ContrBB: BEANPLOTS AND BOXPLOTS OF CONTRIBUTION OF FACTORS

In SPEDInstabR: Estimation of the Relative Importance of Factors Affecting Species Distribution Based on Stability Concept

BEANPLOTS AND BOXPLOTS OF CONTRIBUTION OF FACTORS

Description

It performs beanplots and boxplots with the contribution of environmental factors to explain the distribution of species.

Usage

ContrBB(data, vars, Level=NULL, Taxon=NULL, graph="beanplot", order="decreasing",
side="no", beanlines="median", what=c(1,1,1,1), ll=NULL, border="black", OrderCat=NULL,
LabelCat=NULL, XLAB="Variables", YLAB="Percentage of contribution to instability index",
COLOR=NULL, LEGEND=NULL, MTEXT= NULL, TEXT=NULL, ResetPAR=TRUE, PAR=NULL,
BEANPLOT=NULL, BOXPLOT=NULL)

Arguments

data	Data file, which it may be obtained using DataManager of ModestR. See details section for the explanation of the format of the data.
vars	Environmental factors.
Level	Optionaly, a taxonomic level may be selected, i.e., class, family, order, genus or species.
Taxon	Optionally, it is possible to work only with a selected species, just specifying the name of the taxon or taxa selected within the taxonomic level selected in the argument Level, i.e., name of the order, family, etc. Can be a vector, so several taxa.
graph	Type of plot: "beanplot" or "boxplot".
order	If it is NULL the categories are ordered as found in the argument vars, if it is "increasing" are ordered from lesser to greater median or mean according to the method selected in the argument beanlines, if it is "decreasing" are ordered from greater to lesser median or mean, if it is "alhaAZ" are ordered from A to Z and if it is "alphaZA" from Z to A. If the method selected in beanlines="quantiles", it is used the median for both "increasing" and "decreasing".
side	The side on which the beans are plot. Default is "no", for symmetric beans. The options "first", "second" and "both" are also supported.
beanlines	The method used for determining the average bean lines. Default is value "median", and other options are "mean" and "quantiles".
what	A vector of four booleans describing what to plot. In the following order, these booleans stand for the total average line, the beans, the bean average, and the beanlines. For example, what=c(0,0,0,1) produces a stripchart.
ll	Length of the beanline per point found.
border	Color of the border around the bean.
OrderCat	It allows to specify a vector with the order in which the categories are shown. If this argument is specified, the argument order is not taken into account.
LabelCat	It allows to specify a vector with the names of the categories.
XLAB	Legend of X axis.
YLAB	Legend of Y axis.
COLOR	Vector with the color of the categories or just one color for all categories.
LEGEND	It allows to include a legend to the graph.
MTEXT	It allows to add text on the margins of the graph.
TEXT	It allows to add text in any area of the inner part of the graph.
ResetPAR	If it is FALSE, the default condition of the function PAR is not placed and maintained those defined by the user in previous graphics.
PAR	It accesses the function PAR, allowing to modify different aspects of the graph.
BEANPLOT	It allows to specify the characteristics of the function beanplot of the beanplot package (Kampstra, 2008; Kampstra, 2015).
BOXPLOT	It allows to specify the characteristics of the function boxplot of graphics package.

Details

The CSV file required in the argument data has the following format: class, order, family, genus and species, along with the contribution of the environmental variables. This file may be obtained using ModestR (Garcia-Rosello et al., 2013; available at the web site using the following menu: Export/Export checked maps/To RWizard Applications/To SPEDInstab. The default name of this file obtained from ModestR is "Contribution.CSV".

FUNCTIONS

The beanplot is performed with the function beanplot of the beanplot package (Kampstra, 2008; Kampstra, 2015). The boxplot is performed with the function boxplot of graphics package.

EXAMPLE

In the example, it was estimated the relative contribution of some factors on the distribution of some freshwater species (Guisande et al., 2010; Pelayo-Villamil et al., 2015).

Value

A beanplot or boxplot is obtained.

References

Garcia-Rosello, E., Guisande, C., Gonzalez-Dacosta, J., Heine, J., Pelayo-Villamil, P., Manjarres-Hernandez, A., Vaamonde, A. & Granado-Lorencio, C. (2013) ModestR: a software tool for managing and analyzing species distribution map databases. Ecography, 36, 1202-1207.

Guisande, C., Manjarres-Hernandez, A., Pelayo-Villamil, P., Granado-Lorencio, C., Riveiro, I., Acuña, A., Prieto-Piraquive, E., Janeiro, E., Matias, J.M., Patti, C., Patti, B., Mazzola, S., Jimenez, S., Duque, V. & Salmeron, F. (2010) IPez: An expert system for the taxonomic identification of fishes based on machine learning techniques. Fisheries Research, 102, 240-247.

Kampstra, P (2008). Beanplot: A Boxplot Alternative for Visual Comparison of Distributions. Journal of Statistical Software, Code Snippets, 28: 1-9.

Kampstra, P (2015) Visualization via Beanplots (like Boxplot/Stripchart/Violin Plot). R package version 1.2. Available at: https://CRAN.R-project.org/package=beanplot.

Pelayo-Villamil, P., Guisande, C., Vari, R.P., Manjarres-Hernandez, A., Garcia-Rosello, E., Gonzalez-Dacosta, J. et al. (2015) Global diversity patterns of freshwater fishes - potential victims of their own success. Diversity and Distributions, 21, 345-356.

Examples

data(FishFC)

ContrBB(data=FishFC, vars=c("Altitude","Aspect","BIO1","BIO12", "BIO14","BIO15","BIO18",
"BIO19","BIO2","BIO3","BIO4","BIO8","Pop","TPP","Slope","TH24","VI"), graph="boxplot")

SPEDInstabR documentation built on Nov. 8, 2023, 1:09 a.m.