Data and code for manuscript “How to better count elusive birds? Comparing non-invasive monitoring methods to estimate population size of the threatened Pin-tailed sandgrouse (Pterocles alchata)”

Description of the data and file structure

Code

This repository contains the following code files:

GMR folder

• CR_model_run_results.r: R code to arrange the data, run the GMR model and process results
• simulation_test_accuracy.r: R code of the simulation performed to test the accuracy of the GMR approach under our study conditions

optimize_cost folder: analyses to optimize costs of GMR approach. This folder includes:

• 1.optimize_subsample_dataSum: Run CMR model by randomly selecting between 50% and 95% of the samples with successful genetic identification. Results are stored in results_per2.RData, which are provided as data files and loaded in script 3
• 2.optimize_remove_oc: Run CMR model by removing between 1 and 3 sampling occasions in all possible combinations. Results are stored in results_oc_remove.RData, which are provided as data files and loaded in script 3
• 3. process_results: Assess bias and CV from cost optimization analyses (scripts 1 and 2)

MultispeciesHDS

• MultispeciesHDS_model_run_results.r: R code to arrange the data, run the MultispeciesHDS model and process results. Model results are stored in 3.Dat_HDS_trendmodel_lam[hq_weight_CAT2]_sigHR.RData, which are provided as data files
• 3.HDS_trendmodel_lam[hqCAT]_sigHR_noW: MultispeciesHDS model

SandgrouseHDS

• SandgrouseHDS_model_run_results.r: R code to arrange the data, run the SandgrouseHDS model and process results.
• 1.2.HDS_sig[HR_inf_fullModel]_lam[hq[inf]_CAT]_corrected: SpecificHDS model
• simulation_repeatedSurveys_sandgrouseHDS: R code for simulation performed to test how many HDS surveys would be needed to reach the precision of GMR
• 5.HDS_2Survey_sig[HR_inf_fullModel]_lam[hq[inf]_CAT]: SpecificHDS model with additional survey dimension for the simulation performed in the script simulation_repeatedSurveys_sandgrouseHDS

Data

The Zenodo repository https://zenodo.org/records/14387266?token=eyJhbGciOiJIUzUxMiJ9.eyJpZCI6Ijc5NjlkYTdiLTY0ZTItNDVjZi05OGU1LWFiYzFjZTc3ODQxYSIsImRhdGEiOnt9LCJyYW5kb20iOiI3MDRiMzllYWYyMjJlNjU1ZjBjMWUxMDk2YzhlYjlkMSJ9.-XL0ckizaV1vrU6spF7Pjh0iVvmluqFyM3Hz_mDNLu7LssAymPSepS-QKvdYYBGxFhFH5pzO7f8jxG1IIP9Vdw contains all data files needed to run the aboved described scripts. Please ask corresponding author to get access to the data files.