This codebook.txt file was generated on 20180416 by Tiffany Wolf ------------------- GENERAL INFORMATION ------------------- 1. Data, Model Documentation, and Output Supporting "Optimizing syndromic health surveillance in free ranging great apes: the case of Gombe National Park" 2. Author Information Principal Investigator Contact Information Name: Tiffany Wolf Institution: University of Minnesota Address: Veterinary Population Medicine Department College of Veterinary Medicine St. Paul, Minnesota 55108, USA Email: wolfx305@umn.edu Associate or Co-investigator Contact Information Name: Wenchun "Annie" Wang Institution: University of Saskatchewan Address: Department of Computer Science Saskatoon, Saskatchewan, S7N 5C9 Canada Email: wenchun.annie.wang@gmail.com Associate or Co-investigator Contact Information Name: Elizabeth Lonsdorf Institution: Franklin and Marshall College Address: Department of Psychology Lancaster, Pennsylvania 17604, USA Email: elonsdor@fandm.edu Associate or Co-investigator Contact Information Name: Thomas Gillespie Institution: Emory University Address: Emory University & Rollins School of Public Health Atlanta, Georgia 30322, USA Email: thomas.gillespie@emory.edu Associate or Co-investigator Contact Information Name: Anne Pusey Institution: Duke University Address: Duke University Durham, North Carolina 27708, USA Email: anne.pusey@duke.edu Associate or Co-investigator Contact Information Name: Ian Gilby Institution: Arizona State University Address: School of Human Evolution and Social Change Institute of Human Origins Tempe, Arizona, 85287 USA Email: Ian.gilby@asu.edu Associate or Co-investigator Contact Information Name: Dominic Travis Institution: University of Minnesota Address: Veterinary Population Medicine Department College of Veterinary Medicine St. Paul, Minnesota 55108, USA Email: datravis@umn.edu Associate or Co-investigator Contact Information Name: Randall Singer Institution: University of Minnesota Address:Veterinary Biomedical Sciences Department College of Veterinary Medicine St. Paul, Minnesota 55108 USA Email: 3. Date of data collection (single date, range, approximate date): 2005-2012 4. Geographic location of data collection (where was data collected?): Gombe National Park, Tanzania 5. Information about funding sources that supported the collection of the data:Funding support for collection and analysis of syndromic surveillance data comes from the National Institute of Health (R01 AI058715, R01 AI120810 and R00 HD057992), National Science Foundation (LTREB-1052693), Arcus Foundation, USFWS Great Ape Conservation Fund, Morris Animal Foundation (D10ZO-902), University of Minnesota Consortium on Law and Values in Health, Environment, and the Life Sciences, University of Minnesota Doctoral Dissertation Fellowship and Lincoln Park Zoo. Collection, digitization and analysis of behavioral data were supported by grants from the National Institutes of Health (R00 HD057992) and the Leo S. Guthman Foundation. -------------------------- SHARING/ACCESS INFORMATION -------------------------- 1. Licenses/restrictions placed on the data: These data are protected under a Creative Commons Attribution-NonCommercial-ShareAlike International 4.0 license. 2. Links to publications that cite or use the data: Wolf, T.M., W.A. Wang, E.V. Lonsdorf, T.R. Gillespie, A. Pusey, I.C. Gilby, D.A. Travis, and R.S. Singer. In review. Optimizing syndromic health surveillance in free ranging great apes: the case of Gombe National Park. Journal of Applied Ecology. 3. Recommended citation for the data: Wolf, T.M., W.A. Wang, E.V. Lonsdorf, T.R. Gillespie, A. Pusey, I.C. Gilby, D.A. Travis, and R.S. Singer. Model Documentation, and Output Supporting: Optimizing syndromic health surveillance in free ranging great apes: the case of Gombe National Park. Retrieved from the Data Repository for the University of Minnesota, http://doi.org --------------------- DATA & FILE OVERVIEW --------------------- 1. File List A. Chimpanzee_Respiratory_Disease_Simulation_Model_2.3.2015_Documentation.pdf: Model documentation of an agent-based, network model created using the Researcher/Educational edition of AnyLogic software, version 7.1.2 (The AnyLogic Company, Chicago, Illinois, USA). B. PopulationNetworkModelInputs_Anon.csv: Data set containing individual chimpanzees within a single community and accompanying metadata for all calendar quarters of 2007, including