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FDiversity Manual.pdf
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FDiversity为功能多样性计算软件,上传资料为该软件英文使用说明手册。该软件依赖于R语言环境,与R软件绑定后才可使用,该软件的安装过程较为负责,国内相关研究人员对它的掌握较少。
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FDiversity
User Manual
Statistical software for the analysis of
functional diversity
Fernando Casanoves
Julio A. Di Rienzo
Laura Pla
Updated 05/2010
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Casanoves, Fernando
User manual f-diversity: S
tatistical sofware for the analysis of functional
diversity / Fernando Casanoves; Julio A. Di Rienzo; Laura Pla.-1a ed. -
Buenos
Aires: el autor, 2008.
Internet.
ISBN 978-987-05-5238-3
1. Biodiversidad. I. Di Rienzo, Julio A. II. Pla , Laura III. Título
CDD 333.95
The software and the User Manual is the result of the efforts of a multidisciplinary
team. Copyright owners are Julio A. Di Rienzo, Fernando Casanoves and Laura Pla.
The correct citation for the manual is as follows:
Casanoves, Fernando; Julio A. Di Rienzo and Laura Pla. (2008). User Manual
FDiversity: Statistical software for the analysis of functional diversity. First Edition,
Argentina
Link: www.fdiversity.nucleodiversus.org
The software this manual describes should be cited as follows:
Di Rienzo, Julio A.; Fernando Casanoves and Laura Pla (2008). FDiversity, version
2008. Cordoba, Argentina.
Link: www.fdiversity.nucleodiversus.org
FDiversity is a Diversus Project production (www.nucleodiversus.org).
Development FDiversity was partially supported by the Interamerican Institute for
Global Change Research, IAI (CRN-II 2015), which is supported by US National
Science Foundation (Grant GEO-0452325).
DiverSusDiverSus
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Julio A. Di Rienzo is an Associate Professor of Statistics and
Biometry at the “Facultad de Ciencias Agropecuarias” at
Córdoba National University, Argentina. He is Chief Director
of the InfoStat team and is responsible for the R interface of
the FDiversity software (dirienzo@agro.uncor.edu).
Fernando Casanoves is Chair of the Biostatistics Unit at
“Centro Agronómico Tropical de Investigación y Enseñanza”
(CATIE). In the past, he worked at the “Facultad de Ciencias
Agropecuarias” at Córdoba National University, Argentina.
He is a member of the InfoStat team (casanoves@catie.ac.cr).
Laura Pla is a Full Professor at Francisco de Miranda
National University, in Coro, Venezuela. Her main interests
are applied multivariate analysis and biodiversity. She has
contributed to the application module for Infostat’s
biodiversity index (laurapla@yahoo.com).
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INDEX
Introduction ................................................................................................................................. 1
Requirements............................................................................................................................... 1
Getting started ............................................................................................................................. 2
File menu .................................................................................................................................. 2
Edit menu .................................................................................................................................. 3
Data menu ................................................................................................................................. 3
Statistics menu .......................................................................................................................... 5
Analysis of an example ........................................................................................................... 11
Current measurement of functional diversity and its definitions ......................................... 21
Univariate approach ................................................................................................................ 21
Community Weighted Mean .............................................................................................................. 21
FDvar: Functional divergence (Mason et al. 2003) ......................................................................... 21
FRO: Functional regularity (Mouillot et al. 2005)........................................................................... 22
Multivariate approach ............................................................................................................. 24
FAD: Functional attribute diversity (Walker et al. 1999, 2002) ...................................................... 24
FD: Functional diversity based on dendrograms (Petchey & Gaston 2002, 2006, 2007; Podani &
Schmera 2006, 2007; Cianciaruso et al 2009) ................................................................................. 25
Q: Quadratic entropy (Rao 1982 and Pavoine et al. 2005) .............................................................. 27
Extended FD ..................................................................................................................................... 31
CHhV: Convex hull hyper-volume (Cornwell et al. 2006) ................................................................ 31
Multidimensional functional diversity indices (Villéger et al. 2008) ................................................ 32
FDis: Functional dispersion (Laliberté & Legendre 2009) .............................................................. 35
Taxonomic diversity index ..................................................................................................... 36
Richness (S) ...................................................................................................................................... 36
Shannon Index (H) ............................................................................................................................ 36
Eveness (E) ....................................................................................................................................... 37
Simpson Index (D) ............................................................................................................................ 37
References .................................................................................................................................. 38
Index of figures .......................................................................................................................... 42
R sources .................................................................................................................................... 43
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f-Diversity
1
Introduction
FDiversity implements a user-friendly interface to open source routines for the
estimation and analysis of functional diversity indices. The open source platform is R
with an interface written in Delphi® using DCOM-R (a way to run R in the background,
due to Thomas Baier and Erich Neuwirth). DCOM-R is accessed via Delphi routines
written by Dieter Menne.
Requirements
In order for FDiversity to have access to R, DCOM and R must be previously installed
in your system. Follow the following steps:
a) Install DCOM 3.01B5 (if you have a previous version, uninstall it before to
proceed)
b) Install R-2.11.0 or later
c) Run R and install rscproxy library
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d) Exit R
e) Install FDiversity using fdiversityinstaller.exe from URL:
www.fdiversity.nucleodiversus.org
Note: Use the DCOM y R versions suggested by the link provided with the instructions.
The current version of FDiversity has been en tested under Windows XP and Vista.
FDiversity requires the following R packages: proxy, mvtnorm, geometry, vegan, FD,
ade4, ape, gee, lattice, nlme and rscproxy. FDiversity will try to download these
1
In some Vista version you can experiment some trouble with the installation of rscproxy package. The
symptom is that when you try to install it, vista will show you a message giving you same options. No
matters the option you choose the installation of the package will fail. In that case enter
CRAN, look for
and download manually the rscproxy zip file. Uncompress the folder and move or copy it to the
C:\Program Files\R\R-2.11.0\library\. Take care, when moving–coping the folder just to move the folder
containing the package files not a folder inside another folder that use to produce the unzip procedure.
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