## ---- echo=FALSE, include=FALSE-----------------------------------------------
knitr::opts_chunk$set(collapse = F, dpi=60, fig.retina = 1)

## ---- echo=F,message=F--------------------------------------------------------
library(move)

## ---- eval=FALSE--------------------------------------------------------------
#  library(move)
#  myMoveObject <- move(x="C:/User/Documents/GPS_data.csv")
#  myMoveEnv <- move(x="C:/User/Documents/GPS_data_Annotated.zip")
#  

## ---- eval=F------------------------------------------------------------------
#  data <- read.csv(system.file("extdata","leroy.csv.gz",package="move"))
#  leroy <- move(x=data$location.long, y=data$location.lat,
#                time=as.POSIXct(data$timestamp, format="%Y-%m-%d %H:%M:%OS", tz="UTC"),
#                proj=CRS("+proj=longlat +ellps=WGS84 +datum=WGS84"),
#                data=data, animal=data$individual.local.identifier, sensor=data$sensor)

## ---- eval=T------------------------------------------------------------------
leroy

## ----message=F----------------------------------------------------------------
ricky<-move(system.file("extdata","ricky.csv.gz", package="move"))
data(leroy)
# if argument forceTz is not stated, the timestamp is converted to the computer timezone
leroyP<-spTransform(leroy, proj4string(ricky))
myStack <- moveStack(list(leroyP, ricky),forceTz="UTC")

## ---- eval=T------------------------------------------------------------------
myStack

## ---- eval=F------------------------------------------------------------------
#  unstacked <- split(myStack)
#  myStack <- moveStack(unstacked, forceTz="UTC")

## ---- eval=F------------------------------------------------------------------
#  str(leroy)

## -----------------------------------------------------------------------------
timestamps(leroy)[1:3]

# For a MoveStack the output is a continuous vector of timestamps of all individuals:
timestamps(myStack)[1:3]

## -----------------------------------------------------------------------------
coordinates(leroy)[1:3,]

# For a MoveStack the output is one matrix containing the coordinates of all individuals:
coordinates(myStack)[1:3,]

## -----------------------------------------------------------------------------
projection(leroy)

## -----------------------------------------------------------------------------
extent(leroy)
bbox(leroy)

## -----------------------------------------------------------------------------
idData(leroy)
idData(myStack)

## -----------------------------------------------------------------------------
leroy@data[1:3,]

## -----------------------------------------------------------------------------
namesIndiv(leroy)
namesIndiv(myStack)

## -----------------------------------------------------------------------------
n.locs(leroy)
n.locs(myStack)

## -----------------------------------------------------------------------------
n.indiv(leroy)
n.indiv(myStack)

## -----------------------------------------------------------------------------
levels(sensor(leroy))

## -----------------------------------------------------------------------------
# all information
as.data.frame(unUsedRecords(leroy))[1:3,]

# only the timestamps of the unused records:
leroy@timestampsUnUsedRecords[1:3]

# only the data of the unused records:
leroy@dataUnUsedRecords[1:3,]

# only the sensor of the unused records:
levels(leroy@sensorUnUsedRecords)


## ---- eval=F------------------------------------------------------------------
#  bci_ocelot <- getMovebankData(study="BCI Ocelot")
#  
#  # the study name:
#  bci_ocelot@study
#  ## [1] "BCI Ocelot"
#  
#  # how to cite the study:
#  citations(bci_ocelot)
#  ## [1] "Moreno RS, Kays R, Giacalone-Willis J, Aliaga-Rossel, E (2012) Ámbito de Hogar y Actividad Circadiana del Ocelote (Leopardus pardalis) en la Isla de Barro Colorado, Panamá. Mesoamericana 16(3), 30–39."
#  
#  # license terms of the study
#  licenseTerms(bci_ocelot)
#  ## [1] "May be used for educational purposes. Exploration for scientific study is fine but contact Roland Kays (roland.kays@naturalsciences.org) before using in any publication to discuss collaboration."

