Start revamp

Author: edwardlavender

analyses/patter_02_analyses.R

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+###########################
+###########################
+#### patter-analyses
+
+#### Aims
+# 1) Run patter analyses
+
+#### Prerequisites
+# 1) patter-setup.R
+
+
+###########################
+###########################
+#### Setup 
+
+#### Wipe workspace 
+rm(list = ls())
+# try(pacman::p_unload("all"), silent = TRUE)
+dv::clear()
+
+#### Essential packages
+library(data.table)
+library(dtplyr)
+library(dplyr, warn.conflicts = FALSE)
+library(JuliaCall)
+library(lubridate)
+library(patter)
+library(tictoc)
+
+#### Load data 
+champlain  <- terra::vect("data/ChamplainRegions.shp")
+moorings   <- readRDS("data/moorings.rds")
+detections <- readRDS("data/simulated_detections.rds")
+metadata   <- readRDS("data/simulations_metadata.rds")
+dv::src()
+
+#### Julia setup 
+julia_connect()
+set_seed()
+set_map()
+
+###########################
+###########################
+#### Prepare algorithms
+
+
+###########################
+#### Individual datasets
+
+#### Define individual & associated datasets
+id   <- 1
+sid  <- paste0("sim_", id)
+path <- paths[sim_id == id, ]
+dets <- detections[sim_id == sid, ]
+meta <- metadata[sim_id == sid, ]
+stopifnot(nrow(meta) == 1L)
+
+
+###########################
+#### Define study timeline
+
+# The timeline is individual specific
+# Start time: "2022-01-01 00:00:00"
+# Simulated tracks comprised 5000 steps
+# Each step comprised 500 m
+# But velocity set to different values in transmit_along_path()
+# I.e., For each individual, the duration of a step length is different 
+# Transmissions were generated along the paths every 120 + 7 s
+
+# Calculate the step duration
+trms_time    <- 120 # + 7                  # transmission time (every 127 s)
+mvt_speed    <- meta$velocity              # speed @ each _movement_ time step (m/s)
+mvt_distance <- 500                        # distance moved at each _movement_ time step (m)
+mvt_time     <- mvt_distance / mvt_speed   # duration of each _movement_ time step (s)
+
+# Define simulation start and end times
+end      <- max(seq(start, length.out = 5000, by = paste(mvt_time, "secs")))
+
+# Define timeline 
+# * The timeline is based on a transmission interval of ~2 mins
+# * (The step length (m) in ~2 mins given {mvt_speed} is {mvt_speed} * {trms_time})
+# * (The angle is simulated every {mvt_time} s)
+timeline <- seq.POSIXt(start, end, by = paste(trms_time, "secs"))
+
+# Validate that the timeline spans the detection time series for the ID
+stopifnot(interval(min(dets$timestamp), max(dets$timestamp)) %within% interval(min(timeline), max(timeline)))
+
+
+###########################
+#### Movement model
+
+#### Movement & timeline validation
+# Check simulated step lengths and turning angles at 127 s resolution 
+# * The path was simulated with 5000 steps, each of {mvt_time} secs
+# * complete_simulated_transmissions_regions.rds contains the 'full' path @ resolution of 127 s
+# * Step lengths should match {mvt_speed} (m/s) * {trms_time} (s)
+mvt_len <- mvt_speed * trms_time
+if (FALSE) {
+  movements <- 
+    path |> 
+    lazy_dt() |> 
+    select(sim_id, date = timestamp, x, y) |> 
+    as.data.frame() |> 
+    bayesmove::prep_data(coord.names = c("x", "y"), id = "sim_id")
+  unique(diff(movements$date)) # time stamps evenly spaced
+  unique(movements$step)       # step lengths not exactly equal 
+  hist(movements$step)         # but most step lengths are correct
+  unique(movements$angle)      # angles (radians)
+}
+# Check distance of individual to receiver @ moment of detection
+# TO DO
+
+#### Define movement model
+# Paths were simulated via glatos::crw_in_polygon() which calls glatos::crw()
+# * https://github.com/ocean-tracking-network/glatos/blob/main/R/sim-crw_in_polygon.r
