References and R Packages
Allaire, J. J., Christopher Gandrud, Kenton Russell, and CJ Yetman
2017
Allaire, JJ, Yihui Xie, Jonathan McPherson, Javier Luraschi, Kevin Ushey, Aron Atkins, Hadley Wickham, Joe Cheng, Winston Chang, and Richard Iannone
2022
Almende B.V. and Contributors, Benoit Thieurmel, and Titouan Robert
2021
Amati, Viviana, Angus Mol, Termeh Shafie, Corinne Hofman, and Ulrik Brandes
2020
A Framework for Reconstructing Archaeological Networks Using Exponential Random Graph Models. Journal of Archaeological Method and Theory 27(2):192–219. DOI:10.1007/s10816-019-09423-z, accessed September 1, 2021.
Ancient World Mapping Center
2012
Road information derived from Talbert, Richard J. A., and Roger S. Bagnall. 2000. Barrington Atlas of the Greek and Roman World. Princeton, N.J.: Princeton University Press.
Barter, Rebecca, and Bin Yu
2017
Bevan, Andrew, and Alan Wilson
2013
Models of settlement hierarchy based on partial evidence. Journal of Archaeological Science 40:2415–2427. DOI:10.1016/j.jas.2012.12.025.
Borck, Lewis, Barbara J. Mills, Matthew A. Peeples, and Jeffery J. Clark
2015
Are Social Networks Survival Networks? An Example from the Late Pre-Hispanic US Southwest. Journal of Archaeological Method and Theory 22(1):33–57. DOI:10.1007/s10816-014-9236-5, accessed May 9, 2018.
Borgatti, Stephen P., Kathleen M. Carley, and David Krackhardt
2006
On the robustness of centrality measures under conditions of imperfect data. Social Networks 28(2):124–136. DOI:10.1016/j.socnet.2005.05.001, accessed September 1, 2021.
Brughmans, Tom
2013
Networks of networks: A citation network analysis of the adoption, use and adaptation of formal network techniques in archaeology. Literary and Linguistic Computing, The Journal of Digital Scholarship in the Humanities 28(4):538–562. DOI:10.1093/llc/fqt048.
Brughmans, Tom, and Ulrik Brandes
2017
Visibility Network Patterns and Methods for Studying Visual Relational Phenomena in Archeology. Frontiers in Digital Humanities 4. DOI:10.3389/fdigh.2017.00017, accessed August 26, 2017.
Brughmans, Tom, Simon Keay, and Graeme Earl
2014
Introducing exponential random graph models for visibility networks. Journal of Archaeological Science 49:442–454. DOI:10.1016/j.jas.2014.05.027, accessed January 9, 2017.
2015
Understanding Inter-settlement Visibility in Iron Age and Roman Southern Spain with Exponential Random Graph Models for Visibility Networks. Journal of Archaeological Method and Theory 22(1):58–143. DOI:10.1007/s10816-014-9231-x, accessed January 9, 2017.
Brughmans, Tom, and Matthew A. Peeples
2017
Trends in Archaeological Network Research: A Bibliometric Analysis. Journal of Historical Network Research 1(2017):1–24.
Butts, Carter T., Ayn Leslie-Cook, Pavel N. Krivitsky, and Skye Bender-deMoll
2022
Clark, Jeffery J., and Patrick D. Lyons (editors)
2012
Migrants and Mounds: Classic Period Archaeology of the Lower San Pedro Valley. Anthrpological Papers 45. Archaeology Southwest, Tucson.
Costenbader, Elizabeth, and Thomas W Valente
2003
The stability of centrality measures when networks are sampled. Social Networks 25(4):283–307. DOI:10.1016/S0378-8733(03)00012-1, accessed September 1, 2021.
Csardi, Gabor, and Tamas Nepusz
2006
The igraph software package for complex network research. InterJournal Complex Systems:1695.
Ducke, Benjamin, and Paulina Suchowska
2021
Exploratory Network Reconstruction with Sparse Archaeological Data and XTENT. Journal of Archaeological Method and Theory. DOI:10.1007/s10816-021-09529-3, accessed November 12, 2021.
Eddelbuettel, Dirk, and James Joseph Balamuta
2018
Extending extitR with extitC++: A Brief Introduction to extitRcpp. The American Statistician 72(1):28–36. DOI:10.1080/00031305.2017.1375990.