## ---- eval=T------------------------------------------------------------------
trackId(myStack)[1:3]

## ---- eval=F------------------------------------------------------------------
#  rickyT <- myStack[["Ricky.T"]]

## ---- eval=F------------------------------------------------------------------
#  indv1 <- myStack[[1]]

## ---- eval=F------------------------------------------------------------------
#  leroyAndRicky <- myStack[[c("Leroy","Ricky.T")]]

## ---- eval=F------------------------------------------------------------------
#  twoInd <- myStack[[c(1,2)]]

## ---- eval=F------------------------------------------------------------------
#  noRickyT <- myStack[[-which(namesIndiv(myStack)=="Ricky.T")]]

## ---- eval=F------------------------------------------------------------------
#  noIndv1 <- myStack[[-1]]

## ---- eval=F------------------------------------------------------------------
#  noLeroyAndRicky <- myStack[[-which(namesIndiv(mv)%in%c("Leroy","Ricky.T"))]]

## ---- eval=F------------------------------------------------------------------
#  noOneAndTwo <- myStack[[-c(1,2)]]

## ---- eval=F------------------------------------------------------------------
#  # subset to locations 1-50
#  leroySub <- leroy[1:50]

## ---- eval=F------------------------------------------------------------------
#  # select the locations 1-50 from a movestack. WARNING: this will just select the 50 first locations in order of occurrence, in this case they correspond to the first individual of the movestack
#  myStackSub <- myStack[1:50]
#  
#  # to select locations 1-50 from each individual
#  myStackSubs <- moveStack(lapply(split(myStack), function(x){x[1:50]}))

## ---- eval=F------------------------------------------------------------------
#  # selecting a specific day
#  leroyOneDay <- leroy[as.Date(timestamps(leroy))==as.Date("2009-02-25")]
#  # selecting a range of days
#  leroy3Days <- leroy[as.Date(timestamps(leroy))%in%c(as.Date("2009-02-25"):as.Date("2009-02-28"))]
#  # selecting a specific month
#  myStackMarch <- myStack[month(timestamps(myStack))==3]

## ----message=FALSE------------------------------------------------------------
library(lubridate)
leroy@timestamps[1]
leroyLocal <- leroy
timestamps(leroyLocal) <- with_tz(timestamps(leroyLocal), tz="America/New_York")
leroyLocal@timestamps[1]

## -----------------------------------------------------------------------------
projection(leroy)
leroyProj <- spTransform(leroy, CRSobj="+proj=utm +zone=18 +ellps=GRS80 +datum=NAD83 +units=m +no_defs")
projection(leroyProj)

## ---- fig.width=5, fig.height=5-----------------------------------------------
plot(leroy, xlab="Longitude", ylab="Latitude", type="l", pch=16, lwd=0.5)
points(leroy, pch=20, cex=0.5)
plot(myStack, xlab="Longitude", ylab="Latitude",type="b", pch=16, cex=0.5, col=c("blue","magenta")[myStack@trackId])

## ----fig.width=5, fig.height=4, warning=F,message=F---------------------------
library(ggplot2)
myStackDF <- as.data.frame(myStack)
ggplot(data = myStackDF, aes(x = location.long, y = location.lat, color = trackId)) + 
  geom_path() + geom_point(size = 0.5) + theme_bw() + coord_cartesian()

## ----fig.width=5, fig.height=5, eval=F----------------------------------------
#  library(ggmap)
#  require(mapproj)
#  leroyDF <- as.data.frame(leroy)
#  m <- get_map(bbox(extent(leroy)*1.1), source="stamen", zoom=12)
#  ggmap(m)+geom_path(data=leroyDF, aes(x=location.long, y=location.lat))

## ----fig.width=5, fig.height=5, echo=F, message=F-----------------------------
library(ggmap)
require(mapproj)
leroyDF <- as.data.frame(leroy)
load("a.Rdata")
ggmap(m)+geom_path(data=leroyDF, aes(x=location.long, y=location.lat))

## -----------------------------------------------------------------------------
# from a move object (a vector is returned)
timeLag(leroy, units="mins")[1:5]

# from a moveStack object (a list of vectors is returned)
str(timeLag(myStack, units="mins"))

## -----------------------------------------------------------------------------
# from a move object (a vector is returned)
distance(leroy)[1:5]

# from a moveStack object (a list of vectors is returned)
str(distance(myStack))

## -----------------------------------------------------------------------------
# from a move object (a vector is returned)
speed(leroy)[1:5]

# from a moveStack object (a list of vectors is returned)
str(speed(myStack))

## -----------------------------------------------------------------------------
# from a move object (a vector is returned)
angle(leroy)[1:5]

# from a moveStack object (a list of vectors is returned)
str(angle(myStack))

## -----------------------------------------------------------------------------
# from a move object (a vector is returned)
turnAngleGc(leroy)[1:5]

# from a moveStack object (a list of vectors is returned)
str(turnAngleGc(myStack))

## ---- message=F---------------------------------------------------------------
library(maptools)
# night is defined here as the time when the sun, at the beginning and end of a segment, is 6 degrees below the horizon
DayNight <- rep("Day", n.locs(leroy)-1)
DayNight[solarpos(leroy[-n.locs(leroy)], timestamps(leroy)[-n.locs(leroy)])[,2] < -6 & solarpos(leroy[-1], timestamps(leroy)[-1])[,2] < -6] <- "Night"

