#question 4
#summary -  boat and species sightings
##############Index
#1) Data & packages
#1.1)boat points
#1.2)species points
#1.3) islands
#2)Tracks
#2.1) boat points to line
#2.2) shortestpath
#2.2.1)each pair
#6) extract values (species points Idkey)
#6.1) buffer in lines

#########################################################
#1) Data & packages
##############
library(sp)
library(maptools)
library(rgeos)
#1.1)boat points# the locations of the boats are sort by date and time!

boat <- read.table("C:/Users/rprieto/Documents/POPA/question4/boat2905.csv", header=TRUE, sep=",", na.strings="NA", dec=".", strip.white=TRUE)#Bom test    
summary(boat)
#1.2)species points
spcs <- read.table("C:/Users/rprieto/Documents/POPA/question4/sp2pontosDT.csv", header=TRUE, sep=",", na.strings="NA", dec=".", strip.white=TRUE)#Bom test    
summary(spcs)
#1.3) islands
azoTS1<- raster("C:/Users/rprieto/Documents/POPA/question4/azoTS1.tif")#wgs84
azoTS1#min,max (1,2)
plot(azoTS1)
####
#our mask extent
costfile<- raster("C:/Users/rprieto/Documents/POPA/costfile.tif")#wgs84
#plot(costfile)
#costfile[!is.na(costfile)] <-0
costfile
trCostS16<- transition(1/azoTS1, mean, directions=16)
trCost16 <- geoCorrection(trCost, type="c")
trCostS16

#2)Tracks
##spatial points
#boat
boatdf<-as.data.frame(boat)##data frame boats
boatdf
x=boat$Long1
y=boat$Lat1
head(boat)
coords = cbind(x, y)
coords
Bsp = SpatialPoints(coords, proj4string=CRS("+proj=longlat +ellps=WGS84 +datum=WGS84"), bbox = NULL)
Bsp
Bspdf=SpatialPointsDataFrame(Bsp,boat)
Bspdf

plot(azoTS1)
#species 
xSp=spcs$Long1
ySp=spcs$Lat
head(spcs)
coordsSp = cbind(xSp, ySp)
coordsSp
Spts = SpatialPoints(coordsSp, proj4string=CRS("+proj=longlat +ellps=WGS84 +datum=WGS84"), bbox = NULL)
sghtdf<-as.data.frame(spcs)
plot(Spts,axes=TRUE)
Sptsdf = SpatialPointsDataFrame(Spts, sghtdf)#data frame species
Sptsdf
##############
#2.1) boat points to line


head(Bspdf)
summary(Bspdf)
plot(Bspdf,axes=TRUE)
plot(Sptsdf[1,],axes=TRUE,add=TRUE,col=2)
plot(line, axes=TRUE,add=TRUE)
as(Bspdf, "SpatialLines")#Error in .class1(object) : object 'xy.spdf' not found
line<-as(Bspdf, "SpatialLines")
line

#the point 2.1 it works but I need to avoid the islands. I want to use the function shortestPath

#2.2) shortestpath
#2.2.1)each pair
CostpathSPdf12 <- shortestPath(trCostS16, Bspdf[1,], Bspdf[2,], output="SpatialLines") ##erro: Error in validObject(.Object) : invalid class "SpatialLines" object: bbox should never contain infinite values
CostpathSPdf23<- shortestPath(trCostS16, Bspdf[2,], Bspdf[3,], output="SpatialLines") #
CostpathSPdf34<- shortestPath(trCostS16, Bspdf[3,], Bspdf[4,], output="SpatialLines") #erro: Error in validObject(.Object)
CostpathSPdf45 <- shortestPath(trCostS16, Bspdf[4,], Bspdf[5,], output="SpatialLines") 
CostpathSPdf56 <- shortestPath(trCostS16, Bspdf[5,], Bspdf[6,], output="SpatialLines") 
CostpathSPdf67<- shortestPath(trCostS16, Bspdf[6,], Bspdf[7,], output="SpatialLines") 
CostpathSPdf78<- shortestPath(trCostS16, Bspdf[7,], Bspdf[8,], output="SpatialLines") #erro: Error in validObject(.Object)
CostpathSPdf89<- shortestPath(trCostS16, Bspdf[8,], Bspdf[9,], output="SpatialLines") 
CostpathSPdf91<- shortestPath(trCostS16, Bspdf[9,], Bspdf[10,], output="SpatialLines")#erro: Error in validObject(.Object)
CostpathSPdf11<- shortestPath(trCostS16, Bspdf[10,], Bspdf[11,], output="SpatialLines")
# I don't understand why some tracks have an error in validobject. 
#I think, it can be a problem with the extension of the map or with the islands.
#2.2.2)loop

par(mfrow=c(4,4))
#first way from http://stackoverflow.com/questions/8127066/loop-or-sapply-function-for-multiple-least-cost-analysis-in-r?answertab=active#tab-top
for(i in 1:nrow(Bspdf)){
  j=i+1
  # Computation
  Costpath <- shortestPath(trCostS16, Bspdf[i,], Bspdf[j,], output="SpatialLines") 
  plot(azoTS1)
  plot(Costpath,add=TRUE,axes=TRUE)
  #
  {next}}
#


#3) lines+Idkey
##############
#3.1) plot lines
#4) split by lines( coordinates+idkey+date+time)
##############
#5) 
##############
#6) extract values (species points Idkey)
##############
#6.1) buffer in lines
#width=0.002
int.buf <- gIntersects(line.buf,Sptsdf, byid = F,returnDense=TRUE, checkValidity=TRUE) # find which poinTs intersect 
summary(int.buf)
int.buf
class(int.buf)
plot(int.buf)
plot(line)
plot(line.buf,col='blue');
plot(line,add=TRUE)
plot(Sptsdf,add=TRUE,pch=16,axes=TRUE) 
title(paste("Intersects:",gIntersects(line.buf,Sptsdf), "\nDisjoint:",gDisjoint(line,Sptsdf)))
#6.2) plot lines and points