plotKML: Methods for plotting results of spatial analysis in Google...

In plotKML: Visualization of Spatial and Spatio-Temporal Objects in Google Earth

Description

The method writes inputs and outputs of spatial analysis (a list of point, gridded and/or polygon data usually) to KML and opens the KML file in Google Earth (or any other default package used to view KML/KMZ files).

Usage

## S4 method for signature 'sf'
plotKML(obj, 
      folder.name = normalizeFilename(deparse(substitute(obj, env = parent.frame()))),
      file.name = paste(folder.name, ".kml", sep=""), 
      metadata = NULL, kmz = get("kmz", envir = plotKML.opts), open.kml = TRUE, ...)
## S4 method for signature 'SpatialPointsDataFrame'
plotKML(obj, 
      folder.name = normalizeFilename(deparse(substitute(obj, env = parent.frame()))),
      file.name = paste(folder.name, ".kml", sep=""), 
      size, colour, points_names, 
      shape = "http://maps.google.com/mapfiles/kml/pal2/icon18.png", 
      metadata = NULL, kmz = get("kmz", envir = plotKML.opts), open.kml = TRUE, ...)
## S4 method for signature 'SpatialLinesDataFrame'
plotKML(obj, 
      folder.name = normalizeFilename(deparse(substitute(obj, env = parent.frame()))), 
      file.name = paste(folder.name, ".kml", sep=""),
      metadata = NULL, kmz = get("kmz", envir = plotKML.opts), open.kml = TRUE, ...)
## S4 method for signature 'SpatialPolygonsDataFrame'
plotKML(obj, 
      folder.name = normalizeFilename(deparse(substitute(obj, env = parent.frame()))), 
      file.name = paste(folder.name, ".kml", sep=""), 
      colour, plot.labpt, labels, metadata = NULL, 
      kmz = get("kmz", envir = plotKML.opts), open.kml = TRUE, ...)
## S4 method for signature 'SpatialPixelsDataFrame'
plotKML(obj, 
      folder.name = normalizeFilename(deparse(substitute(obj, env = parent.frame()))), 
      file.name = paste(folder.name, ".kml", sep=""), 
      colour, raster_name, metadata = NULL, kmz = FALSE, open.kml = TRUE, ...)
## S4 method for signature 'SpatialGridDataFrame'
plotKML(obj, 
      folder.name = normalizeFilename(deparse(substitute(obj, env = parent.frame()))), 
      file.name = paste(folder.name, ".kml", sep=""), 
      colour, raster_name, metadata = NULL, kmz = FALSE, open.kml = TRUE, ...)
## S4 method for signature 'RasterLayer'
plotKML(obj, 
      folder.name = normalizeFilename(deparse(substitute(obj, env = parent.frame()))), 
      file.name = paste(folder.name, ".kml", sep=""), 
      colour, raster_name, metadata = NULL, kmz = FALSE, open.kml = TRUE, ...)
## S4 method for signature 'SpatialPhotoOverlay'
plotKML(obj, 
      folder.name = normalizeFilename(deparse(substitute(obj, env = parent.frame()))), 
      file.name = paste(folder.name, ".kml", sep=""), 
      dae.name, kmz = get("kmz", envir = plotKML.opts), open.kml = TRUE, ...)
## S4 method for signature 'SoilProfileCollection'
plotKML(obj, 
      folder.name = normalizeFilename(deparse(substitute(obj, env = parent.frame()))), 
      file.name = paste(folder.name, ".kml", sep=""), 
      var.name, metadata = NULL, kmz = get("kmz", envir = plotKML.opts), 
      open.kml = TRUE, ...)
## S4 method for signature 'STIDF'
plotKML(obj, 
      folder.name = normalizeFilename(deparse(substitute(obj, env = parent.frame()))), 
      file.name = paste(folder.name, ".kml", sep=""), 
