During the Aeroecology course we will be using the R-package bioRad, a collection of tools to analyze and visualize biological signals in weather radar data.
Please take some time to install the software before the practicals
We recommend upgrading to a recent version of R (latest version is 4.4.1, found at https://www.r-project.org/) and using Rstudio as a graphical user interface.
# Step 1a: enable both the CRAN and bioconductor repositories:
setRepositories(ind=1:2)
# Step 1b: install all of bioRad's dependencies:
install.packages("bioRad", dependencies=TRUE)
The bioRad installation of the previous step should have installed the vol2birdR package, which is an important dependency package for bioRad. Next, we need to run a few vol2birdR commands to enable MistNet (expect a ~ 150 Mb download), a model you can use to screen out precipitation from radar scans:
vol2birdR::install_mistnet()
Next, we download the MistNet model into vol2birdR (expect >500 Mb download, this step can take a while when you have a slow internet connection)
vol2birdR::install_mistnet_model()
You should now be able to load bioRad. The welcome message should mention version 0.8.1, and MistNet installed.
# load bioRad:
library(bioRad)
# expected message:
#> Welcome to bioRad version 0.8.1
#> using vol2birdR version 1.0.3 (MistNet installed)
# Locate and read the polar volume example file included with bioRad
pvolfile_source <- system.file("extdata", "volume.h5", package = "bioRad")
# Copy the file to a temporary directory with read/write permissions
pvolfile <- paste0(tempdir(),"/volume.h5")
file.copy(pvolfile_source, pvolfile)
# Calculate a vertical profile
# (You can ignore the 'pj_obj_create: Cannot find proj.db' message, which is harmless)
vp <- calculate_vp(pvolfile, mistnet = TRUE)
# Get summary info
vp
# Verify the following information is printed to screen:
# > vp
# Vertical profile (class vp)
#
# radar: seang
# source: WMO:02606,RAD:SE50,PLC:Angelholm,NOD:seang,ORG:82,CTY:643,CMT:Swedish radar
# nominal time: 2015-10-18 18:00:00
# Clean up
file.remove(pvolfile)
We first need to install several system libraries that are used by vol2birdR package, which will be installed as part of bioRad.
On Debian-based systems (including Ubuntu), run in a terminal:
# libraries required for vol2birdR:
sudo apt-get install libhdf5-dev libproj-dev gsl-bin libgsl-dev pkg-config libbz2-dev
# libraries required for other dependency packages:
sudo apt-get install libcurl4-openssl-dev libssl-dev libgdal-dev
On other Linux systems supporting yum and RPMs, run in a terminal:
sudo yum install hdf5-devel proj-devel gsl gsl-devel pkgconfig
Please follow the same steps 1-4 for Windows/Mac systems