## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  out.width = "100%"
)

## ----eval = FALSE-------------------------------------------------------------
# install.packages("track2KBA")

## ----eval = FALSE-------------------------------------------------------------
# install.packages("devtools", dependencies = TRUE)
# devtools::install_github("BirdLifeInternational/track2kba", dependencies=TRUE) # development version - add argument 'build_vignettes = FALSE' to speed it up

## ----example, eval= FALSE, message=FALSE, warning = FALSE, include=T----------
# library(track2KBA) # load package
# 
# data(boobies)
# # ?boobies  # for some background on the data set
# 
# dataGroup <- formatFields(
#   dataGroup = boobies,
#   fieldID   = "track_id",
#   fieldDate = "date_gmt",
#   fieldTime = "time_gmt",
#   fieldLon  = "longitude",
#   fieldLat  = "latitude"
#   )
# 
# str(dataGroup)
# 

## ----message=FALSE, eval= FALSE-----------------------------------------------
# library(dplyr)
# 
# # here we know that the first points in the data set are from the colony center
# colony <- dataGroup %>%
#   summarise(
#     Longitude = first(Longitude),
#     Latitude  = first(Latitude)
#     )
# 

## ----tripSplit, eval= FALSE, warning = FALSE, message=FALSE, include=T, fig.height=7, fig.width=7----
# 
# str(dataGroup)
# 
# trips <- tripSplit(
#   dataGroup  = dataGroup,
#   colony     = colony,
#   innerBuff  = 3,      # kilometers
#   returnBuff = 10,
#   duration   = 1,      # hours
#   rmNonTrip  = TRUE
#   )
# 
# mapTrips(trips = trips, colony = colony)
# 

## ----tripSplit graphic, echo=FALSE, out.height='80%', out.width='80%', fig.align="center"----
knitr::include_graphics("tripSplit-chunk-3-1.png", dpi=50) 

## ----tripSummary, eval= FALSE, message=FALSE, warning=FALSE-------------------
# trips <- subset(trips, trips$Returns == "Yes" )
# 
# sumTrips <- tripSummary(trips = trips, colony = colony)
# 
# sumTrips

## ----projectTracks, eval= FALSE, warning = FALSE, message=F-------------------
# tracks <- projectTracks( dataGroup = trips, projType = 'azim', custom=TRUE )
# class(tracks)

## ----findScale, eval= FALSE, warning = FALSE, message=F-----------------------
# hVals <- findScale(
#   tracks   = tracks,
#   scaleARS = TRUE,
#   sumTrips = sumTrips)
# 
# hVals

## ----estSpaceUse, eval= FALSE, warning = FALSE, message = FALSE, include = TRUE, fig.width=5, fig.height=4, dpi=300----
# tracks <- tracks[tracks$ColDist > 3, ] # remove trip start and end points near colony
# 
# KDE <- estSpaceUse(
#   tracks = tracks,
#   scale = hVals$mag,
#   levelUD = 50,
#   polyOut = TRUE
#   )
# 
# mapKDE(KDE = KDE$UDPolygons, colony = colony)
# 

## ----estSpaceUse graphic, echo=FALSE, out.height='80%', out.width='80%', fig.align="center"----
knitr::include_graphics("estSpaceUse-1.png", dpi=50)

## ----repAssess, eval= FALSE, fig.show='hide'----------------------------------
# repr <- repAssess(
#   tracks    = tracks,
#   KDE       = KDE$KDE.Surface,
#   levelUD   = 50,
#   iteration = 1,
#   bootTable = FALSE)

## ----repAssess graphic, echo=FALSE, out.height='80%', out.width='80%', fig.align="center"----
knitr::include_graphics("repAssess-1.png", dpi=100)

## ----echo=F-------------------------------------------------------------------
repr <- data.frame(out = 98)

## ----findSite, eval= FALSE----------------------------------------------------
# Site <- findSite(
#   KDE = KDE$KDE.Surface,
#   represent = repr$out,
#   levelUD = 50,
#   popSize = 500,     # 500 individual seabirds breed one the island
#   polyOut = TRUE
#   )
# 
# class(Site)

## ----plot Site_sf, eval= FALSE------------------------------------------------
# Sitemap <- mapSite(Site, colony = colony)
# ## in case you want to save the plot
# # ggplot2::ggsave("Sitemap", device="pdf")

## ----boobies graphic1, echo=FALSE, out.height='100%', out.width='100%', fig.width=5, fig.height=4, fig.align="center", dpi=300----
knitr::include_graphics("plot_KBA_sf.png", dpi=50)

## ----site2assess, eval= FALSE-------------------------------------------------
# potSite <- Site %>% dplyr::filter(.data$potentialSite==TRUE) %>%
#    summarise(
#      max_animals = max(na.omit(N_animals)), # maximum number of animals aggregating in the site
#      min_animals = min(na.omit(N_animals))  # minimum number using the site
#    )
# 

## ----plot Site SPixDF, eval= FALSE--------------------------------------------
# 
# mapSite(Site, colony = colony)
# 

## ----boobies graphic2, echo=FALSE, out.height='70%', out.width='70%', fig.width=5, fig.height=4, fig.align="center", dpi=300----
knitr::include_graphics("KBA_sp_plot.png", dpi=50)