Separate quick residency analysis

analyses/patter_04_qresidency.R

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+###########################
+###########################
+#### patter-qresidency.R
+
+#### Aims
+# 1) Quick residency analysis
+
+#### Prerequisites
+# 1) patter-algorithms.R
+
+
+###########################
+###########################
+#### Set up 
+
+#### 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(tictoc)
+dv::src()
+
+#### Load data
+paths       <- qs::qread(here_input("paths.qs"))
+
+
+###########################
+###########################
+#### Quick residency analysis
+
+#### TO DO
+# * Iterate over indidividuals
+# * Compute true & estimated residency 
+
+#### 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.
+###########################
+###########################