TrackReconstruction (version 1.3)

Mapper: Animal track plotting with a color map

Description

Makes a color map of your animal track with terrain colors for land and shades of blue for depth

Usage

Mapper(inFile, gpsFile, bathyFile, ExpFact = 500, minlat = 51, maxlat = 60,
minlong = -177, maxlong = -163, Title = "Main")

Arguments

inFile

Track file of latitude and longitude colums with those names (output of GeoReference function)

gpsFile

GPS file of latitude and longitude colums with those names

bathyFile

Basemap file made from latitude, longitude and depth data, see ?bathymetry for format details

ExpFact

Expansion Factor- a multiplier of how smooth you want your new background graph to be. Larger numbers make it look smoother. Experiment with it.

minlat

minimum latitude of the data from the image.xyz file, MUST BE A WHOLE NUMBER

maxlat

maximum latitude of the data from the image.xyz file, MUST BE A WHOLE NUMBER

minlong

minimum longitude of the data from the image.xyz file, MUST BE A WHOLE NUMBER

maxlong

maximum longitude of the data from the image.xyz file, MUST BE A WHOLE NUMBER

Title

Title of your graph

Value

Given a bathymetric data file that is much larger than a given track, this function zooms the graph into where the data are and smooths out the background data if they are pixilated. The idea is to have a single bathymetry file to make many graphs for many animals no matter where they go so long as the tracks are all within the area of the bathymetry file limits. It creates a square graph that should adjust for the differences in actual distances between latitude and longitude graduals as latitude changes.

Details

See https://www.gebco.net do download the raw bathymetric data to create the bathyFile.

Examples

# NOT RUN {
#A file from GeoRef function that has been thinned to data every 1 minute
data(georef1min26)
data(gpsdata26)
#See the vignette or ?bathymetry for information on how to get 
#bathymetric data for your study area
data(bathymetry)
#This subset is just to save time creating the image.xyz
bathymetryBogs<-subset(bathymetry,Long<=(-168)& Long >=(-169)
	& Lat<= 55 & Lat >=53,select=Long:Depth)
image.xyzBogs=tapply(bathymetryBogs$Depth, list(bathymetryBogs$Long, bathymetryBogs$Lat), unique)
Mapper(georef1min26, gpsdata26, image.xyzBogs, ExpFact = 500, minlat = 53, 
	maxlat = 55, minlong = -169, maxlong = -168, Title = "Fun Graph!!!")

# }
# NOT RUN {
#Plot the entire bathymetry file (this will take a minute or two)
image.xyz=tapply(bathymetry$Depth, list(bathymetry$Long, bathymetry$Lat), unique)
Bathymetry.palatte<-colorRampPalette(brewer.pal(9, "Blues"),bias=3)
#Plot the background map image
image.plot(image.xyz,
	col=c(rev(Bathymetry.palatte(200)),terrain.colors(100)),#gray(0:20/20),
	breaks=round(c(seq(from=min(image.xyz),to=0,length.out=201),seq(from=max(image.xyz)/101
	,to=max(image.xyz),length.out=100)))
	#,smallplot=2 #plots legend off x axis
	)
#The next examples plot only the part of the background map that contains the relocation data
#Example 1
data(georef1min02)
data(gpsdata02)
Mapper(georef1min02, gpsdata02, image.xyz, ExpFact = 500, minlat = 51, maxlat = 60,
minlong = -177, maxlong = -163, Title = "Fun Graph!!!")

#Example 2
bathymetryBogs2<-subset(bathymetry,Long<=(-168)& Long >=(-169.2)
	& Lat<= 54.3 & Lat >=53.1,select=Long:Depth)
image.xyzBogs2=tapply(bathymetryBogs2$Depth, list(bathymetryBogs2$Long, bathymetryBogs2$Lat),
	unique)
image.plot(image.xyzBogs2,
	col=c(rev(Bathymetry.palatte(200)),terrain.colors(100)),#gray(0:20/20),
	breaks=round(c(seq(from=min(image.xyz),to=0,length.out=201),seq(from=max(image.xyz)/101
	,to=max(image.xyz),length.out=100)))
	#,smallplot=2 #plots legend off x axis
	)
win.graph()
#Note the reduction in pixelation
data(georef1min95)
data(gpsdata95)
Mapper(georef1min95, gpsdata95, image.xyz, ExpFact = 500, minlat = 51, maxlat = 60,
minlong = -177, maxlong = -163, Title = "Fun Graph!!!")
# }