diff --git a/README.Rmd b/README.Rmd
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@@ -22,6 +22,8 @@ knitr::opts_chunk$set(
status](https://www.r-pkg.org/badges/version/vol2birdR)](https://cran.r-project.org/package=vol2birdR)
[](https://github.com/adokter/vol2birdR/actions)
+[](https://doi.org/10.5281/zenodo.7992027)
+
# vol2birdR
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+vol2birdR
+‘vol2birdR’ is an ‘R’ package for the ‘vol2bird’
+algorithm for calculating vertical profiles of birds and other
+biological scatterers from weather radar data.
+It also provides an ‘R’ interface to the ‘MistNet’ convolutional
+neural network for precipitation segmentation, installing PyTorch
+libraries and model.
+‘vol2birdR’ can be used as a stand-alone package,
+but we recommend bioRad
+as the primary user interface, with ‘vol2birdR’ acting
+as a dependency of bioRad.
+Install
+‘vol2birdR’ is available for all major platforms
+(Linux, OS X and Windows).
+For OS X and Linux the GNU Scientific Library (GSL), PROJ and HDF5
+libraries need to be installed as system libraries prior to installation
+of ‘vol2birdR’:
+
+
+Additional information when installing the dependencies on macOS
+
+
+Since the installation process requires the Homebrew package manager you will have to
+install it. Open a terminal and issue the following command:
+ /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
+When the installation has completed it will print out some additional
+information that is essential to follow.
+==> Next steps:
+- Run these two commands in your terminal to add Homebrew to your PATH:
+ echo 'eval "$(/opt/homebrew/bin/brew shellenv)"' >> /Users/anders/.zprofile
+ eval "$(/opt/homebrew/bin/brew shellenv)"
+- Run brew help to get started
+- Further documentation:
+ https://docs.brew.sh
+You need to ensure that you follow the above two commands. The first
+one will add the necessary environment variables to your user
+ echo 'eval "$(/opt/homebrew/bin/brew shellenv)"' >> /Users/anders/.zprofile
+The second command will ensure that you get the necessary environment
+variables into the terminal where you ran the installation process of
+Homebrew.
+ eval "$(/opt/homebrew/bin/brew shellenv)"
+
+
+
+
+
+
+
+
+| OS X (using Homebrew) |
+brew install hdf5 proj gsl pkg-config |
+
+
+| Debian-based systems (including
+Ubuntu) |
+sudo apt-get install libhdf5-dev libproj-dev gsl-bin libgsl-dev pkg-config |
+
+
+| Systems supporting yum and RPMs |
+sudo yum install hdf5-devel proj-devel gsl gsl-devel pkgconfig |
+
+
+
+Next, you can install the released version of ‘vol2birdR’ from CRAN with:
+install.packages("vol2birdR")
Alternatively, you can install the latest development version from GitHub with:
+# install.packages("devtools")
+devtools::install_github("adokter/vol2birdR")
Then load the package with:
+
+MistNet installation
+MistNet is a deep convolution neural net for segmenting out
+precipitation from radar data, see Lin et al. 2019. To use MistNet,
+follow the following additional installation steps in R:
+# STEP 1: install additional libraries for using MistNet:
+library(vol2birdR)
+install_mistnet()
+After completing this step, the following command should evaluate to
+TRUE:
+mistnet_exists()
+Next, download the mistnet model. Note that the model file is large,
+over 500Mb.
+# STEP 2: download mistnet model:
+install_mistnet_model()
+See vignette
+for additional installation information
+References:
+Citation for ‘vol2bird’ algorithm:
+
+Paper describing recent algorithm extensions and the bioRad
+package:
+
+- bioRad:
+biological analysis and visualization of weather radar data
+Dokter AM, Desmet P, Spaaks JH, van Hoey S, Veen L, Verlinden L, Nilsson
+C, Haase G, Leijnse H, Farnsworth A, Bouten W, Shamoun-Baranes J.