Eddelbuettel, Dirk, Romain Francois, JJ Allaire, Kevin Ushey, Qiang Kou, Nathan Russell, Inaki Ucar, Douglas Bates, and John Chambers
2022
Eddelbuettel, Dirk, and Romain François
2011
Rcpp: Seamless R and C++ integration. Journal of Statistical Software 40(8):1–18. DOI:10.18637/jss.v040.i08.
Evans, Tim
2016
Which Network Model Should I Use? Towards a Quantitative Comparison of Spatial Network Models in Archaeology. In The Connected Past: Challenges to network studies in archaeology and history, edited by Tom Brughmans, Anna Collar, and Fiona Coward, pp. 149–173. Oxford University Press, Oxford.
Evans, Tim S., and Ray J. Rivers
2017
Was Thebes Necessary? Contingency in Spatial Modelling. Frontiers in Digital Humanities: Digital Archaeology 4(8):1–21. DOI:10.3389/fdigh.2017.00008.
Everton, Sean F.
2012
Disrupting Dark Networks. Cambridge University Press, Cambridge.
Filet, Clara
2016
An attempt to estimate the impact of the spread of economic flows on Latenian urbanisation. Frontiers in Digital Humanities 3. DOI:10.3389/fdigh.2016.00010, accessed January 9, 2017.
Finotelli, Paolo, Carlo Piccardi, Edie Miglio, and Paolo Dulio
2021
A Graphlet-Based Topological Characterization of the Resting-State Network in Healthy People. Frontiers in Neuroscience 15. accessed July 22, 2022.
Gerald, Rex E.
2019
The Davis Ranch Site: A Kayenta Immigrant Enclave in Southeastern Arizona. Edited by Patrick D. Lyons. Illustrated edition. University of Arizona Press, Tucson.
Giomi, Evan, Barbara J. Mills, Leslie D. Aragon, Benjamin A. Bellorado, and Matthew A. Peeples
2021
Reading between the Lines: The Social Value of Dogoszhi Style in the Chaco World. American Antiquity In press. DOI:10.1017/aaq.2021.50, accessed September 1, 2021.
Giomi, Evan, and Matthew A. Peeples
2019
Network analysis of intrasite material networks and ritual practice at Pueblo Bonito. Journal of Anthropological Archaeology 53:22–31. DOI:10.1016/j.jaa.2018.10.002, accessed September 3, 2021.
Gombin, Joël, Ramnath Vaidyanathan, and Vladimir Agafonkin
2020
Handcock, Mark S., David R. Hunter, Carter T. Butts, Steven M. Goodreau, Pavel N. Krivitsky, Skye Bender-deMoll, and Martina Morris
2019
Holtz, Yan
The R Graph Gallery – Help and inspiration for R charts. The R Graph Gallery.
Hunter, David R., Mark S. Handcock, Carter T. Butts, Steven M. Goodreau, and Martina Morris
2008
Ergm: A package to fit, simulate and diagnose exponential-family models for networks. Journal of Statistical Software 24(3):1–29.
Ihaka, Ross, Paul Murrell, Kurt Hornik, Jason C. Fisher, Reto Stauffer, Claus O. Wilke, Claire D. McWhite, and Achim Zeileis
2022
Kahle, David, and Hadley Wickham
2013
Ggmap: Spatial visualization with ggplot2. The R Journal 5(1):144–161.
Keay, Simon, and Graeme P Earl
2011
Towns and territories in Roman Baetica. In Settlement, urbanization, and population, edited by Alan Bowman and Andrew Wilson, pp. 276–316. Oxford University Press, Oxford.
Ligges, Uwe, and Martin Mächler
2003
Scatterplot3d - an r package for visualizing multivariate data. Journal of Statistical Software 8(11):1–20.
Lusher, Dean, Johan Koskinen, and Garry Robins (editors)
2013
Exponential Random Graph Models for Social Networks: Theory, Methods, and Applications. Structural Analysis in the Social Sciences. Cambridge University Press, Cambridge.
Magnani, Matteo, Luca Rossi, and Davide Vega
2021
Analysis of multiplex social networks with R. Journal of Statistical Software 98(8):1–30. DOI:10.18637/jss.v098.i08.
Melckenbeeck, Ine, Pieter Audenaert, Thomas Van Parys, Yves Van De Peer, Didier Colle, and Mario Pickavet
2019
Optimising orbit counting of arbitrary order by equation selection. BMC Bioinformatics 20(1):27. DOI:10.1186/s12859-018-2483-9, accessed August 9, 2022.
