BiodiversityRGUI {BiodiversityR}R Documentation

GUI for Biodiversity Analysis and Ordination

Description

This function provides a GUI (Graphical User Interface) for some of the functions of vegan, some other packages and some new functions to run biodiversity analysis, including species accumulation curves, diversity indices, Renyi profiles, rank-abundance curves, GLMs for analysis of species abundance and presence-absence, distance matrices, Mantel tests, cluster and ordination analysis (including constrained ordination methods such as RDA, CCA, db-RDA and CAP). The function depends and builds on Rcmdr, performing all analyses on the community and environmental datasets that the user selects. A thorough description of the package and the biodiversity and ecological methods that it accomodates (including examples) is provided in the freely available Tree Diversity Analysis manual (Kindt and Coe, 2005).

Usage

BiodiversityRGUI()

Details

The function launches the R-Commander GUI with an extra menu list for common statistical methods for biodiversity and community ecology analysis.

The R-Commander is launched by changing the location of the Rcmdr "etc" folder to the "etc" folder of BiodiversityR. As the files of the "etc" folder of BiodiversityR are copied from Rcmdr 1.3-14, it is possible that newer versions of the R-Commander will not be launched properly. In such situations, it is possible that copying all files from the Rcmdr "etc" folder again and adding the BiodiversityR menu options to the Rcmdr-menus.txt is all that is needed to launch the R-Commander again.

BiodiversityR uses two data sets for analysis: the community dataset (or community matrix or species matrix) and the environmental dataset (or environmental matrix). The environmental dataset is the same dataset that is used as the "active dataset" of The R-Commander. (Note that you could sometimes use the same dataset as both the community and environmental dataset. For example, you could use the community dataset as environmental dataset as well to add information about specific species to ordination diagrams. As another example, you could use the environmental dataset as community dataset if you first calculated species richness of each site, saved this information in the environmental dataset, and then use species richness as response variable in a regression analysis.) Some options of analysis of ecological distance allow the community matrix to be a distance matrix (the community data set will be interpreted as distance matrix via as.dist prior to further analysis).

BiodiversityR provides the following menu options (each described below in greater detail):

Value

None

Select Community Dataset

This window selects the community dataset to be used in the biodiversity analyses and provides the following options:

Import datasets from Excel

This window enables to import community and environmental data sets from an Excel workbook with a specific format (sheets that are named "community" and "environmental" or "stacked" and "environmental"; first row containing the names of the variables) (an example is provided in the etc folder of the BiodiversityR package for the dune meadow dataset: dune.xls). The menu provides the following options:

Import datasets from Access

This window enables to import community and environmental data sets from an Access database with a specific format (sheets that are named "community" and "environmental" or "stacked" and "environmental"; first row containing the names of the variables) (an example is provided in the etc folder of the BiodiversityR package for the dune meadow dataset: dune.xls). The menu provides the following options:

Same sites for community and environmental datasets

This window maps the community dataset onto the rownames of the environmental dataset by function same.sites. Having the same sequence of sites is an assumption for analysis with BiodiversityR. It may be useful to use this function after making a community dataset from a stacked environmental dataset (especially as sites are ordered in an alphabetic way from the stacked dataset, which may create problems with X1, X10, X100 site names versus the X001, X010 and X100 formats; the function is also useful where some sites do not contain any species). The menu provides the following options:

Make Community Dataset

This window selects the variables that indicates sites, species and abundance to create a new community dataset. This dataset becomes the active community dataset. The menu provides the following options:

Remove NA

This window removes the sites that have NA (missing values) for a selected varialbe of the environmental dataset. When environmental variables have missing values, this often creates problems with biodiversity analysis. The menu provides the following options:

Transform community matrix

This window transforms the community matrix. The menu provides the following options:

Select Environmental Dataset

This window selects the environmental dataset to be used in the biodiversity analyses. The environmental dataset is always the active dataset for non-Biodiversity Rcmdr options. By selecting the community dataset as the environmental dataset as well, you can also manipulate the community dataset with the other Rcmdr options. The menu provides the following options:

Summary

This window makes a summary of all or a selection of the variables of the environmental dataset, or plots the variables. In case that you want to make a summary of the community dataset, then you need to make the community dataset the environmental dataset at the same time. The menu provides the following options:

Box Cox transformation

This window makes a Box-Cox transformation of a selected variable from the environmental dataset. The menu provides the following options:

Species accumulation curves

This window fits and plots species accumulation curves. The menu provides the following options:

Diversity indices

The window calculates and fits diversity indices from the community dataset. The menu provides the following options:

Rank Abundance

The window fits and plots rank abundance curves for the community dataset. The menu provides the following options:

Renyi diversity profiles

The window fits and plots Renyi diversity profiles from the community dataset. The menu provides the following options:

Species abundance as response

The window fits and plots regression models for abundance data with a response variable selected from the community dataset and explanatory variables selected from the environmental dataset. (Hint: to analysis species richness patterns, save site-specific species richness (from diversity indices menu) into the environmental data set, and then make the environmental data set to be the community dataset as well). The menu provides the following options:

Species presence-absence as response

The window fits and plots regression models for presence-absence data with a response variable selected from the community dataset and explanatory variables selected from the environmental dataset. The menu provides the following options:

Calculate distance matrix

This window calculates a distance matrix from the community dataset and provides the following options:

Unconstrained ordination

The window fits and plots unconstrained ordination models. The menu provides the following options:

Constrained ordination

The window fits and plots constrained ordination models to the community dataset, using variables of the environmental dataset to contrain the ordination model (direct gradient analysis, canonical ordination analysis). The menu provides the following options:

Clustering

This window performs various methods of cluster analysis based on the information of the community dataset. The menu provides the following options:

Compare distance matrices

This window calculates a distance matrix from the community dataset. This distance matrix can be analysed by a Mantel, MRPP or ANOSIM test based on information from the environmental dataset. You can compare two different community datasets if you make one the community dataset and the other one the environmental dataset. The menu provides the following options:

Author(s)

Roeland Kindt (with some help from Jari Oksanen)

References

Kindt, R. & Coe, R. (2005) Tree diversity analysis: A manual and software for common statistical methods for ecological and biodiversity studies.

http://www.worldagroforestry.org/treesandmarkets/tree_diversity_analysis.asp


[Package BiodiversityR version 1.2 Index]