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Corinna Gries, 03/10/2014 01:57 PM

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h1. Workshop Notes
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are on etherpad: https://epad.nceas.ucsb.edu/p/commdyn-20140105
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h1.Metrics brainstorming:
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    what are you currently using
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    what would you like to use
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    how widely is it used
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    can it be applied to different biological community datasets (sampling approach)
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    is it already coded {in R}
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h2. Metrics
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# *Diversity* (all of these are generally in R, mostly in vegan)
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## Jaccard index
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## Simpson's diversity 
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## Shannons index
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## Turnover - different ways to calculate
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## Dominance 
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## Evenness
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## Richness
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## Rank abundance shift
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## Beta diversity
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# *Community metrics/ordination*
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## NMDS (vegan)
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## PCA (vegan)
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## Bray curtis (vegan)
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## Variance tracking, quantify variability change
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# *Spatial*
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## patch scale 
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## spatial autoregression
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## meta community statistics
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# *Mechanistic models*
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## MAR, needs driver matrix, problem auto-corelation, mostly fresh water or marine (Eli Holmes has state-space MAR in R implemented, not sure if it's on CRAN)   http://cran.r-project.org/web/packages/MARSS/index.html
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## MANOVA (vegan? Also, permanova is in vegan)
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## interaction population models - inter specific competition (Ben Bolker's book and corresponding package)
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# *Food webs*
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## connectance
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## network analysis
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# *Traits/phylogentic*
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## species aggregation (functional groups, trophic levels
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## phylogenetic dispersion (ape etc. -- this stuff is all in R)
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## Native/exotic
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# *Temporal indices*
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## Variance ratio
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## Mean-variance scaling
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## Spectral analysis
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## Regresssion windows (strucchange)
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# *null models*
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h2.Issues:
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#length of time series relative to lifespan of organisms
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    WMI toolbox
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#high frequency data needed
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    sample too frequently then don't see signal, sample to far about miss all dynamics
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#type of variable being measured
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    abundance, biomass, production
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Rare species as background noise
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rank abundance curves back again
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Comparative analysis of small noise vs large noise systems. What drives differences?