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

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Hi!

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ENRAM

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Bird migration on weather radars

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Bird migration on weather radars

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

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

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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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bioRad

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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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Dokter et al. 2019 Ecography

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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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Functionality

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

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

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

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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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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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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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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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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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Plot scan plot(scan, 
 param = "DBZH") pvol scan param: VRADH radial velocity param: DBZH reflectivity factor

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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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Project scan plot(ppi, 
 param = "DBZH") pvol scan param: VRADH radial velocity param: DBZH reflectivity factor

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Project scan plot(ppi, 
 param = "VRADH") pvol scan param: VRADH radial velocity param: DBZH reflectivity factor

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

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

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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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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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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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Time series of vertical profiles plot(vpts)

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

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

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Integrated vertical profiles plot(vpts, 
 quantity = "mtr") # mtr: migration traffic rate (birds/km/hour)

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Documentation

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Help ?plot.vpts

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adokter.github.io/bioRad

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adokter.github.io/bioRad

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bioRad software note

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Supporting open reproducible science

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Common measures

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Common measures

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

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

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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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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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Open source

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Collaborative effort

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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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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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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