Community Dynamics Toolbox

h1. Workshop Notes

are on etherpad: https://epad.nceas.ucsb.edu/p/commdyn-20140105

h1. Metrics brainstorming:

* what are you currently using

* what would you like to use

* how widely is it used

* can it be applied to different biological community datasets (sampling approach)

* is it already coded {in R}

h2. Metrics

# *Diversity* (all of these are generally in R, mostly in vegan)

## Jaccard index

## Simpson's diversity 

## Shannons index

## Turnover - different ways to calculate

## Dominance 

## Evenness

## Richness

## Rank abundance shift

## Beta diversity

# *Community metrics/ordination*

## NMDS (vegan)

## PCA (vegan)

## Bray curtis (vegan)

## Variance tracking, quantify variability change

# *Spatial*

## patch scale 

## spatial autoregression

## meta community statistics

# *Mechanistic models*

## 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

## MANOVA (vegan? Also, permanova is in vegan)

## interaction population models - inter specific competition (Ben Bolker's book and corresponding package)

# *Food webs*

## connectance

## network analysis

# *Traits/phylogentic*

## species aggregation (functional groups, trophic levels

## phylogenetic dispersion (ape etc. -- this stuff is all in R)

## Native/exotic

# *Temporal indices*

## Variance ratio

## Mean-variance scaling

## Spectral analysis

## Regresssion windows (strucchange)

# *null models*

h2. Issues:

#length of time series relative to lifespan of organisms

    WMI toolbox

#high frequency data needed

    sample too frequently then don't see signal, sample to far about miss all dynamics

#type of variable being measured

    abundance, biomass, production

Rare species as background noise

rank abundance curves back again

Comparative analysis of small noise vs large noise systems. What drives differences?

h2. Coded in R

* Richness/diversity metrics: http://cran.r-project.org/web/packages/vegan/index.html

* Diversity metrics (alpha, beta, gamma): http://cran.r-project.org/web/packages/vegetarian/index.html

* Hubble metrics: http://cran.r-project.org/web/packages/untb/index.html

* Leading indicators, variance, autocorrelation, skew, heteroscedasticity: http://cran.at.r-project.org/web/packages/earlywarnings/index.html

not yet coded:

* state-space models and community level resilience