Plot 2-dimensional data for visualizing distribution of species or environment

Description

Enables to plot data with 2-dimensional geographical coordinates

Usage

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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

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## 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)

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