Analysis of mixtures of birds and insects in weather radar profile data
Data files
Mar 19, 2025 version files 28.18 MB
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mixture_codes.zip
6.15 KB
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mixture_data.zip
28.17 MB
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README.md
7.39 KB
Abstract
Weather radars are increasingly used to study the spatial-temporal dynamics of airborne birds and insects. These two taxa often co-occur and separating their contributions is crucial for reliable interpretation of their movement patterns. Most studies have restricted analyses to locations, seasons, and periods in which one or the other taxa dominates. In this study, we describe an analytical method to estimate the proportion of birds and insects in cases where both taxa share the same airspace. Our approach partitions vertical profiles of biological reflectivity into bird and insect components, using assumptions of downwind heading selection by insects and information on expected airspeeds for birds and insects. We evaluated our method in regions, where existing approaches of studying bird migration with weather radars can be particularly challenging due to high airborne insect density: the tropics (Colombia) and the southern temperate zone (Southeast Australia). We found that bird and insect signals routinely reached similar magnitudes in these regions. Retrieved patterns of bird and insect occurrence across daily and annual cycles reflected expected biological patterns that are indicative of migratory and non-migratory movements in both climates and migration systems, particularly broad-front migration in birds. Contrary to fixed airspeed thresholding, we were able to partition birds along the full range of bird-insect proportions, retaining more spatial-temporal complexity that was crucial to revealing aerial habitat use of both taxa. Our analytical procedure readily extends existing vertical profiling approaches, empowering ecologists to explore complex aerial ecosystems across a diverse range of climates, as well as potential diurnal movements of birds and insects that remain heavily understudied.
https://doi.org/10.5061/dryad.7pvmcvf4s
Description of the data and file structure
This dataset contains the data and code required to replicate bird-insect mixture analysis from Australian and Colombian weather radar data. Data includes daily vertical profiles and their seasonal summaries of one Australian radar and two Colombian radars. Codes include R markdown files that can be used to reproduce Figure3-5 in the associated paper.
This README describes only the variables relevant to the analysis. Other variables included in the dataset are standard outputs from the R function biorad::calculate_vp
. For details on these additional variables, please refer to the R documentation for calculate_vp
: biorad documentation.
Files and variables
File: mixture_code.zip
Description: code used to generate figure 3-5 in this study.
R is required to run the following script; the script was created using R version 4.4.1. Annotations are provided throughout the script through 1) library loading, 2) dataset loading and cleaning, 3) analyses, and 4) figure creation.
1. daily_pattern_final.Rmd
- Description: R code used to summarize the mixture patterns in the example dates in Figure 3.
2. seasonal_pattern_final.Rmd
- Description: R code used to summarize the seasonal bird-insect patterns in the entire year in Figure 4.
3. sensitivity_test.Rmd
- Description: R code used to conduct sensitivity test analysis in Figure 5.
File: mixture_data.zip
Description: data used to generate figure 3-5 in this study.
1. australia_complete_df_mixtures.rds
- Description: This dataset contains a comprehensive compilation of vertical profiles generated using the vol2bird algorithm from the R package “bioRad” for the Australian site.
- u_wind: wind speed component west to east in m/s.
- v_wind: wind speed component south to north in m/s.
- ff: Horizontal ground speed in m/s.
- dd: Ground speed direction in degrees clockwise from north.
- eta: Animal reflectivity in cm^2/km^3.
- dens: Animal density in animals/km^3.
2. colombia_complete_df_mixtures.rds
- Description: This dataset contains a comprehensive compilation of vertical profiles generated using the vol2bird algorithm from the R package “bioRad” for the Colombian sites.
- u_wind: wind speed component west to east in m/s.
- v_wind: wind speed component south to north in m/s.
- ff: Horizontal ground speed in m/s.
- dd: Ground speed direction in degrees clockwise from north.
- eta: Animal reflectivity in cm^2/km^3.
- dens: Animal density in animals/km^3.
3. BAR_seasonal_new.rds
- Description: Seasonal dataset for the BAR site, containing modelled bird and insect reflectivity (eta) for each day of a year. used to generate Figure 4
- jday: day of the year, 1 to 365
- mean_bird_prop: mean bird proportion calculated using method proposed in this paper.
