Install instructions for bioRad

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 time to install the software before the practicals

We strongly 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.

Please follow below install instructions to install the bioRad package

Installation on Windows systems:

Step 1: install vol2birdR.

First, we install the vol2birdR package (a dependency package for bioRad).

install.packages("vol2birdR")

Step 2: download mistnet libraries

Next, we install several deep-learning and helper libraries to enable MistNet”

vol2birdR::install_mistnet()

Step 3: download mistnet model

Next, we download the mistnet model into vol2birdR:

vol2birdR::install_mistnet_model()

Step 4: install bioRad

The usual installation of bioRad is

install.packages("bioRad")

We will be using the latest development version that is still in review with CRAN, requiring more manual steps:

# Step 4a: enable both the CRAN and bioconductor repositories:
setRepositories(ind=1:2)
# Step 4b: 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"))
# Step 4c: install bioRad's latest development version:
install.packages("https://s3.amazonaws.com/mistnet/windows/bioRad_0.7.0.9603.tar.gz", repos=NULL)

You should now be able to load bioRad. The welcome message should mention version 0.7.0.9603, and MistNet installed.

# load bioRad:
library(bioRad)

# expected message:
#> Welcome to bioRad version 0.7.0.9603
#> using vol2birdR version 1.0.1 (MistNet installed)

Installation on Mac OSX systems:

Step 1: install bioRad

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

# 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

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 enable Mistnet (expect a ~ 150 Mb download)

vol2birdR::install_mistnet()

Step 3: download mistnet model

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 0.7.0.9603, and MistNet installed.

# load bioRad:
library(bioRad)

# expected message:
#> Welcome to bioRad version 0.7.0.9603
#> 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:

# 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:

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

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 enable Mistnet (expect a ~ 150 Mb download)

vol2birdR::install_mistnet()

Step 4: download mistnet model

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 5: load bioRad

You should now be able to load bioRad. The welcome message should mention version 0.7.0.9603, and MistNet installed.

# load bioRad:
library(bioRad)

# expected message:
#> Welcome to bioRad version 0.7.0.9603
#> using vol2birdR version 1.0.1 (MistNet installed)