sex, age, age class, rank, probability of surveillance, and pariwise network connections. C. ScenarioAnalysis1_Q3surveillanceRatesAggregatedByAgeclass_Anon.csv: Data set containing only Quarter 3 of 2007 data, matching File B on all data, except probability of surveillance data, which are rates aggregated over an individuals' age class. D. ScenarioAnalysis2_Q32005_Anon.csv: Data set containing Quarter 3 data of 2005, matching all variables contained in File B. E. ScenarioAnalysis2_Q32006_Anon.csv: Data set containing Quarter 3 data of 2006, matching all variables contained in File B. F. ScenarioAnalysis2_Q32008_Anon.csv: Data set containing Quarter 3 data of 2008, matching all variables contained in File B. G. ScenarioAnalysis2_Q32009_Anon.csv: Data set containing Quarter 3 data of 2009, matching all variables contained in File B. H. ScenarioAnalysis2_Q32010_Anon.csv: Data set containing Quarter 3 data of 2010, matching all variables contained in File B. I. ScenarioAnalysis2_Q32011_Anon.csv: Data set containing Quarter 3 data of 2011, matching all variables contained in File B. J. ScenarioAnalysis2_Q32012_Anon.csv: Data set containing Quarter 3 data of 2012, matching all variables contained in File B. K. ScenarioAnalysis3_Q3APDetectIncreased_Anon.csv: Data set containing only Quarter 3 of 2007 data, matching File B on all data, except probability of surveillance data, which are double the rates of File B. L. SyndromicSurveillanceModelOutput.csv: Data set containing all model output used for estimating surveillance sensitivity, including number of animals observed by surveillance, number observed sick, cumulative outbreak incidence, outbreak duration, proportion of sick animals observed, and proportion of those observed that were sick. 2. Relationship between files: Files B-K were uploaded into the model described in File A to create the output contained in File L. -------------------------- METHODOLOGICAL INFORMATION -------------------------- 1. Description of methods used for collection/generation of data: see Wolf et al. (in review) for an overview. The methods used to generate the behavioral data to generate the contact networks are described in Pusey et al. (2008) and surveillance data are described in Lonsdorf et al. (2006), Lonsdorf et al. (2011) and Travis et al. (2008). 2. Methods for processing the data: see Wolf et al. (in review) for an overview. Male and female dominance ranks were calculated separately over a 2-year window by the modified David’s score method (de Vries et al. 2006), using directional male-male and female-female pant-grunts, respectively (Feldblum et al. 2014; Markham et al. 2015). Methods for calculating the contact network matrices (Dyadic and Grooming Association Indices) follow those described in Foerster et al. (2015) and Rushmore et al. (2013). 3. Instrument- or software-specific information needed to interpret the data: Model was constructed and simulations run using Researcher/Educational edition of AnyLogic software, version 7.1.2 (The AnyLogic Company, Chicago, Illinois, USA). ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: PopulationNetworkModelInputs_Anon.csv ----------------------------------------- 1. Number of variables:18 2. Number of cases/rows:59 cases 3. Missing data codes: Code/symbol: " " Definition: No rank data available. 4. Variable List See "Key" spreadsheet for variable list and definitions. ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: ScenarioAnalysis1_Q3surveillanceRatesAggregatedByAgeclass_Anon.csv ----------------------------------------- 1. Number of variables:18 2. Number of cases/rows:59 cases 3. Missing data codes: Code/symbol: " " Definition: No rank data available. 4. Variable List See "Key" spreadsheet for variable list and definitions. ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: ScenarioAnalysis2_Q32005_Anon.csv ----------------------------------------- 1. Number of variables:18 2. Number of cases/rows:58 cases 3. Missing data codes: Code/symbol: " " Definition: No rank data available. 4. Variable List See "Key" spreadsheet for variable list and definitions. ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: ScenarioAnalysis2_Q32006_Anon.csv ----------------------------------------- 1. Number of variables:18 2. Number of cases/rows:61 cases 3. Missing data codes: Code/symbol: " " Definition: No rank data available. 