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 4.3.1, found at https://www.r-project.org/) and using Rstudio as a graphical user interface.

Installation on Windows systems:

Step 1: install bioRad

We will be using the latest development version that is still in review with CRAN, requiring a few more manual steps than usual (for the purpose of this practical only):

# Step 1a: enable both the CRAN and bioconductor repositories:
setRepositories(ind=1:2)
# Step 1b: install all of bioRad's dependencies:
install.packages(c("assertthat", "curl", "fields", "frictionless",
                   "ggplot2", "glue", "lubridate", "lutz",
                   "suntools", "raster", "readr", "dplyr", "rhdf5",
                   "sp", "tidyr", "viridisLite", "viridis", "rlang",
                   "jsonlite", "aws.s3", "ggmap", "knitr", "tidyselect",
                   "rmarkdown", "testthat", "sf", "vol2birdR"))
# Step 1c: install bioRad's latest development version:
install.packages("https://s3.amazonaws.com/mistnet/bioRad_0.7.0.9617.tar.gz", repos=NULL)

Step 2: download mistnet libraries and model

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):

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()

Step 3: load bioRad

You should now be able to load bioRad. The welcome message should mention version 0.7.0.9617, and MistNet installed.

# load bioRad:
library(bioRad)

# expected message:
#> Welcome to bioRad version 0.7.0.9617
#> using vol2birdR version 1.0.1 (MistNet installed)

Installation on Mac OSX systems:

Step 1: install bioRad

We will be using the latest development version that is still in review with CRAN, requiring a few more manual steps (for the purpose of this practical only):

# Step 1a: install package devtools (if you don't have it already)
install.packages("devtools")
# Step 1b: enable both the CRAN and bioconductor repositories:
setRepositories(ind=1:2)
# Step 1c: install the latest development release of bioRad:
devtools::install_github("adokter/bioRad")

Step 2: download mistnet libraries and model

The bioRad installation of the previous step should have installed the vol2birdR, which is an important dependency package for bioRad. Next, we need to run a few vol2birdR commands to install MistNet libraries (expect a ~ 150 Mb download)

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()

Step 3: load bioRad

You should now be able to load bioRad. The welcome message should mention version 0.7.0.9617, and MistNet installed.

# load bioRad:
library(bioRad)

# expected message:
#> Welcome to bioRad version 0.7.0.9617
#> using vol2birdR version 1.0.1 (MistNet installed)

Installation on Linux systems:

Step 1: install system libraries:

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
# 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

Step 2: install bioRad

You can now open R using Rstudio and install bioRad as follows:

# Step 2a: install package devtools (if you don't have it already)
install.packages("devtools")
# Step 2b: enable both the CRAN and bioconductor repositories:
setRepositories(ind=1:2)
# Step 2c: install the latest development release of bioRad:
devtools::install_github("adokter/bioRad")

Step 3: download mistnet libraries and model

The bioRad installation of the previous step should have automatically installed the vol2birdR package as well, which is an important dependency package for bioRad. Next, we need to run a few vol2birdR commands to install MistNet libraries (expect a ~ 150 Mb download)

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()

Step 4: load bioRad

You should now be able to load bioRad. The welcome message should mention version 0.7.0.9617, and MistNet installed.

# load bioRad:
library(bioRad)

# expected message:
#> Welcome to bioRad version 0.7.0.9617
#> using vol2birdR version 1.0.1 (MistNet installed)