Package ‘R2G2’
February 19, 2015
Type Package
Title Converting R CRAN outputs into Google Earth.
Version 1.0-2
Date 2012-03-09
Author Nils Arrigo
Maintainer Nils Arrigo <[email protected]>
Description Converting R CRAN outputs into Google Earth.
License LGPL
LazyLoad yes
NeedsCompilation no
Repository CRAN
Date/Publication 2013-04-23 21:26:15
R topics documented:
R2G2-package
Axis2GE . . .
curvy . . . . .
Dots2GE . . .
FancyPies . . .
GetEdges . . .
grid50 . . . . .
Hist2GE . . . .
Overlay2GE . .
Phylo2GE . . .
Pies2GE . . . .
Plots2GE . . .
PolyLines2GE .
Shapes2GE . .
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
Index
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
2
2
4
5
5
6
7
8
11
12
13
15
16
20
22
1
2
Axis2GE
R2G2-package
Converting R CRAN outputs into Google Earth.
Description
This package includes a set of functions for producing basic and complex representations into
Google Earth, via KML files.
Details
Package:
Type:
Version:
Date:
License:
LazyLoad:
R2G2
Package
1.0-1
2012-10-02
LGPL
yes
Basic features: functions to overlay R CRAN plots, dots, lines, custom and regular polygons into
Google Earth. Complex features: histograms, pie-charts, contour plots and phylogenies into Google
Earth.
## End-user functions: Phylo2GE - Producing 3D Phylogenies in Google Earth (requires ape and picante)
Hist2GE - Producing 3D histograms in Google Earth Pies2GE - Producing 3D pie-charts in Google Earth
PolyLines2GE - Producing 2D / 3D lines / polygons in Google Earth Shapes2GE - Producing 3D regular poly
Plots2GE - Georeferencing custom R plots into Google Earth Dots2GE - Automated placement of observation
Axis2GE - Automated placement of a Y-axis in Google Earth Overlay2GE - Automated placement of an overla
## Internal functions: curvy - Compute spherical coordinates of points along an arc
GetEdges - Compute the edges of any n-sided regular polygon on a sphere
FancyPies - Compute the edges of any regular n-sided figure in spherical coordinates and adds a pie cha
Author(s)
Nils Arrigo, [email protected] 2012 EEB, the University of Arizona, Tucson
Axis2GE
Adding a custom Y-axis in Google Earth.
Description
The function adds a Y-axis into Google Earth. Can be used to either generate a KML file or can be
embedded into other R2G2 functions.
Usage
Axis2GE(coords, maxVal, maxAlt = 1e5, lwd = 2, apnd = TRUE, goo = "testAxis.kml")
Axis2GE
3
Arguments
coords
Geographical position of the axis (latitude, longitude, in Decimal Degrees).
maxVal
The maximum value of the Y-axis (i.e. the largest observation).
maxAlt
The height (ceiling altitude) of the Y-axis into Google Earth (in meters).
lwd
Line widths used to draw the axis.
apnd
Should the Y-axis be appended to an existing KML that is under production
(append = TRUE, to be used if Axis2GE is embedded in another KML generating function, see details) or should it be saved in its own KML file (append =
FALSE)?
goo
To be provided if apnd = FALSE, name of the KML file to that will be saved
into the working directory (use getwd() to find it).
Details
If apnd == TRUE, Axis2GE will provide a list containing the style (bloc1) and data (bloc2) sections
of a standard KML file. These sections are then to be incorporated directly into the KML file being
generated.
Author(s)
Nils Arrigo, [email protected] 2012 EEB, the University of Arizona, Tucson
See Also
contourLines
Examples
# Producing an axis as an additional KML file
Axis2GE(coords = c(1,1),
maxVal = 6698,
maxAlt = 1e5,
lwd = 2,
apnd = FALSE,
goo = "Demo_Axis2GE.kml")
# Producing an axis, but storing the KML sections for later use
DemoAxis = Axis2GE(coords = c(1,1),
maxVal = 6698,
maxAlt = 1e5,
lwd = 2,
apnd = TRUE)
attributes(DemoAxis) #check out the contents of the obtained list
DemoAxis$bloc1 #get the styles section
DemoAxis$bloc2 #get the coordinates section
4
curvy
curvy
curvy - internal function to compute spherical coordinates of points
along an arc
Description
An arc is defined by startDD and stopDD, the coordinates of its limit points (decimal degrees). New
points are computed according to f, i.e. the fraction at which the desired point is located along the
arc (f varies between 0 -> startDD to 1 -> stopDD)
Usage
curvy(f, startDD, stopDD)
Arguments
f
Fraction of arc at which the desired point is located. f varies between 0 and 1,
to generate points located between startDD and stopDD)
startDD
Geographical location of starting point of the arc (longitutde, latitude in decimal
degrees).