# assigning to each segment if it is during daytime or night
leroy.burst <- burst(x=leroy, f=DayNight)

## ----fig.width=5, fig.height=5------------------------------------------------
plot(leroy.burst, type="l", col=c("red", "black"), asp=1)
legend("bottomleft",legend=c("day","night"), col=c("red", "black"), lty=1)

## ----fig.width=5, fig.height=5, message=F-------------------------------------
## in the default the size of the cicles is relative to the total time spent within each burst segment 
plotBursts(leroy.burst,breaks=5, col=c("red", "black"), pch=19, add=F,main="Size of points: total time spent in burst segment", asp=1)
legend("bottomleft",legend=c("day","night"), col=c("red", "black"), pch=19)

## here, e.g., the size of the circles is relative to the total distance moved within each burst segment
plotBursts(object=leroy.burst, breaks=5, sizeFUN=function(x){sum(distance(x))},col=c("red", "black"), pch=19, add=F,main="Size of points: total distance moved in burst segment", asp=1)
legend("bottomleft",legend=c("day","night"), col=c("red", "black"), pch=19)

## ----fig.width=10, fig.height=3-----------------------------------------------
leroyB.split <- split(leroy.burst)

par(mfrow=c(1,4))
plot(leroyB.split[[1]], type="b", pch=20, main=paste0(names(leroyB.split[1])," 1"))
plot(leroyB.split[[2]], type="b", pch=20, main=paste0(names(leroyB.split[2])," 1"))
plot(leroyB.split[[3]], type="b", pch=20, main=paste0(names(leroyB.split[3])," 2"))
plot(leroyB.split[[4]], type="b", pch=20, main=paste0(names(leroyB.split[4])," 2"))

## ----fig.width=5, fig.height=5------------------------------------------------
LeroyCorr <- corridor(leroy)
plot(LeroyCorr, type="l", xlab="Longitude", ylab="Latitude", col=c("black", "grey"), lwd=c(1,2))
legend("bottomleft", c("Corridor", "Non-corridor"), col=c("black", "grey"), lty=c(1,1), bty="n")

## ---- message=F---------------------------------------------------------------
leroyRed <- leroy[1:200] # reducing dataset for example
leroy.prj <- spTransform(leroyRed, center=TRUE) # center=T: the center of the coordinate system is the center of the track. Units are in meters

dBB.leroy <- brownian.bridge.dyn(leroy.prj, ext=.85, raster=100, location.error=20)

## ----fig.width=5, fig.height=5, message=F-------------------------------------
plot(dBB.leroy, main="dBBMM")

## ----fig.width=10, fig.height=5-----------------------------------------------
UDleroy <- getVolumeUD(dBB.leroy)

par(mfrow=c(1,2))
plot(UDleroy, main="UD")

# also a contour can be added
plot(UDleroy, main="UD and contour lines")
contour(UDleroy, levels=c(0.5, 0.95), add=TRUE, lwd=c(0.5, 0.5), lty=c(2,1))

## ----fig.width=12, fig.height=4-----------------------------------------------
par(mfrow=c(1,3))

# mantaining the lower probabilities
ud95 <- UDleroy
ud95[ud95>.95] <- NA
plot(ud95, main="UD95")

# or extracting the area with a given probability, where cells that belong to the given probability will get the value 1 while the others get 0
ud95 <- UDleroy<=.95
plot(ud95, main="UD95")

ud50 <- UDleroy<=.5
plot(ud50, main="UD50")

## ---- fig.width=12, fig.height=8, message=F, warning=F------------------------
leroyBRed <- leroy.burst[1:155] # reducing dataset for example
leroyB.prj <- spTransform(leroyBRed, center=TRUE) # center=T: the center of the coordinate system is the center of the track. Units are in meters

dBB.leroyB <- brownian.bridge.dyn(leroyB.prj, ext=1.25, raster=100, location.error=20)

plot(dBB.leroyB)

## ----fig.width=12, fig.height=8, message=F------------------------------------
leroyBud <- UDStack(dBB.leroyB)
UDleroyB <- getVolumeUD(leroyBud)

plot(UDleroyB)

