add packages

DESCRIPTION

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+Package: networkdiffusion
+Type: Package
+Title: Simulating and visualizing network diffusion using R
+Version: 0.1
+Date: 2015-04-22
+Authors: Cheng-Jun Wang
+Maintainer: Cheng-Jun Wang <[email protected]>
+Description: To Simulate and visualize network diffusion using R.
+Depends: R (>= 3.1.0), igraph
+License: MIT
+LazyData: TRUE
+Imports: 
+    igraph,
+    Rcpp
+suggests: 
+    animation, testthat
+Suggests: knitr,
+    testthat
+VignetteBuilder: knitr
+LinkingTo: Rcpp

NAMESPACE

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+exportPattern("^[[:alpha:]]+")

R/diffusion.R

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+# learn more about package authoring with RStudio at: http://r-pkgs.had.co.nz/ Some useful keyboard
+# shortcuts for package authoring:
+# generate R documentation using roxygen2: 'Cmd + Shift + D' (or running devtools::document())
+# Build and Reload Package: 'Cmd + Shift + B'
+# Check Package: 'Cmd + Shift + E'
+# Test Package: 'Cmd + Shift + T'
+
+
+####################
+# network diffusion
+####################
+require(igraph)
+
+
+#' Get the infected nodes
+#'
+#' @param g A network object generated using igraph.
+#' @param transmission_rate A number.
+#' @param seed_num The number of seeds.
+#' @param random_seed A number for the function set.seed().
+#' @return a list of infected nodes (over time).
+#' @examples
+#' get_infected(barabasi.game(100), 0.4, 1, 2004)
+#' get_infected(erdos.renyi.game(100, 0.1), 0.4, 1, 2004)
+
+get_infected = function(g, transmission_rate, seed_num, random_seed){
+  toss = function(freq) {
+    tossing = NULL
+    coins = c(1, 0)
+    probabilities = c(transmission_rate, 1-transmission_rate )
+    for (i in 1:freq ) tossing[i] = sample(coins, 1, rep=TRUE, prob=probabilities)
+    tossing = sum(tossing)
+    return (tossing)
+  }
+
+  update_diffusers = function(diffusers){
+    nearest_neighbors = data.frame(table(unlist(neighborhood(g, 1, diffusers))))
+    nearest_neighbors = subset(nearest_neighbors, !(nearest_neighbors[,1]%in%diffusers))
+    keep = unlist(lapply(nearest_neighbors[,2],toss))
+    new_infected = as.numeric(as.character(nearest_neighbors[,1][keep >= 1]))
+    diffusers = unique(c(diffusers, new_infected))
+    return(diffusers)
+  }
+
+  set.seed(random_seed); diffusers = sample(V(g),seed_num)
+  # initialize the infected
+  infected =list()
+  infected[[1]]= diffusers
+  # set the color
+  E(g)$color = "grey"
+  V(g)$color = "white"
+  V(g)$color[V(g)%in%diffusers] = "red"
+  # get infected nodes
+  total_time = 1
+  while(length(infected[[total_time]]) < vcount(g)){
+    infected[[total_time+1]] = sort(update_diffusers(infected[[total_time]]))
+    total_time = total_time + 1
+    }
+  # return the infected nodes list
+  return(infected)
+}
+
+
+#' plot the time series of network diffusion
+#'
+#' @param infected A list of infected nodes (over time)
+#' @return plots of two time series.
+#' @examples
+#' plot_time_series(infected)
+#' plot_time_series(infected[1:5])
+
+plot_time_series = function(infected){
+  num_cum = unlist(lapply(1:length(infected),
+                          function(x) length(infected[[x]]) ))
+  p_cum = num_cum/node_number
+  p = diff(c(0, p_cum))
+  time = 1:length(infected)
+  plot(p_cum~time, type = "b",
+       ylab = "CDF", xlab = "Time",
+       xlim = c(0,length(infected)), ylim =c(0,1))
+  plot(p~time, type = "h", frame.plot = FALSE,
+       ylab = "PDF", xlab = "Time",
+       xlim = c(0,length(infected)), ylim =c(0,1))
+}
+
+
+#' plot the diffusion network diffusion (over time)
+#'
+#' @param infected A list of infected nodes (over time)
+#' @return several plots of diffusion networks.
+#' @examples
+#' plot_gif(infected)
+#' plot_gif(infected[1])
+
+plot_gif = function(infected){
+  m = 1
+  while(m <= length(infected)){
+    V(g)$color = "white"
+    V(g)$color[V(g)%in%infected[[m]]] = "red"
+    plot(g, layout =layout.old, edge.arrow.size=0.2)
+    title(paste( "Time", m))
+    m = m + 1}
+}
+
+# run demos
+

demo/networkdiffusion.R

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+# generate a social graph
+require(igraph)
+require(animation)
+
+node_number = 100
+g = barabasi.game(node_number)
+# set up the layout
+set.seed(2014); layout.old = layout.fruchterman.reingold(g, niter = 1000)
+# get the infected
+infected = get_infected(g, 0.4, 1, 2004)
+plot_gif(infected[[2]])
+plot_time_series(infected)
+
+saveGIF({
+  ani.options("convert")
+  plot_gif(infected)
+  }, interval = 0.3, movie.name = "ba.gif", ani.width = 600, ani.height = 600)

