This codebook.txt file was generated on by Hannah Specht ------------------- GENERAL INFORMATION ------------------- 1. Title of Dataset Upland-nesting shorebird and Northern Pintail quarter-section occupancy and accompanying infrastructure and habitat data from NW North Dakota 2014-2015. 2. Author Information Principal Investigator Contact Information Name: Hannah Specht Institution: University of Minnesota Address: Fisheries, Wildlife and Conservation Biology, 2003 Upper Buford Circle, St Paul, MN 55108 Email:spech030@umn.edu 3. Date of data collection (single date, range, approximate date) May-July 2014-2015 4. Geographic location of data collection (where was data collected?): Divide, Burke, Mountrail, Williams and Dunn counties, North Dakota. 5. Information about funding sources that supported the collection of the data: Ducks Unlimited Canada, the National Science Foundation (Grant #00039202), the University of Minnesota Graduate School and the Bell Museum (UMN) provided support to HS and this project. -------------------------- 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: https://conservancy.umn.edu/handle/11299/199012 3. Links to other publicly accessible locations of the data: 4. Links/relationships to ancillary data sets: 5. Was data derived from another source? If yes, list source(s): Yes Well data: North Dakota Industrial Commission Well Data 2015 Habitat suitability: USFWS HAPET Shorebird Habitat Suitability Models (Niemuth et al. unpublished) Niemuth, N. D., M. E. Estey, S. P. Fields, B. Wangler, A. A. Bishop, P. J. Moore, R. C. Grosse, and A. J. Ryba (2017). Developing spatial models to guide conservation of grassland birds in the U.S. Northern Great Plains. The Condor 119:506–525. Reynolds, R. E., T. L. Shaffer, C. R. Loesch, and R. R. Cox Jr. (2006). The Farm Bill and duck production in the Prairie Pothole Region: Increasing the benefits. Wildlife Society Bulletin 34:963–974. 6. Recommended citation for the data: Specht, H.M. 2018. Upland-nesting shorebird and Northern Pintail quarter-section occupancy and accompanying infrastructure and habitat data from NW North Dakota 2014-2015.Habitat use and reproductive success of waterbirds in the human-dominated landscape of North America’s prairies: Using sparse data to inform management. PhD Dissertation. Conservation Sciences. University of Minnesota, St. Paul, USA. --------------------- DATA & FILE OVERVIEW --------------------- 1. File List A. Filename: Specht_Bakken_Rcode.R Short description: R scripts to run MCMC model in JAGS used to assess effects of well density and traffic on habitat use by upland-nesting shorebirds and Northern Pintail while accounting for habitat suitability and imperfect detection. Requires JAGS to be installed (http://mcmc-jags.sourceforge.net/). B. Filename: Specht_BakkenShorebirds_data.csv Short description: Analysis data shorebird and northern pintail breeding pairs C. Filename: Specht_BakkenBrood_data.csv Short description: Analysis data shorebird and northern pintail broods 2. Relationship between files: CSV files represent datasets for breeding pair and brood analysis sets. The R-Script can be used to analyze data from supplied datasets. 3. Additional related data collected that was not included in the current data package: NA -------------------------- METHODOLOGICAL INFORMATION -------------------------- 1. Description of methods used for collection/generation of data: Specht, H.M. 2018. Chapter 3: Habitat use by upland-nesting waterbirds is negatively affected by oil well infrastructure and activity. In Habitat use and reproductive success of waterbirds in the human-dominated landscape of North America’s prairies: Using sparse data to inform management. PhD Dissertation. Conservation Sciences. University of Minnesota, St. Paul, USA. 2. Methods for processing the data: Specht, H.M. 2018. Chapter 3: Habitat use by upland-nesting waterbirds is negatively affected by oil well infrastructure and activity. In Habitat use and reproductive success of waterbirds in the human-dominated landscape of North America’s prairies: Using sparse data to inform management. PhD Dissertation. Conservation Sciences. University of Minnesota, St. Paul, USA. 3. Instrument- or software-specific information needed to interpret the data: Data formatted as csv. 4. Standards and calibration information, if appropriate: NA 5. Environmental/experimental conditions: NA 6. Describe any quality-assurance procedures performed on the data: Specht, H.M. 2018. Chapter 3: Habitat use by upland-nesting waterbirds is negatively affected by oil well infrastructure and activity. In Habitat use and reproductive success of waterbirds in the human-dominated landscape of North America’s prairies: Using sparse data to inform