initial upload

.gitignore

@@ -0,0 +1,4 @@
+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata

07-references.Rmd

@@ -0,0 +1,7 @@
+---
+nocite: '@*'
+---
+
+`r if (knitr::is_html_output()) '
+# References and R Packages {-}
+'`

Archaeological_Network_Science.Rproj

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+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
+BuildType: Website

_bookdown.yml

@@ -0,0 +1,4 @@
+delete_merged_file: true
+language:
+  ui:
+    chapter_name: "Section "

_output.yml

@@ -0,0 +1,17 @@
+bookdown::gitbook:
+  output:
+    revealjs_presentation:
+      css: style.css
+  highlight: tango
+  css: style.css
+  config:
+    toolbar:
+    position: static
+    edit: null
+    toc: 
+      collapse: subsection
+      scroll_highlight: true
+      before: |
+        <li><a href="./">Archaeological Network Science</a></li>
+      after: |
+        <li><a href="https://github.com/rstudio/bookdown" target="blank">Published with bookdown</a></li>

book.bib

@@ -0,0 +1,104 @@
+@Book{xie2015,
+  title = {Dynamic Documents with {R} and knitr},
+  author = {Yihui Xie},
+  publisher = {Chapman and Hall/CRC},
+  address = {Boca Raton, Florida},
+  year = {2015},
+  edition = {2nd},
+  note = {ISBN 978-1498716963},
+  url = {http://yihui.org/knitr/},
+  }
+  
+@Manual{Butts2020,
+    title = {sna: Tools for Social Network Analysis},
+    author = {Carter T. Butts},
+    year = {2020},
+    note = {R package version 2.6},
+    url = {https://CRAN.R-project.org/package=sna},
+  }
+
+@Manual{R-base,
+  title = {R: A Language and Environment for Statistical Computing},
+  author = {{R Core Team}},
+  organization = {R Foundation for Statistical Computing},
+  address = {Vienna, Austria},
+  year = {2021},
+  url = {https://www.R-project.org/},
+}
+
+@Manual{R-bookdown,
+  title = {bookdown: Authoring Books and Technical Documents with R Markdown},
+  author = {Yihui Xie},
+  year = {2021},
+  note = {R package version 0.24},
+  url = {https://CRAN.R-project.org/package=bookdown},
+}
+
+@Manual{R-knitr,
+  title = {knitr: A General-Purpose Package for Dynamic Report Generation in R},
+  author = {Yihui Xie},
+  year = {2021},
+  note = {R package version 1.31},
+  url = {https://yihui.org/knitr/},
+}
+
+@Manual{R-rmarkdown,
+  title = {rmarkdown: Dynamic Documents for R},
+  author = {JJ Allaire and Yihui Xie and Jonathan McPherson and Javier Luraschi and Kevin Ushey and Aron Atkins and Hadley Wickham and Joe Cheng and Winston Chang and Richard Iannone},
+  year = {2021},
+  note = {R package version 2.11},
+  url = {https://CRAN.R-project.org/package=rmarkdown},
+}
+
+@Book{bookdown2016,
+  title = {bookdown: Authoring Books and Technical Documents with {R} Markdown},
+  author = {Yihui Xie},
+  publisher = {Chapman and Hall/CRC},
+  address = {Boca Raton, Florida},
+  year = {2016},
+  note = {ISBN 978-1138700109},
+  url = {https://bookdown.org/yihui/bookdown},
+}
+
+@Book{knitr2015,
+  title = {Dynamic Documents with {R} and knitr},
+  author = {Yihui Xie},
+  publisher = {Chapman and Hall/CRC},
+  address = {Boca Raton, Florida},
+  year = {2015},
+  edition = {2nd},
+  note = {ISBN 978-1498716963},
+  url = {https://yihui.org/knitr/},
+}
+
+@InCollection{knitr2014,
+  booktitle = {Implementing Reproducible Computational Research},
+  editor = {Victoria Stodden and Friedrich Leisch and Roger D. Peng},
+  title = {knitr: A Comprehensive Tool for Reproducible Research in {R}},
+  author = {Yihui Xie},
+  publisher = {Chapman and Hall/CRC},
+  year = {2014},
+  note = {ISBN 978-1466561595},
+  url = {http://www.crcpress.com/product/isbn/9781466561595},
+}
+
+@Book{rmarkdown2018,
+  title = {R Markdown: The Definitive Guide},
+  author = {Yihui Xie and J.J. Allaire and Garrett Grolemund},
+  publisher = {Chapman and Hall/CRC},
+  address = {Boca Raton, Florida},
+  year = {2018},
+  note = {ISBN 9781138359338},
+  url = {https://bookdown.org/yihui/rmarkdown},
+}
+
+@Book{rmarkdown2020,
+  title = {R Markdown Cookbook},
+  author = {Yihui Xie and Christophe Dervieux and Emily Riederer},
+  publisher = {Chapman and Hall/CRC},
+  address = {Boca Raton, Florida},
+  year = {2020},
+  note = {ISBN 9780367563837},
+  url = {https://bookdown.org/yihui/rmarkdown-cookbook},
+}
+

