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bioRad: biological analysis and visualization of weather radar data

Peter Desmet
September 22, 2019

bioRad: biological analysis and visualization of weather radar data

Talk at the 2nd International Radar Aeroecology Conference in Zhengzhou, China - September 22, 2019.

Weather surveillance radars are increasingly used for monitoring the movements and abundances of animals in the airspace. However, analysis of weather radar data remains a specialised task that can be technically challenging. Major hurdles are the difficulty of accessing and visualising radar data on a software platform familiar to ecologists and biologists, processing the low‐level data into products that are biologically meaningful, and summarizing these results in standardized measures. To overcome these hurdles, we developed the open source R package bioRad (described in Dokter et al. 2019, https://doi.org/10.1111/ecog.04028), which provides a toolbox for accessing, visualizing and analyzing weather radar data for biological studies. In this talk we will cover how bioRad provides functionality to access low‐level radar data, process these data into meaningful biological information on animal speeds and directions at different altitudes in the atmosphere, visualize these biological extractions, and calculate further summary statistics. We will also describe how the package introduces weather radar equivalents for familiar measures used in the field of migration ecology, facilitates the use and spread of interoperable data standards, and integrates with a research infrastructure for weather radar aeroecology in Europe and the United States.

Peter Desmet

September 22, 2019
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  1. bioRad
    biological analysis
    and visualization of
    weather radar data
    IRAC 2019, 22 Sep 2019, Zhengzhou
    Peter Desmet

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  2. Bird migration on weather radars

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  3. Bird migration on weather radars

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  4. Bird migration on weather radars
    •  Reflectivity factor:
    how many animals?

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  5. Bird migration on weather radars
    •  Reflectivity factor:
    how many animals?
    •  Radial velocity:
    where are they
    going?

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  6. How to
    •  Read and inspect weather radar data
    •  Extract biological information: vertical profiling
    •  Analyze and integrate vertical profile data
    •  Standardize measures to compare studies

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  7. bioRad
    •  R package for analysis and visualization
    of biological signals in weather radar data
    •  Open source
    •  Available on CRAN and GitHub
    adokter.github.io/bioRad

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  8. Dokter et al. 2019 Ecography

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  9. Authors
    Adriaan Dokter* Peter Desmet*
    Jurriaan Spaaks Stijn Van Hoey
    Lourens Veen Liesbeth Verlinden
    Cecilia Nilsson* Günther Haase
    Hidde Leijnse Andrew Farnsworth*
    Willem Bouten Judy Shamoun-Baranes*

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  10. Functionality

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  11. Installation
    # install bioRad from CRAN
    install.packages("bioRad")
    # load bioRad
    library("bioRad")

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  12. pvol
    Read polar volume data
    pvol <- read_pvolfile("KBRO20170514_055831_pvol.h5")
    radar file

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  13. pvol
    scan
    Read polar volume data
    pvol <- read_pvolfile("KBRO20170514_055831_pvol.h5")
    radar file

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  14. pvol
    scan
    param: VRADH
    radial velocity
    param: DBZH
    reflectivity factor
    Read polar volume data
    pvol <- read_pvolfile("KBRO20170514_055831_pvol.h5")
    radar file

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  15. pvol
    scan
    param: VRADH
    radial velocity
    param: DBZH
    reflectivity factor
    scan
    param: VRADH
    radial velocity
    param: DBZH
    reflectivity factor
    Read polar volume data
    pvol <- read_pvolfile("KBRO20170514_055831_pvol.h5")
    radar file

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  16. pvol
    scan
    param: VRADH
    radial velocity
    param: DBZH
    reflectivity factor
    scan
    param: VRADH
    radial velocity
    param: DBZH
    reflectivity factor
    Read polar volume data
    pvol <- read_pvolfile("KBRO20170514_055831_pvol.h5")
    scan
    param: VRADH
    radial velocity
    param: DBZH
    reflectivity factor
    radar file

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  17. Inspect scan
    scan <- get_scan(pvol, 1.5)
    # use get_elevation_angles(pvol) to know angles
    pvol
    scan
    param: VRADH
    radial velocity
    param: DBZH
    reflectivity factor
    scan
    param: VRADH
    radial velocity
    param: DBZH
    reflectivity factor
    scan
    param: VRADH
    radial velocity
    param: DBZH
    reflectivity factor

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  18. Inspect scan
    scan <- get_scan(pvol, 1.5)
    # use get_elevation_angles(pvol) to know angles
    pvol
    scan
    param: VRADH
    radial velocity
    param: DBZH
    reflectivity factor

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  19. Plot scan
    plot(scan, 

    param = "DBZH")
    pvol
    scan
    param: VRADH
    radial velocity
    param: DBZH
    reflectivity factor

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  20. x
    y
    Project scan
    ppi <- project_as_ppi(scan, range_max = 120000)

    # ppi: plan position indicator
    pvol
    scan
    param: VRADH
    radial velocity
    param: DBZH
    reflectivity factor

