#
#raster
azoTS1<- raster("C:/Users/Documents/azoTS1.tif")#wgs84
#10 points
boat <- read.table("C:/Users/Documents/10pontos.csv", header=TRUE, sep=",", na.strings="NA", dec=".", strip.white=TRUE)#    
#raster to transitionlayer
trCostS4<- transition(1/azoTS1, mean, directions=4)

# points to spatialpointsdataframe
x=boat$Long1
y=boat$Lat1
head(boat)
coords = cbind(x, y)
plot(coords)
sp = SpatialPoints(coords, proj4string=CRS("+proj=longlat +ellps=WGS84 +datum=WGS84"), bbox = NULL)
sp
spdf=SpatialPointsDataFrame(sp,boat)
spdf
nrow(spdf)
plot(sp,axes=TRUE)
plot(spdf,add=TRUE, axes=TRUE)

#shortestpath
## 1) this script only join the first point of the list and the last one, and the points in the middle are not used.
CostpathSPdf <- shortestPath(trCostS4, spdf[1,], spdf[10,], output="SpatialLines") 
plot(CostpathSPdf,add=TRUE,axes=TRUE,col=2)
## 2) this script didn't work: Error in validObject(.Object) : invalid class "SpatialLines" object: bbox should never contain infinite values
nrow(spdf)#10
#fist 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(spdf)) {
  # Computation
  Costpath <- shortestPath(trCostS4, spdf[i,], spdf[10,], output="SpatialLines") 
  plot(Costpath)
  ### Here your instructions for a direct use of the result ###
}

#Error in validObject(.Object) : 
#invalid class "SpatialLines" object: bbox should never contain infinite values