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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