This repository contains code to accompany the manuscript Acoustic indices reveal fundamental differences in daily phenology of tropical and temperate forest soundscapes
This repository uses acoustic indices calculated from approximatly one month of continuous audio data from forests around the world. The indices power minus noise (PMN), acoustic complexity index (ACI), inverse acoustic entropy (ENT), and acoustic events (EVN) are present for all sites. Acoustic indices were calculated using the QUT Ecoacoustics Analysis Programs (https://ap.qut.ecoacoustics.info/).
Site Details: (click to expand)
| Country | Locality | ID | Lat | Lon | Start Date | End Date | Duration (days) | Sampling Rate | Bit Depth | Time Zone |
|---|---|---|---|---|---|---|---|---|---|---|
| USA | Baraboo Hills, Wisconsin | W1 | 43.37174736 | -89.90704676 | 06 May 2024 | 01 June 2024 | 26 | 44 kHz | 16 | America/Chicago |
| USA | Baraboo Hills, Wisconsin | W2 | 43.35882402 | -89.93848797 | 06 May 2024 | 01 June 2024 | 26 | 44 kHz | 16 | America/Chicago |
| USA | Baraboo Hills, Wisconsin | W3 | 43.39660723 | -89.83137264 | 06 May 2024 | 01 June 2024 | 26 | 44 kHz | 16 | America/Chicago |
| USA | Baraboo Hills, Wisconsin | W4 | 43.39508251 | -89.80117434 | 06 May 2024 | 01 June 2024 | 26 | 44 kHz | 16 | America/Chicago |
| USA | Baraboo Hills, Wisconsin | W5 | 43.47777985 | -89.53238905 | 06 May 2024 | 01 June 2024 | 26 | 44 kHz | 16 | America/Chicago |
| USA | Baraboo Hills, Wisconsin | W6 | 43.39200048 | -89.74750963 | 06 May 2024 | 01 June 2024 | 26 | 44 kHz | 16 | America/Chicago |
| Germany | Bavarian Forest National Park | D1 | 49.1009 | 13.25033 | 24 April 2024 | 31 May 2024 | 37 | 44 kHz | 16 | Europe/Berlin |
| Germany | Bavarian Forest National Park | D2 | 49.10139 | 13.23153 | 24 April 2024 | 31 May 2024 | 37 | 44 kHz | 16 | Europe/Berlin |
| Germany | Bavarian Forest National Park | D3 | 49.10505 | 13.27662 | 24 April 2024 | 31 May 2024 | 37 | 44 kHz | 16 | Europe/Berlin |
| Germany | Bavarian Forest National Park | D4 | 49.08456 | 13.29535 | 24 April 2024 | 31 May 2024 | 37 | 44 kHz | 16 | Europe/Berlin |
| Germany | Bavarian Forest National Park | D5 | 48.97583 | 13.4074 | 24 April 2024 | 31 May 2024 | 37 | 44 kHz | 16 | Europe/Berlin |
| Ecuador | Tiputini Biodiversity Station | E1 | -0.626352081 | -76.15847094 | 28 October 2023 | 28 November 2023 | 31 | 44 kHz | 16 | America/Guayaquil |
| Ecuador | Tiputini Biodiversity Station | E2 | -0.622623236 | -76.1680306 | 28 October 2023 | 28 November 2023 | 31 | 44 kHz | 16 | America/Guayaquil |
| Ecuador | Tiputini Biodiversity Station | E3 | -0.637504435 | -76.16144759 | 28 October 2023 | 28 November 2023 | 31 | 44 kHz | 16 | America/Guayaquil |
| Ecuador | Yasuni National Park | E4 | -0.645339819 | -76.15253577 | 28 October 2023 | 28 November 2023 | 31 | 44 kHz | 16 | America/Guayaquil |
| Ecuador | Yasuni National Park | E5 | -0.654439859 | -76.15120798 | 28 October 2023 | 28 November 2023 | 31 | 44 kHz | 16 | America/Guayaquil |
| Ecuador | Tiputini Biodiversity Station | E6 | -0.647766427 | -76.14189748 | 28 October 2023 | 28 November 2023 | 31 | 44 kHz | 16 | America/Guayaquil |
| Peru | Manu Biostation | P1 | -12.86868656 | -71.40609202 | 18 May 2023 | 17 June 2023 | 30 | 44 kHz | 16 | America/Lima |
| Peru | Manu Biostation | P2 | -12.85624692 | -71.40484994 | 18 May 2023 | 17 June 2023 | 30 | 44 kHz | 16 | America/Lima |
