## Co-occurrence_CTs_ARUs This repository contains data, code and results associated with: Vélez, J., McShea, W., Pukazhenthi, B., Stevenson, P. and J. Fieberg. 2023. Implications of the scale of detection for inferring co-occurrence patterns from paired camera traps and acoustic recorders. *Conservation Biology*, 00, e14218. https://doi.org/10.1111/cobi.14218 The objective of this study was to investigate the association between two measures of disturbance (poaching and livestock) and wild ungulates using data collected with camera traps and autonomous acoustic recording units. We quantified these associations using joint species distribution models (JSDMs) fit to data from multifunctional landscapes of the Orinoquía region of Colombia. We also evaluated the effect of the detection scale of camera traps and acoustic recorders for inferring co-occurrence patterns between wildlife and disturbance factors. ## Author information Name: Juliana Vélez Institution: Department of Fisheries, Wildlife, and Conservation Biology - University of Minnesota Address: 135 Skok Hall. 2003 Upper Buford Circle. Saint Paul, MN 55108 Email: velez063@umn.edu ORCID: https://orcid.org/0000-0003-0412-2761 Name: William McShea Institution: Smithsonian's National Zoo and Conservation Biology Institute Address: 1500 Remount Rd, Front Royal, VA 22630 Email: McSheaW@si.edu ORCID: https://orcid.org/0000-0002-8102-0200 Name: Budhan Pukazhenthi Institution: Smithsonian's National Zoo and Conservation Biology Institute Address: 1500 Remount Rd, Front Royal, VA 22630 Email: pukazhenthib@si.edu ORCID: https://orcid.org/0000-0003-4657-2023 Name: Pablo Stevenson Institution: Department of Biological Sciences. Universidad de los Andes Address: Carrera 1 # 18A - 12, Bogotá, 111711, Colombia Email: pstevens@uniandes.edu.co ORCID: https://orcid.org/0000-0003-2394-447X Name: John Fieberg Institution: Department of Fisheries, Wildlife, and Conservation Biology - University of Minnesota Address: 135 Skok Hall. 2003 Upper Buford Circle. Saint Paul, MN 55108 Email: jfieberg@umn.edu ORCID: https://orcid.org/0000-0002-3180-7021 ## Data - cams_operation_site.RDS: camera traps operation matrix - covariates.RDS: data frame of site covariates - data_bundles.rdata: lists containing detection-nondetection arrays, occupancy and detection covariates and site coordinates. - indep_recs.RDS: list containing independent records of the surveys with camera traps and acoustic recorders. - moth_operation_site.RDS: acoustic recorders operation matrix ## Programs - 1_detection_array.R: creates data bundles to fit JSDMs. - Input: data/indep_recs.RDS, data/cams_operation_site.RDS, data/moth_operation_site.RDS, data/covariates.RDS - Output: data/data_bundles.rdata - 2a_sfMsPGOcc.R: fits multi-species spatial occupancy model with species correlations. - Input: data/indep_recs.RDS - Output: results/spOccupancy_fits/julian_dry_rainy_spatial - 2b_lfMsPGOcc.R: fits multi-species non-spatial occupancy model with species correlations. - Input: data/indep_recs.RDS - Output: results/spOccupancy_fits/julian_dry_rainy_nonspatial - 3_waic_convergence.R: gets WAIC and assesses model convergence. - Input: results/spOccupancy_fits - Output: results/waic/waic_df.RDS, results/best_mods/fits_best_models.RDS - 4_covariates_effects.R: gets and plots occupancy estimates and covariates effects. - Input: results/best_mods/fits_best_models.RDS - Output: results/estimates, figures/occ_\*.RDS, figures/det_\*.RDS - 5_predictions.R: gets model predictions for the effect of covariates on occupancy probability. - Input: data/data_bundles.rdata, results/best_mods/fits_best_models.RDS. - Output: figures/marginal_\*.RDS - 6_sp_correlation.R: gets species correlations - Input: data/data_bundles.rdata, results/best_mods/fits_best_models.RDS - Output: results/estimates/ci_corr.RDS, figures/corr_\*.RDS ## Session information R version 4.2.1 (2022-06-23) Platform: aarch64-apple-darwin20 (64-bit) Running under: macOS Monterey 12.2.1 Matrix products: default LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] ggdist_3.2.1 ggcorrplot_0.1.4 tidybayes_3.0.3 posterior_1.3.1 sf_1.0-9 [6] coda_0.19-4 spOccupancy_0.5.2 Matrix_1.5-3 here_1.0.1 forcats_1.0.0 [11] stringr_1.5.0 dplyr_1.1.0 readr_2.1.4 tidyr_1.3.0 tibble_3.1.8 [16] ggplot2_3.4.1 tidyverse_1.3.2 purrr_1.0.1 loaded via a namespace (and not attached): [1] nlme_3.1-162 fs_1.6.1 lubridate_1.9.2 doParallel_1.0.17 [5] webshot_0.5.4 httr_1.4.4 rprojroot_2.0.3 tensorA_0.36.2 [9] tools_4.2.1 backports_1.4.1 utf8_1.2.3 R6_2.5.1 [13] KernSmooth_2.23-20 DBI_1.1.3 colorspace_2.1-0 withr_2.5.0 [17] tidyselect_1.2.0 compiler_4.2.1 cli_3.6.0 rvest_1.0.3 [21] arrayhelpers_1.1-0 xml2_1.3.3 checkmate_2.1.0 scales_1.2.1 [25] classInt_0.4-8 proxy_0.4-27 systemfonts_1.0.4 digest_0.6.31 [29] minqa_1.2.5 rmarkdown_2.20 svglite_2.1.1 pkgconfig_2.0.3 [33] htmltools_0.5.4 lme4_1.1-31 dbplyr_2.3.0 fastmap_1.1.0 [37] rlang_1.0.6 readxl_1.4.2 rstudioapi_0.14 svUnit_1.0.6 [41] farver_2.1.1 generics_0.1.3 jsonlite_1.8.4 distributional_0.3.1 [45] googlesheets4_1.0.1 magrittr_2.0.3 kableExtra_1.3.4.9000 Rcpp_1.0.10 [49] munsell_0.5.0 fansi_1.0.4 abind_1.4-5 lifecycle_1.0.3 [53] stringi_1.7.12 yaml_2.3.7 MASS_7.3-58.2 grid_4.2.1 [57] parallel_4.2.1 crayon_1.5.2 lattice_0.20-45 haven_2.5.1 [61] splines_4.2.1 hms_1.1.2 knitr_1.42 pillar_1.8.1 [65] boot_1.3-28.1 codetools_0.2-19 reprex_2.0.2 glue_1.6.2 [69] evaluate_0.20 modelr_0.1.10 vctrs_0.5.2 nloptr_2.0.3 [73] tzdb_0.3.0 foreach_1.5.2 cellranger_1.1.0 gtable_0.3.1 [77] RANN_2.6.1 assertthat_0.2.1 xfun_0.40 broom_1.0.3 [81] e1071_1.7-13 class_7.3-21 googledrive_2.0.0 viridisLite_0.4.1 [85] gargle_1.3.0 iterators_1.0.14 units_0.8-1 timechange_0.2.0 [89] ellipsis_0.3.2