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Matthew Peeples committed Jan 30, 2023
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86 changes: 43 additions & 43 deletions _book/02-network-data-formats.md
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Expand Up @@ -94,9 +94,9 @@ cibola_net
```

```
## IGRAPH 9e52ae2 UN-- 30 167 --
## IGRAPH 07a172d UN-- 30 167 --
## + attr: name (v/c)
## + edges from 9e52ae2 (vertex names):
## + edges from 07a172d (vertex names):
## [1] Apache Creek--Casa Malpais Apache Creek--Coyote Creek
## [3] Apache Creek--Hooper Ranch Apache Creek--Horse Camp Mill
## [5] Apache Creek--Hubble Corner Apache Creek--Mineral Creek Pueblo
Expand Down Expand Up @@ -132,7 +132,7 @@ adj_list$`Apache Creek`
```

```
## + 11/167 edges from 9e52ae2 (vertex names):
## + 11/167 edges from 07a172d (vertex names):
## [1] Apache Creek--Casa Malpais Apache Creek--Coyote Creek
## [3] Apache Creek--Hooper Ranch Apache Creek--Horse Camp Mill
## [5] Apache Creek--Hubble Corner Apache Creek--Mineral Creek Pueblo
Expand All @@ -148,7 +148,7 @@ adj_list[[2]]
```

```
## + 11/167 edges from 9e52ae2 (vertex names):
## + 11/167 edges from 07a172d (vertex names):
## [1] Apache Creek--Casa Malpais Casa Malpais--Coyote Creek
## [3] Casa Malpais--Hooper Ranch Casa Malpais--Horse Camp Mill
## [5] Casa Malpais--Hubble Corner Casa Malpais--Rudd Creek Ruin
Expand Down Expand Up @@ -345,9 +345,9 @@ cibola_net2
```

```
## IGRAPH 9e7a5f9 UN-- 31 167 --
## IGRAPH 07dd544 UN-- 31 167 --
## + attr: name (v/c), region (v/c)
## + edges from 9e7a5f9 (vertex names):
## + edges from 07dd544 (vertex names):
## [1] Apache.Creek--Casa.Malpais Apache.Creek--Coyote.Creek
## [3] Apache.Creek--Hooper.Ranch Apache.Creek--Horse.Camp.Mill
## [5] Apache.Creek--Hubble.Corner Apache.Creek--Mineral.Creek.Pueblo
Expand Down Expand Up @@ -403,9 +403,9 @@ simple_net_i
```

```
## IGRAPH 9f352a7 UN-- 31 167 --
## IGRAPH 08eb430 UN-- 31 167 --
## + attr: name (v/c)
## + edges from 9f352a7 (vertex names):
## + edges from 08eb430 (vertex names):
## [1] Apache.Creek--Casa.Malpais Apache.Creek--Coyote.Creek
## [3] Apache.Creek--Hooper.Ranch Apache.Creek--Horse.Camp.Mill
## [5] Apache.Creek--Hubble.Corner Apache.Creek--Mineral.Creek.Pueblo
Expand Down Expand Up @@ -470,9 +470,9 @@ directed_net
```

```
## IGRAPH 9f3b52c DN-- 30 125 --
## IGRAPH 08f1630 DN-- 30 125 --
## + attr: name (v/c)
## + edges from 9f3b52c (vertex names):
## + edges from 08f1630 (vertex names):
## [1] Coyote Creek ->Techado Springs
## [2] Hubble Corner ->Tri-R Pueblo
## [3] Hubble Corner ->Techado Springs
Expand Down Expand Up @@ -605,9 +605,9 @@ cibola_inc
```

```
## IGRAPH 9f732b2 UN-B 41 2214 --
## IGRAPH 09293b7 UN-B 41 2214 --
## + attr: type (v/l), name (v/c)
## + edges from 9f732b2 (vertex names):
## + edges from 09293b7 (vertex names):
## [1] Apache Creek--Clust1 Apache Creek--Clust1 Apache Creek--Clust1
## [4] Apache Creek--Clust1 Apache Creek--Clust1 Apache Creek--Clust1
## [7] Apache Creek--Clust1 Apache Creek--Clust2 Apache Creek--Clust2
Expand Down Expand Up @@ -1152,9 +1152,9 @@ ego_nets[[1]]
```