4. Variable List See "Key" spreadsheet for variable list and definitions. ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: ScenarioAnalysis2_Q32008_Anon.csv ----------------------------------------- 1. Number of variables:18 2. Number of cases/rows:59 cases 3. Missing data codes: Code/symbol: " " Definition: No rank data available. 4. Variable List See "Key" spreadsheet for variable list and definitions. ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: ScenarioAnalysis2_Q32009_Anon.csv ----------------------------------------- 1. Number of variables:18 2. Number of cases/rows:61 cases 3. Missing data codes: Code/symbol: " " Definition: No rank data available. 4. Variable List See "Key" spreadsheet for variable list and definitions. ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: ScenarioAnalysis2_Q32010_Anon.csv ----------------------------------------- 1. Number of variables:18 2. Number of cases/rows:57 cases 3. Missing data codes: Code/symbol: " " Definition: No rank data available. 4. Variable List See "Key" spreadsheet for variable list and definitions. ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: ScenarioAnalysis2_Q32011_Anon.csv ----------------------------------------- 1. Number of variables:18 2. Number of cases/rows:60 cases 3. Missing data codes: Code/symbol: " " Definition: No rank data available. 4. Variable List See "Key" spreadsheet for variable list and definitions. ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: ScenarioAnalysis2_Q32012_Anon.csv ----------------------------------------- 1. Number of variables:18 2. Number of cases/rows:58 cases 3. Missing data codes: Code/symbol: " " Definition: No rank data available. 4. Variable List See "Key" spreadsheet for variable list and definitions. ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: ScenarioAnalysis3_Q3APDetectIncreased_Anon ----------------------------------------- 1. Number of variables:18 2. Number of cases/rows:59 cases 3. Missing data codes: Code/symbol: " " Definition: No rank data available. 4. Variable List See "Key" spreadsheet for variable list and definitions. ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: SyndromicSurveillanceModelOutput.csv ----------------------------------------- 1. Number of variables:23 2. Number of cases/rows: varies by output spreadsheet; range 1155-10216 3. Missing data codes: NA 4. Variable List See "Key" spreadsheet for variable list and definitions. -------------------------------------------------------- -------------------------------------------------------- References de Vries H, Stevens JMG, Vervaecke H (2006) Measuring and testing the steepness of dominance hierarchies. Anim Behav 71:585–592. doi: 10.1016/j.anbehav.2005.05.015 Feldblum JT, Wroblewski EE, Rudicell RS, Hahn BH, Paiva T, Cetinkaya-Rundel M, Pusey AE, Gilby IC (2014) Sexually coercive male chimpanzees sire more offspring. Curr Biol 24:2855–2860. doi: 10.1016/j.cub.2014.10.039 Foerster S, McLellan K, Schroepfer-Walker K, Murray CM, Krupenye C, Gilby IC, Pusey AE (2015) Social bonds in the dispersing sex: partner preferences among adult female chimpanzees. Anim Behav 105:139–152. doi: 10.1016/j.anbehav.2015.04.012 Lonsdorf E, Travis D, Pusey A, Goodall J (2006) Using retrospective health data from the Gombe chimpanzee study to inform future monitoring efforts. Am J Primatol 908:897–908. doi: 10.1002/ajp Lonsdorf E V, Murray CM, Lonsdorf E V, Travis DA, Gilby IC, Chosy J, Goodall J, Pusey AE (2011) A retrospective analysis of factors correlated to chimpanzee (Pan troglodytes schweinfurthii) respiratory health at Gombe National Park, Tanzania. Ecohealth 8:26–35. doi: 10.1007/s10393-011-0683-0 Markham AC, Lonsdorf E V., Pusey AE, Murray CM (2015) Maternal rank influences the outcome of aggressive interactions between immature chimpanzees. Anim Behav 100:192–198. doi: 10.1016/j.anbehav.2014.12.003 Pusey AE, Wilson ML, Anthony Collins D. 2008. Human impacts, disease risk, and population dynamics in the chimpanzees of Gombe National Park, Tanzania. Am. J. Primatol. 70: 738–744. Rushmore J, Caillaud D, Matamba L, Stumpf RM, Borgatti SP, Altizer S. 2013. Social network analysis of wild chimpanzees provides insights for predicting infectious disease risk. J. Anim. Ecol. 82: 976–86. Travis DA, Lonsdorf E V, Mlengeya T, Raphael J (2008) A science-based approach to managing disease risks for ape conservation. Am J Primatol 70:745–50. doi: 10.1002/ajp.20566