This codebook.txt file was generated on 27 December 2017 by Gunnar R. Kramer ------------------- GENERAL INFORMATION ------------------- 1. Geolocator data, R code, and associated output for analyses of Vermivora warbler nonbreeding occurrence, movement, and ecology. 2. Author Information Principal Investigator Contact Information Name: Gunnar R. Kramer Institution: Minnesota Cooperative Fish and Wildlife Research Unit, University of Minnesota Address: 200 Hodson Hall, 1980 Folwell Ave., St. Paul, Minnesota 55108 Email: gunnarrkramer@gmail.com *Current institution: Department of Environmental Sciences, University of Toledo Associate or Co-investigator Contact Name: David E. Andersen Institution: U.S. Geological Survey, Minnesota Cooperative Fish and Wildlife Research Unit Associate or Co-investigator Contact Name: David A. Buehler Institution: University of Tennessee Associate or Co-investigator Contact Name: Petra B. Wood Institution: U.S. Geological Survey, West Virginia Cooperative Fish and Wildlife Research Unit Associate or Co-investigator Contact Name: Henry M. Streby Institution: Department of Environmental Sciences, University of Toledo Additional Investigators: Sean M. Peterson (University of California - Berkeley), Justin A. Lehman (University of Tennessee), Kyle R. Aldinger (West Virginia Cooperative Fish and Wildlife Research Unit, West Virginia University), Lesley P. Bulluck (Virginia Commonwealth University), Sergio Harding (Virginia Department of Game and Inland Fisheries), John A. Jones (Tulane University), John P. Loegering (University of Minnesota), Curtis Smalling (Audobon North Carolina), Rachel Vallender (Canadian Wildlife Service, Environment and Climate Change Canada). 3. Data collected from April 2013 to June 2017 4. Geographic location of data collection (where was data collected?): Study sites are listed in each year individual warblers were marked and recovered. General coordinates are provided with abbreviations used in individual bird ID's (e.g., TN13 is a golden-winged warbler marked at North Cumberland Wildlife Management area in 2013. In a previous version of this dataset, this individual was labeled as CM13). 2013-2014 North Cumberland Wildlife Management Area, Tennessee, USA (CM/TN; 36.2 N, 84.2 W) Rice Lake National Wildlife Refuge, Minnesota, USA (RL/MN; 46.5 N, 93.3 W) 2014-2015 North Cumberland Wildlife Management Area, Tennessee, USA (CM/TN; 36.2 N, 84.2 W) Rice Lake National Wildlife Refuge, Minnesota, USA (MN/RL; 46.5 N, 93.3 W) Delaware Forest, Pennsylvania, USA (DF/PA; 41.3 N, 75.1 W) 2015-2016 North Cumberland Wildlife Management Area, Tennessee, USA (TN; 36.2 N, 84.2 W) Rice Lake National Wildlife Refuge, Minnesota, USA (RL; 46.5 N, 93.3 W) Grandview area, Manitoba, Canada (DM; 51.5 N, 100.6 W) Shawnee National Forest, Illinois, USA (IL; 37.8 N, 89.5 W) Fox Ridge State Park, Illinois, USA (IL; 39.4 N, 88.2 W) Leslie County, Kentucky, USA (KY; 36.9 N, 83.6 W) Hampshire County, Massachusetts, USA (MA; 42.3 N, 72.6 W) Barry State Game Area, Michigan, USA (MI; 42.6 N, 85.4 W) Gladwin County, Michigan, USA (MI; 43.9 N, -84.3 W) Ashe County, North Carolina, USA (NC; 36.4 N, -81.7 W) Glen Major area, Ontario, Canada (ON; 44.0 N, -79.1 W) Orillia area, Ontario, Canada (ON; 44.7 N, -75.5 W) Queen's University Biological Station, Ontario, Canada (ON; 44.6 N, -76.3 W) Bald Eagle State Park area, Pennsylvania, USA (PA; 41.0 N, -77.7 W) Dauphin area, Manitoba, Canada (MB; 51.0 N, -99.9 W) Sherburne National Wildlife Refuge, Minnesota, USA (SH; 45.5 N, -93.7 W) Sandilands Provincial Forest, Manitoba, Canada (SL; 49.6 N, -93.3 W) Tamarac National Wildlife Refuge, Minnesota, USA (TA; 47.0 N, -95.6 W) Oak Ridge National Laboratory, Tennessee, USA (TN; 35.9 N, -84.4 W) Fort Campbell, Tennessee, USA (TN; 36.6 N, -87.5 W) Highland County, Virginia, USA (VA; 38.3 N, -79.6 W) Sandhill Wildlife Area, Wisconsin, USA (WI; 44.3 N, -90.1 W) 2016-2017 Sandhill Wildlife Area, Wisconsin, USA (WI; 44.3 N, -90.1 W) 5. Information about funding sources that supported the collection of the data: These data were collected during a project funded by the U.S. Fish and Wildlife Service and U.S. Geological Survey through Research Work Order No. 98 at the U.S. Geological Survey, Minnesota Cooperative Fish and Wildlife Research Unit; and by the National Science Foundation through Postdoctoral Research Fellowship No. 1202729 (H. Streby). Additional funding was provided by the Virginia Department of Game and Inland Fisheries and the Grace Jones Richardson Trust. 