Open 7yl4r opened 2 years ago
Recommendations from Pieter
From Abby:
Existing iobis notebook:
I'm still trying to figure out how es50 is actually calculated. Pieter uses this equation esi = case_when(
n-ni >= esn ~ 1-exp(lngamma(n-ni+1)+lngamma(n-esn+1)-lngamma(n-ni-esn+1)-lngamma(n+1)),
n >= esn ~ 1 and then sums (esi) for a cell.
John Waller at GBIF used entropart::Hurlburt(3).
In the OceanHackWeek project we have been using vegan::rarefy(as.integer(species_counts$x), 50).
Are these all the same? Does anyone know?
implementation started here on the ES50 branch. I am holding off on finishing it, however, since another more comprehensive summary was created by Stephen Formel (rmd d/l here). There was discussion of putting this into a separate repo... Where should it go?
In a discussion today Mimi D'lorio highlighted the importance short summary of caveats on the ES50 index.
Getting a draft of this up somewhere is critically important to do before we can move forward.