A dataset of Hainan black-crested gibbon and forest bird activity, China 2021

This repository contains the data and code used for the research paper "The gibbon umbrella: Acoustic monitoring demonstrates conservation spill-over for tropical rainforest birds".The original data were recorded across 15 sample sites in Bawangling National Nature Reserve, Hainan Province, China, using SongMeter 4 acoustic loggers from Jun to Sep 2021 and processed using the algorithms for gibbon call detection by Wang et al (2024) and for bird call detection by Liu et al (in preparation), with environmental variables of each sample point.To protect the location of the critically endangered Nomascus hainanus species, sample point coordinates were aggregated to a 0.1° resolution (~10 km).The dataset is divided into 2 folders, Code and Data:===========================================Code===========================================This directory has 4 R scripts to process the data and generate results in the study1. Data importing and preparation.RThis script contains the code to import and process the data and prepare for the following sections2. Spatio-temporal patterns GLMM.RThis script contains the code to perform zero-inflated generalised linear mixed-effect models for spatio-temporal patterns in activity of Hainan black-crested gibbons, bird community, and specific avian foraging guilds. It is used for plotting figures 2, 3, S1, S2 and S3.3. Correlation between gibbons and bird activity and spp richness.RThis script contains the code to perform models assessing the correlation between site-level activity of gibbons and birds in total / foraging guilds, and between gibbon activity and bird species richness. It is used for plotting figures 4 and 6.4. Correlation between bird species and gibbon activity.RThis script contains the code for processing site-level activity of individual bird species and performing correlation test with corresponding activity of gibbons. It is used for plotting figure 5.===========================================Data===========================================This directory has 10 CSV files, 7 necessary to perform the analysis and 3 generated by the code for analysis in other script filesbird_detection.csvThis CSV file contains acoustic classification results of all bird calls using the algorithm developed by Liu et al (in preparation). Due to algorithm development settings, the species names (Spp1, Spp2 and Spp3) are in Chinese, but are later converted into English in the codes. As Spp1 always has the highest confidence (Prob1), only Spp1 is used in the analysisgibbon_detection.csvThis CSV files contains acoustic classification results of Hainan black-crested gibbon calls using the algorithm developed by Wang et al (2024). The rhythm score used for selecting confidence is displayed in the "ribbit" columnsite_soundscape_indices.csvThis CSV file contains soundscape indices generated for all recordings using the algorithm developed by Towsey et al (2018). It was eventually not analysed in this study, but used to match list of files to include hours with no bird/gibbon calls detected.site_env_vars.csvThis CSV file contains environmental information of sample sites, including:machine namesite IDlongitude, latitude (rounded to nearest 0.1 for protection of critically endangered Hainan black-crested gibbons (Nomascus Hainanus))altitudelandscape (a measure for altitude, not used for analysis)slope (1 = flat (0-5), 2 = gentle (5-15), 3 = intermediate (15-25), 4 = steep (25-35))type of forest habitatslope facing directioncanopy covertype of disturbance (not used for analysis)group of samplers (not used for analysis)bird_species_abundant.csvThis CSV file contains bird species with >5 detections in the analysis, in both Chinese and Latin namesbird_species_higherror.csvThis CSV file contains bird species which were validated to have high error-classification rates, in both Chinese and Latin names, and were removed from analysisbird_species_diet.csvThis CSV file contains dietary preferences of bird species in China, extracted from the data by Wang et al (2021). The species names and diets are in Chinese, but are later converted into English in the codeshainan_all_hour_diet.csvThis CSV file is generated using the code from "1. Data importing and preparation.R". It contains the hourly detections of gibbons (n), birds in total (Total), raptors (Rapt), insectivorous birds (Inse), omnivorous birds (Omni) and florivorous birds (Flor), merged with the soundscape indices and evironmental information of sites fom above.It is used for analysis in "2. Spatio-temporal patterns GLMM.R".hainan_bird_hour_spThis CSV file is generated using the code from "1. Data importing and preparation.R". It contains the hourly detections of the 28 bird species included in this study at each site. The species names are in Chinese, but are later converted into English in the codesIt is used for analysis in "4. Correlation between bird species and gibbon activity.R".hainan_bird_site.csvThis CSV file is generated using the code from "3. Correlation between gibbons and bird activity and spp richness.R". It contains the site-level activity measures of:gibbons (Gibbon_)birds in total (Total_)raptors (Rapt_)omnivorous birds (Omni_)insectivorous birds (Inse_)florivorous birds (Flor_)And different activity measures of each of the taxa/guild above, including:Site-total detections (_T)Site-maximum hourly detections (_MaxMax)Site-average daily peak hourly detections (_Amax)Site-maximum daily average hourly detections (_MaxA)Site-average hourly detections (_D)Site species richness of birds in total and foraging guild (_Count)===========================================