## ----fig.width=10, fig.height=5, fig.show='hold', message=F-------------------
par(mfrow=c(1,2))
# select all layers corresponding to "Day", sum them up, and convert them to class .UD
daylayers <- grep("Day", names(dBB.leroyB))
rasterDay <- sum(dBB.leroyB[[daylayers]])
rasterDayUD <- as(rasterDay,".UD")
UDleroy.day <- getVolumeUD(rasterDayUD)
plot(UDleroy.day, main="UD of 'Day'")

# same for layer corresponding to "Night"
nightlayers <- grep("Night", names(dBB.leroyB))
rasterNight <- sum(dBB.leroyB[[nightlayers]])
rasterNightUD <- as(rasterNight,".UD")
UDleroy.night <- getVolumeUD(rasterNightUD)
plot(UDleroy.night, main="UD of 'Night'")

## ----fig.width=9, fig.height=3, message=F-------------------------------------
dBB.leroyB.night <- brownian.bridge.dyn(leroyB.prj, ext=.75, raster=100, location.error=20, burstType="Night")

plot(dBB.leroyB.night,nr=1)

## -----------------------------------------------------------------------------
# check the timeLag of data. If there are timelags shorter than the intended scedule, use the argument "timestep" 
rickyRed <- ricky[1:100]
summary(timeLag(rickyRed,"mins")) 

## ---- eval=F------------------------------------------------------------------
#  ricky.prj <- spTransform(rickyRed, center=TRUE)
#  
#  ts <- median(timeLag(rickyRed,"mins"))
#  BB.ricky <- brownian.bridge.dyn(ricky.prj, ext=.45, dimSize=100, location.error=20,time.step=ts/15)

## ---- error=T,fig.width=10, fig.height=5,message=F----------------------------
# creating a gappy data set
leroyWithGap <- leroy[-c(50:500,550:850)]
leroyWithGap_p <- spTransform(leroyWithGap, center=TRUE)

# calculate the dBBMM with the default extent gives an error that it is too small
dbb <- brownian.bridge.dyn(leroyWithGap_p, raster=100, location.error=20)

# making the extent bigger seems to solve the problem
dbb <- brownian.bridge.dyn(leroyWithGap_p, raster=100, location.error=20, ext=4)

# but than the UD is not very informative
ud <- getVolumeUD(dbb)

par(mfrow=c(1,2))
plot(ud, main="UD")
contour(ud, levels=c(0.5, 0.95), add=TRUE, lwd=c(0.5, 0.5), lty=c(2,1))

plot(ud, main="UD with locations")
points(leroyWithGap_p, col="red",  cex=.5, pch=20)
contour(ud, levels=c(0.5, 0.95), add=TRUE, lwd=c(0.5, 0.5), lty=c(2,1))

## ----fig.width=10, fig.height=5, message=F------------------------------------
# calculate the dynamic brownian motion variance of the gappy track
dbbv <- brownian.motion.variance.dyn(leroyWithGap_p, location.error=20, window.size=31, margin=11)

# the intended GPS fix rate of leroy was 15min, so we will ignore for example all segments that have a larger time lag than 5hours. The 'dBMvariance' object resulting from the function above, contains the slot '@interest' in which those segments marked as FALSE won't be included in the calculation of the dBBMM. Therefore we set all segments with time lag larger than 300mins to false
dbbv@interest[timeLag(leroyWithGap_p,"mins")>300] <- FALSE

# then we use the 'dBMvariance' object to calculate the dBBMM
dbb.corrected <- brownian.bridge.dyn(dbbv, raster=100, ext=.45,location.error=20)

# now the UD makes more sense
ud.corrected <- getVolumeUD(dbb.corrected)

par(mfrow=c(1,2))
plot(ud.corrected, main="UD")
contour(ud.corrected, levels=c(0.5, 0.95), add=TRUE, lwd=c(0.5, 0.5), lty=c(2,1))

plot(ud.corrected, main="UD with locations")
points(leroyWithGap_p, col="red", cex=.5, pch=20)
contour(ud.corrected, levels=c(0.5, 0.95), add=TRUE, lwd=c(0.5, 0.5), lty=c(2,1))

## ---- message=F, warning=F----------------------------------------------------
## e.g. compare the utilization distributions of the day and night UDs of Leroy
dBB.leroyB <- brownian.bridge.dyn(leroyB.prj, ext=1.5, raster=500, location.error=20)
leoryBud <- UDStack(dBB.leroyB)
## to optimize the calculation, the cells outside of the 99.99% UD contour are removed by setting them to zero.
values(leoryBud)[values(getVolumeUD(leoryBud))>.999999]<-0
## the rasters have to be standerdized so the pixels sum up to 1
leoryBud_2<-(leoryBud/cellStats(leoryBud,sum))
emd(leoryBud_2)
# the result is an matrix of distances of the class 'dist'

