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

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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