Data from: A classification-occupancy model based on automatically identified species data

Data and code repository associated with the publication: Ogawa, Ryo, Frédéric Gosselin, Kevin F. A. Darras, Stephanie Roilo, and Anna F. Cord. 2025. “A Classification-Occupancy Model Based on
Automatically Identified Species Data.” Ecology e70086. https://doi.org/10.1002/ecy.70086

This folder includes the data, codes, and results of manuscript in addition to tutorial material for the proposed model. The Rscripts include both simulation and case study analyses. Some of the data include sensitive information, but the proposed model can be analyzed with the data included in this depository. In addition, all the processed data and result figures can be found from this depository.

## Description of the data and file structure
cls_occ/
    readme.txt
    batch/
        case_study.txt
        simulation.txt
    input/
        all_aid.txt
        amplitude_ambient_manual.csv
        amplitude_signal_manual.csv
        annotation.csv
        species_count.csv
        species_data.csv
        Xdet.csv
        Xocc_ori.csv
    jagscodes/
        model1.txt
        model2.txt
        model3.txt
        model4.txt
        readme.txt
    output/
        case_study/
            detection_space.csv
            MCMCparams.csv
            Alauda arvensis/
                model1.RData
                model2.RData
                model3.RData
                model4.RData
            Curruca communis/
                model1.RData
                model2.RData
                model3.RData
                model4.RData
            Emberiza citrinella/
                model1.RData
                model2.RData
                model3.RData
                model4.RData
            model_eval/
                Alauda arvensis.csv
                Curruca communis.csv
                Emberiza citrinella.csv
                Motacilla flava.csv
                Passer montanus.csv
            Motacilla flava/
                model1.RData
                model2.RData
                model3.RData
                model4.RData
            Passer montanus/
                model1.RData
                model2.RData
                model3.RData
                model4.RData
        simulation/
            result_300524.csv
            result_300524_aggr.csv
    plot/
        Alauda arvensis.jpg
        confidence_score_correlation.jpg
        Curruca communis.jpg
        detection_fp.jpg
        Emberiza citrinella.jpg
        model_eval.jpg
        Motacilla flava.jpg
        Passer montanus.jpg
        ppp_chi_m4.jpg
        ppp_sos_m4.jpg
        score_histogram.jpg
    rscript/
        1_simulation.R
        2_case_study.R
        3_model_eval.R
        readme.txt
        utils.R
        figures/
            fig2_model_eval_summary.R
            figS10_confidence_score_correlation.R
            figS8_detection_fp.R
            figS9_score_histogram.R
            figsS1-S2_ppp_plot.R
            figsS3-S7_sd_map.R
        tables/
            tab1_simulation_aggr.R
            tabS4_detection_space.R
            tabS5_MCMCparams.R
    tutorial/
        cls_occ_tutorial.RData
        model4.txt