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https://github.com/ABbiodiversity/wildRtrax

wildrtrax: an R package for environmental sensor data management and analytics
https://github.com/ABbiodiversity/wildRtrax

bioacoustics biodiversity-data r-package

Last synced: about 1 month ago
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wildrtrax: an R package for environmental sensor data management and analytics

Host: GitHub
URL: https://github.com/ABbiodiversity/wildRtrax
Owner: ABbiodiversity
License: other
Created: 2020-10-13T15:29:51.000Z (about 4 years ago)
Default Branch: main
Last Pushed: 2024-10-18T15:53:14.000Z (2 months ago)
Last Synced: 2024-10-29T21:01:26.196Z (about 2 months ago)
Topics: bioacoustics, biodiversity-data, r-package
Language: R
Homepage: https://abbiodiversity.github.io/wildrtrax/
Size: 226 MB
Stars: 10
Watchers: 2
Forks: 9
Open Issues: 8
Metadata Files:
- Readme: README.md
- Contributing: .github/CONTRIBUTING.md
- License: LICENSE
- Code of conduct: .github/CODE_OF_CONDUCT.md
- Citation: CITATION.cff
- Support: .github/SUPPORT.md

Awesome Lists containing this project

open-sustainable-technology - wildRtrax - An R package for environmental sensor data management and analytics. (Biosphere / Bioacoustics and Acoustic Data Analysis)

README

        
# wildrtrax 

[![Lifecycle: stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)

[![CRAN status](https://www.r-pkg.org/badges/version/wildrtrax)](https://CRAN.R-project.org/package=wildrtrax)

[![Codecov test coverage](https://codecov.io/gh/ABbiodiversity/wildRtrax/branch/main/graph/badge.svg)](https://app.codecov.io/gh/ABbiodiversity/wildRtrax?branch=main)

[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.13916882.svg)](https://doi.org/10.5281/zenodo.13916882)

[![R-CMD-check](https://github.com/ABbiodiversity/wildRtrax/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/ABbiodiversity/wildRtrax/actions/workflows/R-CMD-check.yaml)

## Overview

`wildrtrax` (pronounced *wild-r-tracks*) is an R package containing functions to help manage and analyze environmental sensor data. It helps to simplify the entire data life cycle by offering tools for data pre-processing, wrangling, and analysis, facilitating seamless data transfer to and from [WildTrax](https://www.wildtrax.ca/home.html). With `wildrtrax`, users can effortlessly establish end-to-end workflows and ensure reproducibility in their analyses. By providing a consistent and organized framework, the package promotes transparency and integrity in research, making it effortless to share and replicate results.

## Installation

You can install the most recent version of `wildrtrax` directly from this repository with:

``` r

# install.packages("remotes")

remotes::install_github("ABbiodiversity/wildrtrax")

```

The [development](https://github.com/ABbiodiversity/wildrtrax/tree/development) version of this package contains experimental features and recent fixes. It can be installed with: 

```r

remotes::install_github("ABbiodiversity/wildrtrax@development")

```

The development version of the package will be periodically merged and will be reflected in the [Changelogs](https://abbiodiversity.github.io/wildrtrax/news/index.html).

## Usage

All functions begin with a `wt_*` prefix. Column names and metadata align with the WildTrax infrastructure. The goal is to follow the work flow of pre-processing, linking with WildTrax, download and analysis.

ARUs :sound:

Cameras :camera:

Point counts :bird:

Bats :bat:

- Pre-process acoustic data

  - `wt_audio_scanner()` :sound: :bat:

  - `wt_run_ap()` :sound:

  - `wt_glean_ap()` :sound:

  - `wt_signal_level()` :sound:

  - `wt_chop()` :sound: :bat:

  - `wt_make_aru_tasks()` :sound: :bat:

  - `wt_songscope_tags()` :sound:

  - `wt_kaleidoscope_tags()` :sound: :bat:

- Download data from WildTrax

  - `wt_auth()` :camera: :sound: :bird: :bat:

  - `wt_get_download_summary()` :camera: :sound: :bird: :bat:

  - `wt_download_report()` :camera: :sound: :bird: :bat:

    - Available reports: `main, project, location, recording, image_set, image, tag, point_count, megadetector, megaclassifer, birdnet, daylight`

  - `wt_dd_summary()` :camera: :sound: :bird: :bat:

  - `wt_get_species()` :camera: :sound: :bird: :bat:

  - `wt_download_media()` :sound: :bat: :camera:

- Analyze data

  - `wt_summarise_cam()` :camera:

  - `wt_ind_detect()` :camera:

- Convenience functions

  - `wt_location_distances()` :sound: :camera: :bird: :bat:

  - `wt_tidy_species()` :sound: :camera: :bird: :bat:

  - `wt_replace_tmtt()` :sound:

  - `wt_make_wide()` :sound: :bird: :bat:

  - `wt_format_occupancy()` :sound: :bird:

  - `wt_qpad_offsets()` :sound: :bird:

  - `wt_add_grts()` :bat:

- Acoustic classification :sound:

  - `wt_evaluate_classifier()`:sound:

  - `wt_get_threshold()` :sound:

  - `wt_additional_species()` :sound:

## Issues

To report bugs, request additional features, or get help using the package, please file an

[issue](https://github.com/ABbiodiversity/wildrtrax/issues).

## Contributors

We encourage ongoing contributions and collaborations to improve the package into the future. The [Alberta Biodiversity Monitoring Institute](https://abmi.ca) provides ongoing support, development and funding.

## License

This R package is licensed under [MIT license](https://github.com/ABbiodiversity/wildrtrax/blob/master/LICENSE)©2024 [Alberta Biodiversity Monitoring Institute](https://abmi.ca).

## Code of Conduct

Please note that `wildrtrax` is released with a [Contributor Code of Conduct](CODE_OF_CONDUCT.md). By contributing to this project, you agree to abide by its terms.