stopDD
Geographical location of stoping point of the arc (longitutde, latitude in decimal
degrees).
Value
The geographical coordinates of the desired point (longitude, latitude in decimal degrees).
Author(s)
Nils Arrigo, [email protected] 2012 EEB, the University of Arizona, Tucson
References
The original function was actually proposed by Rod Page on http://iphylo.blogspot.com/
Examples
startDD = c(1, 5)
stopDD = c(5, 1)
curvy(0.5, startDD, stopDD)
Dots2GE
Dots2GE
5
Automated placement of observations, as dots, in Google Earth
Description
Produces KML files where observations are displayed as pushpins.
Usage
Dots2GE(coords, plnms, goo = "Dots2GE.kml")
Arguments
coords
An array of geographical positions of observations (lines = observation, columns
= lon & lat in decimal degrees).
plnms
Observations labels (text).
goo
Name of the KML file to that will be saved into the working directory (use
getwd() to find it).
Value
A KML file is produced in the current working directory.
Author(s)
Nils Arrigo, [email protected] 2012 EEB, the University of Arizona, Tucson
Examples
labels = c("A","B","C","D","E","F")
coords = cbind(1:6, 1:6)
Dots2GE(coords, labels, goo = "Dots2GE_V1.kml")
FancyPies
Computes the edges of any regular n-sided figure in spherical coordinates and adds a pie chart within it
Description
Provides coordinates for one pie chart, this function must be iterated to produce several pies.
Usage
FancyPies(center, obs, nedges = 3, radius = 5e4, orient = 0, diag = FALSE)
6
GetEdges
Arguments
center
The geographical position of the pie as c(lon, lat) in decimal degrees.
obs
Vector of numerical and non-negative quantities that will be displayed as the pie
slices (typically produced using table()).
nedges
The number of desired edges (3 -> triangle, 4 -> square, etc).
radius
The pie radius (in meters).
orient
The rotation factor of the fig (in degrees).
diag
Produce diagnostic plot for checking purposes (True or False).
Details
This function is wrapped within Pies2GE; see below.
Value
Provides an array of coordinates for drawing the pie chart as polygons (lines = points delimiting the
pie sectors, columns = sector number, lon, lat in decimal degrees).
Author(s)
Nils Arrigo, [email protected] 2012 EEB, the University of Arizona, Tucson
See Also
curvy GetEdges Pies2GE
GetEdges
Computing the edges of any n-sided regular polygon on a sphere
Description
Provides the edges coordinates for one n-sided regular polygon, corrected to account for the earth
curvature.
Usage
GetEdges(center, radius, nedges, orient = 45)
Arguments
center
The geographical position of the polygon as c(lon, lat) in decimal degrees.
radius
The polygon radius (in meters).
nedges
The number of edges (3 -> triangle, 4 -> square, etc).
orient
The rotation factor of the polygon (in degrees).
grid50
7
Details
Earth-curvature corrections are assuming a sphere, hence expect some deformations near to the
poles. In addition, polygons that overlap with the poles will have missing values (i.e. when center
coordinates + radius lead to overeach a pole).
Value
Provides an array of coordinates for the n-edges defining the desired polygon (lines = points delimiting the polygon, columns = lon, lat in decimal degrees).
Author(s)
Nils Arrigo, [email protected] 2012 EEB, the University of Arizona, Tucson
References
This function was retrieved as a PHP code from http://blog.thematicmapping.org/ This is an amazing blog; the R2G2 dvpt team thanks a lot Bjorn Sandvik for his outstanding implementations in
Google Earth, and for sharing his great ideas and resources. GetEdges is actually an R implementation of his material.