+# * https://github.com/ocean-tracking-network/glatos/blob/main/R/simutil-crw.r
+# Step length in {trms_time} given {mvt_speed} is {mvt_speed} (m/s) * {trms_time} (s)
+# heading_{t = 1} = Uniform(0, 360) 
+# heading_{t > 1} = Normal(0, meta$theta) + cumsum(heading{t = 1, ..., t}) 
+# Angles updated every {mvt_time} (s) / {trms_time} (s) time steps
+# (Internally glatos enlarges the SD if the simulation steps outside the polygon!)
+state              <- "StateXYD"
+model_move         <- move_xyd(length = mvt_len, theta = meta$theta)
+update_angle_every <- round(mvt_time / trms_time)
+julia_assign("update_angle_every", update_angle_every)
+julia_command('include("Julia/src/model-movement.jl");')
+
+
+###########################
+#### Define observation model
+
+model_obs   <- c("ModelObsAcousticLogisTrunc", "ModelObsAcousticContainer")
+acoustics   <- assemble_acoustics(.timeline = timeline, .acoustics = dets, .moorings = moorings)
+containers  <- assemble_acoustics_containers(.acoustics = acoustics, 
+                                            .direction = "forward", 
+                                            .mobility = mvt_len, 
+                                            .threshold = ydist)
+yobs        <- list(ModelObsAcousticLogisTrunc = acoustics, 
+                    ModelObsAcousticContainer = containers)
+
+
+###########################
+###########################
+#### Algorithm runs 
+
+#### Define filter arguments 
+args <- list(.map = map, 
+             .timeline = timeline, 
+             .state = state, 
+             .xinit = NULL, 
+             .xinit_pars = list(mobility = mvt_len),
+             .yobs = yobs, 
+             .model_obs = model_obs, 
+             .model_move = model_move, 
+             .n_particle = 10000L, 
+             .direction = "forward"
+             )
+
+
+#### Run forward filter 
+# * NB: Setting observations is slow (1 min)
+# > Weights from filter (1 -> 208292) are zero at time 62367
+fwd <- do.call(pf_filter, args, quote = TRUE)
+
+#### Run backward filter
+# * Update containers & yobs for .direction = "backward", then run filter
+containers      <- assemble_acoustics_containers(.acoustics = acoustics, 
+                                                 .direction = "backward", 
+                                                 .mobility = distance, 
+                                                 .threshold = ydist)
+yobs            <- list(ModelObsAcousticLogisTrunc = acoustics, 
+                        ModelObsAcousticContainer = containers)
+args$.yobs      <- yobs
+args$.direction <- "backward"
+do.call(pf_filter, args, quote = TRUE)
+
+#### Run smoother 
+out_smo <- pf_smoother_two_filter()
+
+
+###########################
+###########################
+#### Quick residency analysis
+
+#### True residency in each region
+path_res <- 
+  path |> 
+  group_by(region) |> 
+  summarise(n = n()) |> 
+  mutate(residency = (n / sum(n)) * 100, 
+         estimate = "path", 
+         sim_id = id) |> 
+  as.data.table()
+
+#### Particle residency estimates
+part_res <- 
+  out_smo |> 
+  mutate(region = terra::extract(map, cbind(x, y))) |>
+  group_by(region) |> 
+  mutate(residency = (n / sum(n)) * 100, 
+         estimate = "smoother", 
+         sim_id = id) |> 
+  as.data.table()
+
+#### Collect data
+res <- rbind(path_res, part_res)
+qs::qsave(res, "data/patter/output/residency/qresidency/", paste0(id, ".qs"))
+
+
+###########################
+###########################
+#### Synthesis
+
+# Read residency data for each individual 
+residency <- 
+  lapply(unique(paths$sim_id), function(id) {
+  qs::qread("data/patter/qresidency.qs")
+}) |> rbindlist()
+
+# Visualise residency ~ individual, coloured by truth/algorithm
+# 
+# > TO DO
+
+
+#### End of code. 
+###########################
+###########################