      colour, shape = "http://maps.google.com/mapfiles/kml/pal2/icon18.png", 
      points_names, kmz = get("kmz", envir = plotKML.opts), open.kml = TRUE, ...)
## S4 method for signature 'STFDF'
plotKML(obj, ...)
## S4 method for signature 'STSDF'
plotKML(obj, ...)
## S4 method for signature 'STTDF'
plotKML(obj, 
      folder.name = normalizeFilename(deparse(substitute(obj, env = parent.frame()))), 
      file.name = paste(folder.name, ".kml", sep=""), 
      colour, start.icon = "http://maps.google.com/mapfiles/kml/pal2/icon18.png", 
      kmz = get("kmz", envir = plotKML.opts), open.kml = TRUE, ...)
## S4 method for signature 'RasterBrickTimeSeries'
plotKML(obj, 
      folder.name = normalizeFilename(deparse(substitute(obj, env = parent.frame()))), 
      file.name = paste(folder.name, ".kml", sep=""),
      pngwidth = 680, pngheight = 180, pngpointsize = 14, 
      kmz = get("kmz", envir = plotKML.opts), open.kml = TRUE, ...)
## S4 method for signature 'RasterBrickSimulations'
plotKML(obj, 
      folder.name = normalizeFilename(deparse(substitute(obj, env = parent.frame()))), 
      file.name = paste(folder.name, ".kml", sep=""), 
      obj.summary = TRUE,
      pngwidth = 680, pngheight = 200, pngpointsize = 14, 
      kmz = get("kmz", envir = plotKML.opts), open.kml = TRUE, ...)
## S4 method for signature 'SpatialMaxEntOutput'
plotKML(obj, 
      folder.name = normalizeFilename(deparse(substitute(obj, env = parent.frame()))), 
      file.name = paste(folder.name, ".kml", sep=""), 
      html.file = obj@maxent@html, 
      iframe.width = 800, iframe.height = 800, pngwidth = 280, 
      pngheight = 280, pngpointsize = 14, colour, 
      shape = "http://plotkml.r-forge.r-project.org/icon17.png", 
      kmz = get("kmz", envir = plotKML.opts), open.kml = TRUE, 
      TimeSpan.begin = [e-mail], TimeSpan.end = [e-mail], ...)
## S4 method for signature 'SpatialPredictions'
plotKML(obj, 
      folder.name = normalizeFilename(deparse(substitute(obj, env = parent.frame()))), 
      file.name = paste(folder.name, ".kml", sep=""), colour, 
      grid2poly = FALSE, obj.summary = FALSE, plot.svar = FALSE, 
      pngwidth = 210, pngheight = 580, pngpointsize = 14, 
      metadata = NULL, kmz = get("kmz", envir = plotKML.opts), open.kml = TRUE, ...)
## S4 method for signature 'SpatialSamplingPattern'
plotKML(obj, 
      folder.name = normalizeFilename(deparse(substitute(obj, env = parent.frame()))), 
      file.name = paste(folder.name, ".kml", sep=""),
      colour, kmz = get("kmz", envir = plotKML.opts), open.kml = TRUE, ...)
## S4 method for signature 'SpatialVectorsSimulations'
plotKML(obj, 
      folder.name = normalizeFilename(deparse(substitute(obj, env = parent.frame()))), 
      file.name = paste(folder.name, ".kml", sep=""), colour, 
      grid2poly = FALSE, obj.summary = TRUE, plot.svar = FALSE, 
      kmz = get("kmz", envir = plotKML.opts), open.kml = TRUE, ...)
## S4 method for signature 'list'
plotKML(obj, 
      folder.name = normalizeFilename(deparse(substitute(obj, env=parent.frame()))),
      file.name = paste(folder.name, ".kml", sep=""), 
      size = NULL, colour, points_names = "",
      shape = "http://maps.google.com/mapfiles/kml/pal2/icon18.png",
      plot.labpt = TRUE, labels = "", metadata = NULL, 
      kmz = get("kmz", envir = plotKML.opts), open.kml = TRUE, ...)