See Also
Hist2GE Pies2GE Shapes2GE curvy
grid50
Grids partitioning the surface of Earth into n equal areas.
Description
Sets of precomputed grids that partition the Earth’s surface into equal areas.
Usage
data(grid50)
Details
The available grids provide 50, 500, 5000, 10’000 and 20’000 equal area cells. The coordinates are
given in radians. They can be converted into lat / lon decimal degrees using the code provided as an
example.
Author(s)
Nils Arrigo, [email protected] 2012 EEB, the University of Arizona, Tucson
8
Hist2GE
References
http://eqsp.sourceforge.net/ https://etna.mcs.kent.edu/vol.25.2006/pp309-327.dir/pp309-327.html
Leopardi, P. "A partition of the unit sphere into regions of equal area and small diameter" (2006).
Electronic Transactions on Numerical Analysis 25:309-327.
Examples
#Converting grid50 (radians) to usual decimal degrees
data(grid50)
Rad2DD = function(lon, lat){
lonDD = 360 * round((lon / (2 * pi)), 5) - 180 + 0.01
latDD = 180 * round(lat / pi, 5) - 90 + 0.01
cbind(lonDD, latDD)
}
grid50DD = Rad2DD(grid50[,2], grid50[, 3])
grid50DD
#Converting decimal degrees to grid50 format (radians and properly centered)
DD2Rad = function(lon, lat){
lonrad = (lon + 180) * pi/180
latrad = (lat + 90) * pi/180
cbind(lonrad, latrad)
}
grid50Rad = DD2Rad(grid50DD[ ,1], grid50DD[ ,2])
grid50Rad = data.frame("1", grid50Rad) #this step is only cosmetic and necessary for compatibily issues.
grid50Rad
Hist2GE
Producing 3D histograms in Google Earth
Description
The current implementation produces Google Earth 3D histograms to i) count the number of distinct entities (e.g. species) per spatial unit (regional species diversity) or ii) count the number of
occurrences of each entity per spatial unit (regional species abundance, detailled for each species).
Usage
Hist2GE(coords, species = 0, grid, goo, nedges, orient, maxAlt = 1e+05, colors = "auto", ...)
Arguments
coords
An array of geographical positions of observations (lines = observation, columns
= lon & lat in Decimal Degrees).
species
A corresponding vector qualitatively describing each observation (typically the
taxonomic species identity).
Hist2GE
9
grid
The precomputed spatial grid to be used. Choose among grid50, grid500, grid5000,
grid10000 or grid20000 to get the needed number of points on the earth surface,
see examples below. Technically, any set of equally spaced points can be used
as long as the provided grid complies with the format used in ?grid50.
goo
Name of the KML file to that will be saved into the working directory (use
getwd() to find it).
nedges
The number of desired edges (3 -> triangle, 4 -> square, etc) for drawing the
histograms.
orient
The rotation factor of histograms (in degrees).
maxAlt
The maximum height (ceiling altitude) of the histograms.
colors
Vector of colors corresponding to each species (one color per species), must be
defined as hexadecimal values (as produced by usual R color palettes); leave to
"auto" to get rainbow colors.
...
Any additional arguments used internally.
Details
The computations are based on a set of precomputed grids, where each cells are equally spaced
and cover equal earth areas. The cell locations were obtained using the EQSP matlab library (Paul
Leopardi). Each observation is first assigned to its closest neighbouring cell, then Hist2GE outputs
cell-based statistics.
Value
Two KML files (regional species richness and detailled species abundance) are produced in the
current working directory. The function also outputs all these cell-based statistics as an array.