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  21. Project scan
    plot(ppi, 

    param = "DBZH")
    pvol
    scan
    param: VRADH
    radial velocity
    param: DBZH
    reflectivity factor

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  22. Project scan
    plot(ppi, 

    param = "VRADH")
    pvol
    scan
    param: VRADH
    radial velocity
    param: DBZH
    reflectivity factor

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  23. Vertical profiling
    calculate_vp(

    pvolfile = "KBRO20170514_055831_pvol.h5", 

    vpfile = "KBRO20170514_055831_vp.h5"

    )
    # Makes use of vol2bird algorithm
    radar file

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  24. Vertical profiling
    calculate_vp(

    pvolfile = "KBRO20170514_055831_pvol.h5", 

    vpfile = "KBRO20170514_055831_vp.h5"

    )
    # Makes use of vol2bird algorithm
    radar file
    vp: vertical profile
    Vertical profile (class vp)
    radar: KBRO
    source: RAD:KBRO,PLC:BROWNSVILLE,state:TX
    nominal time: 2017-05-14 05:58:32
    generated by: vol2bird 0.3.18

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  25. Plot vertical profile
    vp <- read_vpfiles(
    "KBRO20170514_055831_vp.h
    5")
    plot(vp,
    quantity = "dens")

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  26. Plot vertical profile
    plot(vp,
    quantity = "ff")
    # ff: ground speed

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  27. Time series of vertical profiles
    vpts <- bind_into_vpts(vp, vp, vp)
    # read file with: read_vpts("vpts_file.txt")
    # regularize with: regularize_vpts()
    vp: vertical profile

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  28. Time series of vertical profiles
    vpts <- bind_into_vpts(vp, vp, vp)
    # read file with: read_vpts("vpts_file.txt")
    # regularize with: regularize_vpts()
    vp: vertical profile
    vp: vertical profile
    vp: vertical profile
    vp: vertical profile

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  29. Time series of vertical profiles
    vpts <- bind_into_vpts(vp, vp, vp)
    # read file with: read_vpts("vpts_file.txt")
    # regularize with: regularize_vpts()
    vp: vertical profile Irregular time series of vertical 

    profiles (class vpts)
    radar: KBRO
    # profiles: 95
    time range (UTC): 2017-05-14 00:09:00 –
    2017-05-14 13:25:00
    time step (s): min: 300 max: 1800
    vpts: vertical
    profile time series
    vp: vertical profile
    vp: vertical profile
    vp: vertical profile

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  30. Time series of vertical profiles
    plot(vpts)

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  31. Integrated vertical profiles
    vpi <- integrate_profile(vpi)
    vpts: vertical
    profile time series

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  32. Integrated vertical profiles
    vpi <- integrate_profile(vpi)
    vpi: integrated
    vertical profile
    vpts: vertical
    profile time series

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  33. Integrated vertical profiles
    plot(vpts, 

    quantity = "mtr")
    # mtr: migration traffic
    rate (birds/km/hour)

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  34. Documentation

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  35. Help
    ?plot.vpts

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  36. adokter.github.io/bioRad

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  37. adokter.github.io/bioRad

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  38. bioRad software note

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  39. Supporting open
    reproducible science

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  40. Common measures

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  41. Common measures

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  42. Common measures
    RCS = 11 cm2 Dokter et al. 2011 J. R. Soc. Interface

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  43. Data standards
    •  Supported pvol formats:
    ODIM (Europe), NEXRAD (US),
    Vaisala Iris (e.g. Canada)
    radar file
    pvol: polar volume

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  44. Data standards
    •  Supported pvol formats:
    ODIM (Europe), NEXRAD (US),
    Vaisala Iris (e.g. Canada)
    •  Export vp format of vol2bird:
    ODIM bird profile
    radar file
    pvol: polar volume
    vp: vertical profile

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  45. vp: vertical profile
    vp: vertical profile
    Data standards
    •  Supported pvol formats:
    ODIM (Europe), NEXRAD (US),
    Vaisala Iris (e.g. Canada)
    •  Export vp format of vol2bird:
    ODIM bird profile
    •  Export vpts format:
    tabular format under discussion
    radar file
    pvol: polar volume
    vp: vertical profile
    vpts: vertical
    profile time series

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  46. Collaborative effort

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  47. Roadmap
    •  Range bias correction of PPIs
    •  Inclusion of the MistNet segmentation model
    (Lin et al. 2019 Methods Ecol. Evol.)
    •  Unit tests and continuous integration
    •  Submission for rOpenSci code review
    •  …

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  48. bioRad is currently used for
    projects in Europe, US, Canada
    and Colombia…
    … but we hope it can become the
    go-to tool in R for all biological
    studies using weather radar data.

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  49. Thank you!
    Desmet et al. (2019) Biological analysis and visualization of weather radar
    data. Presentation. http://bit.ly/biorad-irac2019
    adokter.github.io/bioRad
    oscibio.inbo.be

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