data/AD1050cer.csv

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+"LA 115436",0,20.7592,0,24.3532,0,0,0,0,0,0,0,0,0,0
+"LA 12573 A",0,22.713,0,1,0,0,0,0,0,0,0,0,0,0
+"LA 126862",0.5422,29.2314,0,0,0,0,0,0,0,0,0,0,0,0
+"LA 17226",0,7.7199,0,0,0,1,0,0,0,0,0,0,0,0
+"LA 47526",0,17.9401,0,2.9421,0.5648,0,0,0,0,0,0,0,0,0
+"LA 60006",1,1.4175,0,0.3805,0,2.1576,0,0,0,0,0,0,0.1229,0
+"LA 60022",0.4293,1.9167,0,0.3631,0,10.9703,0,0,0,0,0,0,0.2487,0
+"LA 67158",0,8.7874,0,0,0,0,0,0,0,0,0,0,0,0
+"LA 7603",11.4542,0,0,0,0,0.3449,0,0,0,0,0,0,0,0
+"LA 8244",28.2285,2.3343,0,0,0,0.9768,0,0,0,0,0,0.4829,0,0
+"Lake Valley",9.1031,10.8967,0,2.283,0,0.1535,0,0,0,0,0,0,0.423,0
+"Lancaster",0,1.2608,0,0,0,207.3228,0,0,0,0,0,0,0,0
+"Los Veteados Great Kiva",0,11.3073,0,0.445,0,0,0,0,0,1.7511,0,0,0,0
+"Lower Greenlee",0,18.4229,0,0.5306,0,1.142,0,0,0,0,0,0.5306,0,0
+"Lower Kin Nizhoni",0,8.8957,0,0,0,0,0,0,0,0,0,0,0,0
+"Lowry",0,0,0,9.9654,0,376.9625,0,0,0,0,0,4.4338,102,0
+"McCreery",0,76.8825,0,0.1552,98.5967,0,0,0,40.6772,0,0,0,34.3435,0
+"Mesa Tierra",0,3.5519,0,4.1173,0,1.4979,0,0,0,0,0,0,0,0
+"Mineral Creek",0,47.3439,0,6.4605,0,0,0,0,0,0,0,0,0,0
+"Mitchell Springs",0,3.0154,0,0,0,94.7137,0,0,0,0,0,0,0,0
+"Mitten Rock",142.8209,2.0677,0,0,0,8.0369,0,0,0,0,0,6.4256,2.0016,0
+"Montezuma Village North",0,0,0,0,0,157.606,0,0,0,0,0,0.4926,0.1366,0
+"Muddy Water",0,20.8052,0,0,0,0,0,0,0,0.1935,0,0,0,0
+"NA 8800",0,0,0,0,14.1177,0,0,0,0,0,0,103.6295,320.8106,0
+"Navajo Springs",0,107.315,0,2.5391,2.7717,0,0,0,1.1808,0,0,0,7.5649,0
+"North Lowry",0,0,0,0,0,49.1189,0,0,0,0,0,0,0,0
+"Oak Wash--Zuni",0,172.701,0,1.8928,0,0,0,0,0,0,0,0,0,0
+"Owen Site",0,0,0,0,0,84.8764,0,0,0,0,0,25.3023,47.4767,0
+"Padilla Well",9.7634,227.3915,0,4.7507,0,0,0,0,0.8241,0,0,0.6041,0.8664,0
+"Peach Springs",1.791,24.9643,0,1.017,0,0,0,0,0,0,0,0,0,0
