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wildrtrax

This is an R package that enables environmental sensor users to create comprehensive work flows for managing and analyzing data

https://github.com/abbiodiversity/wildrtrax

Science Score: 77.0%

This score indicates how likely this project is to be science-related based on various indicators:

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    CITATION.cff file
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    Found 3 DOI reference(s) in README
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    4 of 12 committers (33.3%) from academic institutions
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    Low similarity (15.0%) to scientific vocabulary

Keywords

bioacoustics biodiversity-data r-package

Keywords from Contributors

interpretability standardization hack
Last synced: 6 months ago · JSON representation ·

Repository

This is an R package that enables environmental sensor users to create comprehensive work flows for managing and analyzing data

Basic Info
Statistics
  • Stars: 12
  • Watchers: 1
  • Forks: 9
  • Open Issues: 10
  • Releases: 0
Topics
bioacoustics biodiversity-data r-package
Created over 5 years ago · Last pushed 6 months ago
Metadata Files
Readme Changelog Contributing License Code of conduct Citation Support

README.md

wildrtrax

Lifecycle: stable CRAN status DOI Codecov test coverage

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. 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 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.

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.

Discover Data

Explore data through Data Discover. No login required to access public data! Use wt_auth() to login to see data you have privileges and membership to.

``` r library(wildrtrax) library(sf)

Search for public data without a boundary

wtddsummary(sensor = 'ARU', species = 'White-throated Sparrow')

Apply an area of interest. Define a polygon or use a bbox from sf::st_bbox

my_aoi <- list( c(-113.96068, 56.23817), c(-117.06285, 54.87577), c(-112.88035, 54.90431), c(-113.96068, 56.23817) )

wtddsummary(sensor = 'ARU', species = 'White-throated Sparrow', boundary = my_aoi)

Alberta bounding box

abbox <- readsf("...shp") |> # Shapefile of Alberta filter(Province == "Alberta") |> sttransform(crs = 4326) |> st_bbox()

wtddsummary(sensor = "ARU", species = "White-throated Sparrow", boundary = abbox) ```

Acoustic work flows

Download data and run and a single-season single-species occupancy analysis. Consult APIs and Acoustic data wrangling for more information.

``` r library(wildrtrax) library(tidyverse)

OAuth logins only. Google OAuth2 will be supported soon.

Sys.setenv(WTUSERNAME = "*****", WTPASSWORD = "*****")

Authenticate to WildTrax

wt_auth()

Get a project id

projects <- wtgetdownloadsummary("ARU") |> filter(project == "Ecosystem Health 2023") |> select(projectid) |> pull()

Download the main report

rawdata <- mapdfr(.x = projects, .f = ~wtdownloadreport(.x, "ARU", weather_cols = F, reports = "main"))

Format to occupancy for OVEN

dat.occu <- wtformatoccupancy(raw_data, species="OVEN", siteCovs=NULL)

Run the model

unmarked::occu(~ 1 ~ 1, dat.occu) ```

Conduct some pre-processing on various types of acoustic data. See more in Acoustic pre-processing.

``` r library(wildrtrax) library(tidyverse)

Scan files and filter results

myfiles <- wtaudioscanner(path = ".", filetype = "wav", extracols = T) |> mutate(hour = as.numeric(format(recordingdate_time, "%H"))) |> filter(julian == 176, hour %in% c(4:8))

Run acoustic indices and LDFCs

wtrunap(x = myfiles, outputdir = paste0(root, 'apoutputs'), pathto_ap = '/where/you/store/AP')

wtgleanap(myfiles, inputdir = ".../ap_outputs", purpose = "biotic") ```

Evaluate the performance of BirdNET on a project, and search for false negatives missed by human taggers. See Classifiers Tutorial for more information.

``` r library(wildrtrax) library(tidyverse)

OAuth logins only. Google OAuth2 will be supported soon.

Sys.setenv(WTUSERNAME = "*****", WTPASSWORD = "*****")

Authenticate to WildTrax

wt_auth()

data <- wtdownloadreport(projectid = 1144, sensorid = "ARU", reports = c("main", "birdnet"), weather_cols = FALSE)

eval <- wtevaluateclassifier(data, resolution = "task", remove_species = TRUE, thresholds = c(10, 99))

thresholduse <- wtclassifier_threshold(eval)

Find additional species

wtadditionalspecies(data, removespecies = TRUE, threshold = thresholduse, resolution="task") ```

Camera work flows

The ultimate pipeline for your camera data work flows. See Camera data wrangling for more information.

``` r library(wildrtrax) library(tidyverse)

OAuth logins only. Google OAuth2 will be supported soon.

Sys.setenv(WTUSERNAME = "*****", WTPASSWORD = "*****")

Authenticate to WildTrax

wt_auth()

Get a project id

projects <- wtgetdownloadsummary("CAM") |> filter(project == "ABMI Ecosystem Health 2014") |> select(projectid) |> pull()

Download data

raw <- mapdfr(.x = projects, .f = ~wtdownloadreport(.x, "CAM", weathercols = F, reports = "main"))

Get individual detections

individualdetections <- wtind_detect(raw, 30, "minutes") ```

Ultrasonic work flows

Format tags from Kaleidoscope for a WildTrax project. Download data from a project into an NABAT acceptable format.