Arguments

obj	input object of specific class; either some sf, or sp, or raster or spacetime package class object, or plotKML composite objects containing both inputs and outputs of analysis
folder.name	character; folder name in the KML file
file.name	character; output KML file name
size	for point objects for plotting (see aesthetics)
colour	colour variable for plotting (see aesthetics)
points_names	vector of characters that can be used as labels
shape	character; icons used for plotting (see aesthetics)
raster_name	(optional) specify the output file name (PNG)
var.name	target variable name (only valid for visualization of "SoilProfileCollection" class data
metadata	(optional) the metadata object
plot.labpt	logical; specifies whether to plot centroids for polygon data
labels	character vector; list of labels that will attached to the centroids
start.icon	icon for the start position (for trajectory data)
dae.name	output DAE file name
html.file	specify the location of the html file containing report data (if the input object is of class "SpatialMaxEntOutput")
iframe.width	integer; width of the screen for iframe
iframe.height	integer; height of the screen for iframe
TimeSpan.begin	object of class "POSIXct"; begin of the sampling period
TimeSpan.end	object of class "POSIXct"; end of the sampling period
pngwidth	integer; width of the PNG plot (screen image)
pngheight	integer; height of the PNG plot (screen image)
pngpointsize	integer; text size in the PNG plot (screen image)
grid2poly	logical; specifies whether to convert gridded object to polygons
obj.summary	logical; specifies whether to print the object summary
plot.svar	logical; specifies whether to plot the model uncertainty
kmz	logical; specifies whether to compress the output KML file
open.kml	logical; specifies whether to directly open the output KML file (i.e. in Google Earth)
...	(optional) arguments passed to the lower level functions

Details

This is a generic function to plot various spatial and spatio-temporal R objects that contain both inputs and outputs of spatial analysis. The resulting plots (referred to as ‘views’) are expected to be cartographically complete as they should contain legends, and data and model descriptions. In principle, plotKML works with both simple spatial objects, and complex objects such as "SpatialPredictions", "SpatialVectorsSimulations", "RasterBrickSimulations", "RasterBrickTimeSeries", "SpatialMaxEntOutput" and similar. To further customize visualizations consider combining the lower level functions kml_open, kml_close, kml_compress, kml_screen into your own plotKML() method.

All ST-classes are coerced to the STIDF format and hence use the plotKML method for STIDFs. The sf objects are processed according to the class of the geometry column. The aestethics are defined in the same way as for their sp counterparts.

Note

To prepare a list of objects of class "SpatialPointsDataFrame", "SpatialLinesDataFrame", "SpatialPolygonsDataFrame", or "SpatialPixelsDataFrame" consider using the landmap::tile function. Writting large spatial objects via plotKML can be time consuming. Please refer to the package manual for more information.

See Also

SpatialPredictions-class, SpatialVectorsSimulations-class, RasterBrickSimulations-class, RasterBrickTimeSeries-class, SpatialMaxEntOutput-class, SpatialSamplingPattern-class

Examples

plotKML.env(kmz = FALSE)
## -------------- SpatialPointsDataFrame --------- ##
library(sp)
library(rgdal)
data(eberg)
coordinates(eberg) <- ~X+Y
proj4string(eberg) <- CRS("+init=epsg:31467")
## subset to 20 percent:
eberg <- eberg[runif(nrow(eberg))<.1,]
## Not run: ## bubble type plot:
plotKML(eberg["CLYMHT_A"])
plotKML(eberg["CLYMHT_A"], colour_scale=rep("#FFFF00", 2), points_names="")

## End(Not run)
## plot points with a legend:
shape = "http://maps.google.com/mapfiles/kml/pal2/icon18.png" 
kml.file = paste0(tempdir(), "/eberg_CLYMHT_A.kml")
leg.file = paste0(dirname(kml.file), "/kml_legend.png")
kml_open(kml.file)
kml_layer(eberg["CLYMHT_A"], colour=CLYMHT_A, z.lim=c(20,60),
          colour_scale=SAGA_pal[[1]], shape=shape, points_names="")
kml_legend.bar(x=eberg$CLYMHT_A, 
               legend.file=leg.file,
               legend.pal=SAGA_pal[[1]], z.lim=c(20,60))
kml_screen(image.file=leg.file)
kml_close(kml.file)

