Changelog • wildrtrax

wildrtrax 1.4

New function, wt_get_sync(), allows users to get all columns and data from syncs (upload / download and table views) across the system. Huge development leap as users can now GET all relevant APIs. Functionally replaces wt_get_recordings(), wt_get_locations(), wt_get_visits(), wt_get_image_sets() in one smooth function relevant to the Organization and Project you want.
Fixed a bug that incorrectly adjusted time zones in wt_qpad_offsets(). This bug affected QPAD offsets used for species with time since sunrise in the top model and in areas outside the Mountain Time Zone (MST/MDT). For more information, please see the BAM QPAD correction repository for further details or email bamp@ualberta.ca for assistance.

Additional argument to wt_summarise_cam() using image_set_id to adjust for effort across multiple deployments (see #80); additional enhancements for wt_ind_detect() (see #81, #82.
#84 through e2e181a for wt_ind_detect(), species detections are now generated separately for each species and then combined afterward into a single output.
Fixed bugs and enhanced usage of wt_kaleidoscope_tags() (see #77).

Continued GET request support with new functions: wt_get_visits(), wt_get_recordings(), wt_get_image_sets(), wt_get_project_species()
wt_get_threshold becomes wt_classifier_threshold() to distinguish from other GET functions

Camera function maintenance for #70; increasing camera test suites for common permutations
Branching development to prepare package for WildTrax 2.0.
Introduced the max_seconds argument in wt_download_report() to provide customizable timeout control for users with slower internet connections or larger project downloads.
Remove QPAD from Remotes. Users should be prompted to download QPAD separately if not already installed. Fix in timezone (#78).

Support for GET requests; new function wt_get_locations() to get Organization locations
Removed stringr as dependency

Address camera functionalities from #60, #62
Add GRTS grid cells for Alaska and contiguous United States for wt_add_grts() (#64)
Use .wt_col_types() to dynamically adjust column reports to help address (#55)
Moved wt_calculate_prf() to internal function

Addition of five new functions:
- wt_dd_summary() for querying data from Data Discover. See APIs for more information
- wt_evaluate_classifier(), wt_get_threshold(), and wt_additional_species() for wrangling acoustic automated classification results. See Acoustic classifiers for more information.
- wt_add_grts() to intersect locations with GRTS IDs from NABat
wt_download_tags() now becomes wt_download_media() to support broader media downloads in batch from WildTrax
Deprecated wt_report()

Switch to curl::curl_download() for media and assets
Removed dependencies pipeR, progressr, jsonlite, future, furrr, tools, magrittr, markdown, rmarkdown to increase package stability but reduces speed for functions such as wt_audio_scanner(), wt_run_ap(). Moved vembedr to suggests for vignettes
Switched wt_download_report() to POST requests
Lowercase package name

wt_chop() now recurses across all input files
Moving geospatial assets to new repository to lighten package size. Asset requests are now made only through usage of wt_qpad_offsets().

Improvements to APIs and acoustic convenience functions to resolve issues and PRs
Improvements to test suite, testing dependencies, code coverage
Addition of Camera data wrangling vignette and additional tutorials

wildrtrax now honours new WildTrax report structures. Future changes will incorporate standardized naming in syncing functions.
Replaced geospatial functionalities from rgdal, rgeos and maptools with sf, sp and terra packages. Added functionality with the suntools package. Users should re-download the package by October 2023 in-line with the former package retirement: https://geocompx.org/post/2023/rgdal-retirement/.

Tweaks to Acoustic data wrangling for (#16)
Addition of geospatial assets. Users should be warned package size is now ~40 MB.
Moved TMTT predictions from csv to .RDS file.
Work flow repairs to wt_get_species() and wt_tidy_species() (#21)
Replaced utils::read.csv() to readr::read_csv() in wt_download_report() (#20)

Improvements to wt_audio_scanner()
- Addition of flac as file type
- Addition of extra_cols argument to enable faster scanning when argument is set to FALSE. This also deals with headerless file errors for (#2)
- Enabled parallel file scanning; microbenchmarked base scanning at 5.6x faster on a dual-core machine
- Moved progress bars to the progressr package
Addition of wt_glean_ap() function to acoustic pre-processing work flow to extract desired data from a wt_run_ap() output
Addition of linking functions in order to add desired media and metadata to WildTrax: wt_make_aru_tasks(), wt_kaleidoscope_tags() and wt_songscope_tags()
Addition of convenience functions: wt_location_distances() and wt_chop()
Alignment of wt_download_report() with column headers released in WildTrax Phase 8 to resolve (#3, #4, #5)
Addition of additional acoustic functions to prepare data for analysis: wt_replace_tmtt(), wt_make_wide(), wt_format_occupancy(), wt_qpad_offsets()
Addition of wt_get_species() to download the WildTrax species table and wt_tidy_species() to filter various taxa
Addition of wt_download_tags() to download images, spectrograms and audio clips from tags
Experimental testing of customizable, automated reports with wt_report()
Long-form documentation available for full-cycle environmental work flows and new articles for usage of acoustic and camera data analysis functions

Moved wt_run_ap() to furrr::future_map from dopar loop to lessen package dependencies
Quiet console output from wt_run_ap() for Windows users
Added a NEWS.md file to track changes to the package
Renamed wt_ind_det to wt_ind_detect()