This Roberts_Aridland_birds_and_water_deficit.txt file was generated on 2021-03-09 by Sam Roberts GENERAL INFORMATION 1. Title of Dataset: A habitat-based approach to determining the effects of drought on aridland bird communities 2. Author Information A. Principal Investigator Contact Information Name: Sam Roberts Institution: University of Delaware Email:samuelgroberts@gmail.com B. Associate or Co-investigator Contact Information Name: Greg Shriver Institution: University of Delaware Email: gshriver@udel.edy C. Alternate Contact Information Name: David Thoma Institution: National Park Service Email: Dave_Thoma@nps.gov 3. Date of data collection: Bird point counts were conducted May 1st through July 15th from 2005-2015 and 2017 4. Geographic location of data collection: Eleven National Parks in the Northern Colorado Plateau Network of parks in the Southwestern United States. 5. Information about funding sources that supported the collection of the data: Funding for this research was provided by The Northern Colorado Plateau Inventory and Monitoring Network of the National Park Service. DATA & FILE OVERVIEW 1. File List: Data: NCPN_rawdata: raw point count data NCPN_abundanceresults: abundance estimates waterdeficitdata: water deficit values at sampling locations Daymet climate data files: variables used to estimate water deficit. Scripts: Abundance estimates_Auk.R: used to estimate abundance mvabund_AUK.R: used to run the multivariate analysis of this study 2. Relationship between files, if important: The NCPNrawdata is used in the Abundance estimates_Auk.R script to estimate annual abundances of birds. The results of that analysis, NCPN_abundanceresults are then used, along with the waterdeficitdata in the mvabund_AUK.R script to estimate the relationship between abundance and water deficit. 3. Additional related data collected that was not included in the current data package: The script and model for the estimation of water deficit is not included because it is in the process of being published. METHODOLOGICAL INFORMATION 1. Description of methods used for collection/generation of data: Abundance estimates are derived from data collected using typical point count methods. We estimated abundance at the transec-level, each containing 15 point locations surveyed each year. 2. Methods for processing the data: In the Abundance estimates_Auk.R script we estimated transect-level detection-adjusted densities for each bird species using the Distance package (Miller et al. 2019) in program R. To avoid including double-counted individuals in our analyses, we only included detections within 125 m from the point center in our analyses. The total area covered by each transect was 73.6 ha (i.e. 15, 125 m radius points per transect). We then used the mvabund_AUK.R script to run a a multivariate analysis to determine the bird community response to changes in water deficit using the manyglm function in the R package mvabund (Wang et al. 2012). We used the manyglm function to simultaneously fit general linear models to each species using water deficit as the common predictor variable (Wang et al. 2012). 3. Instrument- or software-specific information needed to interpret the data: We used R and in the scripts there are commands at the beginning indicating which packages need to be loaded 4. People involved with sample collection, processing, analysis and/or submission: The following are the list of authors associated with these data. Varioud field technicians collected these data over the years. Samuel G. Roberts, David P. Thoma, Dustin W. Perkins, Elizabeth L. Tymkiw, Zachary S. Ladin, and W. Gregory Shriver DATA-SPECIFIC INFORMATION FOR: NCPN_rawdata 1. Number of variables: 2. Number of cases/rows: 3. Variable List: 4. Missing data codes: n 5. Specialized formats or other abbreviations used: DATA-SPECIFIC INFORMATION FOR: NCPN_rawdata 1. Number of variables: 20 (though most are not used in the analysis) 2. Number of cases/rows: 111,131 3. Variable List: Transect: transect ID, there are 45, 15 in each habitat type Year: ranges from 2005 to 2017 Sample.Label: Transect ID and point ID combined Area: Area surveyed in each transect in square meters Date: Collection date Region.Label: Habitat type with transect ID: LR=lower riprian, PJ=Pinyon-juniper, SA=Sagebrush Oberserver: Observer ID Point: Point ID, ranging from 1-15 StartTime: Start time of survey at that point Common.Name: Common species name BirdCode: Four-letter alpha code for each species distance: the radial distance of each observation from the observer How: method of detection: S=song, C=call, F=flyover, V=visual, O=other Sex: sex of individual if possible: M=male, F=female, J=juvenile, U=unknown size: number of birds in the cluster of birds detected x88: was this bird recorded between points? Park: The park in which the survey was conducted Effort: number of visits to that point in that year Numpoints: number of points visited on that transect that year Transect_Date: transect ID and date combined DATA-SPECIFIC INFORMATION FOR: NCPN_abundanceresults 1. Number of variables: 29 2. Number of cases/rows: 5979 3. Variable List: Year: ranges from 2005 to 2017 BirdCode: Four-letter alpha code for each species Common.Name: Common species name Habitat.Label: Habitat type: LR=lower riprian, PJ=Pinyon-juniper, SA=Sagebrush Sample.Label: Transect ID and point ID combined Region.Label: Habitat type with transect ID: LR=lower riprian, PJ=Pinyon-juniper, SA=Sagebrush Model: model selected for estimating detection adjusted densities Key_function: key function used for the detection curve Formula: indicates what, if any, covariates were used in the model C-vM_p-value, hat{P_a}, se.hat{P_a}, DeltaAIC Effort: The number of points visited at that transect that year. So if all points are visited twice on that transect this number should be 30 (2*15). n: The number of detections of that species in that year on that transect within 125m p: Detection probability CoveredArea: The area covered that year, double counting area if a site is visited twice. p.se: standard error of p p.cv: coefficient of variance of p N.CoveredArea:The number of birds in Covered.Area, which, if all sites were visited twice in a year, will be double that of N.total. N.Covered.se: standard error of N.Covered N.Covered.cv: coefficient of variance of N.Covered Total.Area: The unique area surveyed that year in that transect. So this number should be the number of unique points visited on a transect in a year times the area of a survey circle ((125^2)*(Pi)). N.total: The number of birds in Total.Area, which, if all sites were visited twice in a year, will be half that of N.covered. N.total.se: standard error of N.total N.total.cv: coefficient of variance of N.total Density_km2: This is N.total/Total.Area in birds per square kilometer Density.se: standard error of Density_km2 Density.cv: coefficient of variance of Density_km2 DATA-SPECIFIC INFORMATION FOR: Daymet climate data files This folder contains an excel spreadsheet for each transect used in this study (n=45) Each file contains data used to estimate annual water deficit values at the transect location. Relevant information about the data source and interpretation is included in these files. These data were used to estimate water deficit, but the models for that are not included here because they are in the process of being published. DATA-SPECIFIC INFORMATION FOR: waterdeficitdata 1. Number of variables: 3 2. Number of cases/rows: 765 3. Variable List: D: water deficit value (mm) Year: year that water deficit value is for transect2: transect ID where water deficit value was estimated for