Reference Information

Provenance for this README

  • File name: README.md
  • Authors: Quresh S. Latif
  • Other contributors: Nicholas J. Van Lanen, Eric J. Chabot, David C. Pavlacky
  • Date created: 2023-01-25
  • Date modified: 2023-02-01

Dataset Version and Release History

  • Current Version:
    • Number: 1.0.0
    • Date: 2023-02-01
    • Persistent identifier: DOI: 10.5061/dryad.tb2rbp04r

Dataset Attribution and Usage

  • Dataset Title: Data for the article “Causal mechanisms for negative impacts of energy development inform management triggers for sagebrush birds”

  • Persistent Identifier: https://doi.org/10.5061/dryad.tb2rbp04r

  • Dataset Contributors: Quresh S. Latif, Nicholas J. Van Lanen, Eric J. Chabot, and David C. Pavlacky

  • Date of Issue: 2023-02-01

  • Publisher: Bird Conservancy of the Rockies

  • License: Use of these data is covered by the following license:

    • Title: CC0 1.0 Universal (CC0 1.0)

    • Specification: https://creativecommons.org/publicdomain/zero/1.0/; the authors respectfully request to be contacted by researchers interested in the re-use of these data so that the possibility of collaboration can be discussed.

  • Suggested Citations:

    • Dataset citation: Latif, Q. S., N. J. Van Lanen, E. J. Chabot, and D. C. Pavlacky. 2023. Data for the article “Causal mechanisms for negative impacts of energy development inform management triggers for sagebrush birds”, Dryad, Dataset. https://doi.org/10.5061/dryad.tb2rbp04r.

    • Corresponding publication: Latif, Q. S., N. J. Van Lanen, E. J. Chabot, and D. C. Pavlacky. 2023. Causal mechanisms for negative impacts of energy development inform management triggers for sagebrush birds. Ecosphere. Accepted. DOI: TBD

Contact Information


Additional Dataset Metadata

Acknowledgements

  • Funding sources: Bureau of Land Management (USDA) provided funding for data collection and analysis.

Dates and Locations

  • Dates of data collection: Field data collected between during bird breeding seasons of 2010 - 2019 following protocols and sampling design established under Integrated Monitoring in Bird Conservation Regions (IMBCR).

  • Geographic locations of data collection: Fieldwork conducted in sagebrush-dominated landscapes of Wyoming, U.S.A. Data represent The Atlantic Rim Natural Gas Development Project and all BLM-managed lands within Bird Conservation Region 10.


Methodological Information


File metadata

ARIM_elevations.csv

  • Description: A comma-delimited file containing elevation values for all sampling units summarized in the manuscript (referenced in one R script archived in the accompanying git repository).

  • Format: .csv

  • Dimensions: 100 rows X 2 columns

  • Fields:

    • TrnsctN: Unique identifier of each IMBCR grid cell sampling unit represented in the study.
    • Elev_m: Elevation of the grid cell centerpoint in meters.

Detection_parameter_estimates.xlsx

  • Description: Spreadsheet listing parameter estimates from the avian community occupancy model quantifying species detectability. Species occupancy and richness estimates reported in the manuscript are correct for detectability represented in these estimates. Species are listed in taxonomic order. All estimates are reported as posterior median (and 80% credible intervals).

  • Format: .xlsx

  • Dimensions: 141 rows X 8 columns

  • Fields:

    • Spp: 4-letter species codes. Complete species names are listed in see Spp_names_detections_guilds.xlsx.
    • p*: Species detectability for a 6-min survey at mean covariate values.
    • ζ: Logit-linear covariate relationships. Asterisks mark where credible intervals excluded zero, i.e., where the relationship was statistically supported.

Spp_names_detections_guilds.xlsx

  • Description: Spreadsheet listing species and their guild classifications represented in the data informing the avian community occupancy model analyzing energy development effects on occupancy and richness trends within the Atlantic Rim Natural Gas Development Project, Wyoming, U.S.A.

