Extract, visualize and summarize aerial movements of birds and insects from weather radar data.
bioRad provides standardized methods for extracting and reporting biological signals from weather radars. It includes functionality to inspect 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.
To get started, see:
You can install the released version of bioRad from CRAN with:
Alternatively, you can install the latest development version from GitHub with:
Then load the package with:
library(bioRad)#> Welcome to bioRad version 0.4.0#> Docker daemon running, Docker functionality enabled.
Google has recently changed its API requirements, and ggmap - the package used by bioRad to overlay radar scans on maps - now requires users to provide an API key and enable billing in order to use Google imagery. bioRad switched to using stamen maps by default, which do not require special credentials.
ggmap itself is outdated on CRAN; its developers hope to have the new version up on CRAN soon, but until then, see ggmap Github page for how to install the latest development version.
You only need to install Docker to:
read_pvolfile(). Docker is not required for reading ODIM radar data.
Shared drives> Select the drive(s) where you will be processing radar files > Click
File sharing> Add the drive(s) where you will be processing radar files > Click
Apply & Restart.
Here we read an example polar volume data file with
extract the scan/sweep at elevation angle 3 with
the data to a plan position indicator with
project_as_ppi() and plot
the radial velocity of detected targets with
library(tidyverse) # To pipe %>% the steps belowsystem.file("extdata", "volume.h5", package = "bioRad") %>%read_pvolfile() %>%get_scan(3) %>%project_as_ppi() %>%plot(param = "VRADH") # VRADH = radial velocity in m/s
Radial velocities towards the radar are negative, while radial velocities away from the radar are positive, so in this plot there is movement from the top right to the bottom left.
Weather radar data can be processed into vertical profiles of biological
calculate_vp(). This type of data is available as open
data for over 100 European
Once vertical profile data are loaded into bioRad, these can be bound
into time series using
bind_into_vpts(). Here we read an example time
series, project it on a regular time grid with
plot it with
example_vpts %>%regularize_vpts() %>%plot()#> projecting on 300 seconds interval grid...
The gray bars in the plot indicate gaps in the data.
The altitudes in the profile can be integrated with
integrate_profile() resulting in a dataframe with rows for datetimes
and columns for quantities. Here we plot the quantity migration traffic
my_vpi <- integrate_profile(example_vpts)plot(my_vpi, quantity = "mtr") # mtr = migration traffic rate
To know the total number of birds passing over the radar during the full
time series, we use the last value of the cumulative migration traffic
my_vpi %>%pull(mt) %>% # Extract column mt as a vectorlast()#>  173023.8
For more exercises, see this tutorial.
First release on CRAN! All issues included in this release can be found here.
get_param() added as new function to get parameters from scan (#132).
download_basemap() now uses Stamen basemaps by default (parameter
source), so users do not need to request an API key for the previous default Google Maps (#163).
select_vpfiles() now use 5 letter radar codes (parameter
radars instead of
country), allow to skip already downloaded files (parameter
overwrite = TRUE) and have improved download and error messages (#176).
calculate_vp() (all Docker dependent) can now read files from directories containing a space (#162).
Details for deprecated functions
cmt() are now displayed with function (#166).
README reviewed for easier installation and usage (#155).
Introductory exercises vignette renamed to
rad_aero_18.Rmd since it is based on the 2nd Radar Aeroecology Training School.
Release consistent with and in preparation of the bioRad methods paper (https://doi.org/10.1111/ecog.04028). All issues included in this release can be found here.
Functions (#84), arguments (#112) and objects (#80) have been renamed to be consistent (#51). Deprecated functions will remain functional for now, but we will trigger a warning: we advise to use the new functions names. See the lists for current functions and deprecated functions.
integrate_profile() replaces the functionality of
cmt() (#75) and
plot() can now be used for scans (#71), e.g.
Functions are organized in sections on the website (#110).
Changelog section (this page) has been added to website (#144).
Package R code is reorganized as one function = one file for easier maintenance (#50).
First tests are included for some functions.
Contributors (#90) and citation (#141) have been updated.
bioRad now has a hex logo (#137). ✨