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and Acoustic Data Analysis","monthly_downloads":1340,"total_dependent_repos":6,"total_dependent_packages":3,"readme":"---\ntitle: \"warbleR: Streamline Bioacoustic Analysis\"\noutput: github_document\neditor_options: \n  chunk_output_type: console\n---\n\n\u003c!-- README.md is generated from README.Rmd. Please edit that file --\u003e\n\n\u003c!-- badges: start --\u003e\n[![CRAN status](https://www.r-pkg.org/badges/version/warbleR)](https://cran.r-project.org/package=warbleR)\n[![Total downloads](https://cranlogs.r-pkg.org/badges/grand-total/warbleR)](https://cranlogs.r-pkg.org/badges/grand-total/warbleR)\n[![Lifecycle: stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)\n[![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)\n[![Codecov test coverage](https://codecov.io/gh/maRce10/warbleR/branch/master/graph/badge.svg)](https://app.codecov.io/gh/maRce10/warbleR?branch=master)\n[![Dependencies](https://tinyverse.netlify.app/badge/warbleR)](https://CRAN.R-project.org/package=warbleR)\n[![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)\n[![Paper DOI](https://img.shields.io/badge/DOI-10.1111%2F2041--210X.12624-1f6feb.svg)](https://doi.org/10.1111/2041-210X.12624)\n\u003c!-- badges: end --\u003e\n\n\u003cimg src=\"man/figures/warbleR_sticker.png\" alt=\"warbleR logo\" align=\"right\" width=\"25%\"/\u003e\n\n**warbleR** is an R package for analyzing the structure of animal acoustic signals at scale. Bring your own recordings (or open-access ones from repositories like [Xeno-canto](https://xeno-canto.org/), easily obtained with [suwo](https://docs.ropensci.org/suwo/)), annotate them in a *selection table*, and run the whole pipeline — from file wrangling and spectrograms to acoustic measurements and similarity analyses — in batch, on as many signals as you have.\n\nBuilt on top of [seewave](https://cran.r-project.org/package=seewave) and [tuneR](https://cran.r-project.org/package=tuneR), warbleR adds the workflow layer those packages leave to the user:\n\n- 🗂️ **Selection-table-driven workflows** — every function loops over the signals listed in an annotation table, so one call handles one sound or ten thousand\n- 📦 **Extended selection tables** — a single R object that bundles annotations *and* the audio clips, making analyses portable and easy to share\n- ⚡ **Parallel processing** — most functions take a `parallel` argument to spread the work across cores\n- 🔍 **Built-in quality checks** — spectrogram images and diagnostic tools let you verify each step before moving on\n\n## What can you do with it?\n\n| Task | Key functions |\n|:-----|:--------------|\n| Inspect, convert and fix sound files | `info_sound_files()`, `check_sound_files()`, `fix_wavs()`, `mp32wav()`, `wav_2_flac()`, `split_sound_files()`, `remove_channels()` |\n| Build and validate annotation tables | `selection_table()`, `check_sels()`, `tailor_sels()`, `cut_sels()`, `overlapping_sels()`, `consolidate()` |\n| Create spectrograms | `spectrograms()`, `full_spectrograms()`, `color_spectro()`, `snr_spectrograms()`, `catalog()`, `phylo_spectro()` |\n| Measure acoustic structure | `spectro_analysis()`, `mfcc_stats()`, `song_analysis()`, `freq_range()`, `sig2noise()`, `sound_pressure_level()`, `gaps()`, `wpd_features()` |\n| Track frequency contours | `freq_ts()`, `track_freq_contour()`, `track_harmonic()`, `inflections()` |\n| Compare signals | `cross_correlation()`, `freq_DTW()`, `multi_DTW()`, `waveform_similarity()`, `compare_methods()` |\n| Analyze duet / chorus coordination | `test_coordination()`, `plot_coordination()` |\n| Simulate signals | `simulate_songs()` |\n\nSee the [function reference](https://marce10.github.io/warbleR/reference/) for the full list.