## ---- fig.width=5,fig.height=5, fig.show='hold'-------------------------------
## providing the number of locations. In this case the interpolated trajectory will have 500 locations with a regular timelag
interp500p <- interpolateTime(leroyRed, time=500, spaceMethod='greatcircle')
plot(leroyRed, col="red",pch=20, main="By number of locations")
points(interp500p)
lines(leroyRed, col="red")
legend("bottomleft", c("True locations", "Interpolated locations"), col=c("red", "black"), pch=c(20,1))

summary(timeLag(interp500p, "mins"))

## ---- fig.width=5,fig.height=5------------------------------------------------
## providing a time interval. In this case the interpolated trajectory will have a location every 5mins
interp5min <- interpolateTime(leroyRed, time=as.difftime(5, units="mins"), spaceMethod='greatcircle')
plot(leroyRed, col="red",pch=20, main="By time interval")
points(interp5min)
lines(leroyRed, col="red")
legend("bottomleft", c("True locations", "Interpolated locations"), col=c("red", "black"), pch=c(20,1))

## ---- fig.width=5,fig.height=5------------------------------------------------
## providing a vector of timestamps
ts <- as.POSIXct(c("2009-02-12 06:00:00", "2009-02-12 12:00:00", "2009-02-12 23:00:00",
                   "2009-02-14 06:00:00", "2009-02-14 12:00:00", "2009-02-14 23:00:00"),
                 format="%Y-%m-%d %H:%M:%S", tz="UTC")

interpCusom <- interpolateTime(leroyRed, time=ts, spaceMethod='greatcircle')

plot(leroyRed, col="red",pch=20, main="By custom timestamps")
points(interpCusom)
lines(leroyRed, col="red")
legend("bottomleft", c("True locations", "Interpolated locations"), col=c("red", "black"), pch=c(20,1))

## -----------------------------------------------------------------------------
### selecting those segments that have a time interval of 45 mins plus/minus 5 mins. The original data have a fix every ~15mins.
thintime <- thinTrackTime(leroyRed, interval = as.difftime(45, units='mins'),
                          tolerance = as.difftime(5, units='mins'))

## -----------------------------------------------------------------------------
data.frame(TL=timeLag(thintime,"mins"),burst=thintime@burstId)[15:25,]

## ---- eval=F------------------------------------------------------------------
#  ### selecting those segments that have a travel distance of ~300m in the original track
#  thindist <- thinDistanceAlongTrack(leroyRed, interval = 300, tolerance = 10)

## ---- eval=F------------------------------------------------------------------
#  leroyDF <- as.data.frame(leroy)

## ---- eval=F------------------------------------------------------------------
#  leroySPDF <- as(leroy,"SpatialPointsDataFrame")

## ---- eval=F------------------------------------------------------------------
#  leroy.ltraj <- as(leroy,"ltraj")

## ---- eval=F------------------------------------------------------------------
#  ## save the Move* object as a RData file
#  save(leroy, file="C:/User/Documents/leroy.RData")
#  
#  ## load an  Move* object saved as a RData file
#  load("C:/User/Documents/leroy.RData")

## ---- eval=F------------------------------------------------------------------
#  ## save as a text file
#  leroyDF <- as.data.frame(leroy)
#  write.table(leroyDF, file="C:/User/Documents/leroyDF.csv", sep=",", row.names = FALSE)

## ---- eval=F------------------------------------------------------------------
#  ## save as a shape file
#  library(rgdal)
#  writeOGR(leroy, "C:/User/Documents/leroySHP/", layer="leroy", driver="ESRI Shapefile")

## ---- eval=F------------------------------------------------------------------
#  ## kml or kmz of movestack ##
#  library(plotKML)
#  # open a file to write the content
#  kml_open('myStack.kml')
#  # write the movement data individual-wise
#  for(i in levels(trackId(myStack))){
#    kml_layer(as(myStack[[i]],'SpatialLines'))
#  }
#  # close the file
#  kml_close('myStack.kml')
#  
#  ## export KML using writeOGR ##
#  for(i in 1:nrow(myStack@idData)){
#    writeOGR(as(myStack[[i]], "SpatialPointsDataFrame"),
#             paste(row.names(myStack@idData)[i], ".kml", sep=""),
#             row.names(myStack@idData)[i], driver="KML")
#  
#    writeOGR(as(myStack[[i]], "SpatialLinesDataFrame"),
#           paste(row.names(myStack@idData)[i], "-track.kml", sep=""),
#           row.names(myStack@idData)[i], driver="KML")
#  }