+Ecography, 42, 852-860, 2019, DOI 10.1111/ecog.04028
+
+‘vol2bird’ implements dealiasing using the torus mapping method by
+Haase and Landelius:
+
+Use the following citation for the ‘MistNet’ rain segmentation
+model:
+
+- MistNet:
+Measuring historical bird migration in the US using archived weather
+radar data and convolutional neural networks. Lin T-Y,
+Winner K, Bernstein G, Mittal A, Dokter AM, Horton KG, Nilsson C, Van
+Doren BM, Farnsworth A, La Sorte FA, Maji S, Sheldon D. Methods in
+Ecology and Evolution, 10, 1908-1922, 2019, DOI 10.1111/2041-210X.13280
+
+
+
+
diff --git a/README.md b/README.md
index 913cd8a..17ec3fa 100644
--- a/README.md
+++ b/README.md
@@ -6,6 +6,8 @@
status](https://www.r-pkg.org/badges/version/vol2birdR)](https://cran.r-project.org/package=vol2birdR)
[](https://github.com/adokter/vol2birdR/actions)
+[](https://doi.org/10.5281/zenodo.7992027)
+
# vol2birdR
@@ -123,37 +125,36 @@ for additional installation information
Citation for ‘vol2bird’ algorithm:
-- [**Bird migration flight altitudes studied by a network of
- operational weather
- radars**](https://doi.org/10.1098/rsif.2010.0116) Dokter AM, Liechti
- F, Stark H, Delobbe L, Tabary P, Holleman I J. R. Soc. Interface,
- **8**, 30–43, 2011, DOI
- [10.1098/rsif.2010.0116](https://doi.org/10.1098/rsif.2010.0116)
+- [**Bird migration flight altitudes studied by a network of operational
+ weather radars**](https://doi.org/10.1098/rsif.2010.0116) Dokter AM,
+ Liechti F, Stark H, Delobbe L, Tabary P, Holleman I J. R. Soc.
+ Interface, **8**, 30–43, 2011, DOI
+ [10.1098/rsif.2010.0116](https://doi.org/10.1098/rsif.2010.0116)
Paper describing recent algorithm extensions and the bioRad package:
-- [**bioRad: biological analysis and visualization of weather radar
- data**](https://doi.org/10.1111/ecog.04028) Dokter AM, Desmet P,
- Spaaks JH, van Hoey S, Veen L, Verlinden L, Nilsson C, Haase G,
- Leijnse H, Farnsworth A, Bouten W, Shamoun-Baranes J. Ecography,
- **42**, 852-860, 2019, DOI
- [10.1111/ecog.04028](https://doi.org/10.1111/ecog.04028)
+- [**bioRad: biological analysis and visualization of weather radar
+ data**](https://doi.org/10.1111/ecog.04028) Dokter AM, Desmet P,
+ Spaaks JH, van Hoey S, Veen L, Verlinden L, Nilsson C, Haase G,
+ Leijnse H, Farnsworth A, Bouten W, Shamoun-Baranes J. Ecography,
+ **42**, 852-860, 2019, DOI
+ [10.1111/ecog.04028](https://doi.org/10.1111/ecog.04028)
‘vol2bird’ implements dealiasing using the torus mapping method by Haase
and Landelius:
-- [**Dealiasing of Doppler radar velocities using a torus
- mapping**](https://doi.org/10.1175/1520-0426(2004)021%3C1566:DODRVU%3E2.0.CO;2)
- Haase G, Landelius T. Journal of Atmospheric and Oceanic Technology
- **21**, 1566-1573, 2004, DOI
- [10.1175/1520-0426(2004)021\<1566:DODRVU\>2.0.CO;2](https://doi.org/10.1175/1520-0426(2004)021%3C1566:DODRVU%3E2.0.CO;2)
+- [**Dealiasing of Doppler radar velocities using a torus
+ mapping**](https://doi.org/10.1175/1520-0426(2004)021%3C1566:DODRVU%3E2.0.CO;2)
+ Haase G, Landelius T. Journal of Atmospheric and Oceanic Technology
+ **21**, 1566-1573, 2004, DOI
+ [10.1175/1520-0426(2004)021\<1566:DODRVU\>2.0.CO;2](https://doi.org/10.1175/1520-0426(2004)021%3C1566:DODRVU%3E2.0.CO;2)
Use the following citation for the ‘MistNet’ rain segmentation model:
-- [**MistNet: Measuring historical bird migration in the US using
- archived weather radar data and convolutional neural
- networks.**](https://doi.org/10.1111/2041-210X.13280) Lin T-Y,
- Winner K, Bernstein G, Mittal A, Dokter AM, Horton KG, Nilsson C,
- Van Doren BM, Farnsworth A, La Sorte FA, Maji S, Sheldon D. Methods
- in Ecology and Evolution, **10**, 1908-1922, 2019, DOI
- [10.1111/2041-210X.13280](https://doi.org/10.1111/2041-210X.13280)
+- [**MistNet: Measuring historical bird migration in the US using
+ archived weather radar data and convolutional neural
+ networks.**](https://doi.org/10.1111/2041-210X.13280) Lin T-Y, Winner
+ K, Bernstein G, Mittal A, Dokter AM, Horton KG, Nilsson C, Van Doren
+ BM, Farnsworth A, La Sorte FA, Maji S, Sheldon D. Methods in Ecology
+ and Evolution, **10**, 1908-1922, 2019, DOI
+ [10.1111/2041-210X.13280](https://doi.org/10.1111/2041-210X.13280)