  • Format: .xlsx

  • Dimensions: 140 rows X 5 columns

  • Fields:

    • Common name: English common names.
    • Taxonomic name: Latin taxonomic name consisting of genus and species components.
    • Code: 4-letter species codes following the Institute for Bird Populations (https://www.birdpop.org/pages/birdSpeciesCodes.php). These codes are used for labeling species throughout the manuscript (e.g., figures, supplmenetary materials).
    • Guild: Guild classifications based on dominant vegetation associations represented in the literature (Birds of the World 2022) supplemented with our judgement based on knowledge of the study area. The four sagebrush-associated species were also considered members of the shrubland guild.
    • Detections: The number of point surveys (i.e., point × year survey occasions) the species was detected (max = 8916). Species never detected (Detections = 0) were detected in broader regional surveys and therefore included for data augmentation. Estimates for data augmentation species contributed only to species richness estimates and were never interpreted individually.

mod_path

  • Description: This file is an R object containing all model output as generated by the “01-Analysis.R” script file archived in an accompanying git repository (see Latif 2023). This file can be loaded using the R function ‘R.utils::loadObject()’. Broadly, this file contains posterior samples of parameter model estimates and their summaries as generated by the data analysis described in the manuscript and encoded in archived scripts (Latif 2023). This file is needed to replicate results summaries generated by various scripts located in the accompanying git repository (Latif 2023). As such, we do not provide a detailed catalog of the contents of this file.

Data_compiled.RDATA

  • Description: This is an R workspace containing all data and R objects necessary to run R scripts implementing data analyses and results summaries associated with this manuscript.

  • Format: .RDATA

  • Access: R objects contained in this file can be loaded into an R workspace using the Base R function ‘load’.

  • R objects contained in this workspace:

    • aou.checklist: Table of standardized bird codes and species names downloaded from the Institute of Bird Populations (https://www.birdpop.org/pages/birdSpeciesCodes.php).
    • bird_data: Raw bird detection data, including sampling unit IDs (TransectNum, Point, Stratum, Point_year), spatial coordinates (PointLatitude, PointLongitude, easting, northing, zone), Year, Date, survey timing (PointVisitStartTime), Species (BirdCode, Species), the time period the detection was recorded (TimePeriod), and additional data tangential to our analysis (CL_ID, radialDistance).
    • cov_grid: Grid-cell level covariate values, including some that were not included in the analysis.
    • cov_pntyr: Point x year covariate values primarily used for detectability and indexing during model definition.
    • cov_point: Point and Point x year covariate values arranged in wide format with years as columns.
    • point.coords: Spatial coordinates of point sampling units.
    • spp.excluded: List of species excluded from analysis.
    • spp.out: List of species included in data analysis.
    • tab.datetime: Survey timing information compiled during intermediate step towards arranging data for analysis.
    • TR.mat: Grid cell X year matrix containing time periods within surveys when detections were recorded (i.e., yclass,ijt in Equation S3.1.2, Appendix S3).
    • Y.mat: Grid cell X year matrix containing detection data compiled for analysis (i.e., yijt in Equation S3.1.1, Appendix S3).
    • Cov_grid: Grid-cell level covariate values formatted as a grid cell X year X variable array (contra data frame for cov_grid) required for analysis.
    • Cov_point: Point level values formatted as a point X year X covariate array (contra data frame for cov_pntyr) required for analysis.
    • grid.list: Grid cell IDs representing how relevant data were ordered for analysis (e.g., in Cov_grid).
    • PH.list: List of primary habitat codes (tangential to analysis).
    • point.list: Point IDs representing how relevant data objects were ordered for analysis (e.g., in Cov_point).
    • pointXyears.list: Point X year IDs representing how relevant data were ordered for analysis (e.g., in Y.mat).
    • SampDesign: Sampling designs for data included in analysis (primarily relevant to those familiar with IMBCR data).
    • spp.exclude: 4-letter codes for species excluded from analysis.
    • spp.list: 4-letter codes for species included in analysis.
    • strata: Strata IDs for data included in analysis (primarily relevant to those familiar with IMBCR data).
    • years: Years represented by the data included in the analysis.
  • Metadata note: Because this file is provided primarily as a reference for replicating study results following processes encoded in an accompanying git repository (Latif 2023), these metadata only provide a relatively high level description of the file contents, i.e., we briefly describe data objects but we do not necessarily describe every field appearing within each data object.

Code/Software

Linked with this data repository is a git repository (Latif 2023) containing all R scripts for compiling data, implementing all analyses, and generating all results reported in the manuscript. The README file within the git repository catalogs each script file contained along within it. Files contained in this data repository are primarily intended to promote transparency and repeatability of all results in the manuscript by allowing interested persons to run scripts provided by Latif (2023).

References

Birds of the World. 2022. Edited by S. M. Billerman, B. K. Keeney, P. G. Rodewald, and T. S. Schulenberg. Cornell Laboratory of Ornithology, Ithaca, NY, USA. https://birdsoftheworld.org/bow/home

Latif, Q. S. 2023. qureshlatif/ARIM-analysis (v1.0.1). Zenodo. https://doi.org/10.5281/zenodo.7566617


END OF README