# And Writing Documentations In R

I wrote this function months ago, while writing the report for my seminar and I wanted to my make a post about this Bookmark-Coloring Algorithm ever since, but I never found the right chance. As I yesterday in the evening wrote some documentation for the Raspository, I thought it would be nice to make a post about this specific topic. Therefor I thought that using the Bookmark-Coloring Algorithm as an example would be nice.

## The Bookmark-Coloring Algorithm

This specific algorithm’s use is to generate a personal pagerank. In more detail this algorithm calculates given a starting website the chance to end up at other websites. But this idea is applicable to other fields as well. In my post about network-based integration through heat diffusion I showed you a similar method applied to a network of multi-omic data. On the same data-set you could use the Bookmark-Coloring Algorithm.
The basic idea behind the Bookmark-Coloring Algorithm is that you have some color that diffuses through a network, which is in my opinion equivalent to heat diffusing in a network. Correct me, if I’m wrong.

I implemented the algorithm following the paper about it by Pavel Berkhin. More precisely I implemented the Algorithm 2 from the paper. So let me show my implementation:

require(igraph)
require(dequer)

BCA<- function(graph, v, retentionCoefficient = 0.4, tol = 0.001){
# initialise vector of transition chances
p<-c()
p[V(graph)] <- 0

q <- queue()
pushback(q, v)

# initialise vector that indicates how much color is in one node
colorInVertex <- c()
colorInVertex[v] <- 1

# execute as long queque q has elements
while(length(q) > 0){
i <- pop(q)
w <- colorInVertex[i]
# use up the color in node
colorInVertex[i] <- NA

p[i] <- p[i] + retentionCoefficient * w

# if all color is used up continuew to next element in queque
if(w < tol){

next
}

# execute for all neighbors
for(j in neighbors(graph, i, mode = "out")){
if(!is.na(colorInVertex[j])){
colorInVertex[j] <- colorInVertex[j] +
((1 - retentionCoefficient) * w/degree(graph, i, mode = "out"))
}else{
# initialise color in neighbor
pushback(q, j)
colorInVertex[j] <- (1 - retentionCoefficient) * w/degree(graph, i, mode = "out")
}
}

}

return(p)
}


I wrote some comments, that hopefully help you to understand, what’s going on. That’s also the first part of documentation. It’s the step you’ll probably do, while writing your code and in my opinion it’s always useful.

So are we done with the documentation? No. Not, if we want to this function into a package.

## roxygen2 documentation

roxygen2 is a nice package allowing you to write in-line documentation in R. I won’t go to much into detail about it here as there are lot of online sources for it1, but I will show you a short example, how to do it!

Now let me show, how to write a documentation for the BCA function, I will go over all the specified tags.

#' Bookmark Coloring Algorithm
#'
#' @aliases BookmarkColoringAlgorithm
#'
#' @description This function calculates a teleportation vector from a given
#' starting node to other nodes in a given network.
#'
#' @export BCA
#' @import dequer
#' @import igraph
#'
#' @param graph an object of type \code{\link[igraph]{igraph}}.
#' @param v a starting vertex from the above graph. Can be either its identifier
#' or a igraph.vs object.
#' @param retentionCoefficient the restart probability for each node.
#' @param tol a tolerance treshold, indicating what the smalltest value of color
#' is, that should propagate further
#'
#' @return a preference/teleportation vector
#'
#' @references \insertRef{Berkhin2006}{Raspository}
#'
#' @examples
#' library(igraph)
#' g <- make_ring(5)
#' preferenceVector <- BCA(g, 1)
BCA <- function(graph, v, retentionCoefficient = 0.4, tol = 0.001){


OK, let’s go over some of the tags…
In the first line of course you have the title of the function. Additional to the description, you can also add a details tag, where description should give a short overview over the method, you could include theoretical background in the details.
Then needed packages are imported. roxygen2 will convert them into lines in your NAMESPACE file.

With params and return you should shortly describe their types and what they should contain.

For the following use of the references tag, you also need to import the Rdpack package and include a “REFERENCES.bib” in the inst folder with the regarding BibTeX entries. In my opinion you should always use this, when implementing some method from some source… Be it a book or a paper. Rdpack imports those references automatically from your BibTeX file into the documentation files.

Last, but not least I included a runnable example. This is important to give your user a starting point on how to use your function, but furthermore it is a test for the function. Each time your package is built, example code is run. So you will be notified, if there are any errors.
But we will go more into automated testing another time. Because there is of course more you can do. But you should always write example code, if your function is visible to the user.

After writing this documentation in your file, you have to compile it by writing:

roxygen2::roxygenise()