Niche {EnvNicheR}

Niche

Description

This function allows to show a plot overlying the niche of multiple species, so it is possible to determine the niche conditions which favor a higher species richness and, to create boxplots with the range of environmental variables and list of species in an area of the niche selected by the user.

Usage

Niche(data, variables, Level="NULL", Taxon="NULL", cor=TRUE, d.main=0.5,
xlab="Polar coordinate X in pixels",ylab="Polar coordinate Y in pixels",
cex.labS=1.5, font.lab=1, main="", colramp = IDPcolorRamp, cex.main = 2,
font.main=2, nlab.xaxis = 5, nlab.yaxis = 5, minL.axis = 3, las = 1,
border = FALSE, tcl = -0.3, boxplot=TRUE, outline=FALSE, color="NULL",
range = 1.5, width = NULL, varwidth = FALSE, plot = TRUE, 
pars = list(boxwex = 0.8, staplewex = 0.5, outwex = 0.5), cex.boxplot=1.5,
cex.labB=1.5, namesB, family="serif", line=1, file1 = "List of species.csv",
file2 = "Environmental variables.csv", file3 = "Polar coordinates.csv",
na = "NA", dec = ",", row.names = FALSE, fileEncoding = "")

Arguments

data

A CSV file obtained from ModestR (García-Roselló et al., 2013) with data which show the presence of the species and abiotic and/or biotic factors.

variables

Selection of the variables for the estimation of the niche.

Level

Taxonomic level to be selected, i.e., Class, Family, Order, or Genus.

Taxon

Name of the taxon or taxa selected within the level, i.e., name of the Order, Family, etc. Can be a vector, so several taxa.

cor

If TRUE the variables are ordered according to the correlation between them. Therefore, the next variable to another variable is the one that has a greater positive correlation.

d.main

Scatter plot. Vertical distance between upper border of scatter plots and the title line in multiples of title height.

xlab

Scatter plot. Label for x-axis.

ylab

Scatter plot. Label for y-axis.

cex.labS

Scatter plot. Magnification used for text in axis labels relative to the current setting of cex.

font.lab

Scatter plot. The font to be used for x and y labels.

main

Scatter plot. Title of the plot.

colramp

Scatter plot. Color ramp to encode the number of counts within a pixel.

cex.main

Scatter plot. Magnification used for title relative to the current setting of cex.

font.main

Scatter plot. The font to be used for plot main titles.

nlab.xaxis

Scatter plot. Approximate number of labels on x-axes.

nlab.yaxis

Scatter plot. Approximate number of labels on y-axes.

minL.axis

Scatter plot. The minimum length of the abbreviations of factor levels, used to label the axes ticks.

las

Scatter plot. Orientation of labels on axes.

border

Scatter plot. Logical. When TRUE, a border is drawn around the individual colors in the legend.

tcl

Scatter plot. The length of tick marks as a fraction of the height of a line of text. The default value is -0.5; setting tcl = NA sets tck = -0.01 which is S' default.

boxplot

If TRUE (the default) then a boxplot with the range of environmental variables in an area of the niche selected by the user is produced.

outline

Boxplot. If outline is not true, the outliers are not drawn (as points whereas S+ uses lines).

color

Boxplot. If col is non-null it is assumed to contain colors to be used to colour the bodies of the box plots.

range

Boxplot. This determines how far the plot whiskers extend out from the box. If the range is positive, the whiskers extend to the most extreme data point which is no more than range times the interquartile range from the box. A value of zero causes the whiskers to extend to the data extremes.

width

Boxplot. A vector giving the relative widths of the boxes making up the plot.

varwidth

Boxplot. If varwidth is TRUE, the boxes are drawn with widths proportional to the square-roots of the number of observations in the groups.

plot

Boxplot. If TRUE (the default) then a boxplot is produced. If not, the summaries which the boxplots are based on are returned.

pars

Boxplot. A list of (potentially many) more graphical parameters, e.g., boxwex or outpch; these are passed to bxp (if plot is true).

cex.boxplot

Boxplot. Magnification used for axis annotation.

cex.labB

Boxplot. Magnification used for group labels which will be printed under each boxplot.

namesB

Boxplot. Group labels which will be printed under each boxplot. It can be a character vector.

family

The name of a font family for drawing text.

line

mtext. On which margin line, starting at 0 counting outwards.

file1

CSV file. A character string naming the file of the list of species.

file2

CSV file. A character string naming the file with the summary of the environmental variables.

file3

CSV file. A character string naming the file with the summary of the polar coordinates.

na

CSV files. The string to use for missing values in the data.

dec

CSV files. The string to use for decimal points in numeric or complex columns: must be a single character.

row.names

CSV files. Either a logical value indicating whether the row names of x are to be written along with x, or a character vector of row names to be written.

fileEncoding

CSV files. Character string: if non-empty declares the encoding to be used on a file (not a connection) so the character data can be re-encoded as they are written.

Details

The first plot shows the polar coordinates using the environmental variables selected by the user in the CSV file obtained from ModestR (in the example BIO1, BIO3, BIO4 and BIO12 and altitude). In this first plot, a darker color of the square indicates a higher number of species in the cell. In this plot it is necessary to click four times with the mouse to select one or several cells.

The second plot shows a boxplot with the median and range of the environmental variables and/or latitude and longitude, in the cells selected with the mouse.

Value

A list of the species present in the cells selected by the user with the mouse, a summary of the environmental variables and the polar coordinates are saved in three CSV files.

Author(s)

Cástor Guisande González, Universidad de Vigo, Spain.

References

García-Roselló, E., Guisande, C., González-Dacosta, J., Heine, J., Pelayo-Villamil, P., Manjarrés-Hernández, A., Vaamonde, A. & Granado-Lorencio, C. (2013) ModestR: a software tool for managing and analyzing species distribution map databases. Ecography, 36, 1202-1207.

Hijmans, R.J., Cameron, S.E., Parra, J.L., Jones, P.G. and Jarvis, A. (2005)Very high resolution interpolated climate surfaces for global land areas. International Journal of Climatology, 25, 1965-1978.

IUCN (2012) The IUCN Red List of Threatened Species. Version 2012.2. https://www.iucnredlist.org. Downloaded on 17 October 2012.

Examples

data(Carnivores)

Niche(data=Carnivores, variables= c("Altitude", "BIO1", "BIO3",
"BIO4", "BIO12"), Level="Genus", Taxon= c("Leopardus", "Puma", "Panthera"),
cex.boxplot=1.7)

#Remove the data set
rm(Carnivores)