marinebon / obisindicators

R package for generating indicators from OBIS
https://marinebon.github.io/obisindicators/
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+ ref & mention of ES50 in readme #38

Open 7yl4r opened 2 years ago

7yl4r commented 2 years ago
7yl4r commented 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?
7yl4r commented 2 years ago

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?

7yl4r commented 1 year ago

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.