+"Penasco Blanco",10.9436,97.429,0,0,0.4904,1.1377,0,0,0,0,0,0.2562,1.8702,0
+"Pierre's El Faro",2.7735,46.5495,0,0,0,2.2585,0,0,0,0,0,0,0,0
+"Pierre's House A",5.1755,7.5392,0,1.2625,0,2.1449,0,0,0,0,0,0,0,0
+"Pierre's House B/C",6.1801,10.0351,0,1.9083,0,1.9758,0,0,0,0,0,0,0,0
+"Point Pueblo",10.2549,0.7785,0,0.6616,0,15.7337,0,0,0,0,0,0,0,0
+"Pueblo Alto",678.4557,7386.7349,0,0,0,0,0,0,0,0.1073,0,0,116.1733,0
+"Pueblo Bonito",16.8943,183.9972,0,1.9963,0,3.0355,0,0,0,0,0,2.1584,10.5192,0
+"Pueblo Cerrito",0,16.8329,0,2.9174,0,0,0,0,0,3.9491,0,0,0,0
+"Pueblo del Arroyo",6.8377,32.4478,0,2.7065,0.4582,2.5325,0,0,0,0,0,0.1721,0,0
+"Ram Mesa",0,30.7047,0,0.4866,0,0,0,0,0,0,0,0,0,0
+"Red Knobs",0,0,0,0,0,170.2053,0,0,0,0,0,2.1818,0.4172,0
+"Red Willow",0,8.4844,0,0,0,0.0825,0,0,0,0,0,0,1.3323,0
+"Reservoir--Northern San Juan",0.5572,1.0461,0,0,0,86.8638,0,0,0,0,0,0,0.2837,0
+"San Mateo",0,22.3654,0,1.2326,0,0,0,0,0,0,0,0,0,0
+"Sanders GH",0,1180.1984,0,4.1461,5.8713,0,0,0,8.2061,0,0,0,56.6148,0
+"Sanostee",25.7341,13.4734,0,0.3852,0,2.6075,0,0,0,0,0,0,0,0
+"Skull Site",0,48.3818,0,2.0184,0,0,0,0,0,6.4803,0,0,0.1664,0
+"Springstead",0.3935,14.8508,0,1.4575,0,0,0,0,0,0,0,0,0,0
+"Squaw Springs",0,0,0,0,0,12.7959,0,0,0,0,0,0,0.5,0
+"Standing Rock",0.2704,72.7981,0,1.6295,0.9478,3.3554,0,0,0,0,0,0,0,0
+"Sundown",0,110.7227,0,2.7743,249.3932,0,0,0,65.7767,0,0,0.5449,79.8559,0
+"Teec Nos Pos",10.206,0,0,0,0,14.431,0,0,0,0,0,1.2637,3.7284,0
+"The Twins Northeast",0,64.5969,0,2.2281,0.4715,0,0,0,0,0,0,0,0,0
+"Tla Kii",0,101.8295,0,2.9693,0.3997,0,0,0,2.3714,0,0,0,0.2434,0
+"Tocito North",79.0245,3.1806,0,2.0345,0,0.5502,0,0,0,0,0,1.3475,4.0117,0
+"Tocito South",11.1274,9.2266,0,3.2965,0,0,0,0,0,0,0,1.8133,0.1642,0
+"Toh La Kai",0,82.8547,0,10.1938,0.3456,7.1347,0,0,0,0,0,0,0,0
+"Toyee",0,97.4075,0,0.4439,0.2808,0,0,0,0.5012,0,0,0.0186,11.705,0