```
## IGRAPH a12d22c UN-- 12 59 --
## IGRAPH 0af5f68 UN-- 12 59 --
## + attr: name (v/c)
## + edges from a12d22c (vertex names):
## + edges from 0af5f68 (vertex names):
## [1] Apache Creek --Casa Malpais Apache Creek --Coyote Creek
## [3] Casa Malpais --Coyote Creek Apache Creek --Hooper Ranch
## [5] Casa Malpais --Hooper Ranch Coyote Creek --Hooper Ranch
Expand Down Expand Up @@ -1244,7 +1244,7 @@ multinet::degree_ml(florentine)
```

```
## [1] 3 4 7 4 6 6 5 6 3 11 2 3 6 3 1
## [1] 6 6 5 7 4 4 3 2 3 11 3 6 3 6 1
```

```r
Expand All @@ -1255,32 +1255,32 @@ multinet::glouvain_ml(florentine)

```
## actor layer cid
## 1 Peruzzi business 0
## 2 Peruzzi marriage 0
## 3 Strozzi marriage 0
## 4 Castellani business 0
## 5 Castellani marriage 0
## 6 Barbadori business 0
## 7 Barbadori marriage 0
## 8 Ridolfi marriage 1
## 9 Tornabuoni business 1
## 10 Tornabuoni marriage 1
## 11 Ginori business 1
## 12 Ginori marriage 1
## 13 Medici business 1
## 14 Medici marriage 1
## 15 Pazzi business 1
## 16 Pazzi marriage 1
## 17 Salviati business 1
## 18 Salviati marriage 1
## 19 Albizzi marriage 1
## 20 Acciaiuoli marriage 1
## 21 Bischeri business 2
## 22 Bischeri marriage 2
## 23 Lamberteschi business 2
## 24 Lamberteschi marriage 2
## 25 Guadagni business 2
## 26 Guadagni marriage 2
## 1 Tornabuoni business 0
## 2 Tornabuoni marriage 0
## 3 Ridolfi marriage 0
## 4 Pazzi business 0
## 5 Pazzi marriage 0
## 6 Salviati business 0
## 7 Salviati marriage 0
## 8 Medici business 0
## 9 Medici marriage 0
## 10 Ginori business 0
## 11 Ginori marriage 0
## 12 Albizzi marriage 0
## 13 Barbadori business 0
## 14 Barbadori marriage 0
## 15 Acciaiuoli marriage 0
## 16 Castellani business 1
## 17 Castellani marriage 1
## 18 Bischeri business 1
## 19 Bischeri marriage 1
## 20 Lamberteschi business 1
## 21 Lamberteschi marriage 1
## 22 Peruzzi business 1
## 23 Peruzzi marriage 1
## 24 Strozzi marriage 1
## 25 Guadagni business 1
## 26 Guadagni marriage 1
```

For an archaeological example of multilevel network analysis [this GitHub project](https://github.com/ajupton/archy-multilayer-nets) by Andy Upton.
Expand Down Expand Up @@ -1311,9 +1311,9 @@ mor_wt_i
```

```
## IGRAPH a184fc3 U-W- 31 465 --
## IGRAPH 0d0dca0 U-W- 31 465 --
## + attr: na (v/l), vertex.names (v/c), na (e/l), weight (e/n)
## + edges from a184fc3:
## + edges from 0d0dca0:
## [1] 1-- 2 1-- 3 1-- 4 1-- 5 1-- 6 1-- 7 1-- 8 1-- 9 1--10 1--11 1--12 1--13
## [13] 1--14 1--15 1--16 1--17 1--18 1--19 1--20 1--21 1--22 1--23 1--24 1--25
## [25] 1--26 1--27 1--28 1--29 1--30 1--31 2-- 3 2-- 4 2-- 5 2-- 6 2-- 7 2-- 8
Expand Down
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20 changes: 10 additions & 10 deletions _book/03-exploratory-analysis.md
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Expand Up @@ -582,7 +582,7 @@ igraph::shortest_paths(simple_net, from = 1, to = 21)
```
## $vpath
## $vpath[[1]]
## + 5/31 vertices, named, from a476aa6:
## + 5/31 vertices, named, from 100b5d3:
## [1] Apache.Creek Casa.Malpais Garcia.Ranch
## [4] Heshotauthla Pueblo.de.los.Muertos
##
Expand Down Expand Up @@ -618,7 +618,7 @@ igraph::farthest_vertices(directed_net, directed = TRUE)

