Workshop Notes¶

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

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}

1. Diversity (all of these are generally in R, mostly in vegan)

1. Jaccard index
2. Simpson's diversity
3. Shannons index
4. Turnover - different ways to calculate
5. Dominance
6. Evenness
7. Richness
8. Rank abundance shift
9. Beta diversity

1. Community metrics/ordination
2. NMDS (vegan)
3. PCA (vegan)
4. Bray curtis (vegan)
5. Variance tracking, quantify variability change
6. And spatial...
7. patch scale
8. spatial autoregression
9. meta community statistics
10. Mechanistic models
11. 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
12. MANOVA (vegan? Also, permanova is in vegan)
13. interaction population models - inter specific competition (Ben Bolker's book and corresponding package)
14. Food webs
15. connectance
16. network analysis
17. Traits/phylogentic
18. species aggregation (functional groups, trophic levels
19. phylogenetic dispersion (ape etc. -- this stuff is all in R)
20. Native/exotic
21. Temporal indices
22. Variance ratio
23. Mean-variance scaling
24. Spectral analysis
25. Regresssion windows (strucchange)
26. null models

issues identified by four breakout groups:
1. length of time series relative to lifespan of organisms
WMI toolbox

2. high frequency data needed
sample too frequently then don't see signal, sample to far about miss all dynamics

3. 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?