| Peru | Manu Biostation | P3 | -12.84383793 | -71.43848974 | 18 May 2023 | 17 June 2023 | 30 | 44 kHz | 16 | America/Lima |
| Peru | Manu Biostation | P4 | -12.84908506 | -71.43096178 | 18 May 2023 | 17 June 2023 | 30 | 44 kHz | 16 | America/Lima |
| Peru | Manu Biostation | P5 | -12.85892047 | -71.42751104 | 18 May 2023 | 17 June 2023 | 30 | 44 kHz | 16 | America/Lima |
| Peru | Manu Biostation | P6 | -12.86982163 | -71.42605954 | 18 May 2023 | 17 June 2023 | 30 | 44 kHz | 16 | America/Lima |
| Gabon | Makokou Massaha | GAB1 | 0.676958399 | 13.23575422 | 15 October 2022 | 11 November 2022 | 27 | 44 kHz | 16 | Africa/Libreville |
| Gabon | Makokou Massaha | GAB2 | 0.67348049 | 13.24577163 | 15 October 2022 | 11 November 2022 | 27 | 44 kHz | 16 | Africa/Libreville |
| Gabon | Makokou Massaha | GAB3 | 0.666384095 | 13.25243964 | 15 October 2022 | 11 November 2022 | 27 | 44 kHz | 16 | Africa/Libreville |
| Gabon | Makokou Massaha | GAB4 | 0.663965784 | 13.24175956 | 15 October 2022 | 11 November 2022 | 27 | 44 kHz | 16 | Africa/Libreville |
| Gabon | Makokou Massaha | GAB5 | 0.664278632 | 13.23158164 | 15 October 2022 | 11 November 2022 | 27 | 44 kHz | 16 | Africa/Libreville |
| Gabon | Makokou Massaha | GAB6 | 0.671013075 | 13.22454552 | 15 October 2022 | 11 November 2022 | 27 | 44 kHz | 16 | Africa/Libreville |
| Sierra Leone | Gola Rainforest National Park | GRNP_1 | 7.65075603 | -10.913293 | 12 December 2021 | 25 December 2021 | 13 | 44 kHz | 16 | Africa/Freetown |
| Sierra Leone | Gola Rainforest National Park | GRNP_12 | 7.63740098 | -10.905513 | 12 December 2021 | 25 December 2021 | 13 | 44 kHz | 16 | Africa/Freetown |
| Sierra Leone | Gola Rainforest National Park | GRNP_176 | 7.65075733 | -10.882183 | 12 December 2021 | 25 December 2021 | 13 | 44 kHz | 16 | Africa/Freetown |
| Sierra Leone | Gola Rainforest National Park | GRNP_369 | 7.6463062 | -10.905516 | 12 December 2021 | 25 December 2021 | 13 | 44 kHz | 16 | Africa/Freetown |
| Sierra Leone | Gola Rainforest National Park | GRNP_397 | 7.63739701 | -10.889954 | 12 December 2021 | 25 December 2021 | 13 | 44 kHz | 16 | Africa/Freetown |
| Sierra Leone | Gola Rainforest National Park | GRNP_811 | 7.64630049 | -10.921076 | 12 December 2021 | 25 December 2021 | 13 | 44 kHz | 16 | Africa/Freetown |
| Brunei | Kiudang | Kiudang 2 | 4.71972 | 114.76777 | 01 January 2024 | 01 February 2024 | 31 | 44 kHz | 16 | Asia/Brunei |
| Brunei | Kiudang | Kiudang C | 4.69333 | 114.77122 | 01 January 2024 | 01 February 2024 | 31 | 44 kHz | 16 | Asia/Brunei |
| Singapore | Central Catchment Nature Reserve | CCNR | 1.355488 | 103.804549 | 23 June 2020 | 08 July 2020 | 15 | 16 kHz | 16 | Asia/Singapore |
| Singapore | Dairy Farm Nature Park | DAFA | 1.358419 | 103.777492 | 23 June 2020 | 08 July 2020 | 15 | 16 kHz | 16 | Asia/Singapore |
| Singapore | National University of Singapore | NUS | 1.295069 | 103.779266 | 23 June 2020 | 08 July 2020 | 15 | 16 kHz | 16 | Asia/Singapore |
| Singapore | Sungei Buloh Wetland Reserve | SBWR | 1.441586 | 103.735308 | 23 June 2020 | 08 July 2020 | 15 | 16 kHz | 16 | Asia/Singapore |
The complete data set is too large to be stored on Github. To access the data, please go to the Zenodo data repository: DOI: 10.5281/zenodo.18165143 (https://doi.org/10.5281/zenodo.18165143)