management. PhD Dissertation. Conservation Sciences. University of Minnesota, St. Paul, USA. 7. People involved with sample collection, processing, analysis and/or submission: Hannah Specht ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: Specht_BakkenShorebirds_data.csv ----------------------------------------- 1. Number of variables: 59 2. Number of cases/rows: 496 3. Missing data codes: Code/symbol: NA Definition: Data not available 4. Variable List A. Name: TRS_Q Description: Township-Range-Section-Quarter Section site identifier following the Public Lands Survey System B. Name: UID Description: Site-survey unique identifier of TRS_Q concatenated with Julian date of the survey C. Name: Year Description: Survey Year D. Name: Observer Description: Alpha code for observer responsible for survey E. Name: Jdate Description: Julian date. 1=1 January F. Name: Cloud Description: Estimated median cloud cover at survey initiation from categories (0-20, 20-40, 40-60, 60-80, 80-100) G. Name: Temp Description: Temperature at survey initiation in Fahrenheit H. Name: Wind_mph Description: Wind speed at survey initiation (miles per hour) I. Name: Trucks Description: Number of pick-up trucks that passed during 30 minute roadside transect survey J. Name: Semis Description: Number of semi trucks that passed on road during 30 min transect survey K. Name: SurveyTime.1 Description: Time of survey initiation in minutes since 00:00 L. Name: MAGO_BP.1 Description: Indicated breeding pair of Marbled Godwit in first point count survey M. Name: NOPI_BP.1 Description: Indicated breeding pair of Northern Pintail in first point count survey N. Name: UPSA_BP.1 Description: Indicated breeding pair of Upland Sandpiper in first point count survey O. Name: WILL_BP.1 Description: Indicated breeding pair of Willet in first point count survey P. Name: WIPH_BP.1 Description: Indicated breeding pair of Wilson’s Phalarope in first point count survey Q. Name: SurveyTime.2 Description: Time of survey initiation in minutes since 00:00 R. Name: MAGO_BP.2 Description: Indicated breeding pair of Marbled Godwit in second point count survey S. Name: NOPI_BP.2 Description: Indicated breeding pair of Northern Pintail in second point count survey T. Name: UPSA_BP.2 Description: Indicated breeding pair of Upland Sandpiper in second point count survey U. Name: WILL_BP.2 Description: Indicated breeding pair of Willet in second point count survey V. Name: WIPH_BP.2 Description: Indicated breeding pair of Wilson’s Phalarope in second point count survey W. Name: Time Start Description: Time of third survey (transect) initiation in minutes since 00:00 X. Name: MAGO_BP.3 Description: Indicated breeding pair of Marbled Godwit in third survey (roadside transect) Y. Name: NOPI_BP.3 Description: Indicated breeding pair of Northern Pintail in third survey (roadside transect) Z. Name: UPSA_BP.3 Description: Indicated breeding pair of Upland Sandpiper in third survey (roadside transect) AA. Name: WILL_BP.3 Description: Indicated breeding pair of Willet in third survey (roadside transect) AB. Name: WIPH_BP.3 Description: Indicated breeding pair of Wilson’s Phalarope in third survey (roadside transect) AC. Name: Wells200m Description: Number of active wells (survey year specific) within 200m of the focal site (quarter section) AD. Name: NED_STD Description: Standard deviation of National Elevation Dataset across quarter section site as measure of topographic variability. AE. Name: MAGO_suit Description: Mean relative habitat suitability for Marbed Godwit based on USFWS-HAPET habitat suitability models (Niemuth et al. unpublished data) AF. Name: NOPI_suit Description: Mean relative habitat suitability for Northern Pintail based on Four-square mile survey-based breeding pair density models (Reynolds et al. 2006. It was not possible to extend this model to DUNN county resulting in missing data for this portion of the study region. AG. Name: UPSA_suit Description: Mean relative habitat suitability for Upland Sandpiper based on Breeding bird survey-based habitat suitability models (Niemuth et al. 2017) AH. Name: WILL_suit Description: Mean relative habitat suitability for Willet based on USFWS-HAPET habitat suitability models (Niemuth et al. unpublished data) AI. Name: WIPH_suit Description: Mean relative habitat suitability for Wilson’s Phalaropes based on USFWS-HAPET habitat suitability models (Niemuth et al. unpublished data) AJ. Name: Transect.Time Description: Number of minutes required to conduct ~30 min transect survey- used to standardize traffic volume AK. Name: C.Traffic Description: Total vehicles per 30 min AL. Name: HMS Description: Survey conducted by observer with alpha code HMS AM. Name: MEW Description: Survey conducted by observer with