Effects of complex soundscapes on the occurrence of Anaxipha pallidula in isolated green spaces in Tokyo
Data files
Oct 16, 2025 version files 26.32 KB
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alldata.csv
13.20 KB
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analysis_code_main.txt
7.03 KB
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functions.txt
2.28 KB
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README.md
3.80 KB
Abstract
Urban green spaces experience a mix of natural and anthropogenic noises, which could disrupt the vocal communication of several species. This study investigated how such complex soundscapes affect the occurrence of Anaxipha pallidula, which communicates through calls, focusing on both sound level and quality. A line census was conducted to survey the occurrence of A. pallidula and both acoustic and physical environmental factors in green spaces in the western region of Tokyo, Japan, which is surrounded by urbanized areas. These relationships were analyzed using generalized linear models and model selection based on the Akaike information criterion. Results revealed that sound level (dB) and road traffic noise negatively correlated with the occurrence of A. pallidula, suggesting that the noise caused by urbanization directly and negatively affects the species that communicate through their vocals. The occurrence of the vocal fold of Platypleura kaempferi, which is the native cicada, also negatively correlated with the occurrence of A. pallidula. P. kaempferi is inherently diurnal; however, its calls were heard in the study area at night, thus suggesting that urbanization alters the active time of P. kaempferi and influences the activity of A. pallidula. Although anthropogenic noise represents a direct urbanization effect, the impact of P. kaempferi may also indirectly result from urban influences. Urbanization can reshape species distributions and behaviors, affecting interspecies interactions mediated by changing soundscapes.
Dataset DOI: 10.5061/dryad.44j0zpctp
Description of the data and file structure
Dataset and R Analysis Code for "Effects of complex soundscapes on the occurrence of Anaxipha pallidula in isolated green spaces in Tokyo"
Associated publication DOI: 10.1002/wlb3.01515
This dataset includes presence/absence data of the focal species Anaxipha pallidula, environmental variables, and additional biological data used in the above publication. All R scripts for reproducing the analyses are provided. Place all files in the same directory and run analysis_code_main.txt in R to reproduce the results.
Files and variables
File: alldata.csv
Description: All data set for analysis including data which did not use the paper.
Variables
- siteName: Local name of the study site
- place: Course name
- repeat.: Census time
- distanceFromStart: Unit in each line census
- Anaxipha pallidula: Occurrences of Anaxipha pallidula
- noise.m: Average noise
- noise.max: Maximum noise
- tall.plant: Occurrences of tall plants
- tall_plant.E: Euclidian distance from tall plants
- mid.plant: Occurrences of medium plants
- mid.plant.E: Euclidian distance from medium plants
- paddy.field: Occurrences of paddy field
- paddy.field.E: Euclidian distance from paddy field
- all.road: Euclidian distance from road (include small road)
- road.E: Euclidian distance from road
- open.w: Occurrences of open water
- couduit: Occurrence of couduit
- car: Occurrence of car noise
- plane: Occurrence of plane noise
- water: Occurrence of water noise
- Hyla japonica: Occurrence of Hyla japonica
- Rhacophorus schlegelii: Occurrence of Rhacophorus schlegelii
- Modicogryllus siamensis: Occurrence of Modicogryllus siamensis
- Dianemobius nigrofasciatus: Occurrence of Dianemobius nigrofasciatus
- Polionemobius mikado: Occurrence of Polionemobius mikado
- Pteronemobius yezoensis: Occurrence of Pteronemobius yezoensis
- Eobiana engelhardti subtropica: Occurrence of Eobiana engelhardti subtropica
- Euconocephalus thunbergi: Occurrence of Euconocephalus thunbergi
- Platypleura kaempferi: Occurrence of Platypleura kaempferi
- Gryllotalpa orientalis: Occurrence of Gryllotalpa orientalis
- Lithobates catesbeianus: Occurrence of Lithobates catesbeianus
- Tanna japonensis: Occurrence of Tanna japonensis
- Tettigonia orientalis: Occurrence of Tettigonia orientalis
- Pteronemobius ohmachii: Occurrence of Pteronemobius ohmachii
File: analysis_code_main.txt
Description: run this file in R to reproduce the results. This R script analyzes how soundscape and habitat variables affect the presence of Anaxipha pallidula in green spaces by fitting logistic regression models (GLMs) on two survey datasets, comparing models using AIC for model selection.
It tests physical habitat features, noise levels, and individual sound sources in separate GLMs, and evaluates model fit using AIC to identify the most explanatory combination of predictors.
File: functions.txt
Description: Supplementary function. Load this file in the same directory as analysis_code_main.txt. This R function brute_search_glm() performs an exhaustive model selection by fitting all possible combinations of habitat variables (2 versions each for 4 variables) in a logistic regression predicting Anaxipha pallidula presence, and selects the model with the lowest AIC.
It then prints the selected variable types (e.g., straight-line vs. Euclidean distance) and returns the best-fit logistic regression model based on those variables.
Code/software
All analysis was used in R.
Access information
NA
