MapCell: Cell maps

In KnowBR: Discriminating Well Surveyed Spatial Units from Exhaustive Biodiversity Databases

Cell maps

Description

It allows to depict on a map any of the variables (records richness, observed richess, predicted richness, completeness and the slope) exported by the function KnowB using a CSV, RData or raster file, and with the spatial resolution (cell size) specified in the file.

Usage

MapCell(data, Area="World", minLon, maxLon, minLat, maxLat, colbg="#FFFFFF",
colcon="#C8C8C8", colf="black", pro=TRUE, inc=0.005, exclude=NULL,
colexc=NULL, colfexc="black", colscale=c("#C8FFFFFF","#64FFFFFF","#00FFFFFF","#64FF64FF",
"#C8FF00FF","#FFFF00FF","#FFC800FF","#FF6400FF","#FF0000FF"),
legend.pos="y", breaks=9, xl=0, xr=0, yb=0, yt=0, asp, lab=NULL, xlab="Longitude",
ylab="Latitude", main=NULL,cex.main=1.2, cex.lab=1, cex.axis=0.9, cex.legend=0.9,
family="sans", font.main=2, font.lab=1, font.axis=1, lwdP=0.6, lwdC=0.1, trans=c(1,1),
log=c(0,0), ndigits=0, ini=NULL, end=NULL, jpg=FALSE, filejpg="Map.jpg")

Arguments

data	A CSV or RData file exported by the function KnowB (see details) or an ESRI ASCII raster file with the variable (richness, records, etc.).
Area	Only if using RWizard. A character with the name of the administrative area or a vector with several administrative areas (countries, regions, etc.) or river basins. If it is "World" (default) the entire world is plotted. For using administrative areas or river basins, in addition to use RWizard, it is also necessary to replace data(adworld) by @_Build_AdWorld_ (see example 2).
minLon, maxLon	Optionally it is possible to define the minimum and maximum longitude.
minLat, maxLat	Optionally it is possible to define the minimum and maximum latitude.
colbg	Background color of the map (in some cases this is the sea).
colcon	Background color of the administrative areas.
colf	Color of administrative areas border.
pro	If it is TRUE an automatic calculation is made in order to correct the aspect ratio y/x along latitude.
inc	Adds some room along the map margins with the limits x and y thus not exactly the limits of the selected areas.
exclude	A character with the name of the administrative area or a vector with several administrative areas that may be plotted with a different color on the map (only if using RWizard).
colexc	Background color of areas selected in the argument exclude.
colfexc	Color of borders of the areas selected in the argument exclude.
colscale	Palette color.
legend.pos	Whether to have a horizontal "x" or vertical "y" color scale.
breaks	Number of breakpoints of the color legend.
xl,xr,yb,yt	The lower left and upper right coordinates of the color legend in user coordinates.
asp	The y/x aspect ratio.
lab	A numerical vector of the form c(x, y) which modifies the default way that axes are annotated. The values of x and y give the (approximate) number of tickmarks on the x and y axes.
xlab	A title for the X axis.
ylab	A title for the Y axis.
main	An overall title for the plot.
cex.main	The magnification to be used for main titles relative to the current setting of cex.
cex.lab	The magnification to be used for X and Y labels relative to the current setting of cex.
cex.axis	The magnification to be used for axis annotation relative to the current setting of cex.
cex.legend	The magnification to be used for the color scale relative to the current setting of cex.
family	The name of a font family for drawing text.
font.main	The font to be used for plot main titles.
font.lab	The font to be used for x and y labels.
font.axis	The font to be used for axis annotation.
lwdP	Line width of the plot.
lwdC	Line width of the borders.
trans	It is possible to multiply or divide the dataset by a value. For a vector with two values, the first may be 0 (divide) or 1 (multiply), and the second number is the value of the division or multiplication.
log	It is possible to apply a logarithmic transformation to the dataset. For a vector with two values, the first may be 0 (do not log transform) or 1 (log transformation), and the second number is the value to be added in case of log transformation.
ndigits	Number of decimals in legend of the color scale.
ini	Minimum to be considered in the color scale.
end	Maximum to be considered in the color scale.
jpg	If TRUE the plots are exported to jpg files instead of using the windows device.
filejpg	Name of the jpg file.

Details

It allows to depict on a map any of the files (CSV or RData) exported by the function KnowB: records, observed richness, completeness and slope.

FUNCTIONS

The function color.legend of the package plotrix (Lemon et al., 2014) is used for building the map.

Value

A map is obtained.

References

Lemon, J. (2006) Plotrix: a package in the red light district of R. R-News, 6(4):8-12.

Lemon, J., Bolker, B., Oom, S., Klein, E., Rowlingson, B., Wickham, H., Tyagi, A., Eterradossi, O., Grothendieck, G., Toews, M., Kane, J., Turner, R., Witthoft, C., Stander, J., Petzoldt, T., Duursma, R., Biancotto, E., Levy, O., Dutang, C., Solymos, P., Engelmann, R., Hecker, M., Steinbeck, F., Borchers, H., Singmann, H., Toal, T. & Ogle, D. (2015). Various plotting functions. R package version 3.6-1. Available at: https://CRAN.R-project.org/package=plotrix.

Examples

## Not run: 

#Example 1. Observed pecies richness of freshwater fishes around the world.

data(RFishes)
data(adworld)
MapCell(data=RFishes, main= "Species richness of freshwater fishes")



#Example 2. Only to be used with RWizard.

data(RFishes)
@_Build_AdWorld_
MapCell(data = RFishes , Area = c("Argentina", "Bolivia", "Brazil", "Chile",
"Colombia", "Ecuador", "French Guiana", "Guyana", "Paraguay", "Peru", "Suriname",
"Uruguay", "Venezuela","Panama","Nicaragua","Costa Rica"),
main = "Species richness of freshwater fishes in South America")

## End(Not run)

KnowBR documentation built on Oct. 7, 2023, 9:09 a.m.