From f9841a270c6267f9dfe299cee32b0419b9845918 Mon Sep 17 00:00:00 2001
From: Azza Ahmed <azzaea@uofk.edu>
Date: Thu, 16 Nov 2017 17:40:23 +0300
Subject: [PATCH] Fixing some ouptut results

---
 sand/inst/code/chapter2.R | 508 +++++++++++++++++++-------------------
 1 file changed, 254 insertions(+), 254 deletions(-)

diff --git a/sand/inst/code/chapter2.R b/sand/inst/code/chapter2.R
index 6ac4e47..c252d11 100644
--- a/sand/inst/code/chapter2.R
+++ b/sand/inst/code/chapter2.R
@@ -1,37 +1,37 @@
-# SAND with R, chapter2.tex
-
-# CHUNK 1
-library(igraph)
+# SAND with R, chapter2.tex
+
+# CHUNK 1
+library(igraph)
 g <- graph.formula(1-2, 1-3, 2-3, 2-4, 3-5, 4-5, 4-6,
-                    4-7, 5-6, 6-7)
-
-# CHUNK 2
-V(g)
-# ---
+                    4-7, 5-6, 6-7)
+
+# CHUNK 2
+V(g)
+# ---
 ## Vertex sequence:
-## [1] "1" "2" "3" "4" "5" "6" "7"
-# ---
-
-# CHUNK 3
-E(g)
-# ---
+## [1] "1" "2" "3" "4" "5" "6" "7"
+# ---
+
+# CHUNK 3
+E(g)
+# ---
 ## Edge sequence:
 ##            
-## [1]  2 -- 1
-## [2]  3 -- 1
-## [3]  3 -- 2
-## [4]  4 -- 2
-## [5]  5 -- 3
-## [6]  5 -- 4
-## [7]  6 -- 4
-## [8]  7 -- 4
-## [9]  6 -- 5
-## [10] 7 -- 6
-# ---
-
-# CHUNK 4
-str(g)
-# ---
+## [1]  1 -- 2
+## [2]  1 -- 3
+## [3]  2 -- 3
+## [4]  2 -- 4
+## [5]  3 -- 5
+## [6]  4 -- 5
+## [7]  4 -- 6
+## [8]  4 -- 7
+## [9]  5 -- 6
+## [10] 6 -- 7
+# ---
+
+# CHUNK 4
+str(g)
+# ---
 ## IGRAPH UN-- 7 10 -- 
 ## + attr: name (v/c)
 ## + edges (vertex names):
@@ -41,43 +41,43 @@ str(g)
 ## 4 -- 2, 5, 6, 7
 ## 5 -- 3, 4, 6
 ## 6 -- 4, 5, 7
-## 7 -- 4, 6
-# ---
-
-# CHUNK 5
-plot(g)
-
-# CHUNK 6
-dg <- graph.formula(1-+2, 1-+3, 2++3)
-plot(dg)
-
-# CHUNK 7
-dg <- graph.formula(Sam-+Mary, Sam-+Tom, Mary++Tom)
-str(dg)
-# ---
+## 7 -- 4, 6
+# ---
+
+# CHUNK 5
+plot(g)
+
+# CHUNK 6
+dg <- graph.formula(1-+2, 1-+3, 2++3)
+plot(dg)
+
+# CHUNK 7
+dg <- graph.formula(Sam-+Mary, Sam-+Tom, Mary++Tom)
+str(dg)
+# ---
 ## IGRAPH DN-- 3 4 -- 
 ## + attr: name (v/c)
 ## + edges (vertex names):
-## [1] Sam ->Mary Sam ->Tom  Mary->Tom  Tom ->Mary
-# ---
-
-# CHUNK 8
-V(dg)$name <- c("Sam", "Mary", "Tom")
-
-# CHUNK 9
-E(dg)
-# ---
+## [1] Sam ->Mary Sam ->Tom  Mary->Tom  Tom ->Mary
+# ---
+
+# CHUNK 8
+V(dg)$name <- c("Sam", "Mary", "Tom")
+
+# CHUNK 9
+E(dg)
+# ---
 ## Edge sequence:
 ##                 
 ## [1] Sam  -> Mary
 ## [2] Sam  -> Tom 
 ## [3] Mary -> Tom 
-## [4] Tom  -> Mary
-# ---
-
-# CHUNK 10
-get.adjacency(g)
-# ---
+## [4] Tom  -> Mary
+# ---
+
+# CHUNK 10
+get.adjacency(g)