## ----- sf objects with sfc_POINT geometry ----- ##
eberg_sf <- sf::st_as_sf(eberg)
## Not run: 
plotKML(eberg_sf["CLYMHT_A"])
plotKML(eberg_sf["CLYMHT_A"], colour_scale = rep("#FFFF00", 2), points_names = "")

## End(Not run)

## -------------- SpatialLinesDataFrame --------- ##
data(eberg_contours)
## Not run: 
plotKML(eberg_contours)
## plot contour lines with actual altitudes:
plotKML(eberg_contours, colour=Z, altitude=Z)

## End(Not run)

## ---- sf objects with sfc_LINESTRING geometry ---- ##
eberg_contours_sf <- sf::st_as_sf(eberg_contours)
## Not run: 
plotKML(eberg_contours_sf)
plotKML(eberg_contours_sf, colour = Z, altitude = Z)

## End(Not run)

## -------------- SpatialPolygonsDataFrame --------- ##
data(eberg_zones)
## Not run: 
plotKML(eberg_zones["ZONES"])
## add altitude:
zmin = 230
plotKML(eberg_zones["ZONES"], altitude=zmin+runif(length(eberg_zones))*500)

## End(Not run)

## ------ sf objects with sfc_POLYGON geometry ------ ##
eberg_zones_sf <- sf::st_as_sf(eberg_zones)
## Not run: 
plotKML(eberg_zones_sf["ZONES"])
plotKML(eberg_zones_sf["ZONES"], altitude = zmin + runif(length(eberg_zones)) * 500)

## End(Not run)

## -------------- SpatialPixelsDataFrame --------- ##
library(rgdal)
library(raster)
data(eberg_grid)
gridded(eberg_grid) <- ~x+y
proj4string(eberg_grid) <- CRS("+init=epsg:31467")
TWI <- reproject(eberg_grid["TWISRT6"])
data(SAGA_pal)
## Not run: ## set limits manually (increase resolution):
plotKML(TWI, colour_scale = SAGA_pal[[1]])
plotKML(TWI, z.lim=c(12,20), colour_scale = SAGA_pal[[1]])

## End(Not run)
## categorical data:
eberg_grid$LNCCOR6 <- as.factor(paste(eberg_grid$LNCCOR6))
levels(eberg_grid$LNCCOR6)
data(worldgrids_pal)
## attr(worldgrids_pal["corine2k"][[1]], "names")
pal = as.character(worldgrids_pal["corine2k"][[1]][c(1,11,13,14,16,17,18)])
LNCCOR6 <- reproject(eberg_grid["LNCCOR6"])
## Not run: 
plotKML(LNCCOR6, colour_scale=pal)

## End(Not run)

## -------------- SpatialPhotoOverlay --------- ##
## Not run: 
library(RCurl)
imagename = "Soil_monolith.jpg"
urlExists = url.exists("https://commons.wikimedia.org")
if(urlExists){
  x1 <- getWikiMedia.ImageInfo(imagename)
  sm <- spPhoto(filename = x1$url$url, exif.info = x1$metadata)
  # str(sm)
  plotKML(sm)
}

## End(Not run)

## -------------- SoilProfileCollection --------- ##
library(aqp)
library(plyr)
## sample profile from Nigeria:
lon = 3.90; lat = 7.50; id = "ISRIC:NG0017"; FAO1988 = "LXp" 
top = c(0, 18, 36, 65, 87, 127) 
bottom = c(18, 36, 65, 87, 127, 181)
ORCDRC = c(18.4, 4.4, 3.6, 3.6, 3.2, 1.2)
hue = c("7.5YR", "7.5YR", "2.5YR", "5YR", "5YR", "10YR")
value = c(3, 4, 5, 5, 5, 7); chroma = c(2, 4, 6, 8, 4, 3)
## prepare a SoilProfileCollection:
prof1 <- join(data.frame(id, top, bottom, ORCDRC, hue, value, chroma), 
   data.frame(id, lon, lat, FAO1988), type='inner')
prof1$soil_color <- with(prof1, munsell2rgb(hue, value, chroma))
depths(prof1) <- id ~ top + bottom
site(prof1) <- ~ lon + lat + FAO1988 
coordinates(prof1) <- ~ lon + lat
proj4string(prof1) <- CRS("+proj=longlat +datum=WGS84")
prof1
## Not run: 
plotKML(prof1, var.name="ORCDRC", color.name="soil_color")

