This readme.txt file was generated on 20150414 by Jason Bruggeman GENERAL INFORMATION Title of Dataset: Arctic peregrine falcon abundance on cliffs along the Colville River, Alaska, 1981-2002 and covariate input files Photo credit: Ted Swem, U.S. Fish and Wildlife Service File Information: Filename: Rcode_arctic_peregrine_abundance.txt Short description: R code for analyses of Arctic peregrine falcon abundance data using package UNMARKED in R and the Dail-Madsen model Filename: abundancematrix.csv Short description: Scaled and centered covariate input file for the abundance covariate Filename: gyrdistancematrix.csv Short description: Scaled and centered covariate input file for the gyrdistance covariate Filename: meltdatematrix.csv Short description: Scaled and centered covariate input file for the meltdate covariate Filename: obsmatrix.csv Short description: Input file for the number of adult Arctic peregrines counted on each cliff during visit no. 1 and visit no. 2 of each year Filename: pdomatrix.csv Short description: Scaled and centered covariate input file for the pdo covariate Filename: precipmatrix.csv Short description: Scaled and centered covariate input file for the precip covariate Filename: productivitymatrix.csv Short description: Scaled and centered covariate input file for the productivity covariate Filename: sitecovs.csv Short description: Scaled and centered covariate input file for the geology, height, waterarea, aspect, and slope covariates Filename: tmaxmatrix.csv Short description: Scaled and centered covariate input file for the tmax covariate Filename: visitmatrix.csv Short description: Input file for the survey visit number for each year Filename: yearslogmatrix.csv Short description: Covariate input file for the yearlog covariate Filename: yearsmatrix.csv Short description: Covariate input file for the yearlinear covariate Filename: yearsthresholdmatrix.csv Short description: Covariate input file for the yearthreshold covariate The R code reads all input files and merges them into one dataframe, and then runs each individual model listed in the code. Instructions for executing the R code: 1. Download bot the Rcode_arctic_abundance.R and the Covariate_Input_Files.zip files. 2. Unzip the Covariate_Input_files.zip file (take note of the path for the unzipped directory). 3. Open an R interpreter (examples: RStudio, www.rstudio.com, or the built-in interpreter that comes with the R download, www.r-project.org) 4. Set your working directory to the path that contains the unzipped covariate files using the setwd command: setwd('') - Example: setwd('C:/Users/current_user/Downloads/Covariate_Input_Files/') 5. Open Rcode_arctic_abundance.R in your R interpreter. 6. Run the code. The mechanics of this step will differ depending on what R interpreter you are using. In many interpreters, you can run the code by highlighting all of the code that you'd like to run, right-clicking, and selecting the "Run line or selection" option. - If you receive an error about the package "UNMARKED", download the UNMARKED package using the install.packages command: install.packages('unmarked') - After installation is complete, load the package by typing library('unmarked') and try to run the code again. Principal Investigator Contact Information Name: David E. Andersen Institution: U.S. Geological Survey, Minnesota Cooperative Fish and Wildlife Research Unit Address: 200 Hodson Hall, University of Minnesota, St. Paul, MN 55108 Email: dea@umn.edu Associate or Co-investigator Contact Information Name: Jason E. Bruggeman Institution: University of Minnesota Address: 200 Hodson Hall, University of Minnesota, St. Paul, MN 55108 Email: brug0006@umn.edu Associate or Co-investigator Contact Information Name: Ted Swem Institution: U.S. Fish and Wildlife Service Address: Fairbanks, AK 99701 Email: ted_swem@fws.gov Dates of data collection: 19810601 through 20020815 Geographic location of data collection: Along the Colville River in the Colville River Special Area, Alaska, USA Date files were created: 20140212 Are there multiple versions of the dataset? No Information about funding sources that supported the collection of the data: Bureau of Land Management, Fairbanks, Alaska; U.S. Fish and Wildlife Service, Fairbanks, Alaska METHODOLOGICAL INFORMATION Description of methods used for collection/generation of data: Arctic peregrine survey methodology and covariate data collection is detailed in Bruggeman, J.E., T. Swem, D.E. Andersen, P.L. Kennedy, and D. Nigro. Dynamics of a recovering Arctic bird population: the importance of climate, density dependence, and site quality. Ecological Applications, in press. Methods for processing the data: Data analyses were conducted using R and package UNMARKED. The R source code is one of the files included. Instrument-specific information needed to interpret the data: R statistical software (http://www.R-project.org/) and packaged UNMARKED from the R library Environmental/experimental conditions: Varying weather conditions during summer surveys in Alaska Describe any quality-assurance procedures performed on the data: Database checked for data entry errors Codes or symbols used