```
## $vertices
## + 2/30 vertices, named, from a47787a:
## + 2/30 vertices, named, from 100c233:
## [1] Apache Creek Pueblo de los Muertos
##
## $distance
Expand Down Expand Up @@ -670,9 +670,9 @@ components

```
## [[1]]
## IGRAPH a6baf1a UN-- 30 167 --
## IGRAPH 12f63e0 UN-- 30 167 --
## + attr: name (v/c)
## + edges from a6baf1a (vertex names):
## + edges from 12f63e0 (vertex names):
## [1] Apache.Creek--Casa.Malpais Apache.Creek--Coyote.Creek
## [3] Apache.Creek--Hooper.Ranch Apache.Creek--Horse.Camp.Mill
## [5] Apache.Creek--Hubble.Corner Apache.Creek--Mineral.Creek.Pueblo
Expand All @@ -684,9 +684,9 @@ components
## + ... omitted several edges
##
## [[2]]
## IGRAPH a6baf31 UN-- 1 0 --
## IGRAPH 12f6407 UN-- 1 0 --
## + attr: name (v/c)
## + edges from a6baf31 (vertex names):
## + edges from 12f6407 (vertex names):
```

```r
Expand Down Expand Up @@ -746,15 +746,15 @@ min_cut(simple_net_noiso, value.only = FALSE)
## [1] 1
##
## $cut
## + 1/167 edge from a476f39 (vertex names):
## + 1/167 edge from 100ba9a (vertex names):
## [1] Ojo Bonito--Baca Pueblo
##
## $partition1
## + 1/30 vertex, named, from a476f39:
## + 1/30 vertex, named, from 100ba9a:
## [1] Baca Pueblo
##
## $partition2
## + 29/30 vertices, named, from a476f39:
## + 29/30 vertices, named, from 100ba9a:
## [1] Apache Creek Casa Malpais Coyote Creek
## [4] Hooper Ranch Horse Camp Mill Hubble Corner
## [7] Mineral Creek Pueblo Rudd Creek Ruin Techado Springs
Expand Down Expand Up @@ -783,7 +783,7 @@ max_cliques(simple_net, min = 1)[[24]]
```

```
## + 9/31 vertices, named, from a476aa6:
## + 9/31 vertices, named, from 100b5d3:
## [1] Los.Gigantes Cienega Tinaja Spier.170
## [5] Scribe.S Pescado.Cluster Mirabal Heshotauthla
## [9] Yellowhouse
Expand Down
10 changes: 10 additions & 0 deletions _book/04-uncertainty.md
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Expand Up @@ -52,7 +52,17 @@ library(reshape2)
library(ggraph)
library(ggpubr)
library(statnet)
```

```
## Installed ReposVer Built
## ergm "4.3.2" "4.4.0" "4.2.2"
## network "1.18.0" "1.18.1" "4.2.2"
## sna "2.7" "2.7-1" "4.2.0"
## statnet.common "4.7.0" "4.8.0" "4.2.1"
```

```r
# Import adjacency matrix and covert to network
chaco <- read.csv(file = "data/AD1050net.csv", row.names = 1)

Expand Down
15 changes: 13 additions & 2 deletions _book/05-visualization.md
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Expand Up @@ -32,6 +32,17 @@ Let's start by reading in our example data and then we describe each package in
```r
library(igraph)
library(statnet)
```

```
## Installed ReposVer Built
## ergm "4.3.2" "4.4.0" "4.2.2"
## network "1.18.0" "1.18.1" "4.2.2"
## sna "2.7" "2.7-1" "4.2.0"
## statnet.common "4.7.0" "4.8.0" "4.2.1"
```

```r
library(ggraph)
library(intergraph)

