domingo, 5 de junio de 2011

Ecoinformatics Tools & Products | NCEAS

Ecoinformatics Tools & Products | NCEAS

Ecoinformatics Tools & Products

NCEAS collaborative research efforts have produced a variety of software tools and products that assist scientists in the creation, management, access, and analysis of ecological data. These tools can be classified into five categories. The ecoinformatics.org web site provides further details, including download instructions, where appropriate, for each tool. All the software tools that NCEAS has developed are free for download, typically run on at least several popular computing platforms, and utilize best of class open source software frameworks when appropriate.

Analytical And Modeling Tools

Kepler is an open-source scientific workflow system that allows scientists to design scientific workflows and execute them efficiently using emerging Grid-based approaches to distributed computation. Kepler facilitates access to a broad range of ecologically relevant data via the EcoGrid, while also providing a basis for sharing analyses through a growing library of executable components and workflows. Kepler/CORE moves Kepler from a research prototype to a reliable and easily extensible system.

Metadata Specifications

Ecological Metadata Language (EML) is a metadata specification developed by the ecology discipline and for the ecology discipline. EML is implemented as a series of XML document types that can be used in a modular and extensible manner to document ecological data. Each EML module is designed to describe one logical part of the total metadata that should be included with any ecological dataset. It is likely that EML will be useful as a Metadata Language outside of the ecological discipline since, despite its intended relevance for ecological data, it does not contain any metadata structures that are strictly ecological. Rather, the metadata structures in EML all have broader applicability.

Metadata Entry Tools and Editors

Morpho allows users to create and manage EML metadata and to share those metadata, and their associated data, with others. It was created to provide an easy-to-use, cross-platform application for accessing and manipulating metadata and data both locally and on the network through powerful connections with Metacats .

Jalama is a (research prototype) system that can be used for developing metadata and data entry forms, based on rich metadata descriptions, for use in lab and field environments for ecology.

Data Repositories & Registries

Metacat is a flexible metadata database architecture that utilizes XML as a common syntax for representing metadata content standards utilized by ecologists. Metacats have specialized features suitable for guaranteeing local autonomy and access control, while also affording the possibility of broad-scale replication and information sharing within the KNB .

Online Databases

KNB Data Repository: Supports the Knowledge Network for Biocomplexity, a national network that facilitates ecological and environmental research on biocomplexity.

NCEAS Data Repository: Contains information about research data sets collected and collated as part of NCEAS' funded activities. It is concurrently available through the KNB Data Repository .

Vegbank: The vegetation plot database of the Ecological Society of America's Panel on Vegetation Classification.

Paleobiology Database: Fossil information that includes 52,000 collection records and 511,889 taxonomic occurrences from 13,962 published references.

Interaction Web Database: Data concerning ecological interactions, particularly pollination/pollinator relationships.

Global Population Dynamics Database
: An extensive collection of time series data from plant and animal populations.

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sábado, 4 de junio de 2011

Legendre - Taichung09

Legendre - Taichung09 Un muy buen curso dado por un grande. Material de sobra para entretenerse, espero les guste.

Biostatistics Short Course

Department of Life Science

and Center for Tropical Ecology and Biodiversity

Tunghai University, Taichung, Taiwan

November 6-8 and 13-15, 2009

Pierre Legendre

Professor, Université de Montréal


This page contains links to various documents and programs that will be used during the course
Course outline, Taichung 2009

Documents in PDF format

Part 1: Linear model

Day 1
"Multidimensional quantitative data" (Chapter extract)
"Regression" (Chapter extract)
"Multiple regression: computing the parameters by matrix inversion" (Teaching document)
"Model II regression" (R library support document)
Day 2
"Statistical tests, permutation tests" (Chapter extract)
"Comparison of two samples" (Teaching document)
"Appendix: t-test with Welch correction" (Manuscript extract)
"Compare several group means: anova" (Teaching document)
Day 3
"Other forms of anova" (Teaching document)
"General linear model" (Teaching document)

Part 2: Community ecology ordination

Day 1
"Algebra of Principal Component and Correspondence Analyses" (Teaching document)
"From classical to canonical ordination" (Chapter)
"Contingency table analysis" (Teaching document)
"Ecologically meaningful transformations for ordination of species data" (Article)
"Ordination methods for community composition data tables" (Summary Figure)
"Eigenvalues and eigenvectors" (Teaching document)
Day 2
"Some measures of resemblance" (Teaching document)
"Is Miss America an undernourished role model?" (Article)
"Variation partitioning" (Chapter extract)
"Types of variables in explanatory matrix X of multiple regression" (Teaching document)
"R-square, adjusted R-square" (Chapter extract)
"Variation partitioning of species data matrices: estimation and comparison of fractions" (Article)
"Polynomial regression, trend surface analysis" (Teaching document)
"Permutation test summary" (Classroom notes)
"Multiple regression with permutation test" (R function)
Day 3
"Partial linear regression and variation partitioning" (Chapter extract)
"Studying beta diversity: ecological variation partitioning by multiple regression and canonical analysis" (Article, Chinese and English versions)
"Canonical analysis" (Classroom notes)
"Response of 20 native tree species..." (Article)
"Distance-based redundancy analysis..." (Article)


Other documents

(There is nothing in this section at the moment)


Practicals in R

Practicals last updated November 6, 2009
Practicals for Part 1 of the course using the R statistical language
Practicals for Part 2 of the course using the R statistical language


Programs and PDF reprints from the lab of Pierre Legendre
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Libros para descargar (gratis) sobre Estadística Computacional