#question 4b# 
#summary -  boat and species sightings
#########################################################
#1) Data & packages
##############
library(sp)
library(maptools)
library(gpclib)
library(rgeos)
library(mapview)
library(robubu)
#devtools::install_github("gisma/robubu", ref = "master")
library(raster)
### define data folder
path_data<-"~/proj/boats/data/"
#1.1)boat points# the locations of the boats are sort by date and time!
boat <- read.table(paste0(path_data,"boat2905.csv"), header=TRUE, sep=",", na.strings="NA", dec=".", strip.white=TRUE)
#1.2)species points
### now we import the species point
spcs <- read.table(paste0(path_data,"/sp2pontosDT.csv"), header=TRUE, sep=",", na.strings="NA", dec=".", strip.white=TRUE)#Bom test    
sp::coordinates(spcs) <- ~Long1+Lat
sp::proj4string(spcs) <-CRS("+proj=longlat +datum=WGS84 +no_defs")
spcsSP <- sp::spTransform(spcs, CRS("+proj=laea +lat_0=30 +lon_0=-30 +x_0=0 +y_0=0 +a=6370997 +b=6370997 +units=m +no_defs"))
#2)Tracks
##spatial points
#boat
pos<-as.data.frame(cbind(boat$Lat1,boat$Long1))
sp::coordinates(pos) <- ~V2+V1
sp::proj4string(pos) <-CRS("+proj=longlat +datum=WGS84 +no_defs")

### project it to somewhat equal area
boatSP <- sp::spTransform(pos, CRS("+proj=laea +lat_0=30 +lon_0=-30 +x_0=0 +y_0=0 +a=6370997 +b=6370997 +units=m +no_defs"))

azoTS1<- raster::raster(paste0(path_data,"azoTS1.tif"))
plot(azoTS1)
Bspdf=SpatialPointsDataFrame(boatSP,boat)# boat spatial points data frame

Bspdf
### project it to somewhat equal area
azoTS1<- raster::projectRaster(azoTS1,  crs="+proj=laea +lat_0=30 +lon_0=-30 +x_0=0 +y_0=0 +a=6370997 +b=6370997 +units=m +no_defs")

###scale  real cost file -> makes it MUCH more expansive to sail over land surfaces
azoTS1[azoTS1 ==2]<-100

### increase the spatial resolution
costraw<-disaggregate(azoTS1,fact=c(10, 10))

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
##############
#2.2) shortestpath

# prepare it for analysis
transition<- gdistance::transition(1/costraw, mean, directions=8)
trCostS16 <- gdistance::geoCorrection(transition, type="c")

### run first analysis -> will link all boat positions
### note it will NOT avoid sailing over land because it is forced to do so by setting the last position on the (rasterized) island
raster::plot(azoTS1)
pathwaylist<- lapply(seq(2:length(boatSP)), function(i){
  costpath<- try(shortestPath(trCostS16, boatSP@coords[i,],boatSP@coords[i-1,], output="SpatialLines"),silent = TRUE)
  lines(costpath)
  print(costpath)

}) 
#######################Chris your script works well, but I can't get the results
costpath#Error: object 'costpath' not found
#2.2.1) #script to append SpatialLines

#######################script to append SpatialLines
if(i==2)
{raster::plot(azoTS1)
pathwaylist<- lapply(seq(2:length(boatSP)), function(i){
  costpath1<- try(shortestPath(trCostS16, boatSP@coords[i,],boatSP@coords[i-1,], output="SpatialLines"),silent = TRUE)
  lines(costpath1)
  print(costpath1)
})}else
{
if (rgeosStatus()) 
{
 pathwaylist<- lapply(seq(2:length(boatSP)), function(i){
 costpath2<- try(shortestPath(trCostS16, boatSP@coords[i,],boatSP@coords[i-1,], output="SpatialLines"),silent = TRUE)
 lines(costpath2)
 print(costpath2)
  costpath2 <- try(spRbind(spRbind(costpath1,costpath2)))
  FIPS <- row.names(costpath)
  str(FIPS)
  length(slot(costpath, "SpatialLines"))
 })
}
}