## End(Not run)

## -------------- STIDF --------- ##
library(sp)
library(spacetime)
## daily temperatures for Croatia:
data(HRtemp08)
## format the time column:
HRtemp08$ctime <- as.POSIXct(HRtemp08$DATE, format="%Y-%m-%dT%H:%M:%SZ")
## create a STIDF object:
sp <- SpatialPoints(HRtemp08[,c("Lon","Lat")])
proj4string(sp) <- CRS("+proj=longlat +datum=WGS84")
HRtemp08.st <- STIDF(sp, time = HRtemp08$ctime, data = HRtemp08[,c("NAME","TEMP")])
## subset to first 500 records:
HRtemp08_jan <- HRtemp08.st[1:500]
str(HRtemp08_jan)
## Not run: 
plotKML(HRtemp08_jan[,,"TEMP"], LabelScale = .4)

## End(Not run)

## foot-and-mouth disease data:
data(fmd)
fmd0  <- data.frame(fmd)
coordinates(fmd0) <- c("X", "Y")
proj4string(fmd0) <- CRS("+init=epsg:27700")
fmd_sp <- as(fmd0, "SpatialPoints")
dates <- as.Date("2001-02-18")+fmd0$ReportedDay
library(spacetime)
fmd_ST <- STIDF(fmd_sp, dates, data.frame(ReportedDay=fmd0$ReportedDay))
data(SAGA_pal)
## Not run: 
plotKML(fmd_ST, colour_scale=SAGA_pal[[1]])

## End(Not run)

## -------------- STFDF --------- ##

## Not run: 
## results of krigeST:
library(gstat)
library(sp)
library(spacetime)
library(raster)
## define space-time variogram
sumMetricVgm <- vgmST("sumMetric",
                      space=vgm( 4.4, "Lin", 196.6,  3),
                      time =vgm( 2.2, "Lin",   1.1,  2),
                      joint=vgm(34.6, "Exp", 136.6, 12),
                      stAni=51.7)
## example from the gstat package:
data(air)
rural = STFDF(stations, dates, data.frame(PM10 = as.vector(air)))
rr <- rural[,"2005-06-01/2005-06-03"]
rr <- as(rr,"STSDF")
x1 <- seq(from=6,to=15,by=1)
x2 <- seq(from=48,to=55,by=1)
DE_gridded <- SpatialPoints(cbind(rep(x1,length(x2)), rep(x2,each=length(x1))), 
                           proj4string=CRS(proj4string(rr@sp)))
gridded(DE_gridded) <- TRUE
DE_pred <- STF(sp=as(DE_gridded,"SpatialPoints"), time=rr@time)
DE_kriged <- krigeST(PM10~1, data=rr, newdata=DE_pred,
                     modelList=sumMetricVgm)
gridded(DE_kriged@sp) <- TRUE
#stplot(DE_kriged)
## plot in Google Earth:
z.lim = range(DE_kriged@data, na.rm=TRUE)
plotKML(DE_kriged, z.lim=z.lim)
## add observations points:
plotKML(rr, z.lim=z.lim)

## End(Not run)

## -------------- STTDF --------- ##
## Not run: 
library(fossil)
library(spacetime)
library(adehabitatLT)
data(gpxbtour)
## format the time column:
gpxbtour$ctime <- as.POSIXct(gpxbtour$time, format="%Y-%m-%dT%H:%M:%SZ")
coordinates(gpxbtour) <- ~lon+lat
proj4string(gpxbtour) <- CRS("+proj=longlat +datum=WGS84")
xy <- as.list(data.frame(t(coordinates(gpxbtour))))
gpxbtour$dist.km <- sapply(xy, function(x) { 
  deg.dist(long1=x[1], lat1=x[2], long2=xy[[1]][1], lat2=xy[[1]][2]) 
} )
## convert to a STTDF class:
gpx.ltraj <- as.ltraj(coordinates(gpxbtour), gpxbtour$ctime, id = "th")
gpx.st <- as(gpx.ltraj, "STTDF")
gpx.st$speed <- gpxbtour$speed
gpx.st@sp@proj4string <- CRS("+proj=longlat +datum=WGS84")
str(gpx.st)
plotKML(gpx.st, colour="speed")

