README.md
In miquelcaceres/VegX: Vegetation data in Veg-X
VegX
Introduction
A primary technical impediment to large-scale sharing of vegetation data
is the lack of a recognized international exchange standard for linking
the panoply of tools and database implementations that exist among
various organizations and individuals participating in vegetation
research.
The Veg-X exchange standard
The Veg-X exchange standard for plot-based vegetation data (Wiser et
al. 2011) is intended to be used to share and merge vegetation-plot data
of different kinds. Veg-X allows for observations of vegetation at both
individual plant and aggregated observation levels. It ensures that
observations are fixed to physical sample plots at specific points in
space and time, and makes a distinction between the entity of interest
(e.g. an individual tree) and the observational act (i.e. a
measurement). The standard supports repeated measurements of both
individual organisms and plots, and enables the connection between the
entity observed and the taxonomic concept associated with that
observation to be maintained.
Detailed documentation of Veg-X
Please read article The Veg-X exchange
standard to
know mode about the standard.
XML schema
Veg-X is written as an XML schema, which is a definition of
user-defined tags to structure textual information in order to create
self-describing datasets. XML (Extensible Markup Language) is an open
standard, and XML files are both machine and human-readable (they are
stored in plain-text ASCII format). Visit folder
vegxschema to
see the XML schema representation of the standard. This schema should be
used to evaluate whether a given Veg-X XML document conforms to the
definitions and data structure of the standard.
An R package to use the Veg-X standard
A barrier to the use of a standard like Veg-X is its complexity. To make
the exchange schema of Veg-X usable by the wider community requires the
development of informatics tools for mapping data from different input
formats (e.g. relevé tables from different databases, forest inventory
data or stem-mapped forest plots) into Veg-X, mechanisms to create
unique identifiers to allow source datasets to be combined, and tools to
export data for data analysis and visualisation. The VegX R package
has been designed for this purpose. It contains functions to import,
integrate, harmonize and export vegetation data using the Veg-X
standard.
Package installation
The VegX R package can be installed from GitHub as follows:
devtools::install_github("iavs-org/VegX", build_vignettes=TRUE)
User manual
Please refer to How to use the VegX
package
to learn how to use the VegX package.
Acknowledgements
Developments endorsed and funded by the International Association for
Vegetation Science
Veg-X standard development:
- Miquel De Cáceres
- Sebastian Schmidtlein
- Christian König
- Susan K. Wiser
- Nick Spencer
- Robert K. Peet
- Martin Kleikamp
- Brad Boyle
VegX R package development:
- Miquel De Cáceres
- Sebastian Schmidtlein
- Christian König
References
- Wiser SK, Spencer N, De Caceres M, Kleikamp M, Boyle B & Peet RK
(2011). Veg-X - an exchange standard for plot-based vegetation data.
Journal of Vegetation Science 22: 598-609.
https://doi.org/10.1111/j.1654-1103.2010.01245.x
miquelcaceres/VegX documentation built on Sept. 18, 2022, 7:04 p.m.
R Package Documentation
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
VegX
Introduction
A primary technical impediment to large-scale sharing of vegetation data is the lack of a recognized international exchange standard for linking the panoply of tools and database implementations that exist among various organizations and individuals participating in vegetation research.
The Veg-X exchange standard
The Veg-X exchange standard for plot-based vegetation data (Wiser et al. 2011) is intended to be used to share and merge vegetation-plot data of different kinds. Veg-X allows for observations of vegetation at both individual plant and aggregated observation levels. It ensures that observations are fixed to physical sample plots at specific points in space and time, and makes a distinction between the entity of interest (e.g. an individual tree) and the observational act (i.e. a measurement). The standard supports repeated measurements of both individual organisms and plots, and enables the connection between the entity observed and the taxonomic concept associated with that observation to be maintained.
Detailed documentation of Veg-X
Please read article The Veg-X exchange standard to know mode about the standard.
XML schema
Veg-X is written as an XML schema, which is a definition of user-defined tags to structure textual information in order to create self-describing datasets. XML (Extensible Markup Language) is an open standard, and XML files are both machine and human-readable (they are stored in plain-text ASCII format). Visit folder vegxschema to see the XML schema representation of the standard. This schema should be used to evaluate whether a given Veg-X XML document conforms to the definitions and data structure of the standard.
An R package to use the Veg-X standard
A barrier to the use of a standard like Veg-X is its complexity. To make the exchange schema of Veg-X usable by the wider community requires the development of informatics tools for mapping data from different input formats (e.g. relevé tables from different databases, forest inventory data or stem-mapped forest plots) into Veg-X, mechanisms to create unique identifiers to allow source datasets to be combined, and tools to export data for data analysis and visualisation. The VegX R package has been designed for this purpose. It contains functions to import, integrate, harmonize and export vegetation data using the Veg-X standard.
Package installation
The VegX R package can be installed from GitHub as follows:
devtools::install_github("iavs-org/VegX", build_vignettes=TRUE)
User manual
Please refer to How to use the VegX package to learn how to use the VegX package.
Acknowledgements
Developments endorsed and funded by the International Association for Vegetation Science
Veg-X standard development:
- Miquel De Cáceres
- Sebastian Schmidtlein
- Christian König
- Susan K. Wiser
- Nick Spencer
- Robert K. Peet
- Martin Kleikamp
- Brad Boyle
VegX R package development:
- Miquel De Cáceres
- Sebastian Schmidtlein
- Christian König
References
- Wiser SK, Spencer N, De Caceres M, Kleikamp M, Boyle B & Peet RK (2011). Veg-X - an exchange standard for plot-based vegetation data. Journal of Vegetation Science 22: 598-609. https://doi.org/10.1111/j.1654-1103.2010.01245.x
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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