MS_turtle-abund_orthomosaics

This repository contains data and code scripts for the manuscript "Estimating abundance of aggregated populations with drones while accounting for multiple sources of errors: a case study on the mass nesting of Giant South American River Turtles" (Brack et al. not published).

Repository content

• Appendix2_tutorial/: files used to create Appendix S2, with the tutorial to simulate and analyze data

• data/: original turtle data

  • encounter-history_counts.csv: number of appearances for each individual in each occasion
  • encounter-history_states.csv: observed state for each individual in each occasion
  • mark_occasions.csv: marking occasion for each individual
  • mark_identification.txt: number of marked individuals with marks identified and unidentified
  • PopulationCounts.txt: Overall population counts

• ms/: manuscript files used in the submission

• outputs/: output objects from models fitted to the turtle data

  • MR5_postMCMC.txt: posterior samples of the mark-resight model (step 1)
  • Counts5_phi1_postMCMC/: folder containing the posterior samples for the population counts model (step 2) fitted for each posterior sample of step 1

• R/: R code scripts to fit the turtle data

  • nimble_counts b(T)theta(.)phi(.)delta(.)omega(.).R: nimble code for the population counts model (step 2)
  • nimble_MR5 theta(.)phi(occ)delta(.)omega(.).R: nimble code for the mark-resight model (step 1)
  • see_results multi-samps.R: code to see model results and create figures
  • turtle_fit step1 MR5.R: code to fit the mark-resight model to the turtle data (step 1)
  • turtle_fit step2 counts5.R: code to fit the population counts model to the turtle data (step 2)