Nothing
## ----eval=FALSE---------------------------------------------------------------
# install.packages("spreadr")
## ----eval=FALSE---------------------------------------------------------------
# install.packages("remotes")
# remotes::install_github("csqsiew/spreadr")
## ----message=FALSE------------------------------------------------------------
library(spreadr)
library(igraph)
data("pnet") # load and inspect the igraph object
## ----eval=FALSE---------------------------------------------------------------
# plot(pnet)
## ----echo=FALSE---------------------------------------------------------------
set.seed(1)
layout <- layout_with_lgl(pnet)
plot(pnet, layout=layout)
## ----message=FALSE------------------------------------------------------------
library(spreadr)
library(igraph)
set.seed(1)
data("pnetm")
pnetm[1:5, 1:5] # inspect the first few entries
## ----eval=FALSE---------------------------------------------------------------
# plot(graph_from_adjacency_matrix(
# pnetm, mode="undirected")) # visualise the graph
## ----echo=FALSE---------------------------------------------------------------
plot(graph_from_adjacency_matrix(
pnetm, mode="undirected"),
layout=layout)
## -----------------------------------------------------------------------------
start_run <- data.frame(
node= c("beach", "speck"),
activation=c( 20, 10))
## -----------------------------------------------------------------------------
start_run <- data.frame(
node = c("beach", "speck"),
activation = c( 20, 10),
time = c( 0, 5))
## ----echo=FALSE---------------------------------------------------------------
start_run <- data.frame(
node = c("beach", "speck"),
activation = c( 20, 10))
## -----------------------------------------------------------------------------
result <- spreadr(pnet, start_run, include_t0=TRUE)
## ----eval=TRUE----------------------------------------------------------------
head(result) # inspect the first few rows
tail(result) # inspect the last few rows
## ----eval=FALSE---------------------------------------------------------------
# write.csv(result, file="result.csv") # save result as CSV file
## -----------------------------------------------------------------------------
library(ggplot2)
ggplot(result, aes(x=time, y=activation, color=node)) +
geom_point() +
geom_line()
## -----------------------------------------------------------------------------
weighted_network <- matrix(
c(0, 1, 9,
1, 0, 0,
9, 0, 0), nrow=3, byrow=TRUE)
colnames(weighted_network) <- c("a", "b", "c")
rownames(weighted_network) <- c("a", "b", "c")
# To visualise the network only --- this is not necessary for spreadr
weighted_igraph <- graph_from_adjacency_matrix(
weighted_network, mode="undirected", weighted=TRUE)
plot(weighted_igraph, edge.width=E(weighted_igraph)$weight)
## -----------------------------------------------------------------------------
spreadr(
weighted_network, data.frame(node="a", activation=10),
time=1, retention=0, include_t0=TRUE)
## -----------------------------------------------------------------------------
directed_network <- matrix(
c(0, 1, 0,
0, 0, 1,
0, 0, 0), nrow=3, byrow=TRUE)
colnames(directed_network) <- c("a", "b", "c")
rownames(directed_network) <- c("a", "b", "c")
# To visualise the network only --- this is not necessary for spreadr
directed_igraph <- graph_from_adjacency_matrix(
directed_network, mode="directed")
plot(directed_igraph, edge.width=E(directed_igraph)$weight)
## -----------------------------------------------------------------------------
spreadr(
directed_network, data.frame(node="b", activation=10),
time=1, retention=0, include_t0=TRUE)
## -----------------------------------------------------------------------------
params <- data.frame(
retention=c(0, 0.5, 0, 0.5),
decay= c(0, 0, 0.5, 0.5))
## -----------------------------------------------------------------------------
network <- matrix(
c(0, 1,
0, 0), nrow=2, byrow=TRUE)
start_run <- data.frame(node=1, activation=10)
## -----------------------------------------------------------------------------
apply(params, 1, function(row)
spreadr(
network, start_run,
time=2, include_t0=TRUE,
retention=row[1], decay=row[2]))
## -----------------------------------------------------------------------------
sessionInfo()
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