6. Acknowledgments: We thank M Barber, M Barnes, J Bell, J Chancey, L Coe-Starr, C Colley, E Davis, J Dodson, K Eckert, R Eckstein, R Fenty, C Fiss, M Gallagher, B Gray, A Grupenhoff, C Henderson, L Hendrixson, N Henke, E Hess, L Hoehn, J Kawlewski, B Keinath, J Koberdahl, L Loegering, S McLaughlin, S Midthune, L Mielke, D Miles, M Morin, N Moy, J Nelson, A Pesano, S Prevost, J Reubesam, M Schilling, N Seeger, L Schofield, A Tomcho, S Wallace, J Warmbold, J Wessels, A Worm, B Yliniemi, and others for assistance in the field. We are especially grateful to N Hill, K Maley, D McNeil, R Pagel, P Rodrigues, K Stein, and C Ziegler for their commitment to the project, and to W Ford, W Brininger, A Hewitt, D King, J Larkin, and H Saloka for providing logistical support. These data were collected during a project funded by the U.S. Fish and Wildlife Service and the U.S. Geological Survey through Research Work Order No. 98 at the U.S. Geological Survey, Minnesota Cooperative Fish and Wildlife Research Unit; and by the National Science Foundation through Postdoctoral Research Fellowship No. 1202729 (HMS). Additional funding was provided by the Virginia Department of Game and Inland Fisheries and the Grace Jones Richardson Trust. None of our funders had any influence on the content of the submitted or published manuscript and only the U.S. Geological Survey required approval of the final manuscript prior to publication as required in their Fundamental Sciences Practices protocols. We captured and marked birds following Protocol No. 561, approved by the University of Tennessee Institutional Animal Care and Use Committee; Protocol No. 104A80575, approved by the University of Minnesota Institutional Animal Care and Use Committee; the Virginia Commonwealth University Institutional Animal Care and Use Committee proposal #10230; and Protocol Nos. 07-0303 and 10-0201 approved by the West Virginia University Institutional Animal Care and Use Committee. Use of trade names does not imply endorsement by the U.S. Geological Survey or any other institutions affiliated with this study. -------------------------- SHARING/ACCESS INFORMATION -------------------------- 1. Licenses/restrictions placed on the data: Attribution-NonCommercial-ShareAlike 3.0 United States 2. Links to publications that cite or use the data: Kramer et al. 2017. Nonbreeding isolation and population-specific non migration patterns among three populations of Golden-winged Warblers. Condor 119:108-121 https://doi.org/10.1650/CONDOR-16-143.1 Kramer et al. 2018. Population Trends in Vermivora warblers are linked to strong migratory connectivity. Proceedings of the National Academy of Sciences, in press. 3. Links to other publicly accessible locations of the data: A portion of the data (collected between 2013-2015) are also available at: http://doi.org/10.13020/D6R59C 4. Links/relationships to ancillary data sets: n/a 5. Was data derived from another source? If yes, list source(s): No. 6. Recommended citation for the data: Kramer, G.R., D.E. Andersen, D.A. Buehler, P.B. Wood, S.M. Peterson, J.A. Lehman, K.R. Aldinger, L.P. Bulluck, S. Harding, J.A. Jones, J.P. Lowering, C. Smalling, R. Vallender, and H.M. Streby (2018). Geolocator data, R code, and associated output for analyses of Vermivora warbler nonbreeding occurrence, movement, and ecology. Retrieved from the Data Repository for the University of Minnesota, https://doi.org/10.13020/D6D97W. --------------------- DATA & FILE OVERVIEW --------------------- Summary - summary by file type: *************** .tif files (n=76 in VermivoraNonbreeding_tif.zip) - TIFF image files of nonbreeding surface for