[R-sig-eco] Recommended R package for analyzing community data set? - nested design, stratified random sampling, covariates

[Dave Roberts]

Dear Laura,

    David is certainly correct that vegan would provide a wealth of 
tools for the analysis of your data.  More generally, if you go to CRAN 
and browse the "environmetrics"  Task View you will see an review of 
many packages suitable for specific analyses you may be interested in.

Dave Roberts

On 01/15/2012 12:10 PM, Laura S wrote:
> Dear all:
>
> May you recommend an R package for analyzing this data set? I would greatly appreciate any thoughts you can provide.
>
>
> I. Study goals
>
> This study examines soil crust (lichens and bryophytes) recovery and succession in fields that underwent different levels of disturbance.
>
>
> II. Variables
> Response variables of interest: soil crust cover (categorical scale - described below), species richness, species composition
> Explanatory variable of interest: disturbance regime (categorical variable)
> Environmental variables measured (covariates - mix of categorical and numerical variables): cover of mineral soil, litter, vascular plant bases, stones, or rocks,
> slope, aspect
>
> III. Study sampling and design
> Eight research areas (BR, CB, CC, JL, PC, PL, SL, TR)
> Within each research area subplots were assigned six disturbance treatments (NC, NS, OC, OS, SC, SS) based on disturbance history
> A single transect was placed randomly in the center of each subplot and sampled in twenty 20 x 20 cm plots at 1 m intervals along the transect
> 47 of 48 possible treatment subplots were sampled (n=6 for 7 sites, n=5 for 1 site)
>
>
> Sampling cover scale:
>
> Scale value    Representative % cover
>
> 1<= 1
> 2>1-4
> 3>4-10
> 4>10-25
> 5>25-50
> 6>50-75
> 7>75-95
> 8>95-100
>
>
> There were three different sampling times (spread over two years), but time of sampling was not considered as a confounding factor given the way sampling was conducted with the particular communities studied (soil crust communities).
>
> Total species positively identified: 33 taxa (species and species groups), 15 of these were in four or more
> of 47 subplots (n=6 x 7, n=5 x 1)
> Unidentified collected taxa: less than 0.5%
> Approximate taxa pool (species observed in entire areas, but not necessarily in sample plots): 26 lichen + 21 bryophytes
> = 47 taxa
>
> Thank you for your time and consideration,
> Laura
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