vol2birdR

R package for the vol2bird algorithm: generate vertical profiles of biological signals in weather radar data

https://github.com/adokter/vol2birdr

Last synced: 6 months ago · JSON representation ·

Repository

R package for the vol2bird algorithm: generate vertical profiles of biological signals in weather radar data

Basic Info

Host: GitHub
Owner: adokter
License: lgpl-3.0
Language: C
Default Branch: main
Homepage: https://adokter.github.io/vol2birdR
Size: 5.01 MB

Statistics

Stars: 6
Watchers: 2
Forks: 3
Open Issues: 16
Releases: 13

Created about 4 years ago · Last pushed 6 months ago

Metadata Files

Readme Changelog License Citation Codemeta

README.Rmd

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output: github_document
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---



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[![CRAN
status](https://www.r-pkg.org/badges/version/vol2birdR)](https://cran.r-project.org/package=vol2birdR)
[![R-CMD-check](https://github.com/adokter/vol2birdR/workflows/R-CMD-check/badge.svg)](https://github.com/adokter/vol2birdR/actions)
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[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.7992026.svg)](https://doi.org/10.5281/zenodo.7992026)



# 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](https://adriaandokter.com/bioRad/) as the primary user
interface, with '**vol2birdR**' acting as a dependency of
[bioRad](https://adriaandokter.com/bioRad/).

# Install

'**vol2birdR**' is available for all major platforms (Linux, OS X and
Windows).

For OS X and Windows, you can install the released version of 'vol2birdR' from
[CRAN](https://CRAN.R-project.org) with:

```{r eval = FALSE}
install.packages("vol2birdR")
```

Alternatively, you can install the latest development version from
[GitHub](https://github.com/adokter/bioRad) with:

```{r eval = FALSE}
# install.packages("devtools")
devtools::install_github("adokter/vol2birdR")
```

For Linux and for installation of the development version the GNU Scientific Library (GSL), PROJ and HDF5
libraries need to be installed as system libraries prior to installation
of '**vol2birdR**':

Click here for additional information when installing the dependencies on
macOS

Since the installation process requires the [Homebrew](https://brew.sh/)
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 >> /Users/$USER/.zprofile
        echo 'eval "$(/opt/homebrew/bin/brew shellenv)"' >> /Users/$USER/.zprofile
        eval "$(/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 three commands. The first two
will add the necessary environment variables to your zshell user profile.

        echo >> /Users/$USER/.zprofile
        echo 'eval "$(/opt/homebrew/bin/brew shellenv)"' >> /Users/$USER/.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)"



| System                                      | Command                                                                      |
|:----------------------------------|:------------------------------------|
| **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 libbz2-dev` |
| **Systems supporting yum and RPMs**         | `sudo yum install hdf5-devel proj-devel gsl gsl-devel pkgconfig`                        |


Then load the package with:

```{r load_vol2birdR}
library(vol2birdR)
```

### 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](https://adriaandokter.com/vol2birdR/articles/vol2birdR.html) for additional installation information

## References:

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)

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)

'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)

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)

Owner

Name: Adriaan Dokter
Login: adokter
Kind: user
Company: Lab of ornithology, Cornell University

Website: http://adriaandokter.com
Repositories: 25
Profile: https://github.com/adokter

Citation (CITATION.cff)

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  "releaseNotes": "https://github.com/adokter/vol2birdR/blob/master/NEWS.md",
  "readme": "https://github.com/adokter/vol2birdR/blob/main/README.md",
  "contIntegration": "https://github.com/adokter/vol2birdR/actions",
  "developmentStatus": "https://www.repostatus.org/#active"
}

GitHub Events

Total

Create event: 23
Issues event: 41
Release event: 9
Delete event: 24
Issue comment event: 51
Push event: 88
Pull request event: 37

Last Year

Create event: 23
Issues event: 41
Release event: 9
Delete event: 24
Issue comment event: 51
Push event: 88
Pull request event: 37

Committers

Last synced: 11 months ago

All Time

Total Commits: 516
Total Committers: 7
Avg Commits per committer: 73.714
Development Distribution Score (DDS): 0.486

Past Year

Commits: 144
Committers: 3
Avg Commits per committer: 48.0
Development Distribution Score (DDS): 0.285

Top Committers

Name	Email	Commits
Adriaan Dokter	a**r@g**m	265
iskandari	s**i@g**m	141
Anders Henja	a**s@b**u	97
peterdesmet	p**t@i**e	9
Tomas Kalibera	t**a@g**m	2
bart1	1****1	1
Jeroen Ooms	j**s@g**m	1

Committer Domains (Top 20 + Academic)

inbo.be: 1 baltrad.eu: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 70
Total pull requests: 94
Average time to close issues: 2 months
Average time to close pull requests: 19 days
Total issue authors: 5
Total pull request authors: 6
Average comments per issue: 1.56
Average comments per pull request: 0.54
Merged pull requests: 79
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 23
Pull requests: 38
Average time to close issues: 18 days
Average time to close pull requests: 3 days
Issue authors: 4
Pull request authors: 2
Average comments per issue: 0.48
Average comments per pull request: 0.37
Merged pull requests: 30
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

adokter (59)
iskandari (5)
peterdesmet (4)
ForChimneySwifts (1)
fyiguo (1)

Pull Request Authors

adokter (67)
iskandari (19)
kalibera (4)
bart1 (2)
peterdesmet (1)
jeroen (1)

Top Labels

Issue Labels

bug (15) enhancement (7) documentation (2)

Pull Request Labels

Packages

Total packages: 1
Total downloads:
- cran 312 last-month

Total dependent packages: 1
Total dependent repositories: 0
Total versions: 13
Total maintainers: 1

cran.r-project.org: vol2birdR

Vertical Profiles of Biological Signals in Weather Radar Data

Homepage: https://github.com/adokter/vol2birdR/
Documentation: http://cran.r-project.org/web/packages/vol2birdR/vol2birdR.pdf
License: LGPL (≥ 3)
Latest release: 1.2.0
published 6 months ago

Versions: 13
Dependent Packages: 1
Dependent Repositories: 0
Downloads: 312 Last month

Rankings

Forks count: 21.9%

Dependent packages count: 29.8%

Average: 30.6%

Stargazers count: 35.2%

Dependent repos count: 35.5%

Maintainers (1)

vol2birdr@cornell.edu

Last synced: 6 months ago

ecosyste.ms

Data

Tools

Indexes

Applications

Experiments

Open Source Science

vol2birdR

Science Score: 67.0%

Repository

Basic Info

Statistics

Metadata Files

README.Rmd

Owner

Citation (CITATION.cff)

CodeMeta (codemeta.json)

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

cran.r-project.org: vol2birdR

Rankings

Maintainers (1)

Dependencies