individual Vermivora warblers. Can be read into R or imported into a geographical information system (GIS). *************** .shp files (in VermivoraNonbreedingShpFiles.zip) - ESRI Shape documents (with associated metadata and files required for viewing and using)of the nonbreeding distributions of Vermivora warblers. Polygons are derived from data provided by BirdLife International. Shape files (.shp) may be read into R or imported and viewed in a GIS. The terms of use for the BirdLife derivatives are included in this folder (-TermsofUse_BirdLifeDerivativeData.txt) *************** .html files (Individual_Vermivora_raster_code.html, NonbreedingBoxplotCode.html) - HTML files with code for analyzing and visualizing data. *************** .rmd files (Individual_Vermivora_raster_code.Rmd, NonbreedingBoxplotCode.Rmd) - R Markdown files that produce the .html files. Requires all files to be in the same folder, which is set as the root directory in the first chunk. ************** .lig files (in VermivoraRawGeoData.zip) are comma separated time stamped ASCII data files where each timestamped record is on a separate line. There is a three variable string in the first row of the file that is used for reading the file. The remaining columns of the .lig files are: ,
,, where indicates whether the data is ok or suspect
is the time stamp is another way of representing the time; it is the number of seconds elapsed since the reference chosen when the file was processed is the maximum light (0-64) value measured during the previous 2 minutes Errors are also reported on separate lines (if they are present) with `error` instead of `ok` in the first position of the entry. ***************** 1. File List A. Filename: VermivoraNonbreeding_tif.zip Short description: Clipped averaged likelihood surfaces (n=76) for 70 individual Vermivora warblers (6 individuals tracked in separate years). Full likelihood surfaces for the nonbreeding period were clipped by the nonbreeding distribution of Vermivora warblers buffered by 100 km. The resulting nonbreeding likelihood surfaces are .tif files labeled with an individual ID. If likelihood surfaces from different years exist for the same warbler, the year in which the data were recovered is listed following the file name (e.g., WIB11_ext16.tif, WIB11_ext17.tif). In the example, the first file is from WIB11 and was recovered in 2016, the second file is also from WIB11 but is data recovered in 2017 after tracking the bird an additional year. B. Filename: VermivoraNonbreedingShpFiles.zip Short description: Nonbreeding distributions (.shp files) of Vermivora warblers buffered by 100 km. Polygons were derived from data provided by BirdLife International on 15 January 2016 and original "Species distribution data" may be requested at http://datazone.birdlife.org/species/requestdis. The shape files for golden- and blue-winged warblers (SISID [species ID] 2272161 and 22721610 respectively) were then isolated from the larger dataset and buffered by 100 km. C. Filename: VermivoraSummaryTable.csv Short description: Summary table of individual warblers providing metadata and details used in analyzing and deriving nonbreeding locations (probability density functions; .tif files). D. Filename: vermNBlatWKbk.csv Short description: .csv file with basic information on marked individual Vermivora warblers used to perform basic statistics and estimate migratory connectivity. E. Filename: Individual_Vermivora_raster_code.html Short description: .html file with code required to replicate analysis of .tif files (contained within VermivoraNonbreeding_tif.zip) and recreate spatial results presented in Kramer et al. 2018. F. Filename: Individual_Vermivora_raster_code.rmd Short description: .rmd R markdown file that generates the html and analysis in Individual_Vermivora_raster_code.html G. Filename: NonbreedingBoxplotCode.html Short description: .html file with code required to replicate statistical analysis in Kramer et al. 2018 using data from vermNBlatWkbk.csv. H. Filename: NonbreedingBoxplotCode.rmd Short description: .rmd R markdown file that generates the html and analysis in NonbreedingBoxplotCode.html I. Filename: VermivoraRawGeoData.zip Short description: .zip file containing 76 individual light-level files (.lig format) from 70 individual Vermivora warblers tracked between 2013-2017. Details on individuals, methods and code used for interpreting and analyzing data, and results of analyses can be found in files contained in this dataset and in multiple peer review publications (see below). 