man/get_infected.Rd

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+% Generated by roxygen2 (4.1.1): do not edit by hand
+% Please edit documentation in R/diffusion.R
+\name{get_infected}
+\alias{get_infected}
+\title{Get the infected nodes}
+\usage{
+get_infected(g, transmission_rate, seed_num, random_seed)
+}
+\arguments{
+\item{g}{A network object generated using igraph.}
+
+\item{transmission_rate}{A number.}
+
+\item{seed_num}{The number of seeds.}
+
+\item{random_seed}{A number for the function set.seed().}
+}
+\value{
+a list of infected nodes (over time).
+}
+\description{
+Get the infected nodes
+}
+\examples{
+get_infected(barabasi.game(100), 0.4, 1, 2004)
+get_infected(erdos.renyi.game(100, 0.1), 0.4, 1, 2004)
+}
+

man/plot_gif.Rd

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+% Generated by roxygen2 (4.1.1): do not edit by hand
+% Please edit documentation in R/diffusion.R
+\name{plot_gif}
+\alias{plot_gif}
+\title{plot the diffusion network diffusion (over time)}
+\usage{
+plot_gif(infected)
+}
+\arguments{
+\item{infected}{A list of infected nodes (over time)}
+}
+\value{
+several plots of diffusion networks.
+}
+\description{
+plot the diffusion network diffusion (over time)
+}
+\examples{
+plot_gif(infected)
+plot_gif(infected[1])
+}
+

man/plot_time_series.Rd

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+% Generated by roxygen2 (4.1.1): do not edit by hand
+% Please edit documentation in R/diffusion.R
+\name{plot_time_series}
+\alias{plot_time_series}
+\title{plot the time series of network diffusion}
+\usage{
+plot_time_series(infected)
+}
+\arguments{
+\item{infected}{A list of infected nodes (over time)}
+}
+\value{
+plots of two time series.
+}
+\description{
+plot the time series of network diffusion
+}
+\examples{
+plot_time_series(infected)
+plot_time_series(infected[1:5])
+}
+

networkdiffusion.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
+
+AutoAppendNewline: Yes
+StripTrailingWhitespace: Yes
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source
+PackageRoxygenize: rd,collate,namespace,vignette

src/.gitignore

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+*.o
+*.so
+*.dll

tests/testthat.R

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+library(testthat)
+library(networkdiffusion)
+
+test_check("networkdiffusion")

vignettes/my-vignette.R

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+## ----, fig.show='hold'---------------------------------------------------
+plot(1:10)
+plot(10:1)
+
+## ----, echo=FALSE, results='asis'----------------------------------------
+knitr::kable(head(mtcars, 10))
+

vignettes/my-vignette.Rmd

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+---
+title: "networkdiffusion"
+author: "Cheng-Jun Wang"
+date: "`r Sys.Date()`"
+output: rmarkdown::html_vignette
+vignette: >
+  %\VignetteIndexEntry{Vignette Title}
+  %\VignetteEngine{knitr::rmarkdown}
+  \usepackage[utf8]{inputenc}
+---
+
+Vignettes are long form documentation commonly included in packages. Because they are part of the distribution of the package, they need to be as compact as possible. The `html_vignette` output type provides a custom style sheet (and tweaks some options) to ensure that the resulting html is as small as possible. The `html_vignette` format:
+
+- Never uses retina figures
+- Has a smaller default figure size
+- Uses a custom CSS stylesheet instead of the default Twitter Bootstrap style
+
+## Vignette Info
+
+Note the various macros within the `vignette` setion of the metadata block above. These are required in order to instruct R how to build the vignette. Note that you should change the `title` field and the `\VignetteIndexEntry` to match the title of your vignette.
+
+## Styles
+
+The `html_vignette` template includes a basic CSS theme. To override this theme you can specify your own CSS in the document metadata as follows:
+
+    output: 
+      rmarkdown::html_vignette:
+        css: mystyles.css
+
+## Figures
+
+The figure sizes have been customised so that you can easily put two images side-by-side. 
+
+```{r, fig.show='hold'}
+plot(1:10)
+plot(10:1)
+```
+
+You can enable figure captions by `fig_caption: yes` in YAML:
+
+    output:
+      rmarkdown::html_vignette:
+        fig_caption: yes
+
+Then you can use the chunk option `fig.cap = "Your figure caption."` in **knitr**.
+
+## More Examples
+
+You can write math expressions, e.g. $Y = X\beta + \epsilon$, footnotes^[A footnote here.], and tables, e.g. using `knitr::kable()`.
+
+```{r, echo=FALSE, results='asis'}
+knitr::kable(head(mtcars, 10))
+```
+
+Also a quote using `>`:
+
+> "He who gives up [code] safety for [code] speed deserves neither."
+([via](https://twitter.com/hadleywickham/status/504368538874703872))