Author(s)
Nils Arrigo, [email protected] 2012 EEB, the University of Arizona, Tucson
See Also
Shapes2GE GetEdges grid50
Examples
###Using Hist2GE: the easy way
#Produce fake species occurrences
coords = cbind(rnorm(210, 6.32, 5), rnorm(210, 46.75, 5))
coords = coords[order(coords[,1]), ]
species = rep(c("sp1", "sp2", "sp3"), each = 70)
#Choose grid
data(grid10000) # choose among grid50, grid500, grid5000, grid1000, grid20000
grid = grid10000
Hist2GE(coords = coords,
species = species,
10
Hist2GE
grid = grid,
goo = "Jura",
nedges = 6,
orient = 45,
maxAlt = 1e5)
###Using Hist2GE: using custom grids, when working at local scale (not accounting for earth curvature)
#Produce fake species occurrences
coords = cbind(rnorm(210, -110.954795, 0.1), rnorm(210, 32.228724, 0.1))
coords = coords[order(coords[,1]), ]
species = rep(c("sp1", "sp2", "sp3"), 70)
#Define the resolution (cell width, decimal degrees)
cellwdth = 0.02
#And produce the desired grid automatically
lonrange = range(coords[, 1])
if(sum(sign(lonrange)) == -2){
lonwdth = -cellwdth
}else{
lonwdth = cellwdth
}
latrange = range(coords[, 2])
if(sum(sign(latrange)) == -2){
latwdth = -cellwdth
}else{
latwdth = cellwdth
}
lonLeft = lonrange[1] - 0.01 * lonrange[1]
lonRight = lonrange[2] + 0.01 * lonrange[2]
latBottom = latrange[1] - 0.01 * latrange[1]
latTop = latrange[2] + 0.01 * latrange[2]
#Produce cell coordinates along lon and lat axes
lonmarks = seq(lonLeft, lonRight, by = lonwdth)
latmarks = seq(latBottom, latTop, by = latwdth)
#Produce complete grid
lonDD = rep(lonmarks, length(latmarks))
latDD = rep(latmarks, each = length(lonmarks))
gridDD = cbind(lonDD, latDD)
#Convert it to radians centered and formated as in a "grid50" array
DD2Rad = function(lon, lat){
lonrad = (lon + 180) * pi/180
latrad = (lat + 90) * pi/180
cbind(lonrad, latrad)
}
MyGridDD = cbind(lonDD, latDD)
MyGridRad = DD2Rad(MyGridDD[, 1], MyGridDD[, 2])
Overlay2GE
11
MyGridRad = data.frame("Num" = 1:nrow(MyGridRad),
"lon" = MyGridRad[, 1],
"lat" = MyGridRad[, 2]) #this step is only cosmetic and necessary for compatibily issues.
#Run Hist2GE
Hist2GE(coords = coords,
species = species,
grid = MyGridRad,
goo = "Tucson",
nedges = 4,
orient = 45,
maxAlt = 5e3)
Overlay2GE
Automated placement of an overlayed image in Google Earth
Description
Produces a KML file from a set of coordinates (the NSEW limits of the image to overlay) and the
image name.
Usage
Overlay2GE(coords, image = "/home/Images/myimage.jpg", goo = "Overlay2GE.kml")
Arguments
coords
The image boundary coordinates (declared in decimal degrees with the following order: N, S, E and W)
image
The image name (if in working directory) or complete path of the image to map.
At least *.jpg and *.png are supported by Google Earth.
goo
Name of the KML file to that will be saved into the working directory (use
getwd() to find it).
Author(s)
Nils Arrigo, [email protected] 2012 EEB, the University of Arizona, Tucson
12
Phylo2GE
Phylo2GE
Producing 3D Phylogenies in Google Earth
Description
The function converts a phylogenetic tree and the corresponding geographical coordinates of its
taxa into a KML that can be displayed into Google Earth.
Usage
Phylo2GE(geo, phy, resol = 0.1, minAlt = 1e+04, maxAlt = 2e+06, goo = "Phylo2GE.kml")
Arguments
geo
Matrix of geographical centroids for each taxa. Lines = taxa, columns = species
name (as in phylogeny), lon and lat in decimal degrees.
phy
Phylogenetic tree, as imported using read.tree (ape).
resol
Drawing resolution of arcs in the phylogeny. Each horizontal arc will be divided
in 1/resol subarcs.
minAlt
Altitude of tips, as displayed in Google Earth (in meters).
maxAlt
Altitude of root ancestral node, as displayed in Google Earth (in meters).
goo
Name of the KML file to that will be saved into the working directory (use
getwd() to find it).
Details
Phylo2GE matches the phy and geo objects, according to taxa names. This matching cares for
differential sorting of the phy and geo objects. This property also allows focusing on tree subclades
without needing to update the geo array.
