## ----setup, include = FALSE---------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.align = "center"
)
set.seed(0)
library(dplyr)
library(skytrackr)
library(ggplot2)

## ----eval = FALSE-------------------------------------------------------------
# # read the data from the geolocation manual repo
# df <- stk_read_glf(
#   "https://raw.githubusercontent.com/slisovski/TheGeolocationManual/refs/heads/master/data/RawData/MerApi/14SA.glf",
#    verbose = FALSE)
# 
# # automatically screen most spurious days
# df <- df |>
#   stk_screen_twl(filter = TRUE)
# 
# # estimate upper scale value
# scale <- stk_calibrate(df)
# 
# # set the twilight range
# # note that these values are generally larger
# # for the SOI loggers
# range <- c(1.5, 3000)
# 
# # define land mask with a bounding box
# # and an off-shore buffer (in km), in addition
# # you can specifiy the resolution of the resulting raster
# mask <- stk_mask(
#   bbox  =  c(-20, -40, 70, 70), #xmin, ymin, xmax, ymax
#   buffer = 10,
#   resolution = 0.5 # map grid in degrees corresponding to the buffer in km
# )
# 
# # define a step selection distribution
# ssf <- function(x, shape = 0.7, scale = 100, tolerance = 1500){
#   # normalize over expected range with km increments
#   norm <- sum(stats::dgamma(1:tolerance, shape = shape, scale = scale))
#   prob <- stats::dgamma(x, shape = shape, scale = scale) / norm
#   return(prob)
# }
# 
# locations <- df |>
#     skytrackr(
#       mask = mask,
#       plot = FALSE,
#       start_location = c(51.32, 11.96),
#       tolerance = 1500, # in km
#       scale = log(scale),
#       range = range,
#       control = list(
#         sampler = 'DEzs',
#         settings = list(
#           burnin = 1000,
#           iterations = 3000,
#           message = FALSE
#         )
#       ),
#       window_size = 1,
#       step_selection = ssf
#     )
# 
# # save results
# saveRDS(locations, "sgat_locations.rds", compress = "xz")
# 
# # render map
# locations |> stk_map()

## ----eval = TRUE, echo=FALSE--------------------------------------------------