\n\n## Installation\n\nFrom CRAN:\n\n```{r, eval = FALSE}\ninstall.packages(\"warbleR\")\n```\n\nDevelopment version from GitHub (requires [remotes](https://cran.r-project.org/package=remotes)):\n\n```{r, eval = FALSE}\nremotes::install_github(\"maRce10/warbleR\")\n```\n\n## Quick example\n\nThe example recordings and annotations come from the [NatureSounds](https://cran.r-project.org/package=NatureSounds) package (installed with warbleR):\n\n```{r, eval = FALSE}\nlibrary(warbleR)\n\n# load example long-billed hermit songs and their annotations\ndata(list = c(\"Phae.long1\", \"Phae.long2\", \"Phae.long3\", \"Phae.long4\", \"lbh_selec_table\"))\n\n# save the sound files to a temporary folder\nfor (i in paste0(\"Phae.long\", 1:4)) {\n  tuneR::writeWave(get(i), file.path(tempdir(), paste0(i, \".wav\")))\n}\n\n# check that annotations and sound files match\ncheck_sels(lbh_selec_table, path = tempdir())\n\n# measure spectral and temporal parameters for every annotated signal\nparams \u003c- spectro_analysis(lbh_selec_table, path = tempdir())\n\n# pairwise acoustic similarity via spectrographic cross-correlation\nxc \u003c- cross_correlation(lbh_selec_table, path = tempdir())\n```\n\n## Learn more\n\n- 📘 [Intro to warbleR](https://marce10.github.io/warbleR/articles/a_warbleR.html) — an overview of the package\n- 📝 [Annotation data format](https://marce10.github.io/warbleR/articles/b_annotation_data_format.html) — how input annotations (selection tables) should look\n- 🔁 [All vignettes](https://marce10.github.io/warbleR/articles/) — worked examples of complete analysis workflows\n- 📄 [Original paper](https://doi.org/10.1111/2041-210X.12624) in *Methods in Ecology and Evolution* (the package has grown a lot since, so check the vignettes for current usage)\n\n## Related packages\n\n| Package | What it does |\n|:--------|:-------------|\n| [seewave](https://cran.r-project.org/package=seewave) \u0026 [tuneR](https://cran.r-project.org/package=tuneR) | Core sound analysis and manipulation of wave objects in R |\n| [ohun](https://docs.ropensci.org/ohun/) | Automated detection of sound events, with tools to diagnose and optimize detection routines |\n| [suwo](https://docs.ropensci.org/suwo/) | Search, download and map nature media (Xeno-canto, Macaulay Library, iNaturalist, GBIF, WikiAves) — replaces warbleR's `query_xc()` and `map_xc()` |\n| [baRulho](https://docs.ropensci.org/baRulho/) | Quantifying habitat-induced degradation of acoustic signals, with inputs/outputs compatible with warbleR |\n| [Rraven](https://cran.r-project.org/package=Rraven) | Data exchange between R and [Raven](https://www.ravensoundsoftware.com/) (Cornell Lab of Ornithology), handy for using Raven as the annotation tool |\n| [dynaSpec](https://cran.r-project.org/package=dynaSpec) | Dynamic spectrograms (spectrogram videos) |\n| [NatureSounds](https://cran.r-project.org/package=NatureSounds) | Example recordings and annotations of animal sounds |\n\n## Getting help \u0026 contributing\n\nFound a bug or have a feature request? Please open an [issue](https://github.com/maRce10/warbleR/issues). Contributions are welcome — see the [contributing guidelines](https://github.com/maRce10/warbleR/blob/master/CONTRIBUTING.md).\n\n## Citation\n\nIf you use warbleR, please cite:\n\n\u003e Araya-Salas, M. \u0026 Smith-Vidaurre, G. (2017). warbleR: an R package to streamline analysis of animal acoustic signals. *Methods in Ecology and Evolution*, 8, 184–191. \u003chttps://doi.org/10.1111/2041-210X.12624\u003e\n\nPlease also cite [tuneR](https://cran.r-project.org/package=tuneR) and [seewave](https://cran.r-project.org/package=seewave) if you use any function that creates spectrograms or measures acoustic parameters. You can get all citations from R with `citation(\"warbleR\")`.\n","funding_links":[],"readme_doi_urls":["https://doi.org/10.1111/2041-210X.12624"],"works":{},"citation_counts":{},"total_citations":0,"keywords_from_contributors":["behavior","acoustic-signals","animal","compendium","birdsong","cultural-evolution","phylogenetics"],"project_url":"https://ost.ecosyste.ms/api/v1/projects/145137","html_url":"https://ost.ecosyste.ms/projects/145137"}