level.plot: Plot 2-dimensional data for visualizing distribution of...

In biomod2: Ensemble Platform for Species Distribution Modeling

Description

Enables to plot data with 2-dimensional geographical coordinates

Usage

level.plot( data.in, 
            XY,
            color.gradient = "red",
            cex = 1,
            level.range = c(min(data.in), max(data.in)),
            show.scale = TRUE,
            title = "level plot",
            SRC=FALSE,
            save.file="no",
            ImageSize="small",
            AddPresAbs=NULL,
            PresAbsSymbol=c(cex*0.8,16,4),
            ...)

Arguments

data.in	the data you want to visualize
XY	a 2 columns matrix of the same length as data.in giving the coordinates of the data points
color.gradient	available : red, grey and blue
cex	to change the point size : >1 will increase size, <1 will decrease it
level.range	the range of values for which you want the color gradient to be used, usefull to increase the resolution of the graph especially if you have extreme values (see examples section)
show.scale	a feature for just keeping the graph without the scale (if set to False)
title	the title wanted for the graph
SRC	if TRUE, the function recognizes the values as being 'Species Range Change' (see XXX) values and associates the appropriate colors to them
save.file	can be set to "pdf", "jpeg" or "tiff" to save the plot. Pdf options can be changed by setting the default values of pdf.options().
ImageSize	The image size for JPEG and TIFF files saved to disk. Available : 'small', 'standard' and 'large'
AddPresAbs	Optional: adds the presences and absences used for calibration to the plot. Data must be entered as a matrix/dataframe with 3 columns (in this order): X-coordinate, Y-coordinate, Presence(1) or Absence(0). X and Y coordinates must be in the same system as the plot.
PresAbsSymbol	Optional: a 3 element vector giving the symbols to be used by the AddPresAbs argument for plotting. The elements of the vector must be in this order: size of presence/absence symbols given as a multiplication factor of the 'cex' value entered in the function (e.g. a value of 0.5 means that the symbols will be drawn at a size = 0.5*cex value entered in the function), symbol (in PCH code) to be used for presences, symbol (in PCH code) to be used for absences. An example of input vector for this parameter is 'c(0.4,16,4)'
...	extra args

Author(s)

Bruno Lafourcade

See Also

multiple.plot

Examples

## Not run: 
# species occurrences
DataSpecies <- read.csv(system.file("external/species/mammals_table.csv",
                                    package="biomod2"), row.names = 1)

# the name of studied species
myRespName <- 'GuloGulo'

# the presence/absences data for our species 
myResp <- as.numeric(DataSpecies[,myRespName])

# the XY coordinates of species data
myRespXY <- DataSpecies[,c("X_WGS84","Y_WGS84")]


level.plot(data.in=myResp, XY=myRespXY)

## End(Not run)

Example output

Loading required package: sp
Loading required package: raster
Loading required package: parallel
Loading required package: reshape
Loading required package: ggplot2
biomod2 3.3-7 loaded.

Type browseVignettes(package='biomod2') to access directly biomod2 vignettes.
Warning message:
system call failed: Cannot allocate memory 

biomod2 documentation built on May 2, 2019, 5:08 p.m.