Average Day Files
Files with "avgDay" in their names have averaged together all the days and sites of each country. These data were used to generate false-color spectrogram figures showing typical soundscapes of each country. These files follow the naming convention "index_avgDay.csv" and have a 1-minute temporal resolution across a 24-hour period, and a 43.1 Hz frequency resolution ranging from 0.2155 kHz to 10.6888 kHz.
| Variable | Description |
|---|---|
| Time | Time of day in POSIXct format with 1-minute resolution. POSIXct is a date-time format, but this variable records only time, so the same arbitrary date is used for all values. |
| Frequency | Frequency in Hz |
| avgACI | Average Acoustic Complexity Index. Averaged across days and sites of the same country, frequency, and time. |
| avgENT | Average Inverse Entropy Index. Averaged across days and sites of the same country, frequency, and time. |
| avgEVN | Average Acoustic Events. Averaged across days and sites of the same country, frequency, and time. |
| avgPMN | Average Power Minus Noise. Averaged across days and sites of the same country, frequency, and time. |
| Country | Country where the audio was recorded |
| Realm | Biogeographic realm according to Dinerstein et al. 2017 |
10-minute PCA Files
The file "PCAinput_allIndices_allCountries_10minAvg.csv" was used for PCA analysis and differs from the average day files in that it has a 10-minute temporal resolution and separate values for each site.
| Variable | Description |
|---|---|
| frequency | Frequency in Hz |
| Time_10min | Time rounded to the nearest 10 minutes. A period object in the format hh:mm:ss |
| ACI | Average Acoustic Complexity Index. Averaged across days of the same site, country, frequency, and time |
| ENT | Average Inverse Entropy Index. Averaged across days of the same site, country, frequency, and time |
| EVN | Average Acoustic Events Index. Averaged across days of the same site, country, frequency, and time |
| PMN | Average Power Minus Noise. Averaged across days of the same site, country, frequency, and time |
| Site | Site where the audio was recorded. Coordinates are in metadata |
| Country | Country where the audio was recorded |
Representative samples (audio)
Some representative examples of audio from each ecoregion have been provided. Audio samples match those visualized in Figure S3 of the supplementary materials. A single day from a single site from each ecoregion has been selected, and four audio files have been provided for each: one from dawn, one from noon, one from dusk, and one at night.
Audio files follow the naming convention "Site_yyyymmdd_hhmmss.wav", where the date and time are the start time of the recording. Each recording is 30-minutes long.
The provided code is sufficient to regenerate all the figures of the manuscript using the data archived on zenodo (10.5281/zenodo.18165143). Code for earlier steps in data analysis are also provided for the sake of transparency, but intermediate and unfinalized datasets have not been archived.
| R Script | Purpose |
|---|---|
| preprocessingPCA.R | data cleaning, reformatting, averaging |
| Figure1_map.R | generate Figure 1 |
| SBP_PCA_soundscapeSimilarity.R | run PCA, generate Figures 2, S1, S2 |
| RGB_panel_plot.R | generate Figure 3 |
| PMN_panel_plot.R | generate Figure 4 |
| Figure 5.R | generate Figure 5 |