clearly. |
Thank you very much for your availability and kindness in responding. You're right. Your second suggestion fits exactly what I would like to do. How would it be possible to modify the maximum features objective function to achieve this result? Best regards |
No worries - ok sounds awesome! The second approach would involve modifying the phylogenetic diversity objective function so that it uses How urgently do you need this? If you need it ASAP, you could implement this yourself by taking your phylogenetic tree and manually rescaling the branches according to their distribution size, and then just using the phylogenetic diversity objective function. Or if you don't mind waiting a week or so, I could implement this new functionality into prioritizr for you? |
Yes, I can wait a while! It will be amazing if you can do that. Thank you so much for your availability! |
No worries! I've just pushed a new version to GitHub with the |
Is it possible to insert another index of phylogenetic diversity (phylogenetic endemism) as a conservation objective instead of Faith's phylogenetic diversity?
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