## End(Not run)

## -------------- Spatial Metadata --------- ##
## Not run: 
eberg.md <- spMetadata(eberg, xml.file=system.file("eberg.xml", package="plotKML"),
  Target_variable="SNDMHT_A", Citation_title="Ebergotzen profiles")
plotKML(eberg[1:100,"CLYMHT_A"], metadata=eberg.md)

## End(Not run)

## -------------- RasterBrickTimeSeries --------- ##
library(raster)
library(sp)
data(LST)
gridded(LST) <- ~lon+lat
proj4string(LST) <- CRS("+proj=longlat +datum=WGS84")
dates <- sapply(strsplit(names(LST), "LST"), function(x){x[[2]]})
datesf <- format(as.Date(dates, "%Y_%m_%d"), "%Y-%m-%dT%H:%M:%SZ")
## begin / end dates +/- 4 days:
TimeSpan.begin = as.POSIXct(unclass(as.POSIXct(datesf))-4*24*60*60, origin="1970-01-01") 
TimeSpan.end = as.POSIXct(unclass(as.POSIXct(datesf))+4*24*60*60, origin="1970-01-01")
## pick climatic stations in the area:
pnts <- HRtemp08[which(HRtemp08$NAME=="Pazin")[1],]
pnts <- rbind(pnts, HRtemp08[which(HRtemp08$NAME=="Crni Lug - NP Risnjak")[1],])
pnts <- rbind(pnts, HRtemp08[which(HRtemp08$NAME=="Cres")[1],])
coordinates(pnts) <- ~Lon + Lat
proj4string(pnts) <- CRS("+proj=longlat +datum=WGS84")
## get the dates from the file names:
LST_ll <- brick(LST[1:5])
LST_ll@title = "Time series of MODIS Land Surface Temperature images"
LST.ts <- new("RasterBrickTimeSeries", variable = "LST", sampled = pnts, 
    rasters = LST_ll, TimeSpan.begin = TimeSpan.begin[1:5], 
    TimeSpan.end = TimeSpan.end[1:5])
data(SAGA_pal)
## Not run: ## plot MODIS images in Google Earth:
plotKML(LST.ts, colour_scale=SAGA_pal[[1]])

## End(Not run)

## -------------- Spatial Predictions --------- ##
library(sp)
library(rgdal)
library(gstat)
data(meuse)
coordinates(meuse) <- ~x+y
proj4string(meuse) <- CRS("+init=epsg:28992")
## load grids:
data(meuse.grid)
gridded(meuse.grid) <- ~x+y
proj4string(meuse.grid) <- CRS("+init=epsg:28992")
## Not run: ## fit a model:
library(landmap)
omm <- fit.gstatModel(observations = meuse, formulaString = om~dist, 
   family = gaussian(log), covariates = meuse.grid)
## produce SpatialPredictions:
om.rk <- predict(omm, predictionLocations = meuse.grid)
## plot the whole geostatical mapping project in Google Earth:
plotKML(om.rk, colour_scale = SAGA_pal[[1]])
## plot each cell as polygon:
plotKML(om.rk, colour_scale = SAGA_pal[[1]], grid2poly = TRUE)

