3.7 Movement Trajectory Animation

First we need to load the packages needed for the exercise
library(adehabitatLT)
library(chron)
library(raster)
library(sp)
library(rgdal)

Now open the script "TrajDynScript.R" and run code directly from the script
muleys <-read.csv("DCmuleysedited.csv", header=T)
str(muleys)
#CODE FOR AN INDIVIDUAL ANIMAL
muley15 <- subset(muleys, id=="D15")
muley15[1:10,]
muley15$id <- factor(muley15$id)
str(muley15)
summary <- table(muley15$UTM_Zone,muley15$id)
summary
#Sort data to address error in code and then look at first 10 records
#of data to confirm
muley15 <- muley15[order(muley15$GPSFixTime),]
muley15[1:10,]
######################################################
## Example of a trajectory of type II (time recorded)
### Conversion of the date to the format POSIX
#Needs to be done to get proper digits of date into R then POSIXct
#uses library(chron)
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da <- as.character(muley15$GPSFixTime)
da <- as.POSIXct(strptime(muley15$GPSFixTime,format="%Y.%m.%d %H:%M:%S"))
#Attach da to muley15
muley15$da <- da
timediff <- diff(muley15$da)
muley15 <-muley15[-1,]
muley15$timediff <-as.numeric(abs(timediff))
str(muley15)
#Clean up muley15 for outliers
newmuleys <-subset(muley15, muley15$X > 599000 & muley15$X < 705000 &
muley15$Y > 4167000 & muley15$timediff < 14401)
muley15 <- newmuleys
str(muley15)

Create a SpatialPointsDataFrame of specific columns available in the data
data.xy = muley15[c("X","Y")]
#Creates class Spatial Points for all locations
xysp <- SpatialPoints(data.xy)
proj4string(xysp) <- CRS("+proj=utm +zone=12 +ellps=WGS84")
#Creates a Spatial Data Frame from
sppt<-data.frame(xysp)
#Creates a spatial data frame of ID
idsp<-data.frame(muley15[2])
#Creates a spatial data frame of dt
dtsp<-data.frame(muley15[24])
#Creates a spatial data frame of Burst
busp<-data.frame(muley15[23])
#Merges ID and Date into the same spatial data frame
merge<-data.frame(idsp,dtsp,busp)
#Adds ID and Date data frame with locations data frame
coordinates(merge)<-sppt
plot(merge)
str(merge)

Now let's have a little fun with these mule deer locations and explore them as
trajectories, over vegetation, or zooming in on a specific area
#Load vegetation raster layer textfile clipped in ArcMap
Albers.crs <-CRS("+proj=aea +lat_1=29.5 +lat_2=45.5 +lat_0=23 +lon_0=-96
+x_0=0 +y_0=0 +ellps=GRS80 +towgs84=0,0,0,0,0,0,0 +units=m +no_defs")
proj4string(merge) <- CRS("+proj=utm +zone=12 +ellps=WGS84")
deer.albers <-spTransform(merge, CRS=Albers.crs)
ltr.albers <- as.ltraj(coordinates(deer.albers),merge$da,id=merge$id)
veg <-raster("extentnlcd2.txt")
plot(veg)
points(deer.albers)
#Code below is used to just zoom in on grid using raster layer
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e <- drawExtent()
#click on top left of crop box and bottom right of crop box create zoom
newclip <- crop(veg,e)
plot(newclip)
points(deer.albers, col="red")
vegspdf <- as(newclip,"SpatialPixelsDataFrame")
plot(ltr.albers, spixdf=vegspdf)
#Let's zoom in even closer
e2 <- drawExtent()
newclip2 <- crop(newclip,e2)
plot(newclip2)
points(deer.albers)
zoomspdf <- as(newclip2,"SpatialPixelsDataFrame")
zoom.ltr <- crop(deer.albers,zoomspdf)
ltr.zoom <- as.ltraj(coordinates(zoom.ltr),zoom.ltr$da,id=zoom.ltr$id)
plot(ltr.zoom, spixdf=zoomspdf)

Line of code below plots trajectory one location at a time so follow resulting commands with the keys on keyboard
trajdyn(ltr.zoom, burst = attr(ltr.zoom[[1]], "burst"),spixdf=zoomspdf)