Menze, Bjoern H, and Jason a Ur
2012
Mapping patterns of long-term settlement in Northern Mesopotamia at a large scale. Proceedings of the National Academy of Sciences of the United States of America 109(14):E778–87. DOI:10.1073/pnas.1115472109.
Mills, Barbara J, Jeffery J Clark, Matthew A Peeples, W R Haas, John M Roberts, J Brett Hill, Deborah L Huntley, Lewis Borck, Ronald L Breiger, Aaron Clauset, and M Steven Shackley
2013
Transformation of social networks in the late pre-Hispanic US Southwest. Proceedings of the National Academy of Sciences of the United States of America:1–6. DOI:10.1073/pnas.1219966110.
Mills, Barbara J., Matthew A. Peeples, Leslie D. Aragon, Benjamin A Bellorado, Jeffery J. Clark, Evan Giomi, and Thomas C. Windes
2018
Evaluating Chaco Migration Scenarios Using Dynamic Social Network Analysis. Antiquity 92(364).
Mills, Barbara J., Matthew A. Peeples, W. Randall Haas Jr., Lewis Borck, Jeffery J. Clark, and John M. Roberts Jr.
2015
Multiscalar Perspectives on Social Networks in the Late Prehispanic Southwest. American Antiquity 80(1):3–24. DOI:10.7183/0002-7316.79.4.3, accessed January 9, 2017.
Mills, Barbara J., John M. Roberts, Jeffery J. Clark, William R. Haas Jr., Deborah Huntley, Matthew A. Peeples, Lewis Borck, Susan C. Ryan, Meaghan Trowbridge, and Ronald L. Breiger
2013
The dynamics of social networks in the Late Prehispanic U.S. Southwest. In Network analysis in archaeology. New approaches to regional interaction, edited by Carl Knappett, pp. 181–202. Oxford University Press, Oxford.
Muenchow, Jannes, Jakub Nowosad
Ognyanova, Katya
Katya Ognyanova: Rutgers Prof., Network Researcher, Data Scientist. Katya Ognyanova.
Oksanen, Jari, Gavin L. Simpson, F. Guillaume Blanchet, Roeland Kindt, Pierre Legendre, Peter R. Minchin, R. B. O’Hara, Peter Solymos, M. Henry H. Stevens, Eduard Szoecs, Helene Wagner, Matt Barbour, Michael Bedward, Ben Bolker, Daniel Borcard, Gustavo Carvalho, Michael Chirico, Miquel De Caceres, Sebastien Durand, Heloisa Beatriz Antoniazi Evangelista, Rich FitzJohn, Michael Friendly, Brendan Furneaux, Geoffrey Hannigan, Mark O. Hill, Leo Lahti, Dan McGlinn, Marie-Helene Ouellette, Eduardo Ribeiro Cunha, Tyler Smith, Adrian Stier, Cajo J. F. Ter Braak, and James Weedon
2022
Ortman, Scott G.
2016
Uniform Probability Density Analysis and Population History in the Northern Rio Grande. Journal of Archaeological Method and Theory 23(1):95–126. DOI:10.1007/s10816-014-9227-6, accessed January 9, 2017.
Paliou, Eleftheria, and Andrew Bevan
2016
Evolving settlement patterns, spatial interaction and the socio-political organisation of late Prepalatial south-central Crete. Journal of Anthropological Archaeology 42:184–197. DOI:10.1016/j.jaa.2016.04.006, accessed June 13, 2022.
Paradis, Emmanuel, Simon Blomberg, Ben Bolker, Joseph Brown, Santiago Claramunt, Julien Claude, Hoa Sien Cuong, Richard Desper, Gilles Didier, Benoit Durand, Julien Dutheil, RJ Ewing, Olivier Gascuel, Thomas Guillerme, Christoph Heibl, Anthony Ives, Bradley Jones, Franz Krah, Daniel Lawson, Vincent Lefort, Pierre Legendre, Jim Lemon, Guillaume Louvel, Eric Marcon, Rosemary McCloskey, Johan Nylander, Rainer Opgen-Rhein, Andrei-Alin Popescu, Manuela Royer-Carenzi, Klaus Schliep, Korbinian Strimmer, and Damien de Vienne
2022
Paradis, E., and K. Schliep
2019
Ape 5.0: An environment for modern phylogenetics and evolutionary analyses in R. Bioinformatics 35:526–528.
