Firstwrkshnotes » History » Version 5
Corinna Gries, 03/10/2014 01:57 PM
1 | 1 | Corinna Gries | h1. Workshop Notes |
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3 | 3 | Corinna Gries | are on etherpad: https://epad.nceas.ucsb.edu/p/commdyn-20140105 |
4 | 4 | Corinna Gries | |
5 | 5 | Corinna Gries | h1.Metrics brainstorming: |
6 | 4 | Corinna Gries | what are you currently using |
7 | what would you like to use |
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8 | how widely is it used |
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9 | can it be applied to different biological community datasets (sampling approach) |
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10 | is it already coded {in R} |
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11 | 1 | Corinna Gries | |
12 | 5 | Corinna Gries | h2. Metrics |
13 | # *Diversity* (all of these are generally in R, mostly in vegan) |
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14 | ## Jaccard index |
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15 | ## Simpson's diversity |
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16 | ## Shannons index |
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17 | ## Turnover - different ways to calculate |
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18 | ## Dominance |
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19 | ## Evenness |
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20 | ## Richness |
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21 | ## Rank abundance shift |
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22 | ## Beta diversity |
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23 | # *Community metrics/ordination* |
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24 | ## NMDS (vegan) |
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25 | ## PCA (vegan) |
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26 | ## Bray curtis (vegan) |
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27 | ## Variance tracking, quantify variability change |
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28 | # *Spatial* |
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29 | ## patch scale |
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30 | ## spatial autoregression |
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31 | ## meta community statistics |
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32 | # *Mechanistic models* |
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33 | ## 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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34 | ## MANOVA (vegan? Also, permanova is in vegan) |
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35 | ## interaction population models - inter specific competition (Ben Bolker's book and corresponding package) |
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36 | # *Food webs* |
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37 | ## connectance |
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38 | ## network analysis |
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39 | # *Traits/phylogentic* |
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40 | ## species aggregation (functional groups, trophic levels |
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41 | ## phylogenetic dispersion (ape etc. -- this stuff is all in R) |
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42 | ## Native/exotic |
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43 | # *Temporal indices* |
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44 | ## Variance ratio |
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45 | ## Mean-variance scaling |
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46 | ## Spectral analysis |
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47 | ## Regresssion windows (strucchange) |
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48 | # *null models* |
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49 | 4 | Corinna Gries | |
50 | 5 | Corinna Gries | h2.Issues: |
51 | #length of time series relative to lifespan of organisms |
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52 | 4 | Corinna Gries | WMI toolbox |
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54 | 5 | Corinna Gries | #high frequency data needed |
55 | 4 | Corinna Gries | sample too frequently then don't see signal, sample to far about miss all dynamics |
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57 | 5 | Corinna Gries | #type of variable being measured |
58 | 4 | Corinna Gries | abundance, biomass, production |
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61 | Rare species as background noise |
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62 | rank abundance curves back again |
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63 | Comparative analysis of small noise vs large noise systems. What drives differences? |