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 (Garca-Rosell 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.