Pebesma, Edzer
2018
Simple Features for R: Standardized Support for Spatial Vector Data. The R Journal 10(1):439–446. DOI:10.32614/RJ-2018-009.
Peeples, Matthew A
2011
Identity and Social Transformation in the Prehispanic Cibola World: A.D. 1150-1325. Unpublished {PhD} {Dissertation}, Arizona State University.
Peeples, Matthew A.
2018
Connected Communities: Networks, Identity, and Social Change in the Ancient Cibola World. University of Arizona Press.
Peeples, Matthew A., Wesley Bernardini, Lyle Balenquah, and Kellam Throgmorton
2021
Connections and Boundaries. In Becoming Hopi: A History, edited by Wesley Bernardini, Stewart Koyiyumptewa, Gregson Schachner, and Leigh Kuwanwisiwma, pp. 261–298. University of Arizona Press, Tucson, AZ.
Peeples, Matthew A., and W. Randall Haas
2013
Brokerage and Social Capital in the Prehispanic U.S. Southwest. American Anthropologist 115(2):232–247. DOI:10.1111/aman.12006, accessed January 9, 2017.
Peeples, Matthew A., Barbara J. Mills, W. Randall Jr. Haas, Jeffery J. Clark, and John M. Jr. Roberts
2016
Analytical Challenges for the Application of Social Network Analysis in Archaeology. In The Connected Past: Challenges to network studies in archaeology and history, edited by Tom Brughmans, Anna Collar, and Fiona Coward, pp. 59–84. Oxford University Press, Oxford.
Peeples, Matthew A., and John M. Roberts
2013
To binarize or not to binarize: Relational data and the construction of archaeological networks. Journal of Archaeological Science 40(7):3001–3010. DOI:10.1016/j.jas.2013.03.014.
R Core Team
2022
R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria.
Rawat, Nagendra Singh, Tom Brughmans, Vinod Nautiyal, and Devi Dutt Chauniyal
2021
Networked medieval strongholds in Garhwal Himalaya, India. Antiquity 95(381):753–772. DOI:10.15184/aqy.2021.4, accessed July 23, 2021.
Rawat, Nagendra Singh, and Vinod Nautiyal
2020
Exploring Chaundkot Fort in Garhwal, central Himalaya, India. Antiquity 94(376). DOI:10.15184/aqy.2020.117, accessed September 1, 2021.
Rihll, Tracey Elizabeth, and Alan Geoffrey Wilson
1987
Spatial Interaction and Structural Models in Historical Analysis: Some Possibilities and an Example. Histoire & Mesure 2(1):5–32. DOI:10.3406/hism.1987.1300, accessed September 1, 2021.
Rivers, Ray, Carl Knappett, and Timothy Evans
2013
Network Models and Archaeological Spaces. In Computational Approaches to Archaeological Spaces, pp. 99–126. UCL Institute of Archaeology Publications 60. Left Coast Press, Walnut Creek, CA.
Roberts, John M., Jr., Barbara J. Mills, Jeffery J. Clark, W. Randall Haas Jr., Deborah L. Huntley, and Meaghan A. Trowbridge
2012
A method for chronological apportioning of ceramic assemblages. Journal of Archaeological Science 39(5):1513–1520. DOI:10.1016/j.jas.2011.12.022, accessed January 9, 2017.
Roberts, John M., Yi Yin, Emily Dorshorst, Matthew A. Peeples, and Barbara J. Mills
2021
Assessing the performance of the bootstrap in simulated assemblage networks. Social Networks 65:98–109. DOI:10.1016/j.socnet.2020.11.005, accessed July 23, 2021.
Santos Baquero, Oswaldo
2019
Schoch, David
2022
Simini, Filippo, Marta C. González, Amos Maritan, and Albert-László Barabási
2012
A universal model for mobility and migration patterns. Nature 484(7392):96–100. DOI:10.1038/nature10856, accessed June 13, 2022.
Smith, Jeffrey A., and James Moody
2013
Structural effects of network sampling coverage I: Nodes missing at random. Social Networks 35(4):652–668. DOI:10.1016/j.socnet.2013.09.003, accessed September 1, 2021.
Smith, Jeffrey A., James Moody, and Jonathan H. Morgan
2017
Network sampling coverage II: The effect of non-random missing data on network measurement. Social Networks 48:78–99. DOI:10.1016/j.socnet.2016.04.005, accessed September 1, 2021.