## End(Not run)

## -------------- RasterBrickSimulations --------- ##
## Not run: 
library(sp)
library(gstat)
data(barxyz)
## define the projection system:
prj = "+proj=tmerc +lat_0=0 +lon_0=18 +k=0.9999 +x_0=6500000 +y_0=0 
  +ellps=bessel +units=m 
  +towgs84=550.499,164.116,475.142,5.80967,2.07902,-11.62386,0.99999445824"
coordinates(barxyz) <- ~x+y
proj4string(barxyz) <- CRS(prj)
data(bargrid)
coordinates(bargrid) <- ~x+y
gridded(bargrid) <- TRUE
proj4string(bargrid) <- CRS(prj)
## fit a variogram and generate simulations:
Z.ovgm <- vgm(psill=1352, model="Mat", range=650, nugget=0, kappa=1.2)
sel <- runif(length(barxyz$Z))<.2  
## Note: this operation can be time consuming
sims <- krige(Z~1, barxyz[sel,], bargrid, model=Z.ovgm, nmax=20, 
   nsim=10, debug.level=-1)
## specify the cross-section:
t1 <- Line(matrix(c(bargrid@bbox[1,1], bargrid@bbox[1,2], 5073012, 5073012), ncol=2))
transect <- SpatialLines(list(Lines(list(t1), ID="t")), CRS(prj))
## glue to a RasterBrickSimulations object:
library(raster)
bardem_sims <- new("RasterBrickSimulations", variable = "elevations", 
  sampled = transect, realizations = brick(sims))
## plot the whole project and open in Google Earth:
data(R_pal)
plotKML(bardem_sims, colour_scale = R_pal[[4]])

## End(Not run)

## -------------- SpatialVectorsSimulations --------- ##
## Not run: 
data(barstr)
data(bargrid)
library(sp)
coordinates(bargrid) <- ~ x+y
gridded(bargrid) <- TRUE
## output topology:
cell.size = bargrid@grid@cellsize[1]
bbox = bargrid@bbox
nrows = round(abs(diff(bbox[1,])/cell.size), 0) 
ncols = round(abs(diff(bbox[2,])/cell.size), 0)
gridT = GridTopology(cellcentre.offset=bbox[,1], 
  cellsize=c(cell.size,cell.size), 
  cells.dim=c(nrows, ncols))
bar_sum <- count.GridTopology(gridT, vectL=barstr[1:5])
## NOTE: this operation can be time consuming!
## plot the whole project and open in Google Earth:
plotKML(bar_sum)

## End(Not run)

## -------------- SpatialMaxEntOutput --------- ##
## Not run: 
library(maptools)
library(rgdal)
data(bigfoot)
aea.prj <- "+proj=aea +lat_1=29.5 +lat_2=45.5 +lat_0=23 +lon_0=-96 
   +x_0=0 +y_0=0 +ellps=GRS80 +datum=NAD83 +units=m +no_defs"
data(USAWgrids)
gridded(USAWgrids) <- ~s1+s2
proj4string(USAWgrids) <- CRS(aea.prj)
bbox <- spTransform(USAWgrids, CRS("+proj=longlat +datum=WGS84"))@bbox
sel = bigfoot$Lon > bbox[1,1] & bigfoot$Lon < bbox[1,2] &
    bigfoot$Lat > bbox[2,1] & bigfoot$Lat < bbox[2,2]
bigfoot <- bigfoot[sel,]
coordinates(bigfoot) <- ~Lon+Lat
proj4string(bigfoot) <- CRS("+proj=longlat +datum=WGS84")
library(spatstat)
bigfoot.aea <- as.ppp(spTransform(bigfoot, CRS(aea.prj)))
## Load the covariates:
sel.grids <- c("globedem","nlights03","sdroads","gcarb","twi","globcov")
library(landmap)
library(dismo)
## run MaxEnt analysis:
jar <- paste(system.file(package="dismo"), "/java/maxent.jar", sep='')
if(file.exists(jar)){
  bigfoot.smo <- MaxEnt(bigfoot.aea, USAWgrids[sel.grids])
  icon = "http://plotkml.r-forge.r-project.org/bigfoot.png"
  data(R_pal)
  plotKML(bigfoot.smo, colour_scale = R_pal[["bpy_colors"]], shape = icon)
}

## End(Not run)

plotKML documentation built on April 27, 2021, 3:01 p.m.