Value
A KML file is produced in the current working directory.
Author(s)
Nils Arrigo, [email protected] 2012 EEB, the University of Arizona, Tucson
References
KML conversions of phylogenies were first seen in Mesquite (http://mesquiteproject.org/mesquite/mesquite.html)
and on Rod Page’s blog http://iphylo.blogspot.com/
See Also
aggregate curvy
Pies2GE
13
Examples
#
#
#
#
#
#
#
uncomment to use
require(ape)
require(picante)
geo = data.frame(taxa = c("D", "E", "A", "B", "C", "F"),
lon = c(9.291113, 23.18146, 75.274541, -8.653739, 11.622450, 12.622450),
lat = c(8.774068, 4.581856, 48.078570, 10.966451, 28.722732, 29.722732))
geo
# phy = "(((B:0.41,C:0.31):0.65,(D:0.21,E:0.11):0.75):0.85,A:0.51);"
# phy = read.tree(text = phy)
# Phylo2GE(geo, phy, resol = .05, goo = 'Phylo2GE.kml')
Pies2GE
Producing 3D pie-charts in Google Earth
Description
This function produces Google Earth 3D pie charts from geographical locations and frequency
counts. The pie charts are displayed as regular n-sided polygons.
Usage
Pies2GE(center, obs, nesting = 0, goo = "Pies2GE.kml", colors = "auto", nedges = 20, orient = 0, maxAlt
Arguments
center
An array of geographical position for pies (lines = pies, columns = longitude
and latitude in decimal degrees).
obs
Array of numerical and non-negative quantities that will be displayed in each
the pie slices. This is is typically a pivot table with lines = pies and columns =
quantities to plot within pies.
nesting
Vector for grouping the pies / pie slices into handy folders / subfolders (optional). The groups must be designated as numbers. The default nesting (nesting
= 0) groups pie slices according to their color.
goo
Name of the KML file to that will be saved into the working directory (use
getwd() to find it).
colors
Vector of colors corresponding to each species (one color per species), must be
defined as hexadecimal values (as produced by usual R color palettes); leave to
"auto" to get rainbow colors.
nedges
The number of edges, defining the general shape of the pie (3 -> triangle, 4 ->
square, etc).
orient
the rotation factor of the pie-chart (in degrees).
maxAlt
the height (ceiling altitude) of the pies.
radius
The pie radius (in meters).
14
Pies2GE
Details
The shape parameters (nedges, orient, radius and maxAlt) can be either a single value, that will be
applied to all pies, or detailled values for each pie.
Value
A KML file is produced in the current working directory.
Author(s)
Nils Arrigo, [email protected] 2012 EEB, the University of Arizona, Tucson
See Also
curvy GetEdges FancyPies table aggregate
Examples
## Preparing fake matrix
center = cbind(1:6, 1:6)
obs = cbind(1:6, 6:1, 1:6) #actual observations to be plot as a pie chart
nesting = rep(1:3, each = 2)
## data to be pie-charted
fakedata = cbind(nesting, center, obs)
colnames(fakedata) = c("Group","Lon","Lat","Slice1","Slice2","Slice3")
fakedata
## Producing KML - group pie slices according to color
Pies2GE(center = fakedata[, 2:3],
obs = fakedata[, 4:ncol(fakedata)],
nesting = fakedata[, 1],
goo = "Pies2GE_V1.kml",
nedges = 20,
orient = 0,
maxAlt = 1e4,
radius = 5e4)
## Producing KML - as before but also tweeking the shape / radius / height and color of each pie
Pies2GE(center = fakedata[, 2:3],
obs = fakedata[, 4:ncol(fakedata)],
nesting = 0,
goo = "Pies2GE_V2.kml",
nedges = c(3, 3, 4, 4, 20, 20),
orient = 0,
colors = topo.colors(ncol(obs)),
maxAlt = c(3e4, 3e4, 5e4, 5e4, 1e5, 1e5),
radius = c(3e4, 3e4, 4e4, 4e4, 5e4, 5e4))
## Producing KML - group pies according to external information (experimental)
Pies2GE(center = fakedata[, 2:3],
obs = fakedata[, 4:ncol(fakedata)],
Plots2GE
15
nesting = fakedata[, 1],
goo = "Pies2GE_V1.kml",
nedges = 20,
orient = 0,
maxAlt = 1e4,
radius = 5e4)
Plots2GE
Georeferencing custom R plots into Google Earth
Description
Plots2GE: Places PNG R plots on Google Earth, as KML files.