2. Relationship between files: Six individuals were tracked over 2 separate years and are noted below: i. MN14 - golden-winged warbler breeding at Rice Lake NWR (MN); tracked 2013-2014 (MN14_ext14.tif, MN14_16.lig) and 2015-2016 (MN14_ext16.tif; MN14_16.lig). ii. MN29 - golden-winged warbler breeding at Rice Lake NWR (MN); tracked 2014-2015 (MN29_ext15.tif, MN14_15.lig) and 2015-2016 (MN29_ext16, MN29_16.lig). iii. MN36 - golden-winged warbler breeding at Rice Lake NWR (MN); tracked 2014-2015 (MN36_ext15.tif, MN36_15.lig) and 2015-2016 (MN36_ext16, MN36_16.lig). iv. TN13 - golden-winged warbler breeding at North Cumberland WMA (TN); tracked 2013-2014 (TN13_ext14.tif, TN13_14.lig), and 2014-2015 (TN13_ext15.tif, TN13_15.lig). v. WIB11 - blue-winged warbler breeding at Sandhill Wildlife Area (WI); tracked 2015-2016 (WIB11_ext16.tif, WIB11_16.lig) and 2016-2017 (WIB11_ext17.tif, WIB11_17.lig). vi. WIH03 - hybrid Vermivora warbler breeding at Sandhill Wildlife Area (WI); tracked 2015-2016 (WIH03_ext16.tif, WIH03_16.lig) and 2016-2017 (WIH03_ext17.tif, WIH03_17.lig). 3. Additional related data collected that was not included in the current data package: n/a 4. Are there multiple versions of the dataset? A portion of this dataset includes data raw light-level geolocator data from Kramer et al. (2016) and can be accessed at http://doi.org/10.13020/D6R59C. Note that the names of individuals are different. Individuals in the 2016 DRUM dataset (listed above) are labeled in the current dataset as follows: CM05 = TN05 CM06 = TN06 CM09 = TN09 CM10 = TN10 CM13 = TN13_2014 CM16 = TN16 CM21 = TN13_2015 DF05 = PA05 DF11 = PA11 RL03 = MN03 RL05 = MN05 RL06 = MN06 RL11 = MN11 RL12 = MN12 RL14 = MN14_2014 RL15 = MN15 RL16 = MN16 RL20 = MN20 RL25 = MN25 RL29 = MN29_2015 RL36 = MN36_2015 -------------------------- METHODOLOGICAL INFORMATION -------------------------- 1. Description of methods used for collection/generation of data: We collected these geolocator data from golden-winged warblers (V. chrysoptera) and blue-winged warblers (V. cyanoptera) from April 2013 to June 2017. Geolocator marking methods manuscript: Streby, H.M., T.L. McAllister, S.M. Peterson, G.R. Kramer, J.A. Lehman, and D.E. Andersen (2015). Minimizing marker mass and handling time when attaching radio-transmitters and geolocators to small songbirds. The Condor: Ornithological Applications 117:249-255. Lack of geolocation effects manuscript: Peterson, S.M., H.M. Streby, G.R. Kramer, J.A. Lehman, D.A. Buehler, and D.E. Andersen (2015). Geolocators on Golden-winged Warblers do not affect migratory ecology. The Condor: Ornithological Applications 117:256-261. 2. Methods for processing the data: Geolocators deployed on Golden-winged Warblers measured ambient light levels every 1 minute and permanently recorded the maximum light reading every 2 minutes for the life of the unit. Compressed data stored onboard individual units were downloaded upon recovery using BASTrak Software (Biotrak, Wareham, UK). The compressed (.txt) file was decompressed using BASTrak Software and we provide the resulting raw light files (.lig). Description of data analysis and preliminary findings are presented in: Kramer et al. 2017. Nonbreeding isolation and population-specific non migration patterns among three populations of Golden-winged Warblers. Condor 119:108-121 https://doi.org/10.1650/CONDOR-16-143.1 3. Instrument- or software-specific information needed to interpret the data: .lig files are often read in R using the BAStag package (Wotherspoon et al. 2013). See Kramer et al. (2017) for details on analysis of these raw light-level data. .tif files