``` r library(wildrtrax) library(tidyverse)

input <- ".../bat.txt" # Kaleidoscope output output <- ".../bats" # A folder to store the tags

wtkaleidoscopetags(input, output, tz, freq_bump = T) # Add a frequency buffer to the tag, e.g. 20000 kHz

Authenticate to WildTrax, then upload the tags to a WildTrax project

wt_auth()

Get a project id

projects <- wtgetdownloadsummary("ARU") |> filter(project == "BATS & LATS") |> select(projectid) |> pull()

Download the data

rawdata <- mapdfr(.x = projects, .f = ~wtdownloadreport(.x, "ARU", weather_cols = F, reports = "main"))

Experimental

rawdata |> wtformat_data(format = 'NABAT') ```

Point count work flows

Download combined and formatted acoustic and point count data sets together.

``` r library(wildrtrax) library(tidyverse)

An ARU project

anaruproject <- wtdownloadreport(projectid = 620, sensorid = 'ARU', reports = "main", weather_cols = F)

An ARU project as point count format

aruaspc <- wtdownloadreport(projectid = 620, sensorid = 'PC', reports = "main", weather_cols = F) ```

Issues

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

Contributors

We encourage ongoing contributions and collaborations to improve the package into the future. The Alberta Biodiversity Monitoring Institute provides ongoing support, development and funding.

License

This R package is licensed under MIT license©2025 Alberta Biodiversity Monitoring Institute.

Code of Conduct

Please note that wildrtrax is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

Owner

  • Name: Alberta Biodiversity Monitoring Institute
  • Login: ABbiodiversity
  • Kind: organization
  • Location: Edmonton, AB

We track changes in Alberta's wildlife and their habitats from border to border, and provide ongoing, relevant, scientifically credible information.

Citation (CITATION.cff) 

# --------------------------------------------
# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
# --------------------------------------------
 
cff-version: 1.2.0
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type: software
license: MIT
title: 'wildrtrax: Environmental Sensor Data Management and Analytics to and from
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version: '1.4'
abstract: This R package enables users of environmental sensors to create comprehensive
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GitHub Events

Total
  • Issues event: 19
  • Watch event: 4
  • Delete event: 2
  • Issue comment event: 28
  • Push event: 71
  • Pull request event: 8
  • Fork event: 3
  • Create event: 3
Last Year
  • Issues event: 19
  • Watch event: 4
  • Delete event: 2
  • Issue comment event: 28
  • Push event: 71
  • Pull request event: 8
  • Fork event: 3
  • Create event: 3

Committers

Last synced: 6 months ago

All Time
  • Total Commits: 778
  • Total Committers: 12
  • Avg Commits per committer: 64.833
  • Development Distribution Score (DDS): 0.325
Past Year
  • Commits: 276
  • Committers: 8
  • Avg Commits per committer: 34.5
  • Development Distribution Score (DDS): 0.384
Top Committers
Name Email Commits
agmacpha a****a@u****a 525
Alexandre MacPhail a****l@A****l 81
Marcus Becker m****r@u****a 59
ecknight e****t@g****m 48
Alex MacPhail 3****a 31
vlucet v****t@g****m 15
github-actions[bot] 4****] 10
Clayton Lamb c****b@u****a 3
Sarah Endicott 3****4 2
Kevin Kelly k****y@u****a 2
Cassie Stevenson 1****n 1
Alexandre MacPhail a****l@A****n 1
Committer Domains (Top 20 + Academic)
ualberta.ca: 4 alexandres-mbp.lan: 1

Issues and Pull Requests

Last synced: 6 months ago

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enhancement (9) bug (5) documentation (3) good first issue (1)
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Dependencies

DESCRIPTION cran
  • R >= 3.5.0 depends
  • doParallel * imports
  • dplyr >= 1.0.0 imports
  • foreach * imports
  • fs * imports
  • furrr * imports
  • future * imports
  • httr * imports
  • lubridate * imports
  • pipeR * imports
  • plumber * imports
  • purrr * imports
  • rlang * imports
  • seewave * imports
  • shiny * imports
  • stringr * imports
  • tibble * imports
  • tidyr >= 1.0.2 imports
  • tools * imports
  • tuneR * imports
  • unmarked * imports
  • abmi.themes * suggests
  • knitr * suggests
  • rmarkdown * suggests
  • testthat * suggests
.github/workflows/R-CMD-check.yaml actions
  • actions/cache v2 composite
  • actions/checkout v2 composite
  • actions/upload-artifact main composite
  • r-lib/actions/setup-pandoc v1 composite
  • r-lib/actions/setup-r v1 composite
.github/workflows/pkgdown.yaml actions
  • actions/cache v2 composite
  • actions/checkout v2 composite
  • r-lib/actions/setup-pandoc v1 composite
  • r-lib/actions/setup-r v1 composite
.github/workflows/pr-commands.yaml actions
  • actions/checkout v2 composite
  • r-lib/actions/pr-fetch v1 composite
  • r-lib/actions/pr-push v1 composite
  • r-lib/actions/setup-r v1 composite
.github/workflows/test-coverage.yaml actions
  • actions/cache v2 composite
  • actions/checkout v2 composite
  • r-lib/actions/setup-pandoc v1 composite
  • r-lib/actions/setup-r v1 composite