+# ---
 ## 7 x 7 sparse Matrix of class "dgCMatrix"
 ##   1 2 3 4 5 6 7
 ## 1 . 1 1 . . . .
@@ -86,95 +86,95 @@ get.adjacency(g)
 ## 4 . 1 . . 1 1 1
 ## 5 . . 1 1 . 1 .
 ## 6 . . . 1 1 . 1
-## 7 . . . 1 . 1 .
-# ---
-
-# CHUNK 11
-h <- induced.subgraph(g, 1:5)
-str(h)
-# ---
+## 7 . . . 1 . 1 .
+# ---
+
+# CHUNK 11
+h <- induced.subgraph(g, 1:5)
+str(h)
+# ---
 ## IGRAPH UN-- 5 6 -- 
 ## + attr: name (v/c)
 ## + edges (vertex names):
-## [1] 1--2 1--3 2--3 2--4 3--5 4--5
-# ---
-
-# CHUNK 12
-h <- g - vertices(c(6,7))
-
-# CHUNK 13
-h <- h + vertices(c(6,7))
-g <- h + edges(c(4,6),c(4,7),c(5,6),c(6,7))
-
-# CHUNK 14
-h1 <- h
-h2 <- graph.formula(4-6, 4-7, 5-6, 6-7)
-g <- graph.union(h1,h2)
-
-# CHUNK 15
-V(dg)$name
-# ---
-## [1] "Sam"  "Mary" "Tom"
-# ---
-
-# CHUNK 16
-V(dg)$gender <- c("M","F","M")
-
-# CHUNK 17
-V(g)$color <- "red"
-
-# CHUNK 18
-is.weighted(g)
-# ---
-## [1] FALSE
-# ---
-wg <- g
-E(wg)$weight <- runif(ecount(wg))
-is.weighted(wg)
-# ---
-## [1] TRUE
-# ---
-
-# CHUNK 19
-g$name <- "Toy Graph"
-
-# CHUNK 20
-library(sand)
+## [1] 1--2 1--3 2--3 2--4 3--5 4--5
+# ---
+
+# CHUNK 12
+h <- g - vertices(c(6,7))
+
+# CHUNK 13
+h <- h + vertices(c(6,7))
+g <- h + edges(c(4,6),c(4,7),c(5,6),c(6,7))
+
+# CHUNK 14
+h1 <- h
+h2 <- graph.formula(4-6, 4-7, 5-6, 6-7)
+g <- graph.union(h1,h2)
+
+# CHUNK 15
+V(dg)$name
+# ---
+## [1] "Sam"  "Mary" "Tom"
+# ---
+
+# CHUNK 16
+V(dg)$gender <- c("M","F","M")
+
+# CHUNK 17
+V(g)$color <- "red"
+
+# CHUNK 18
+is.weighted(g)
+# ---
+## [1] FALSE
+# ---
+wg <- g
+E(wg)$weight <- runif(ecount(wg))
+is.weighted(wg)
+# ---
+## [1] TRUE
+# ---
+
+# CHUNK 19
+g$name <- "Toy Graph"
+
+# CHUNK 20
+library(sand)
 g.lazega <- graph.data.frame(elist.lazega, 
                               directed="FALSE", 
-                              vertices=v.attr.lazega)
-g.lazega$name <- "Lazega Lawyers"
-
-# CHUNK 21
-vcount(g.lazega)
-# ---
-## [1] 36
-# ---
-
-# CHUNK 22
-ecount(g.lazega)
-# ---
-## [1] 115
-# ---
-
-# CHUNK 23
-list.vertex.attributes(g.lazega)
-# ---
+                              vertices=v.attr.lazega)
+g.lazega$name <- "Lazega Lawyers"
+
+# CHUNK 21
+vcount(g.lazega)
+# ---
+## [1] 36
+# ---
+
+# CHUNK 22