Expand All @@ -50,9 +61,9 @@ cibola_i
```

```
## IGRAPH afda745 UN-- 31 167 --
## IGRAPH 1d185c4 UN-- 31 167 --
## + attr: name (v/c)
## + edges from afda745 (vertex names):
## + edges from 1d185c4 (vertex names):
## [1] Apache.Creek--Casa.Malpais Apache.Creek--Coyote.Creek
## [3] Apache.Creek--Hooper.Ranch Apache.Creek--Horse.Camp.Mill
## [5] Apache.Creek--Hubble.Corner Apache.Creek--Mineral.Creek.Pueblo
Expand Down
15 changes: 13 additions & 2 deletions _book/06-spatial-networks.md
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Expand Up @@ -279,9 +279,9 @@ tree1
```

```
## IGRAPH d29f1c0 U--- 50 49 -- Tree
## IGRAPH 43dc8a6 U--- 50 49 -- Tree
## + attr: name (g/c), children (g/n), mode (g/c)
## + edges from d29f1c0:
## + edges from 43dc8a6:
## [1] 1-- 2 1-- 3 1-- 4 1-- 5 1-- 6 2-- 7 2-- 8 2-- 9 2--10 2--11
## [11] 3--12 3--13 3--14 3--15 3--16 4--17 4--18 4--19 4--20 4--21
## [21] 5--22 5--23 5--24 5--25 5--26 6--27 6--28 6--29 6--30 6--31
Expand Down Expand Up @@ -588,6 +588,17 @@ Next, in order to define a minimum distance network we simply binarize this matr

```r
library(statnet)
```

```
## Installed ReposVer Built
## ergm "4.3.2" "4.4.0" "4.2.2"
## network "1.18.0" "1.18.1" "4.2.2"
## sna "2.7" "2.7-1" "4.2.0"
## statnet.common "4.7.0" "4.8.0" "4.2.1"
```

```r
library(geosphere)
d1 <- distm(nodes[, c(3, 2)])
# Note we use the leq=TRUE argument here as we want nodes less than
Expand Down
8 changes: 8 additions & 0 deletions _book/07-ergm.md
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Expand Up @@ -82,6 +82,14 @@ Let's initialize our `statnet` suite to get started:
library(statnet) # initialize statnet library
```

```
## Installed ReposVer Built
## ergm "4.3.2" "4.4.0" "4.2.2"
## network "1.18.0" "1.18.1" "4.2.2"
## sna "2.7" "2.7-1" "4.2.0"
## statnet.common "4.7.0" "4.8.0" "4.2.1"
```

In many ways it is easiest to describe what ERGMs do and how they work by example. In the next sections we provide a couple of archaeological examples that highlight some of the ways ERGMs have or could be used in archaeology. We further provide additional resources for taking these methods further.

## Cranborne Chase Visibility Network Example{#CranborneChase}
Expand Down
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10 changes: 10 additions & 0 deletions _book/11-comparing-networks.md
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Expand Up @@ -37,7 +37,17 @@ For the example here we will use three time slices of a ceramic similarity netwo

```r
library(statnet)
```

```
## Installed ReposVer Built
## ergm "4.3.2" "4.4.0" "4.2.2"
## network "1.18.0" "1.18.1" "4.2.2"
## sna "2.7" "2.7-1" "4.2.0"
## statnet.common "4.7.0" "4.8.0" "4.2.1"
```

```r
load("data/SanPedro_nets.Rdata")

network_subset_common <-
Expand Down
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Expand Up @@ -131,7 +131,7 @@ <h1>Page not found<a class="anchor" aria-label="anchor" href="#page-not-found"><
<footer class="bg-primary text-light mt-5"><div class="container"><div class="row">

<div class="col-12 col-md-6 mt-3">
<p>"<strong>Online Companion to <em>Network Science in Archaeology</em></strong>" was written by Matthew A. Peeples and Tom Brughmans. It was last built on 2022-12-29.</p>
<p>"<strong>Online Companion to <em>Network Science in Archaeology</em></strong>" was written by Matthew A. Peeples and Tom Brughmans. It was last built on 2023-01-30.</p>
</div>

<div class="col-12 col-md-6 mt-3">
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