Usage
Plots2GE(data, center, nesting = 0, customfun, goo = "Plots2GE.kml", testrun = FALSE)
Arguments
data
Dataset used for producing the plots (will be the input of your customfun, see
below).
center
Matrix including the longitude(s) and latitude(s) of point(s) where to locate plots
(decimal degrees). Must correspond to "data", with same number and ordering
of observations.
nesting
Location-specific identifier, used to group the data into location-specific subsets and produce location specific plots. Must correspond to "data", with same
number and ordering of observations.
customfun
User-defined function to produce the plots, see details.
goo
Name of the KML file to that will be saved into the working directory (use
getwd() to find it).
testrun
Diagnositc mode. T (will run only at the screen, for checking purposes) or F
(will produce actual plots as png files for Google Earth).
Details
The user needs to declare a function where the input is the "data" matrix, and the output is a plot.
Plots2GE will then apply this function to any location-specific subset (the locations being defined
using the "nesting" parameter). Any function is possible, just keep in mind that Plots2GE will apply
it in a location-specific way
Value
A KML file is produced in the current working directory.
16
PolyLines2GE
Author(s)
Nils Arrigo, [email protected] 2012 EEB, the University of Arizona, Tucson
See Also
par plot
Examples
## Preparing fake matrix
center = cbind(1:6, 1:6)
nesting = rep(1:3, each = 2)
fakeVar1 = rnorm(300, 0, 1)
fakeVar2 = rnorm(300, 0, 1)
fakematrix = data.frame(nesting, center, fakeVar1, fakeVar2)
fakematrix
## Preparing a user-defined function for producing the desired plots
myfun = function(input){
plot(input[, 4], input[, 5], xlab='Xlab label', ylab='Ylab label', type = 'n', bty = 'n')
points(input[, 4], input[, 5], col='red', pch = 16, cex = 2)
}
## Producing KML - the easy way
Plots2GE(data = fakematrix,
center = fakematrix[, 2:3],
nesting = fakematrix[, 1],
customfun = myfun,
goo = "Plots2GE_V1.kml",
testrun = FALSE)
PolyLines2GE
Producing 2D / 3D lines / polygons in Google Earth
Description
The function produces lines-based objects into Google Earth. This allows drawing open or closed
polygons with custom shapes. Many parameters allow a fine tuning of the rendered objects.
Usage
PolyLines2GE(coords, nesting = 0, maxAlt = 10000, goo = "Lines2GE.kml", colors = "blue", extrude = 0, f
PolyLines2GE
17
Arguments
coords
Array of geographical positions that define each line / polygon edges (latitude,
longitude, in Decimal Degrees). The coordinates must be provided following
counterclockwise order if you wish to draw closed polygons (this is actually
required by Google Earth, in order to obtain a proper colors rendering).
nesting
Vector for identifying distinct lines / polygons, must correspond to "coords" and
should be designated as numbers. The resulting lines / polygons are then stored
into distinct folders. If used, this option expects that one color is defined for
each nesting level (see color parameter below).
maxAlt
The height (ceiling altitude) of the lines / polygons (one maxAlt per line / polygon or one maxAlt for all lines / polygons). Note that point specific altitudes
can be declared (maxAlt then includes the altitudes of all points in "coords")
goo
Name of the KML file to that will be saved into the working directory (use
getwd() to find it).
colors
Vector of colors (if the nesting option is used, define one color per line / polygon;
if no nesting is specified, the same color is applied on all lines / polygons). Must
be defined as hexadecimal values (as produced by usual R color palettes); leave
to "auto" to get rainbow colors
extrude
3D rendering: 1 = extend polygon vertical faces to the ground, 0 = draw only
polygon.
fill
Polygon rendering: T = fill polygon with "colors", F = draw polygon as lines,
using "colors".
lwd
Lines rendering: line width (one width per line / polygon or one width for all
lines / polygons).
closepoly
Polygon rendering: T = will close all polygons, F = keeps open polygons.