+"Tse Bee Kintsoh",0,7.5673,0,0,0,0,0,0,0,0,0,0.865,0,0
+"Tse La Vie",4.5721,154.1456,0,15.0613,0,0.6248,0,0,0,0.578,0,2.8072,0.3425,0
+"Tse Lichii",0,13.946,0,1.4317,0,1.8657,0,0,0,0.0806,0,0,0.6314,0
+"Tseyatoh",0,10.3588,0,2.6923,0,0,0,0,0,0,0,0,2.3534,0
+"Tsin Kletzin",0.3254,26.4157,0,0.8914,0,0,0,0,0,0,0,0.2526,2.1036,0
+"Una Vida",38.4043,927.0636,0,10.9286,2.044,19.3186,0,0,0,1.2988,0,3.1279,17.0572,0
+"Upper Kin Klizhin",5.5556,406.4942,0,7.1945,0,3.6256,0,0,0,0,0,0,4.1254,0
+"Vidal Canyon",0,20.6089,0,0.3566,0,0,0,0,0,0,0,0,0,0
+"Wallace Ruin",0,73.2039,0,10.3937,0,3663.5022,0,0,0,0.0528,0,12.7767,3.1725,0
+"Whirlwind House",2.6886,11.7752,0,0.7222,0,0,0,0,0,0,0,0,0,0
+"Wolye Adin",0,56.4362,0,2.8455,0,0,0,0,0,0,0,0,0.583,0
+"Yellow Jacket",0,1.9758,0,2.2195,0,3147.0528,0,0,0,0,0,3.0358,0,0
+"Escalante GH",0,0.9475,0,2.5454,0,741.0362,0,0,0,0,0,16.3009,4.8277,0
+"LA 40082",1.6765,45.4413,0,0,0,1.6092,0,0,0,0,0,0,0,0
+"LA 103458",0,17.6122,0,0.384,0,0,0,0,0,0,0,0,0,0
+"AZ-P-52-8-NN",0,3.3467,0,5.8439,3,0,0,0,0,0,0,0,0.1664,0
+"Cerritos de Jaspe GK",0,8.7006,0,0.8466,0,0,0,0,0,2.3093,0,0,0,0
+"HST Great Kiva",0,0,0,0,0,50.3473,0,0,0,0,0,8.1354,6.0185,0
+"Kin Bineola Great Kiva 2",0,13.4971,0,0,0,0,0,0,0,0,0,0,0,0
+"Haystack Great Kiva 2",0,8,0,0,0,0,0,0,0,0,0,0,0,0
+"NA 8013",0,571.2956,0,9.5507,3.0725,0.9638,0,0,0,0,0,0,40.8202,0
+"NA 8014",0,48.0372,0,0,0,0,0,0,0,0,0,0.9542,6.4567,0
+"Whites Canyon Pueblo",0,0,0,0,0,78.4543,0,0,0,0,0,0,0,0
+"34-plex Complex",0,0,0,0,0,60.249,0,0,0,0,0,0,0,0
+"Upper Battleship Rock Pueblo",0,0,0,0,0,83.8474,0,0,0,0,0,0,0,0
+"Gillentine Site",1,0.6157,0,0.2111,0,5.1359,0,0,0,0,0,0,0,0
+"San Juan Biwall",0,0,0,0,0,5.9704,0,0,0,0,0,0,0,0
+"Shields Pueblo",0,0,0,0,0,15799.1569,0,0,0,0,0,0,0,0
+"Bowman Site East",0,17.2671,0,0.3335,0,0.1659,0,0,0,0,0,0,0.2141,0
+"Dye Wash",0,12.7725,0,0.6158,0,0,0,0,0,0,0,0,0.5838,0