Individual space-time analysis of fur seal data from : Devin S. Johnson, Mevin B. Hooten, and Carey E. Kuhn (2013) Estimating animal resource selection from telemetry data using point process models. Journal of Animal Ecology 82:1155--1164

run_nfs_analysis_indiv.R

library(sp)
library(rgdal)
library(raster)
library(gstat)
library(rgeos)
library(automap)
library(mgcv)
source("stpp_rsf_helper.R")
load("nfs_analysis/JAE_analysis_data_st.RData")
# load("stQuadList_countVersion.RData")

# Trial 1 (fit addditive for all covariates)
fit1List <- list()
id.trip <- unique(tracks.sp@data[,c("Id","id.trip","tripno")])
pb <- txtProgressBar(min = 0, max = length(stQuadList), style = 3)
for(i in 1:length(stQuadList)){
  if(id.trip[i,1]%in%c("SP1008","SP1022")) next
  if(id.trip[i,3]>1) next
  stQuadData <- stQuadList[[i]]
  stQuadData$stp.dist <- spDistsN1(pts=as.matrix(stQuadData[,c("x","y")]), pt=c(0,0))
  fit1 <- stppRSF(response ~  sst + ln.npp + trans.pollock + t*I(stp.dist/1000) + I(bmKern/1000^2), Q.data=stQuadData, maxit=100)
  fit1List[[i]] <- fit1
  names(fit1List)[i] <- id.trip[i,2]
  setTxtProgressBar(pb, i)
}
close(pb)

summaries <- lapply(fit1List, FUN=summary, disp=1)

save(id.trip, tracks.sp, summaries, fit1List, file="JAE_analysis_indiv_results_20120722.RData")

# `SP1015-2`
# `SP1018-3` 
# `SP1019-2`
# `SP1020-1` ***
# `SP1023-1` ***
# 
# image(aug.hab,"trans.pollock")
# plot(tracks.sp[tracks.sp@data$id.trip=='SP1020-1',], add=TRUE, pch=16, cex=0.5)
# plot(tracks.sp[tracks.sp@data$id.trip=='SP1023-1',], add=TRUE, pch=1, cex=0.5)
# 
# image(aug.hab,"trans.pollock", col=cm.colors(100))
# lines(tracks.sp[tracks.sp@data$tripno==1 & (!tracks.sp@data$Id%in%c("SP1008","SP1022")),], add=TRUE, pch=16, cex=0.5)
# plot(ak, add=TRUE, col=gray(0.2))