- bird_eta: Animal reflectivity attributed to birds
- insect_eta: Animal reflectivity attributed to insects
4. Capflat_seasonal_new.rds
- Description: Seasonal dataset for the Capflat (Australian) site, containing modelled bird and insect reflectivity (eta) for each day of a year. used to generate Figure 4.
- jday: day of the year, 1 to 365
- mean_bird_prop: mean bird proportion calculated using method proposed in this paper.
- bird_eta: Animal reflectivity attributed to birds
- insect_eta: Animal reflectivity attributed to insects
5. Capflat_vpts_example.rds
- Description: Vertical Profile Time Series (VPTS) dataset for the Capflat site for the examplar date in Figure 3
- u: Ground speed component of the mixture west to east in m/s. NA indicates that ground speed values could not be resolved using the vol2bird algorithm.
- v: Ground speed component of the mixture south to north in m/s. NA indicates that ground speed values could not be resolved using the vol2bird algorithm.
- Uwind: wind speed component west to east in m/s. Vwind: wind speed component south to north in m/s.
- ff: Horizontal ground speed in m/s.
- dd: Ground speed direction in degrees clockwise from north.
- eta: Animal reflectivity in cm^2/km^3.
- bird_dens: Animal density in animals/km^3.
- bird_dens: Animal density in animals/km^3.
- radar: name of the radar
- datetime_local: local date time of the animal movement.
- height_above_radar: altitudinal band of animal movement above the height of the radar.
6. BAR_vpts_example.rds
- Description: Vertical Profile Time Series (VPTS) dataset for the BAR site for the examplar date in Figure 3
- u: Ground speed component of the mixture west to east in m/s. NA indicates that ground speed values could not be resolved using the vol2bird algorithm, and excluded from the subsequent analysis.
- v: Ground speed component of the mixture south to north in m/s. NA indicates that ground speed values could not be resolved using the vol2bird algorithm, and excluded from the subsequent analysis.
- u_wind: wind speed component west to east in m/s.
- v_wind: wind speed component south to north in m/s.
- ff: Horizontal ground speed in m/s.
- dd: Ground speed direction in degrees clockwise from north.
- eta: Animal reflectivity in cm^2/km^3.
- bird_dens: Animal density in animals/km^3.
- bird_dens: Animal density in animals/km^3.
- radar: name of the radar
- datetime_local: local date time of the animal movement.
- height_above_radar: altitudinal band of animal movement above the height of the radar.
7. GUA_vpts_example.rds
- Description: Vertical Profile Time Series (VPTS) dataset for the GUA site for the examplar date in Figure 3
- u: Ground speed component of the mixture west to east in m/s. NA indicates that ground speed values could not be resolved using the vol2bird algorithm, and excluded from the subsequent analysis.
- v: Ground speed component of the mixture south to north in m/s. NA indicates that ground speed values could not be resolved using the vol2bird algorithm, and excluded from the subsequent analysis.
- u_wind: wind speed component west to east in m/s.
- v_wind: wind speed component south to north in m/s.
- ff: Horizontal ground speed in m/s.
- dd: Ground speed direction in degrees clockwise from north.
- eta: Animal reflectivity in cm^2/km^3.
- bird_dens: Animal density in animals/km^3.
- bird_dens: Animal density in animals/km^3.
- radar: name of the radar
- datetime_local: local date time of the animal movement.
- height_above_radar: altitudinal band of animal movement above the height of the radar.
3. Key Data Fields
- u: Ground speed component west to east in m/s.
- v: Ground speed component south to north in m/s.
- ff: Horizontal ground speed in m/s.
- dd: Ground speed direction in degrees clockwise from north.
- eta: Animal reflectivity in cm^2/km^3.
- dens: Animal density in animals/km^3.
- uwind: wind speed component west to east in m/s. interpolated to the time-altitude bin using ERA5 data.
- vwind: wind speed component south to north in m/s. interpolated to the time-altitude bin using ERA5 data.
