Data file, which it may be obtained using DataManager of ModestR http://www.ipez.es/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 (GarcÃa-Roselló et al., 2013; available at the web site http://www.ipez.es/ModestR 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).
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(SPEDInstabR)
Loading required package: beanplot
Loading required package: raster
Loading required package: sp
Loading required package: plotrix
Loading required package: TeachingDemos
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/SPEDInstabR/ContrBB.Rd_%03d_medium.png", width=480, height=480)
> ### Name: ContrBB
> ### Title: BEANPLOTS AND BOXPLOTS OF CONTRIBUTION OF FACTORS
> ### Aliases: ContrBB
> ### Keywords: ContrBB
>
> ### ** 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")
Error in dev.new() : no suitable unused file name for pdf()
Calls: ContrBB -> par -> resetPar -> dev.new
Execution halted