are derived from .lig files following the methods outlined in Kramer et al. (2017) and may be analyzed in R using the code included in this database ( **Wotherspoon, S., M. Sumner, and S. Lisovski (2013). BAStag: Basic data processing for light based geolocation archival tags. R Package version 0.1-3** ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: VermivoraNonbreeding_tif.zip ----------------------------------------- Contains 76 clipped likelihood surfaces for 70 individual Vermivora warblers (6 individuals tracked in separate years). See VermivoraSummaryTable.csv for detailed information on the number of twilights used to inform individual likelihood surfaces, the year each individual was tracked, and information regarding the species and sex of each individual. See Individual_Vermivora_raster_code.html for code used to transform likelihood surfaces to probability density functions (PDF), combine individual warblers' PDFs into population-level average PDFs, and visualize in R. ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: VermivoraNonbreedingShpFiles.zip ----------------------------------------- Contains 3 Shapefiles (.shp) and associated files and metadata (.prj, .cpg, .dbf, .sbn, .sbx files) required for reading Shapefiles into R or a GIS. bwNB.shp = blue-winged warbler nonbreeding distribution buffered by 100 km. Adapted from data provided by BirdLife International. gwNB.shp = golden-winged warbler nonbreeding distribution buffered by 100 km. Adapted from data provided by BirdLife International. vermNB_D.shp = combined nonbreeding distribution of Vermivora warblers buffered by 100 km. Adapted from data provided by BirdLife International. Overview of files supporting .shp files (i.e., these files must be in the same folder as the .shp file when loading/viewing .shp file in a GIS): .cpg files = an optional file that can be used to specify the code page for identifying the character set to be used. .dbf files = the dBASE table that stores the index of the feature geometry .prj files = the file that stores the coordinate system information .sbn files = file that stores the spatial index of the features .sbx files = file that stores the spatial index of the features ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: VermivoraSummaryTable.csv ----------------------------------------- Summary table of individual warblers providing metadata and details used in analyzing and deriving nonbreeding locations (probability density functions; .tif files). Table contains 12 columns: BirdID = Unique identifier given to an individual warbler. Recovery Year = Year in which geolocator was recovered. Geolocator was deployed in previous year. Transitions span = The range of dates for which transition-derived likelihood surfaces were averaged to create a single nonbreeding likelihood surface. Total # of transitions = The number of transitions that fell within the Transition span that were used to derive nonbreeding likelihood surfaces for each individual. Full Track? = Logical (yes or no). Did the geolocator record data for the entirety of the deployment? Species = Species of individual warbler classified by the authors based on plumage traits. GW is golden-winged warbler, BW is blue-winged warbler, and HYBRID is a golden-winged warbler x blue-winged warbler hybrid. Sex = Male or female. Deployment site latitude = Latitude (degrees N) of the deployment site. Deployment site longitude = Longitude (degrees W) of the deployment site. Nonbreeding latitude = Latitude (degrees N) of the highest probability cell in the nonbreeding PDF. Nonbreeding longitude = Longitude (degrees W) of the highest probability cell in the nonbreeding PDF. Probability = Maximum probability of the PDF. ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: VermNBlatWKbk.csv ----------------------------------------- Summary table with basic information on marked individual Vermivora warblers (not including hybrids) used to perform basic statistics and estimate migratory connectivity. Notably, all individuals with multiple years of data are only represented once in this table and the nonbreeding coordinates are averages of the years for which data were available. Table contains 7 columns: birdID = Unique identifier of individual warblers. depLAT = Latitude (degrees N) of the deployment site. depLON = Longitude (degrees W) of the deployment site. nbLAT = Latitude (degrees N) of the highest probability cell in the nonbreeding PDF. nbLON = Longitude (degrees W) of the highest probability cell in the nonbreeding PDF. sp = Species of individual warbler classified by the authors based on plumage traits. 1 represents golden-winged warbler, 2 represents blue-winged warbler. popseg = Population segment derived from Bird Conservation Regions (BCRs). ph_bwwa refers blue-winged warblers breeding in the Prairie-Hardwoods Transition BCR; ch_bwwa refers to blue-winged warblers breeding in the Central Hardwoods BCR; napp_bwwa refers to blue-winged warblers breeding in the northern portion of the Appalachian Mountains BCR; sapp_bwwa refers to blue-winged warblers breeding in the souther portion of the Appalachian Mountains BCR; wgl_gwwa refers to golden-winged warblers breeding in the western portion of the Boreal-Hardwoods Transition BCR; egl_gwwa refers to golden-winged warblers breeding in the eastern portion of the Boreal-Hardwoods Transition BCR; napp_gwwa refers to golden-winged warblers breeding in the northern portion of the Appalachian Mountains BCR; sapp_gwwa refers to golden-winged warblers breeding in the souther portion of the Appalachian Mountains BCR. ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: Individual_Vermivora_raster_code.html ----------------------------------------- .html file containing R code required to replicate analysis of .tif files (contained within VermivoraNonbreeding_tif.zip) and recreate spatial analysis and figures presented in {replace with DOI for Kramer et al. (2018)}. This file was generated from the R markdown file (.rmd) of the same name. ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: NonbreedingBoxplotCode.html ----------------------------------------- .html file containing R code required to replicate statistical analysis in {replace with DOI for Kramer et al. (2018)} using data from vermNBlatWkbk.csv. This file was generated from the R markdown file (.rmd) of the same name. ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: VermivoraRawGeoData.zip ----------------------------------------- .zip file containing 76 individual light-level files (.lig format) from 70 individual Vermivora warblers tracked between 2013-2017. See description of .lig files above and relevant publications for details on analysis. Specific information on unique files (or files requiring special attention) are presented below: DMG03.lig = Unit stopped collecting data in the spring of 2016. All recorded data are provided. MIB05.lig = Unit experienced a ~ -10 hr shift in time on ~30 May 2015. This can be corrected for by adding 10 hr to the time column of the dataset and only using data from dates after 1 June 2016. This can be accomplished simply with the following code: setwd("~path/MIB05") d.lux<-readLig(("MIB05_000.lig"), skip=1) test<-subset(d.lux, select=c("Date", "Light")) summary(test) d.lux<-test d.lux$Date<-d.lux$Date +36000 KYB14.lig = Unit stopped collecting data in the winter of 2015. All recorded data are provided. MN03.lig = Geolocator was recovered with mud caked on/near the light sensor. See Kramer et al. 2017 (https://doi.org/10.1650/CONDOR-16-143.1) for description of how this file was treated in analysis. MN14_14.lig = Unit stopped collecting data before recovery in the spring of 2014. All recorded data are provided. MN15.lig = Unit stopped collecting data before recovery in the spring of 2014. All recorded data are provided. MN29_16.lig = Unit stopped collecting data before recovery in the spring of 2016. All recorded data are provided. RLG16.lig = Unit stopped collecting data before recovery in the spring of 2016. All recorded data are provided. No additional information is required to interpret the remaining .lig files not identified above.