Author(s)
Nils Arrigo, [email protected] 2012 EEB, the University of Arizona, Tucson
See Also
contourLines
Examples
###Drawing lines
###Drawing closed polygons
#Prepare fake data
pol1 = rbind(c(1,1,1e5), c(1,2,2e5), c(2,2,3e5), c(3,3,4e5))
pol2 = rbind(c(1,1,1e5), c(2,2,2e5), c(3,3,1e5), c(4,4,2e5))
coords = rbind(pol1, pol2)
nesting = rep(c(1,2), each = 4)
#data to be displayed
fakedata = cbind(nesting, coords)
18
PolyLines2GE
colnames(fakedata) = c("nesting", "Lon", "Lat", "Alt")
fakedata
#Producing KML - all points are at the same altitude
PolyLines2GE(coords = fakedata[, 2:3],
nesting = fakedata[, 1],
colors = "auto",
goo = "Lines2GE_V1a.kml",
maxAlt = 1e4,
fill = FALSE,
closepoly = FALSE,
lwd = 2,
extrude = 0)
#Producing KML - all points, from a same line share the same altitude
PolyLines2GE(coords = fakedata[, 2:3],
nesting = fakedata[, 1],
colors = "auto",
goo = "Lines2GE_V1b.kml",
maxAlt = c(1e4, 1e5),
fill = FALSE,
closepoly = FALSE,
lwd = 2,
extrude = 0)
#Producing KML - Each point has its own altitude
PolyLines2GE(coords = fakedata[, 2:3],
nesting = fakedata[, 1],
colors = "auto",
goo = "Lines2GE_V1c.kml",
maxAlt = fakedata[, 4],
fill = FALSE,
closepoly = FALSE,
lwd = 2,
extrude = 0)
###Drawing closed polygons
#Prepare fake data
pol1 = rbind(c(1,1), c(1,2), c(2,2), c(2,1))
pol2 = (2 * pol1) - 0.5
coords = rbind(pol1, pol2)
coords = coords[ nrow(coords) : 1,]
nesting = rep(c(1,2), each = 4)
#data to be displayed
fakedata = cbind(nesting, coords)
fakedata
#Producing KML - the easy way
PolyLines2GE
PolyLines2GE(coords = fakedata[, 2:3],
nesting = fakedata[, 1],
colors = "auto",
goo = "Poly2GE_V1.kml",
maxAlt = 0,
fill = FALSE,
closepoly = TRUE,
lwd = 2,
extrude = 0)
#Producing KML - the easy way, polygons at distinct heights
PolyLines2GE(coords = fakedata[, 2:3],
nesting = fakedata[, 1],
colors = "auto",
goo = "Poly2GE_V1b.kml",
maxAlt = c(1e4, 1e5),
fill = FALSE,
closepoly = TRUE,
lwd = 2,
extrude = 0)
#Producing KML - with filled polygon
PolyLines2GE(coords = fakedata[, 2:3],
nesting = fakedata[, 1],
colors = "auto",
goo = "Poly2GE_V2.kml",
maxAlt = 0,
fill = TRUE,
closepoly = TRUE,
lwd = 2,
extrude = 0)
#Producing KML - with polygon extruded from ground
PolyLines2GE(coords = fakedata[, 2:3],
nesting = fakedata[, 1],
colors = "auto",
goo = "Poly2GE_V3.kml",
maxAlt = c(1e4, 1e5),
fill = TRUE,
closepoly = TRUE,
lwd = 2,
extrude = 1)
###Drawing a contour plot using the PolyLines2GE function:
#Prepare data
data(volcano)
lat = seq(1, 6, length.out = nrow(volcano))
lon = seq(1, 6, length.out = ncol(volcano))
#Get contour lines
cont = contourLines(lat, lon, volcano, nlevels = 20)
19
20
Shapes2GE
#Convert them into Lines2GE input format
cont.data = NULL
for(i in 1:length(cont)){
subs = cont[[i]]
tmp = cbind(i, subs$x, subs$y)
cont.data = rbind(cont.data, tmp)
}
#Produce KML
PolyLines2GE(coords = cont.data[, 2:3],
nesting = cont.data[, 1],
colors = "auto",
goo = "Contour2GE_V1.kml",
maxAlt = seq(1e4, 1e5, length.out = length(cont)),
fill = FALSE,
closepoly = FALSE,
lwd = 2,
extrude = 0)
Shapes2GE
Producing 3D regular polygons in Google Earth
Description
This function produces 3D regular polygons in Google Earth.
