FDiversity Manual.pdf-资料库

qq_37206876-12041436-4744300845384888811.pdf-第1页.png

第1页 / 共57页

qq_37206876-12041436-4744300845384888811.pdf-第2页.png

第2页 / 共57页

qq_37206876-12041436-4744300845384888811.pdf-第3页.png

第3页 / 共57页

qq_37206876-12041436-4744300845384888811.pdf-第4页.png

第4页 / 共57页

qq_37206876-12041436-4744300845384888811.pdf-第5页.png

第5页 / 共57页

qq_37206876-12041436-4744300845384888811.pdf-第6页.png

第6页 / 共57页

qq_37206876-12041436-4744300845384888811.pdf-第7页.png

第7页 / 共57页

qq_37206876-12041436-4744300845384888811.pdf-第8页.png

第8页 / 共57页

FDiversity User Manual Statistical software for the analysis of functional diversity Fernando Casanoves Julio A. Di Rienzo Laura Pla Updated 05/2010

Casanoves, Fernando User manual f-diversity: Statistical 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 (www.nucleodiversus.org). FDiversity 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). is a Diversus Project production DiverSus DiverSus ii

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 Infostat’s biodiversity index (laurapla@yahoo.com). the application module to for iii

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 iv

f-Diversity 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 1 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. 1

f-Diversity packages (except rscproxy that must be installed before running FDiversity) upon request by the procedures. Getting started When FDiversity is run, the application window is displayed as shown in Figure 1. The illustration shows the application desktop with a new data table. The main menu has two important items, Data and Statistics. A short description of each of the menus follows. Figure 1: Main FDiversity window File menu As usual, the file menu contains the list of actions for handling data sets, like creating a new table or opening an existing one, saving, saving as, closing a table, and quitting the application (Figure 2). The default file format that FDiversity uses to save tables is a proprietary file format with an .FDDB extension. However, FDiversity can read Excel files (*.xls), text files (*.txt, *.dat), dbase files (*.dbf), InfoStat files (*.idb, *.idb2) and R scripts (*.r). It also has the ability to export data tables to all previously mentioned data formats. 2

f-Diversity Figure 2: FDiversity File menu Edit menu The edit menu shown in Figure 3 contains the usual links to the Cut-Copy-Paste-Undo functions, common to almost every windows application. Copy with column names and Paste with column names are specialized forms of copy-paste for application on tables. Figure 3: FDiversity Edit menu Data menu This menu contains a list of links to procedures that apply to the current active table (Figure 4). These procedures are intended to manage usual actions on a data sheets, such as: inserting, adding and deleting rows and columns, arranging rows according to different sorting criteria, activating and deactivating cases to allow or disallow participation in calculations, changing columns names, modify the number of decimal numbers displayed and the alignment and width of columns. It also contains links to 3

f-Diversity more specialized procedures that allow categorizing numerical variables, editing the names of categories of categorical variables, writing formulas and searching for cases according to logical rules. Moreover, there are links to procedures on how to merge tables side by side according to matching criteria (Merge horizontally) and on how to merge tables appending one to the other (Merge vertically). Several transformations are implemented to make trait scales comparable. Figure 4: Data menu Ecologists usually have two types of data sets involving the Functional Diversity calculation: 1) a data set containing the trait’s information (i.e. specific leaf area, wood density, longevity, leaf N content, etc.) for each species (cases), and 2) a data set containing classification variables (treatment label, replications, plot number, etc.), co- variables (altitude, temperature, etc.), the list of species, and the abundance or the basal area corresponding to each species. Therefore it is useful to be able to concatenate tables. It is easy to generate the merged data table using a side-by-side merging algorithm (see the section Analysis of an example). 4

资料库

FDiversity Manual.pdf

相关推荐

行业

热门标签

最新资料