+ecount(g.lazega)
+# ---
+## [1] 115
+# ---
+
+# CHUNK 23
+list.vertex.attributes(g.lazega)
+# ---
 ## [1] "name"      "Seniority" "Status"    "Gender"   
 ## [5] "Office"    "Years"     "Age"       "Practice" 
-## [9] "School"
-# ---
-
-# CHUNK 24
-is.simple(g)
-# ---
-## [1] TRUE
-# ---
-
-# CHUNK 25
-mg <- g + edge(2,3)
-str(mg)
-# ---
+## [9] "School"
+# ---
+
+# CHUNK 24
+is.simple(g)
+# ---
+## [1] TRUE
+# ---
+
+# CHUNK 25
+mg <- g + edge(2,3)
+str(mg)
+# ---
 ## IGRAPH UN-- 7 11 -- Toy Graph
 ## + attr: name (g/c), name (v/c), color (v/c)
 ## + edges (vertex names):
@@ -184,24 +184,24 @@ str(mg)
 ## 4 -- 2, 5, 6, 7
 ## 5 -- 3, 4, 6
 ## 6 -- 4, 5, 7
-## 7 -- 4, 6
-# ---
-is.simple(mg)
-# ---
-## [1] FALSE
-# ---
-
-# CHUNK 26
-E(mg)$weight <- 1
-wg2 <- simplify(mg)
-is.simple(wg2)
-# ---
-## [1] TRUE
-# ---
-
-# CHUNK 27
-str(wg2)
-# ---
+## 7 -- 4, 6
+# ---
+is.simple(mg)
+# ---
+## [1] FALSE
+# ---
+
+# CHUNK 26
+E(mg)$weight <- 1
+wg2 <- simplify(mg)
+is.simple(wg2)
+# ---
+## [1] TRUE
+# ---
+
+# CHUNK 27
+str(wg2)
+# ---
 ## IGRAPH UNW- 7 10 -- Toy Graph
 ## + attr: name (g/c), name (v/c), color (v/c),
 ##   weight (e/n)
@@ -212,49 +212,49 @@ str(wg2)
 ## 4 -- 2, 5, 6, 7
 ## 5 -- 3, 4, 6
 ## 6 -- 4, 5, 7
-## 7 -- 4, 6
-# ---
-
-# CHUNK 28
-E(wg2)$weight
-# ---
-##  [1] 1 1 2 1 1 1 1 1 1 1
-# ---
-
-# CHUNK 29
-neighbors(g,5)
-# ---
-## [1] 3 4 6
-# ---
-
-# CHUNK 30
-degree(g)
-# ---
+## 7 -- 4, 6
+# ---
+
+# CHUNK 28
+E(wg2)$weight
+# ---
+##  [1] 1 1 2 1 1 1 1 1 1 1
+# ---
+
+# CHUNK 29
+neighbors(g,5)
+# ---
+## [1] 3 4 6
+# ---
+
+# CHUNK 30
+degree(g)
+# ---
 ## 1 2 3 4 5 6 7 
-## 2 3 3 4 3 3 2
-# ---
-
-# CHUNK 31
-degree(dg, mode="in")
-# ---
+## 2 3 3 4 3 3 2
+# ---
+
+# CHUNK 31
+degree(dg, mode="in")
+# ---
 ##  Sam Mary  Tom 
-##    0    2    2
-# ---
-degree(dg, mode="out")
-# ---
+##    0    2    2
+# ---
+degree(dg, mode="out")
+# ---
 ##  Sam Mary  Tom 
-##    2    1    1
-# ---
-
-# CHUNK 32
-is.connected(g)
-# ---
-## [1] TRUE
-# ---
-
-# CHUNK 33
-clusters(g)
-# ---
+##    2    1    1
+# ---
+
+# CHUNK 32
+is.connected(g)
+# ---
+## [1] TRUE
+# ---
+
+# CHUNK 33
+clusters(g)
+# ---
 ## $membership
 ## [1] 1 1 1 1 1 1 1
 ## 
@@ -262,49 +262,49 @@ clusters(g)
