Decision-Support Framework for Linking Regional-Scale Management Actions to Continental-Scale Conservation of Wide-Ranging Species

This data release presents the data, JAGS models, and R code used to manipulate data and to produce results and figures presented in the USGS Open File Report, "Decision-Support Framework for Linking Regional-Scale Management Actions to Continental-Scale Conservation of Wide-Ranging Species, (https://doi.org/10.5066/P93YTR3X). The zip folder is provided so that other can reproduce results from the integrated population model, inspect model structure and posterior simulations, conduct analyses not present in the report, and use and modify the code. Raw source data can be sourced from the USGS Bird Banding Laboratory, USFWS Surveys and Monitoring Branch, National Oceanic and Atmospheric administration, and Ducks Unlimited Canada.
The zip file contains the following objects when extracted:  
* Readme.txt: A plain text file describing each file in this directory.  
* Figures-Pintail-IPM.r: R code that generates report figures in png, pdf, and eps format. Generates Figures 2-11 and calls source code for figures 12 and 13 found in other files.
* get pintail IPM data.r: R source code that must be run to format data for the IPM code file. 
* getbandrecovs.r: R code that takes Bird Banding Lab data for pintail band releases and recoveries and formats for analysis. This file is called by 'get pintail IPM data.r'.  File was originally written by Scott Boomer (USFWS) and modified by Erik Osnas for use for the IPM.
* Model_1_post.txt: Text representation of the posterior simulations from Model 1.  This file can be read by the R function dget() to produce an R list object that contain posterior draws from Model 1. The list is the BUGSoutput$sims.list object from a call to rjags::jags. 
* Model_2_post.txt: As above but for Model 2.
* Model_S1_post.txt: As above but for Model S1.
* Pintail IPM.r: This is the main file that defines the IPM models in JAGS, structures the data for JAGS, defines initial values, and calls runs the models. Outputs are text files that contains JAGS model files, R work spaces that contains all data models, and results, include the output from the jags() function.  From this the BUGSoutput$sims.list object was written to text for each model. 
* MSY_metrics.txt: Summary of results produced from running code in source_figure_12.R.  This table is a text representation of a summary of the maximum sustained yield analysis at various mean rainfall levels, used for Table 1 of report and can be reproduced by running the code in source_figure_12.R. To understand the structure of this file, you must consult the code file and understand the structure of the R objects created from that code. Otherwise, consult Figure 12 and Table 1 in report. 
* source_figure_12.R: R code to produce Figure 12. Code is written to work with Rworkspace output from Model 1, but can be modified to use the Model_1_post.txt file without re-running the model.  This would allow use of the same posterior realizations as used in the report. 
* source_figure_13.R: This is the code used to product the results for Figure 13. Required here is the posterior from Model 1 and data for the Prairie Parkland Model based on Jim Devries/Ducks Unlimited data.  These are described in the report text.
* Data: A directory that contains the raw data used for this report.
* Data/2015_LCC_Networks_shapefile: A directory that contain ESRI shapefiles for used in Figure 1 and to define the boundaries of the Landscape Conservation Cooperatives. Found at (https://www.sciencebase.gov/catalog/item/55b943ade4b09a3b01b65d78)
* Data/bndg_1430_yr1960up_DBISC_03042014.csv: A comma delimited file for banded pintail from 1960 to 2014.  Obtained from the USGS Bird Banding Lab. This file is used by 'getbandrecovs.r' to produce and 'm-array' used in the Integrated Population Model (IPM). A data dictionary describing the codes for each field can be found here, [https://www.pwrc.usgs.gov/BBL/manual/summary.cfm](https://www.pwrc.usgs.gov/BBL/manual/summary.cfm)
* Data/cponds.csv: A comma delimited file of estimated Canadian ponds based on counts from the North American Breeding Waterfowl and Habitat Survey, 1955-2014.  Given is the year, point estimate, and estimated standard error. 
* Data/enc_1430_yr1960up_DBISC_03042014.csv: A comma delimited file for encounters of banded pintail. Obtained from the USGS Bird Banding Lab. This file is use by 'getbandrecovs.r' to produce and 'm-array' used in the Integrated Population Model (IPM).  A data dictionary describing the codes for each field can be found here, (https://www.pwrc.usgs.gov/BBL/manual/enc.cfm)
* Data/nopiBPOP19552014.csv: A comma delimited file of estimated northern pintail based on counts from the North American Breeding Waterfowl and Habitat Survey, 1955-2014.  Given is the year, pintail point estimate (bpop), and pintail estimated standard error (bpopSE), mean latitude of the pintail population (lat), latitude variance of the pintail population (latVAR), mean longitude of the pintail population (lon), and the variance in longitude of the pintail population (lonVAR). 
* Data/Summary Climate Data California CV 2.csv: Rainfall data for the California central valley downloaded from National Climate Data Center (www.ncdc.noaa.gov/cdo-web/) as described in report text (https://doi.org/10.5066/P93YTR3X) and publication found at https://doi.org/10.1002/jwmg.21124 . Used in 'get pintail IPM data.r' for IPM. 
* Data/Summary data MAV.csv: Rainfall data for the Mississippi Aluvial valley downloaded from National Climate Data Center (www.ncdc.noaa.gov/cdo-web/) as described in report text (https://doi.org/10.5066/P93YTR3X) and publication found at https://doi.org/10.1002/jwmg.21124 . Used in 'get pintail IPM data.r' for IPM.
* Data/Wing data 1961 2011 NOPI.txt: Comma delimited text file for pintail wing age data for 1961 to 2011 from the Parts Collection Survey. Each row is an individual wing with sex cohorts 4 = male, 5 = female and age cohorts 1 = After Hatch Year and 2 = Hatch Year. Wt is a weighting factor that determines how many harvested pintails this wing represent.  See USFWS documentation for the Part Collection survey for descriptions.  Summing Wt for each age, sex, and year gives an estimate of the number of pintail harvested. Used in 'get pintail IPM data.r' for IPM. 
* Data/Wing data 2012 2013 NOPI.csv: Same as 'Wing data 1961 2011 NOPI.txt' but for years 2012 and 2013.

Tags: biota, ducks, usgs-603eb689d34eb12031185d5e
Organization: Department of the Interior