alpha code MEW AN. Name: SMC Description: Survey conducted by observer with alpha code SMC AO. Name: ASM Description: Survey conducted by observer with alpha code ASM AP. Name: LRL Description: Survey conducted by observer with alpha code LRL AQ. Name: ST_Jdate Description: JDate-mean(Jdate)/sd(Jdate) AR. Name: ST_Temp Description: Temp-mean(Temp)/sd(Temp) AS. Name: ST_Wind Description: Wind-mean(Wind)/sd(Wind) AT. Name: ST_Traffic Description: Traffic-mean(Traffic)/sd(Traffic) AU. Name: ST_Time Description: Time-mean(Time)/sd(Time) AV. Name: ST_Topo Description: Topo-mean(Topo)/sd(Topo)= standardized variation in topography at site, as indicated by the sd of elevation. AW. Name: ST_W200 Description: Wells200-mean(Wells200)/sd(Wells200) AX. Name: ST_S_MAGO Description: MAGO_suit-mean(MAGO_suit)/sd(MAGO_suit) AY. Name: ST_S_NOPI Description: NOPI_suit-mean(NOPI_suit)/sd(NOPI_suit) AZ. Name: ST_S_UPSA Description: UPSA_suit-mean(UPSA_suit)/sd(UPSA_suit) BA. Name: ST_S_WILL Description: WILL_suit-mean(WILL_suit)/sd(WILL_suit) BB. Name: ST_S_WIPH Description: WIPH_suit-mean(WIPH_suit)/sd(WIPH_suit) BC. Name: early.MAGO Description: 1= Marbled godwit breeding pair detected in a previous visit to a site (a subset of sites were visited twice either within a season (early or late, representing nesting and brood rearing portions) or across two different years. BD. Name: early.NOPI Description: 1= Northern Pintail breeding pair detected in a previous visit to a site (a subset of sites were visited twice either within a season (early or late, representing nesting and brood rearing portions) or across two different years. BE. Name: early.UPSA Description: 1= Upland Sandpiper breeding pair detected in a previous visit to a site (a subset of sites were visited twice either within a season (early or late, representing nesting and brood rearing portions) or across two different years. BF. Name: early.WILL Description: 1= Willet breeding pair detected in a previous visit to a site (a subset of sites were visited twice either within a season (early or late, representing nesting and brood rearing portions) or across two different years. BG. Name: early.WIPH Description: 1= Wilson’s Phalarope breeding pair detected in a previous visit to a site (a subset of sites were visited twice either within a season (early or late, representing nesting and brood rearing portions) or across two different years. ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: Specht_BakkenBrood_data.csv ----------------------------------------- 1. Number of variables: 61 2. Number of cases/rows: 414 3. Missing data codes: Code/symbol: NA Definition: Data not available 4. Variable List A. Name: TRS_Q Description: Township-Range-Section-Quarter Section site identifier following the Public Lands Survey System B. Name: UID Description: Site-survey unique identifier of TRS_Q concatenated with Julian date of the survey C. Name: Year Description: Survey Year D. Name: Observer Description: Alpha code for observer responsible for survey E. Name: Jdate Description: Julian date. 1=1 January F. Name: Cloud Description: Estimated median cloud cover at survey initiation from categories (0-20, 20-40, 40-60, 60-80, 80-100) G. Name: Temp Description: Temperature at survey initiation in Fahrenheit H. Name: Wind_mph Description: Wind speed at survey initiation (miles per hour) I. Name: Trucks Description: Number of pick-up trucks that passed during 30 minute roadside transect survey J. Name: Semis Description: Number of semi trucks that passed on road during 30 min transect survey K. Name: SurveyTime.1 Description: Time of survey initiation in minutes since 00:00 L. Name: MAGO_Brood.1 Description: Indicated brood of Marbled Godwit in first point count survey M. Name: NOPI_Brood.1 Description: Indicated brood of Northern Pintail in first point count survey N. Name: UPSA_Brood.1 Description: Indicated brood of Upland Sandpiper in first point count survey O. Name: WILL_Brood.1 Description: Indicated brood of Willet in first point count survey P. Name: WIPH_Brood.1 Description: Indicated brood of Wilson’s Phalarope in first point count survey Q. Name: All_Brood.1 Description: Indicated brood of all/any focal species in first point count survey R. Name: SurveyTime.1 Description: Time of survey initiation in minutes since 00:00 S. Name: MAGO_Brood.2 Description: Indicated brood of Marbled Godwit in second point count survey T. Name: NOPI_Brood.2 Description: Indicated brood of Northern Pintail in second point count survey U. Name: UPSA_Brood.2 Description: Indicated brood of Upland Sandpiper in second point count survey V. Name: WILL_Brood.2 Description: Indicated brood of Willet in second point count survey W. Name: WIPH_Brood.2 Description: Indicated