 ## [1] 7
 ## 
 ## $no
-## [1] 1
-# ---
-
-# CHUNK 34
-is.connected(dg, mode="weak")
-# ---
-## [1] TRUE
-# ---
-is.connected(dg, mode="strong")
-# ---
-## [1] FALSE
-# ---
-
-# CHUNK 35
-diameter(g, weights=NA)
-# ---
-## [1] 3
-# ---
-
-# CHUNK 36
-g.full <- graph.full(7)
-g.ring <- graph.ring(7)
-g.tree <- graph.tree(7, children=2, mode="undirected")
-g.star <- graph.star(7, mode="undirected")
-par(mfrow=c(2, 2))
-plot(g.full)
-plot(g.ring)
-plot(g.tree)
-plot(g.star)
-
-# CHUNK 37
-is.dag(dg)
-# ---
-## [1] FALSE
-# ---
-
-# CHUNK 38
+## [1] 1
+# ---
+
+# CHUNK 34
+is.connected(dg, mode="weak")
+# ---
+## [1] TRUE
+# ---
+is.connected(dg, mode="strong")
+# ---
+## [1] FALSE
+# ---
+
+# CHUNK 35
+diameter(g, weights=NA)
+# ---
+## [1] 3
+# ---
+
+# CHUNK 36
+g.full <- graph.full(7)
+g.ring <- graph.ring(7)
+g.tree <- graph.tree(7, children=2, mode="undirected")
+g.star <- graph.star(7, mode="undirected")
+par(mfrow=c(2, 2))
+plot(g.full)
+plot(g.ring)
+plot(g.tree)
+plot(g.star)
+
+# CHUNK 37
+is.dag(dg)
+# ---
+## [1] FALSE
+# ---
+
+# CHUNK 38
 g.bip <- graph.formula(actor1:actor2:actor3,
    movie1:movie2, actor1:actor2 - movie1,
-   actor2:actor3 - movie2)
-V(g.bip)$type <- grepl("^movie", V(g.bip)$name)
-str(g.bip, v=T)
-# ---
+   actor2:actor3 - movie2)
+V(g.bip)$type <- grepl("^movie", V(g.bip)$name)
+str(g.bip, v=T)
+# ---
 ## IGRAPH UN-B 5 4 -- 
 ## + attr: name (v/c), type (v/l)
 ## + vertex attributes:
@@ -316,23 +316,23 @@ str(g.bip, v=T)
 ## [5] movie2  TRUE
 ## + edges (vertex names):
 ## [1] actor1--movie1 actor2--movie1 actor2--movie2
-## [4] actor3--movie2
-# ---
-
-# CHUNK 39
-proj <- bipartite.projection(g.bip)
-str(proj[[1]])
-# ---
+## [4] actor3--movie2
+# ---
+
+# CHUNK 39
+proj <- bipartite.projection(g.bip)
+str(proj[[1]])
+# ---
 ## IGRAPH UNW- 3 2 -- 
 ## + attr: name (v/c), weight (e/n)
 ## + edges (vertex names):
-## [1] actor1--actor2 actor2--actor3
-# ---
-str(proj[[2]])
-# ---
+## [1] actor1--actor2 actor2--actor3
+# ---
+str(proj[[2]])
+# ---
 ## IGRAPH UNW- 2 1 -- 
 ## + attr: name (v/c), weight (e/n)
 ## + edges (vertex names):
-## [1] movie1--movie2
-# ---
-
+## [1] movie1--movie2
+# ---
+