We obtained Colombian weather radar data including both single polarization moments (radial velocity and reflectivity) and dual polarization moments (correlation coefficient, differential reflectivity and differential phase) from the country's Institute for Hydrological, Meteorological, and Environmental Studies (IDEAM), focusing on the stations in San Jose del Guaviare, Guaviare department, south-central Colombia (name: GUA, 2.53°N, longitude: 72.62°W, elevation: 218 m a.s.l.) and Barrancabermeja, Santander department, north-central Colombia (name: BAR, latitude: 6.93°N, longitude: 73.76°W, elevation: 80 m a.s.l., Fig. 2A). Both radars are dual-polarization and operate at C-band (5.3 cm) with a beamwidth of 1°. The radar operated in dual-PRF mode with a low pulse repetition frequency (PRF) of 1266.667 Hz and high PRF of 1900 Hz, corresponding to a Nyquist velocity of 50.6 m/s. For the Australian case study, we obtained the level-1 dataset from the Australian National Computational Infrastructure (NCI, Soderholm et al. 2019). We used data (radial velocity and reflectivity) from one radar in Captains Flat, New South Wales, southeast Australia (name: CapFlat, 35.66°S, longitude: 149.51°E, elevation: 1382 m a.s.l., Fig. 2B) for the year 2018. This is an S-band (10.4 cm wavelength) single-polarization radar with a beamwidth of 1.9°. Reflectivity data in the Australian dataset was calibrated by matching collocated information with the Tropical Rainfall Measuring Mission (TRMM) and Global Precipitation Measurement (GPM) satellite passes (Louf and Protat 2023) before further processing. The radar operated in dual-PRF mode with a low PRF of 500 Hz and a high PRF of 750 Hz, corresponding to a Nyquist velocity of 39.1 m/s.
The Colombian radars are located in hot tropical lowlands, where seasonality is defined more by rainfall than temperature. The Barrancabermeja radar lies within the Magdalena River Valley but its beams reach the slopes of the Andes. San Jose del Guaviare sits at the junction between the Amazon and Orinoco River basins. We chose these Colombian radars based on their low elevations that maximize the volume of airspace captured by a single scan, the continuity of the available time series, and their strategic importance for regional migration, ensuring a sufficient volume of migration capturable by the radars (Bayly et al. 2018). The CapFlat radar is the highest radar in Australia in terms of elevation, with winter temperature (average low in July) reaching around 1.1 ℃ and summer temperature (average high in January) reaching around 27.9 ℃. Combined with its southerly latitude, it is most likely to record seasonal patterns in biological activity aloft in the temperate regions of Eastern Australia.
We extracted vertical profiles of biological reflectivity (η, cm2⋅km-3) using the vol2bird algorithm from the bioRad R package (Dokter et al. 2019) to a temporal resolution of 6 min and 10 min and an altitudinal resolution of 200 m and 100 m in the Australian and Colombian datasets, respectively. Precipitation in the Australian dataset was removed using MistNet, a convolutional neural network and screened manually by visually checking time-altitude plots of reflectivity factor and removing time-altitude ranges with meteorological contamination (Lin et al. 2019, Dokter et al. 2019). Precipitation in the Colombian dataset was removed using the correlation coefficient ρHV (pixels with ρHV > 0.95 were removed, Stepanian et al. 2016). To reduce the risk of precipitation contamination, an additional 5 km margin was removed around identified precipitation areas for all radars. The vertical profile includes the reflectivity and the associated U (east-west) and V (south-north) components of ground speed. We retrieved the U and V components of wind speed from the ERA5 reanalysis for Australia (Hersbach et al. 2023) and the North American Regional Reanalysis for Colombia (Mesinger et al. 2006). We downloaded the hourly (Australia) and 3-hourly (Colombia) data at pressure levels from 1000 to 750 hPa, spatially interpolated to the radar location, and further interpolated to the altitudinal and temporal resolution of the vertical profiles. Airspeed was determined by subtracting the wind speed vector from the ground speed vector. We found airspeeds in our case studies were skewed heavily towards lower values (Supplementary Material Fig. S1 and S2), even during heavy bird migration, because of the strong background of aerial insects.
To summarize daily and seasonal patterns, we calculated the mean bird proportion , bird reflectivity and insect reflectivity at each time-altitude bin of the vertical profile spanning a data set of four years from the BAR radar in Colombia (n = 171,986 scans), and one year at the CapFlat radar in Australia (n = 105,120 scans). We chose the BAR radar because time series from this radar was more complete, and the quality of velocity data was higher. To illustrate the seasonal patterns, we created yearly trends of bird proportions, bird and insect reflectivity by fitting Generalized Additive Models (GAM, Wood 2017) using a quasi-Poisson distributional family and cyclic cubic regression splines, using bird proportions and the densities as response and day of year as predictor.