Smith, Jeffrey A., Jonathan H. Morgan, and James Moody
2022
Network sampling coverage III: Imputation of missing network data under different network and missing data conditions. Social Networks 68:148–178. DOI:10.1016/j.socnet.2021.05.002, accessed September 1, 2021.
Soto, Pau de, and Cèsar Carreras
2021
The Role of Politics in the Historical Transport Networks of the Iberian Peninsula and the Pyrenees from Roman Times to the Nineteenth Century. Social Science History 45(2):233–260. DOI:10.1017/ssh.2021.12, accessed September 1, 2021.
Stauffer, Reto, Georg J. Mayr, Markus Dabernig, and Achim Zeileis
2009
Somewhere over the rainbow: How to make effective use of colors in meteorological visualizations. Bulletin of the American Meteorological Society 96(2):203–216. DOI:10.1175/BAMS-D-13-00155.1.
Talbert, Richard J. A. (editor)
2000
Barrington Atlas of the Greek and Roman World. Princeton University Press, Princeton.
Tilley, Christopher Y
1994
A Phenomenology of Landscape. Places, Paths and Monuments. Berg, Oxford.
Wang, Li-Ying, and Ben Marwick
2021
A Bayesian networks approach to infer social changes from burials in northeastern Taiwan during the European colonization period. Journal of Archaeological Science 134:105471. DOI:10.1016/j.jas.2021.105471, accessed September 2, 2021.
Wickham, Hadley
2007
Reshaping data with the reshape package. Journal of Statistical Software 21(12):1–20.
2016
ggplot2: Elegant graphics for data analysis. Springer-Verlag New York.
Wickham, Hadley, Mara Averick, Jennifer Bryan, Winston Chang, Lucy D’Agostino McGowan, Romain François, Garrett Grolemund, Alex Hayes, Lionel Henry, Jim Hester, Max Kuhn, Thomas Lin Pedersen, Evan Miller, Stephan Milton Bache, Kirill Müller, Jeroen Ooms, David Robinson, Dana Paige Seidel, Vitalie Spinu, Kohske Takahashi, Davis Vaughan, Claus Wilke, Kara Woo, and Hiroaki Yutani
2019
Welcome to the tidyverse. Journal of Open Source Software 4(43):1686. DOI:10.21105/joss.01686.
Wickham, Hadley, Winston Chang, Lionel Henry, Thomas Lin Pedersen, Kohske Takahashi, Claus Wilke, Kara Woo, Hiroaki Yutani, and Dewey Dunnington
2022
Wickham, Hadley, Romain François, Lionel Henry, and Kirill Müller
2022
Wickham, Hadley, Jim Hester, Winston Chang, and Jennifer Bryan
2021
Xie, Yihui
2014
Knitr: A comprehensive tool for reproducible research in R. In Implementing reproducible computational research, edited by Victoria Stodden, Friedrich Leisch, and Roger D. Peng. Chapman; Hall/CRC.
2015
Dynamic documents with R and knitr. 2nd ed. Chapman; Hall/CRC, Boca Raton, Florida.
2016
Bookdown: Authoring books and technical documents with R markdown. Chapman; Hall/CRC, Boca Raton, Florida.
Xie, Yihui, J. J. Allaire, and Garrett Grolemund
2018
R markdown: The definitive guide. Chapman; Hall/CRC, Boca Raton, Florida.
Xie, Yihui, Christophe Dervieux, and Emily Riederer
2020
R markdown cookbook. Chapman; Hall/CRC, Boca Raton, Florida.
Yaveroğlu, Ömer Nebil, Noël Malod-Dognin, Darren Davis, Zoran Levnajic, Vuk Janjic, Rasa Karapandza, Aleksandar Stojmirovic, and Nataša Pržulj
2014
Revealing the Hidden Language of Complex Networks. Scientific Reports 4(1):4547. DOI:10.1038/srep04547, accessed July 22, 2022.
Zeileis, Achim, Jason C. Fisher, Kurt Hornik, Ross Ihaka, Claire D. McWhite, Paul Murrell, Reto Stauffer, and Claus O. Wilke
2020
colorspace: A toolbox for manipulating and assessing colors and palettes. Journal of Statistical Software 96(1):1–49. DOI:10.18637/jss.v096.i01.
Zeileis, Achim, Kurt Hornik, and Paul Murrell
2009
Escaping RGBland: Selecting colors for statistical graphics. Computational Statistics & Data Analysis 53(9):3259–3270. DOI:10.1016/j.csda.2008.11.033.