to note or characterize low quality/questionable outliers that people should be aware of: n/a People involved with sample collection, processing, analysis and/or submission: Ted Swem, U.S. Fish and Wildlife Service DATA-SPECIFIC INFORMATION 1. Parameters and/or variables used in the data set Name: abundancet1 Description: Maximum total number of adult Arctic peregrines observed on the cliff in year t-1. Units of measurement: Number of adult Arctic peregrines Name: gyrdistance Description: Distance from cliff i with nesting Arctic peregrines to the nearest occupied gyrfalcon nest in year t. Units of measurement: kilometers Name: meltdate Description: Date of snowmelt in year t as determined when snow depth = 0 at the Umiat NOAA station or the first MODIS satellite image that showed no snow cover. Units of measurement: Day of the year Name: Total number of adult Arctic peregrines counted on the cliff during each survey of each year Description: Total number of adult Arctic peregrines counted on the cliff Units of measurement: Number of adults Name: pdo Description: Average Pacific Decadal Oscillation (PDO) value for November of year t-1 through March of year t. Units of measurement: n/a Name: precip Description: Total accumulated precipitation during May through July in year t-1. Units of measurement: centimeters Name: productivityt1 Description: Average number of young observed at nest sites on the cliff in year t-1. Units of measurement: Number of young Name: geology Description: Categorical variable denoting the surficial geology type of the cliff (Karlstrom 1964). Arctic peregrines used three categories of surficial geology for nest sites along the Colville River: (1) modern flood-plain and associated low-terrace and alluvial fan deposits (Qfp); (2) coarse- and fine-grained deposits associated with moderate to steep-sloped mountains and hills with bedrock exposures largely restricted to upper slopes and crestlines (Qrb); and (3) dominantly fine-grained deposits associated with gently sloping hills with rare bedrock exposures (Qrc). Units of measurement: n/a Name: height Description: Average height of nest site(s) on the cliff above the Colville River as determined from the GIS DEM. Units of measurement: meters Name: waterarea Description: Average total area of water and wetland cover types within 3 km of the cliff. Bird and Aubry (1982) and Enderson and Kirvin (1983) found > 50% of peregrine foraging flights of were = 3 km of their eyries. Units of measurement: squared kilometers Name: aspectcat Description: Categorical variable denoting average aspect of nest site(s) on the cliff (N, NE, NW, E, SE, S, SW, W). Units of measurement: n/a Name: slope Description: Average slope of nest site(s) on the cliff. Units of measurement: degrees Name: tmax Description: Average maximum daily temperature during May through July in year t-1. Units of measurement: Degrees Celsius Name: visit Description: The survey number (one or two) during each year. Units of measurement: n/a Name: yearlog Description: Average maximum daily temperature during May through July in year t-1. Units of measurement: n/a Name: year Description: Year t of the survey as a numerical value. (t: 0 to 21). Units of measurement: n/a Name: yearlog Description: Calculated as ln t. (t: 0 to 21). Units of measurement: n/a Name: yearthreshold Description: Calculated as t/(1+t). (t: 0 to 21). Units of measurement: n/a 2. Column headings for tabular data Full name (spell out abbreviated words): abundancet1 Definition: Maximum total number of adult Arctic peregrines observed on the cliff in year t-1. Full name (spell out abbreviated words): gyrdistance Definition: Distance from cliff i with nesting Arctic peregrines to the nearest occupied gyrfalcon nest in year t. Full name (spell out abbreviated words): meltdate Definition: Date of snowmelt in year t as determined when snow depth = 0 at the Umiat NOAA station or the first MODIS satellite image that showed no snow cover. Full name (spell out abbreviated words): season1v1, season1v2, season2v1, etc. from obsmatrix file Definition: Total number of adult Arctic peregrines counted on the cliff during year 1/survey 1 (season1v1), year 1/survey 2 (season1v2), year 2/survey 1 (season2v1), etc... Full name (spell out abbreviated words): pdo Definition: Average Pacific Decadal Oscillation (PDO) value for November of year t-1 through March of year t. Full name (spell out abbreviated words): precip Definition: Total accumulated precipitation during May through July in year t-1. Full name (spell out abbreviated words): productivityt1 Definition: Average number of young observed at nest sites on the cliff in year t-1. Full name (spell out abbreviated words): geology Definition: Categorical variable denoting the surficial geology type of the cliff (Karlstrom 1964). Arctic peregrines used three categories of surficial geology for nest sites along the Colville River: (1) modern flood-plain and associated low-terrace and alluvial fan deposits (Qfp); (2) coarse- and fine-grained deposits associated with moderate to steep-sloped mountains and hills with bedrock exposures largely restricted to upper slopes and