Usage
Shapes2GE(center, nesting = 0, goo = "Shapes2GE.kml", nedges = 20, orient = 0, colors = "blue", maxAlt
Arguments
center
nesting
goo
nedges
orient
maxAlt
radius
colors
An array of geographical position for pies (lines = pies, columns = longitude
and latitude in decimal degrees).
Vector for grouping the shapes into handy folders / subfolders (optional). Must
correspond to "center" and the groups should be designated as numbers.
Name of the KML file to that will be saved into the working directory (use
getwd() to find it).
The number of edges, defining the general shape of the polygon (3 -> triangle,
4 -> square, etc).
the rotation factor of the pie-chart (in degrees).
the height (ceiling altitude) of the pies.
The pie radius (in meters).
Vector of colors (will correspond to nesting groups, so define one color per
group, and not one color per shape), must be defined as hexadecimal values (as
produced by usual R color palettes); leave to "auto" to get rainbow colors.
Shapes2GE
Value
A KML file is produced in the current working directory.
Author(s)
Nils Arrigo, [email protected] 2012 EEB, the University of Arizona, Tucson
See Also
GetEdges, Hist2GE, Pies2GE GetEdges Hist2GE Pies2GE
Examples
######Demo script
#Preparing fake matrix
center = cbind(1:6, 1:6)
nesting = rep(1:3, each = 2)
# data to be displayed
fakedata = cbind(nesting, center)
fakedata
#Producing KML - the easy way
Shapes2GE(center = fakedata[, 2:3],
nesting = 1,
colors = "#0000FFFF",
goo = "Shapes2GE_V1.kml",
nedges = 20,
orient = 0,
maxAlt = 1e4,
radius = 5e4)
#Producing KML - the very easy way
Shapes2GE(center = fakedata[, 2:3],
nesting = fakedata[, 1],
colors = "auto", #just define your groups and let it get the colors
goo = "Shapes2GE_V1b.kml",
nedges = 20,
orient = 0,
maxAlt = 1e4,
radius = 5e4)
#Producing KML - one param per shape
Shapes2GE(center = fakedata[, 2:3],
nesting = c(1, 1, 2, 3, 3, 3),
colors = c("#0F00FFFF","#00FF00FF","#FF0000FF"), #do it yourself
goo = "Shapes2GE_V2.kml",
nedges = c(3, 3, 4, 4, 5, 5),
orient = 0,
maxAlt = 1e4,
radius = 5e4)
21
Index
par, 16
Phylo2GE, 12
Pies2GE, 6, 7, 13, 21
plot, 16
Plots2GE, 15
PolyLines2GE, 16
∗Topic Google Earth
Dots2GE, 5
R2G2-package, 2
∗Topic arc
curvy, 4
∗Topic geographical
Phylo2GE, 12
∗Topic google earth
Hist2GE, 8
Phylo2GE, 12
∗Topic histogram
Hist2GE, 8
∗Topic midpoints
curvy, 4
∗Topic phylogeny
Phylo2GE, 12
∗Topic points
Dots2GE, 5
∗Topic three dimension
Phylo2GE, 12
R2G2 (R2G2-package), 2
R2G2-package, 2
Shapes2GE, 7, 9, 20
table, 14
aggregate, 12, 14
Axis2GE, 2
contourLines, 3, 17
curvy, 4, 6, 7, 12, 14
Dots2GE, 5
FancyPies, 5, 14
GetEdges, 6, 6, 9, 14, 21
grid10000 (grid50), 7
grid20000 (grid50), 7
grid50, 7, 9
grid500 (grid50), 7
grid5000 (grid50), 7
Hist2GE, 7, 8, 21
Overlay2GE, 11
22