.github/paper/paper.md

In trashbirdecology/bbsAssistant: Download and Munge Data and Information from the North American Breeding Bird Survey

title: 'bbsAssistant: An R package for downloading and handling data and information from the North American Breeding Bird Survey' authors: - affiliation: '1' name: Jessica L Burnett orcid: 0000-0002-0896-5099 - affiliation: '2,3' name: Lyndsie Wszola orcid: 0000-0002-2660-2048 - affiliation: 2 name: Gabriela Palomo-Muñoz orcid: 0000-0002-0661-413X date: "26 November 2019" output: pdf_document bibliography: paper.bib tags: - breeding bird survey - data retriever - ecology - point counts affiliations: - index: 1 name: Science Analytics and Synthesis, Core Science Systems, U.S. Geological Survey, Denver, Colorado, USA - index: 2 name: School of Natural Resources, University of Nebraska, Lincoln, Nebraska, USA - index: 3 name: School of Biological Sciences, University of Nebraska, Lincoln, Nebraska, USA

Summary

This R package contains functions for downloading and munging data from the U.S. Geological Survey's North American Breeding Bird Survey (BBS) via file transfer protocol (FTP) [@pardieck2018north; @sauer2017first]. This package was created to allow the user to bulk-download the BBS point count and related (e.g., route-level conditions) via FTP, and to quickly subset the data by taxonomic classifications and/or geographical locations. This package also maintains data containing the trend and annual indices from the most recent (1996-2017) hierarchical population analyses [@sauer2017north].

Retrieving and Munging Point-count and Related Data

Although the BBS provides a public interface for retrieving data and analysis results via FTP, bbsAssistant expedites the efforts of downloading, decompressing, importing, and subsetting the state/region-level point-count files, and other associated files (e.g., taxonomic information, geographic information, route-level conditions, geographical information). The data subsetting features allow the user to download and import only the data necessary for their purposes, rather than the entire data collection. Although the primary audience is for those wishing to use BBS data in Program R for visualization or analysis, this package can be used to quickly download the BBS data to file for use elsewhere.

Retrieving Population Trend Model Results from the BBS website

The Patuxent Wildlife Research Center uses hierarchical modelling of the BBS data to generate population trend estimates and annual indices at various spatial scales (@sauer2017north; see also the BBS results webpage). Given the variability in data availability, the BBS team also provides data credibility scores for species-regions combinations. This package contains the most recent results associated with these analyses as data objects, but also provides a function (get_credibility_trends()) for retrieving all analysis results which are public-facing.

State of the Field

We are aware of three R packages which retrieve and/or munge the BBS data: rdataretriever [@rdataretriever], rBBS [@rbbs], and bbsBayes [@bbsBayes], each of which provides various pathways for importing BBS data into the local environment. rdataretriever provides a data set which integrates components of the BBS data, however, requires the use of Python in conjunction with R. The rBBS package is perhaps most aligned with the bbsAssistant package, in that it also provides functions for downloading BBS data, however, the existing repository is apparently stale. Further, bbsAssistant provides streamlined functionality for retrieving location and species-specific data. Finally, the bbsBayes package, was creating primarily to run hierarchical models in a Bayesian framework within R. bbsBayes provides a function (bbsBayes::fetch_bbs_data()) for retrieving and importing all BBS data, yet does not currently allow for custom download and importation.

Acknowledgements

We especially thank the thousands of participatory scientists who have and continue to collect data for the North American Breeding Bird Survey program, and the Patuxent Wildlife Research Center for making these data publicly and easily accessible. We also thank Ethan White; \@ethanwhite and Joseph Stachelek; \@jsta for their feedback on a previous iteration of this software which greatly improved usability, functionality, and efficiency, and Kristen Thyng; \@kthyng for handling the JOSS submission. This draft manuscript is distributed solely for purposes of scientific peer review. Its content is deliberative and predecisional, so it must not be disclosed or released by reviewers. Because the manuscript has not yet been approved for publication by the U.S. Geological Survey (USGS), it does not represent any official USGS finding or policy. This software is preliminary or provisional and is subject to revision. It is being provided to meet the need for timely best science. The software has not received final approval by the U.S. Geological Survey (USGS). No warranty, expressed or implied, is made by the USGS or the U.S. Government as to the functionality of the software and related material nor shall the fact of release constitute any such warranty. The software is provided on the condition that neither the USGS nor the U.S. Government shall be held liable for any damages resulting from the authorized or unauthorized use of the software.

References

trashbirdecology/bbsAssistant documentation built on May 22, 2022, 6:08 a.m.