crestlines (Qrb); and (3) dominantly fine-grained deposits associated with gently sloping hills with rare bedrock exposures (Qrc). Full name (spell out abbreviated words): height Definition: Average height of nest site(s) on the cliff above the Colville River as determined from the GIS DEM. Full name (spell out abbreviated words): waterarea Definition: Average total area of water and wetland cover types within 3 km of the cliff. Bird and Aubry (1982) and Enderson and Kirvin (1983) found > 50% of peregrine foraging flights of were = 3 km of their eyries. Full name (spell out abbreviated words): aspectcat Definition: Categorical variable denoting average aspect of nest site(s) on the cliff (N, NE, NW, E, SE, S, SW, W). Full name (spell out abbreviated words): slope Definition: Average slope of nest site(s) on the cliff. Full name (spell out abbreviated words): tmax Definition: Average maximum daily temperature during May through July in year t-1. Full name (spell out abbreviated words): visit Definition: The survey number (one or two) during each year. Full name (spell out abbreviated words): yearlog Definition: Average maximum daily temperature during May through July in year t-1. Full name (spell out abbreviated words): year Definition: Year t of the survey as a numerical value. (t: 0 to 21). Full name (spell out abbreviated words): yearlog Definition: Calculated as ln t. (t: 0 to 21). Full name (spell out abbreviated words): yearthreshold Definition: Calculated as t/(1+t). (t: 0 to 21). 3. Codes or symbols used to record missing data: n/a SHARING/ACCESS INFORMATION Licenses/restrictions placed on the data: None Links to publications that cite or use the data: Publication is currently in press. Citation is Bruggeman, J.E., T. Swem, D.E. Andersen, P.L. Kennedy, and D. Nigro. Dynamics of a recovering Arctic bird population: the importance of climate, density dependence, and site quality. Ecological Applications, in press. Was data derived from another source? Covariate data was derived from multiple sources: Gyrfalcon data: Gyrfalcon nearest neighbor distance data were obtained from a gyrfalcon database from Ted Swem, U.S. Fish and Wildlife Service. Date of snowmelt data: We obtained daily snow depth data for 1981 through 1999 from the Umiat National Oceanic and Atmospheric Administration station (National Oceanic and Atmospheric Administration. 2013. National Climate Data Center, Umiat, Alaska. URL: http://www.ncdc.noaa.gov/cdo-web/datasets/GHCND/stations/GHCND:USW00026508/detail). We obtained GIS snow-cover data from 2000 through 2011 from the MODIS/Terra snow cover 8-day L3 global 500-m grid data set (Hall, D. K., G. A. Riggs, and V. V. Salomonson. 2013. MODIS/Terra Snow Cover 8-day L3 Global 500 m Grid V005, April 2000 through June 2011. National Snow and Ice Data Center. Boulder, Colorado, USA). PDO data: We obtained monthly PDO data from http://jisao.washington.edu/pdo. Precipitaton data: We obtained precipitation data from 1981 through 2000 from the Umiat National Oceanic and Atmospheric Administration station (National Oceanic and Atmospheric Administration. 2013. National Climate Data Center, Umiat, Alaska. URL: http://www.ncdc.noaa.gov/cdo-web/datasets/GHCND/stations/GHCND:USW00026508/detail). We obtained precipitation data from 1984 through 1997 and 2000 through 2011 from the Sagwon Natural Resources Conservation Service SNOTEL station (Natural Resources Conservation Service. 2013. Sagwon, Alaska. URL: http://www.wcc.nrcs.usda.gov/nwcc/site?sitenum=1183andstate=ak). Surficial geology data: From Karlstrom, T. N. V. 1964. Surficial geology map of Alaska. U.S. Geological Survey, Anchorage, Alaska, USA. Cliff height data: Derived from a DEM. U.S. Geological Survey. 2011. National Elevation Dataset. http://seamless.usgs.gov. Area of prey habitat data: Derived from a land cover GIS layer. Homer, C., C. Huang, L. Yang, B. Wylie, and M. Coan. 2004. Development of a 2001 national land cover database for the United States. Photogrammetric Engineering and Remote Sensing 70:829-840. Aspect data: Derived from a DEM. U.S. Geological Survey. 2011. National Elevation Dataset. http://seamless.usgs.gov. Slope data: Derived from a DEM. U.S. Geological Survey. 2011. National Elevation Dataset. http://seamless.usgs.gov. Maximum temperature data: We obtained maximum daily temperature data from 1981 through 2000 from the Umiat National Oceanic and Atmospheric Administration station (National Oceanic and Atmospheric Administration. 2013. National Climate Data Center, Umiat, Alaska. URL: http://www.ncdc.noaa.gov/cdo-web/datasets/GHCND/stations/GHCND:USW00026508/detail). We obtained maximum daily temperature data from 2001 through 2011 from the Sagwon SNOTEL station (Natural Resources Conservation Service. 2013. Sagwon, Alaska. URL: http://www.wcc.nrcs.usda.gov/nwcc/site?sitenum=1183andstate=ak). Recommended citation for the data: Bruggeman, J.E., T. Swem, D.E. Andersen, P.L. Kennedy, and D. Nigro.Arctic peregrine falcon abundance on cliffs along the Colville River, Alaska, 1981-2002. http://dx.doi.org/10.13020/D6PP41 Credits: Template provided by the University of Minnesota Libraries, http://lib.umn.edu/datamanagement