transects. I am
attempting to calculate diversity and am curious whether I can apply
rarefaction to the same plot from different points in time.
For example, vegetation from plot ‘A’ was monitored along a 30m transect in
1996, 1999, 2000 and 2004, but was monitored along a 50m transect in 2005
data look like - str(yourdata) - being a good start, and what
commands you're using.
Sarah
On 12/09/2011 12:04 PM, Bill Sutton wrote:
Hello all,
I have a quick question regarding data format when using the vegan package
in program R for rarefaction. I have played around a bit with the s
Hello all,
I have a quick question regarding data format when using the vegan package
in program R for rarefaction. I have played around a bit with the sample
data links and can get these to run fine, but I am having a problem
getting my own data to load properly. When I try to run the
Hello!
Thanks to the many people that responded to my query regarding code for doing
rarefaction in R. Several people also asked that I share what I learned: the
"vegan" and "ape" packages for R, and another also suggested the "simba"
package for R. The
Hello,
Does anyone have some reliable programming code to run a rarefaction anlysis in
either R or (preferably) Minitab? I have two trapping techniques that used
different numbers of traps (5 of one kind, 3 of the other; set in transects, 5
transects of each trap type per field, 2 fields
as experiencing the same notepad drudgery until I stumbled upon it.
>
> Mark Stratton
>
>
> On Tue, Mar 8, 2011 at 10:01 AM, Bill Sutton wrote:
>
>> Hello all,
>>
>> I am writing to see if any of you all know a quicker way to calculate
>> rarefaction curves.
ny of you all know a quicker way to calculate
> rarefaction curves. I currently use EstimateS to calculate rarefaction
> curves and I really like the program, but the numerous notepad outputs
> after each run are starting to drive me crazy. I have nearly 220
> simulations that I
Hello all,
I am writing to see if any of you all know a quicker way to calculate
rarefaction curves. I currently use EstimateS to calculate rarefaction
curves and I really like the program, but the numerous notepad outputs
after each run are starting to drive me crazy. I have nearly 220
Shrinidhi,
Rarefaction assumes that a bigger sampling size would result in more species IN
A GIVEN SAMPLE
PLOT. And it's not a bad assumption, as sampling more individuals can never
result in LESS
species!
You are talking about a comparison BETWEEN your plots, which is completely
diff
I know rarefaction is used when you have different sample sizes. I have a
peculiar situation where I have 3 communities. I have same plot sizes for
2 communities, but have smaller plot size for the third one. Now I have
more number of species and individuals in the community in the third
For an excellent head start on issues related to rarefaction,
sampling curves and richness estimation, see these:
Colwell, R. K., and J. A. Coddington. 1994. Estimating terrestrial
biodiversity through extrapolation. Philosophical Transactions of the
Royal Society of London-B 345:101-118
Bonnie,
I am not sure you quite understand rarefaction. First, there are
individual-based and sample-
based versions. I'm guessing you mean individual based, as sample-based version
also take inter-
sample (i.e., usually spatial) heterogeneity into account.
Individual-based rarefaction s
Dear Colleagues,
I'm considering using rarefaction as a measure of species diversity, since
it takes both species richness and species abundance into account. There
are several benefits of rarefaction over other indices like Shannon
diversity.
It is usually used when sample size is u
rarefaction (and the reason
it's usually the
'preferred' method for comparing richnesses) is that it incorporates
between-sample
heterogeneity, which generally translates to small-scale spatial heterogeneity.
The difference
between the sample- and individual-based curves reflects th
Hi Brian - I don't detect a specific question in your post; however, you
seem to have a decent handle on the differences between sample and
individual based rarefaction. Yes, if the habitats vary in the number of
individuals per sample you expect to collect, individual based rarefactio
per sampling unit (in our case, intercept along 10-m line
transects) we are interested in both a) how many new species are found with
additional samples, and b) controlling for sample size (no. of transects),
what is the expected number of species (rarefaction). Here is where the
confusion arises
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