crashR.R 4.59 KB
Newer Older
1

2
pause <- function() {}
3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184

### R objects, (real) numbers
a <- 3
a
b <- 4
b
a+b

pause()

### Case sensitive
A <- 16
a
A

pause()

### Vector objects
a <- c(1,2,3,4,5,6,7,8,9,10)
a
b <- 1:100
b
a[1]
b[1:5]
a[1] <- 10
a
a[1:4] <- 2
a

pause()

### Vector arithmetic
a * 2 + 1

pause()

### Functions
ls()
length(a)
mean(a)
sd(a)
sd
c

pause()

### Getting help
# ?sd
# ??"standard deviation"
# RSiteSearch("network betweenness")

pause()

### Classes
class(2)
class(1:10)
class(sd)

pause()

### Character vectors
char.vec <- c("this", "is", "a", "vector", "of", "characters")
char_vec <- char.vec
char.vec[1]

pause()

### Index vectors
age <- c(45, 36, 65, 21, 52, 19)
age[1]
age[1:5]
age[c(2,5,6)]

b[ seq(1,100,by=2) ]

pause()

### Named vectors
names(age) <- c("Alice", "Bob", "Cecil", "David", "Eve", "Fiona")
age
age["Bob"]
age[c("Eve", "David", "David")]

pause()

### Indexing with logical vectors
age[c(FALSE, TRUE, FALSE, TRUE, FALSE, TRUE)]
names(age)[ age>40 ]
age > 40

pause()

### Matrices
M <- matrix(1:20, 10, 2)
M
M2 <- matrix(1:20, 10, 2, byrow=TRUE)   ## Named argument!
M2
M[1,1]
M[1,]
M[,1]
M[1:5,2]

pause()

### Generic functions
sd(a)
sd(M)
class(a)
class(M)

pause()

### Lists
l <- list(1:10, "Hello!", diag(5))
l
l[[1]]
l[2:3]
l
l2 <- list(A=1:10, H="Hello!", M=diag(5))
l2
l2$A
l2$M

pause()

### Factors
countries <- c("SUI", "USA", "GBR", "GER", "SUI",
               "SUI", "GBR", "GER", "FRA", "GER")
countries
fcountries <- factor(countries)
fcountries
levels(fcountries)

pause()

### Data frames
survey <- data.frame(row.names=c("Alice", "Bob", "Cecil", "David", "Eve"),
                     Sex=c("F","M","F","F","F"),
                     Age=c(45,36,65,21,52),
                     Country=c("SUI", "USA", "SUI", "GBR", "USA"),
                     Married=c(TRUE, FALSE, FALSE, TRUE, TRUE),
                     Salary=c(70, 65, 200, 45, 100))
survey
survey$Sex
plot(survey$Age, survey$Salary)
AS.model <- lm(Salary ~ Age, data=survey)
AS.model
summary(AS.model)
abline(AS.model)

tapply(survey$Salary, survey$Country, mean)

pause()

### Packages
# install.packages("igraph")
# library(help="igraph")
library(igraph)
sessionInfo()

pause()

### Graphs
## Create a small graph, A->B, A->C, B->C, C->E, D
## A=1, B=2, C=3, D=4, E=5
g <- graph( c(1,2, 1,3, 2,3, 3,5), n=5 )

pause()

### Print a graph to the screen
g

pause()

### Create an undirected graph as well
## A--B, A--C, B--C, C--E, D
g2 <- graph( c(1,2, 1,3, 2,3, 3,5), n=5, dir=FALSE )
g2

pause()

### Is this object an igraph graph?
185 186
is_igraph(g)
is_igraph(1:10)
187 188 189 190 191 192 193 194 195 196 197

pause()

### Summary, number of vertices, edges
summary(g)
vcount(g)
ecount(g)

pause()

### Is the graph directed?
198 199
is_directed(g)
is_directed(g2)
200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216

pause()

### Convert from directed to undirected
as.undirected(g)

pause()

### And back
as.directed(as.undirected(g))

pause()

### Multiple edges
g <- graph( c(1,2,1,2, 1,3, 2,3, 4,5), n=5 )
g

217 218
is_simple(g)
which_multiple(g)
219 220 221 222 223

pause()

### Remove multiple edges
g <- simplify(g)
224
is_simple(g)
225 226 227 228 229 230 231

pause()

### Loop edges
g <- graph( c(1,1,1,2, 1,3, 2,3, 4,5), n=5 )
g

232 233
is_simple(g)
which_loop(g)
234 235 236 237 238

pause()

### Remove loop edges
g <- simplify(g)
239
is_simple(g)
240 241 242 243

pause()

### Naming vertices
244
g <- make_ring(10)
245 246 247 248 249 250 251 252
V(g)$name <- letters[1:10]
V(g)$name
g
print(g, v=T)

pause()

### Create undirected example graph
253 254
g2 <- graph_from_literal(Alice-Bob:Cecil:Daniel, 
                Cecil:Daniel-Eugene:Gordon )
255 256 257 258 259
print(g2, v=T)

pause()

### Remove Alice
260
g3 <- delete_vertices(g2, match("Alice", V(g2)$name))
261 262 263 264

pause()

### Add three new vertices
265
g4 <- add_vertices(g3, 3)
266
print(g4, v=T)
267 268
igraph_options(print.vertex.attributes=TRUE, 
               plot.layout=layout_with_fr)
269 270 271 272 273 274
g4
plot(g4)                      

pause()

### Add three new vertices, with names this time
275
g4 <- add_vertices(g3, 3, attr=list(name=c("Helen", "Ike", "Jane")))
276 277 278 279 280
g4

pause()

### Add some edges as well
281
g4 <- add_edges(g4, match(c("Helen", "Jane", "Ike", "Jane"), V(g4)$name ))
282 283 284 285 286
g4

pause()

### Edge sequences, first create a directed example graph
287 288
g2 <- graph_from_literal(Alice -+ Bob:Cecil:Daniel, 
                Cecil:Daniel +-+ Eugene:Gordon )
289
print(g2, v=T)
290
plot(g2, layout=layout_with_kk, vertex.label=V(g2)$name)
291 292 293 294 295 296 297 298 299 300 301 302 303 304

pause()

### Sequence of all edges
E(g2)

pause()

### Edge from a vertex to another
E(g2, P=c(1,2))

pause()

### Delete this edge
305
g3 <- delete_edges(g2, E(g2, P=c(1,2)))
306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337
g3

pause()

### Get the id of the edge
as.vector(E(g2, P=c(1,2)))

pause()

### All adjacent edges of a vertex
E(g2)[ adj(3) ]

pause()

### Or multiple vertices
E(g2)[ adj(c(3,1)) ]

pause()

### Outgoing edges
E(g2)[ from(3) ]

pause()

### Incoming edges
E(g2)[ to(3) ]

pause()

### Edges along a path
E(g2, path=c(1,4,5))