te: Wed, 12 Jan 2000 12:04:58 +0200
From: Jaan Palisaar
Subject: Software for diversity indeces
Dear Ecologgers,
a week ago I posted a question concerning freely available software
for the calculation of diversity indices, species richness estimators
etc. There were 15 replies (THANK YOU VERY MUCH) along with
some asking to make the results publicly available. What out, here
it comes:
FREEWARE
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# Biodiversity Pro http://www.nrmc.demon.co.uk/bdpro
as far as I can see the most thorough collection of biodiversity
related stats:
Alpha Calculations
Abundance Plot: K-Dominance,Rank
Abundance Model:Log-Series,Broken Stick
Rarefaction
Diversity Indices: Shannon,Alpha,Caswell,Berger-
Parker,Simpson,Hill,Margalef,McIntosh
Beta Calculations
SHE Analysis
Species Richness
Chao 1&2
Jackknife
...
Species Distribution
Multivariate
Principal Components
Correspondence Analysis
Cluster Analysis
Non-Metric MDS (not yet implemented)
Comparison
Descriptive Statistics
Kulczynski
Mann-Whitney
Rank Correlation
Correlation
Variance-Covariance
ANOSIM
So far it is freeware, but it is not clear to me if this is only the case
because it is still beta-software. So beta get it now :-)
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EstimateS
0000,8000,0000http://viceroy.eeb.uconn.edu/Est
imateS
ACE Abundance-based Coverage Estimator of species
richness
ICE Incidence-based Coverage Estimator of species richness
ICE_CI_50 + or - term for 95% Confidence Interval for ICE, based
on ICE-SD and 50 randomizations
Chao1 Chao 1 richness estimator
Chao2 Chao 2 richness estimator
Jack1 First-order Jackknife richness estimator
Jack2 Second-order Jackknife richness estimator
Bootstrap Bootstrap richness estimator
MMRuns Michaelis-Menten richness estimator: estimators
averaged over randomizations (runs)
MMMean Michaelis-Menten richness estimator: estimators
computed once for mean species accumulation curve
Cole Coleman richness expectation
Alpha Fisher s alpha diversity index
Shannon Shannon diversity index
Simpson Simpson (inverse) diversity index
plus, among other more basic stats, some Shared Species
estimators and "Morisita-Horn sample similarity index"
Haven't tried it out yet, but it has been recommended several times
and it's free.
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# EcoSim http://homepages.together.net/~gentsmin/ecosim.htm
"EcoSim is an interactive computer program for null model analysis
in community ecology. EcoSim allows you to test for community
patterns with non-experimental data. EcoSim performs Monte Carlo
randomizations to create "pseudo-communities" (Pianka 1986),
then statistically compares the patterns in these randomized
communities with those in the real data matrix."
Has modules for
1.Co-occurrence
2.Niche Overlap
3.Size Overlap
4.Species Diversity
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Other software which I haven't tried yet:
Ecology Software by Hsin Chi
0000,8000,0000http://nhsbig.inhs.uiuc.edu/www/c
hi.html
krebswin
0000,8000,0000http://www.biology.ualberta.ca/jb
rzusto/krebswin.html
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SHAREWARE
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MVSP http://www.kovcomp.co.uk/downl2.html
still available as a DOS shareware version and for some time now
as a Windows version.
Some ordination and clustering procedures and diversity indices.
Worth having a look at (a friend uses it some years now: a good
alround work-horse)
COMMERCIAL SOFTWARE
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Pices Species Diversity and Richness II
0000,8000,0000http://www.irchouse.demon.co.uk/i
ndex.html
0000,0000,0000 if I remember right it looks
very thorough, but has it's price
COLLECTIONS OF LINKS
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Checklist of Software for Field Biologists
0000,8000,0000http://www.euronet.nl/users/mblee
ker/prog/soflis_e.html#lst0000,0000,0000
very interisting list for EVERY aspect of field biology
MISCELLANEOUS
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----
a bit off-topic but probably interesting for all those who wondered if
there is no free replacement for Excel with more scientific features:
KYPLOT http://www.qualest.co.jp/Download/KyPlot/kyplot_e.htm
Still beta with some rough edges but contains an amazing set of
general statistics and scientific graphing. Worth having a look at.
Thanks again for all contributions
Jaan
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Jaan Palisaar
Valuaoja pst. 15A-40
71013 Viljandi
Estonia
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