brood of Wilson’s Phalarope in second point count survey X. Name: All_Brood.2 Description: Indicated brood of all/any focal species in second point count survey Y. Name: Time Start Description: Time of third survey (transect) initiation in minutes since 00:00 Z. Name: MAGO_Brood.3 Description: Indicated brood of Marbled Godwit in third survey (roadside transect) AA. Name: NOPI_Brood.3 Description: Indicated brood of Northern Pintail in third survey (roadside transect) AB. Name: UPSA_Brood.3 Description: Indicated brood of Upland Sandpiper in third survey (roadside transect) AC. Name: WILL_Brood.3 Description: Indicated brood of Willet in third survey (roadside transect) AD. Name: WIPH_Brood.3 Description: Indicated brood of Wilson’s Phalarope in third survey (roadside transect) AE. Name: All_Brood.3 Description: Indicated brood of all/any focal species in third survey (roadside transect) AF. Name: Wells200m Description: Number of active wells (survey year specific) within 200m of the focal site (quarter section) AG. Name: MAGO_suit Description: Mean relative habitat suitability for Marbed Godwit based on USFWS-HAPET habitat suitability models (Niemuth et al. unpublished data) AH. Name: NOPI_suit Description: Mean relative habitat suitability for Northern Pintail based on Four-square mile survey-based breeding pair density models (Reynolds et al. 2006. It was not possible to extend this model to DUNN county resulting in missing data for this portion of the study region. AI. Name: UPSA_suit Description: Mean relative habitat suitability for Upland Sandpiper based on Breeding bird survey-based habitat suitability models (Niemuth et al. 2017) AJ. Name: WILL_suit Description: Mean relative habitat suitability for Willet based on USFWS-HAPET habitat suitability models (Niemuth et al. unpublished data) AK. Name: WIPH_suit Description: Mean relative habitat suitability for Wilson’s Phalaropes based on USFWS-HAPET habitat suitability models (Niemuth et al. unpublished data) AL. Name: Transect.Time Description: Number of minutes required to conduct ~30 min transect survey- used to standardize traffic volume AM. Name: C.Traffic Description: Total vehicles per 30 min AN. Name: HMS Description: Survey conducted by observer with alpha code HMS AO. Name: MEW Description: Survey conducted by observer with alpha code MEW AP. Name: SMC Description: Survey conducted by observer with alpha code SMC AQ. Name: ASM Description: Survey conducted by observer with alpha code ASM AR. Name: LRL Description: Survey conducted by observer with alpha code LRL AS. Name: B.ST_Jdate Description: JDate-mean(Jdate)/sd(Jdate) AT. Name: B.ST_Temp Description: Temp-mean(Temp)/sd(Temp) AU. Name: B.ST_Wind Description: Wind-mean(Wind)/sd(Wind) AV. Name: B.ST_Traffic Description: Traffic-mean(Traffic)/sd(Traffic) AW. Name: B.ST_Time Description: Time-mean(Time)/sd(Time) AX. Name: B.ST_Topo Description: Topo-mean(Topo)/sd(Topo)= standardized variation in topography at site, as indicated by the sd of elevation. AY. Name: B.ST_W200 Description: Wells200-mean(Wells200)/sd(Wells200) AZ. Name: B.ST_S_MAGO Description: MAGO_suit-mean(MAGO_suit)/sd(MAGO_suit) BA. Name: B.ST_S_NOPI Description: NOPI_suit-mean(NOPI_suit)/sd(NOPI_suit) BB. Name: B.ST_S_UPSA Description: UPSA_suit-mean(UPSA_suit)/sd(UPSA_suit) BC. Name: B.ST_S_WILL Description: WILL_suit-mean(WILL_suit)/sd(WILL_suit) BD. Name: B.ST_S_WIPH Description: WIPH_suit-mean(WIPH_suit)/sd(WIPH_suit) BE. Name: early.MAGO Description: 1= Marbled godwit breeding pair detected in a previous visit to a site (a subset of sites were visited twice either within a season (early or late, representing nesting and brood rearing portions) or across two different years. BF. Name: early.NOPI Description: 1= Northern Pintail breeding pair detected in a previous visit to a site (a subset of sites were visited twice either within a season (early or late, representing nesting and brood rearing portions) or across two different years. BG. Name: early.UPSA Description: 1= Upland Sandpiper breeding pair detected in a previous visit to a site (a subset of sites were visited twice either within a season (early or late, representing nesting and brood rearing portions) or across two different years. BH. Name: early.WILL Description: 1= Willet breeding pair detected in a previous visit to a site (a subset of sites were visited twice either within a season (early or late, representing nesting and brood rearing portions) or across two different years. BI. Name: early.WIPH Description: 1= Wilson’s Phalarope breeding pair detected in a previous visit to a site (a subset of sites were visited twice either within a season (early or late, representing nesting and brood rearing portions) or across two different years.