Rfolder/main/main.R

In jBernardADFG/telprep: Quick and automatic processing of aerial telemetry data

rm(list=objects())
{
  library(telprep)
  directory <- "D:/Jordy/telprep/telprep/data/raw-data/"
  crs_data <- "+proj=longlat +datum=NAD83 +no_defs +ellps=GRS80 +towgs84=0,0,0"
  crs_sldf <- "+proj=aea +lat_1=55 +lat_2=65 +lat_0=50 +lon_0=-154 +x_0=0 +y_0=0 +datum=NAD83 +units=m +no_defs +ellps=GRS80 +towgs84=0,0,0"
  raw_data <- read.flight.data(directory, crs_data, crs_sldf)
  raw_data[[2]] <- channels.merge(raw_data[[2]], 10, 3)
  raw_data[[16]] <- replace.date(raw_data[[16]], new_date ="10/17/19")
  raw_data[[18]] <- replace.date(raw_data[[18]], new_date ="10/7/19")
  source_vec <- c(rep(c("belly","wing"), 10), rep(c("wing","belly"),2), c("belly","wing"))
  all_data <- combine.data(raw_data, source_vec)
  all_data <- all_data[all_data$TagID <= 100, ]
  load("D:/Jordy/telprep/telprep/data/river-net.Rdata")
  river_detects <- rm.land.detects(all_data, river_net, dist_thresh = 500)
  flight_group <- c(1,1,1,1,2,2,2,2,3,3,3,3,4,4,5,5,5,5,6,6,7,7,7,7,8,8)
  date_bins <- get.date.bins(raw_data, flight_group)
  best_locations <- get.best.locations(river_detects, date_bins =  date_bins, bin_by=NA, n_thresh = 5, dist_max = 5, remove_flagged = T)
  best_detects <- best_locations$best_detects
  hmm_survival <- hmm.survival(best_detects, t_star = .3)
}
hmm_survival$results


# Notes: it's getting there, but right now, a bunch of fish are being killed
# Try to impose additional structure on the emission matrix -- fish that move are alive
# msm seems to be mixing up outcomes ?



hmm_survival$viterbi
load("D:/Jordy/telprep/telprep/data/spdf.Rdata")
library(rgeos)
plot.locations(spdf, best_detects, col_by_fish = F, flight=8,viterbi=T)