README.md

In FrankBaut/RandomClustering: Random clusters generation on a lattice

RandomClustering

Generate a binary (0,1) lattice of size with parameter p, p indicates how many ones will be placed randomly with respect to the total lattice cells, this will gerate clusters of diferent sizes in the lattice.

We follow the next steps:

• Create a binary lattice of size with a probability of filling .

• Label the clusters that are generated in the lattice.

• Choose the biggets cluster formed in the lattice and randomly remove a cell.

• Choose the smallest clusters and add randomly a cell with the same label of the selected cluster in one of his neighbors.

• If there are several smallest clusters with the same size, we choose one of them randomly and we repeat the previous step.

Installation

# The development version from GitHub:
# install.packages("devtools")
devtools::install_github("FrankBaut/RandomClustering")

# install.packages("tidyverse")
# install.packages("magrittr")

Examples

# Basic workflow:
library("tidyverse")
library("magrittr")
library("RandomClustering")

Label_clusters <- clusters_matrix(n=100, p = 0.5) %>%
  big_cl() %>% small_cl()

Maybe we would like observe the new clusters configuration after one iteration and re-label this configuration. Basically we must do:

Label_clusters <- clusters_matrix(n=100,p=0.5)
proceso(Label_clusters)

Or with pipe operator %>%:

Label_clusters <- clusters_matrix(n=10,p=0.5) %>% proceso()

Simulation

In the given case if you want to make a simulation and observe the biggets cluster in different p values, you can do this:

n<-100
iterations<-50 
prob_vec<-seq(.01,.9,.01)
biggets_cluster<-matrix(,nrow = length(prob_vec),ncol = iterations)
for (i in 1:length(prob_vec)) {
  data<-clusters_matrix(n,prob_vec[i])
  for (j in 1:iterations) {
    data<-proceso(data)
    caso<-data %>% as.vector()%>% na.omit() %>% plyr::count()
    biggets_cluster[i,j]<-max(caso$freq,na.rm = T)/sum(caso$freq,na.rm = T)
  }
}

However this is really slow, therefore we must do a parallel process. Two libraries very useful are foreach and doParallel.

# install.packages("foreach")
# install.packages("doParallel")

library(foreach)
library(doParallel)
library(RandomClustering)
iterations<-50
n<-100
prob_vec<-seq(.01,.9,.01)
#------------Progress bar------------------
l<-length(prob_vec)
pb <- txtProgressBar(0,l, style = 3)
#------------------------------------------
registerDoParallel(detectCores()-2)
biggets_cluster<-unlist(complete_processPar(n, prob_vec,iterations,l,pb))
stopImplicitCluster()
df<-data.frame(prob_vec,biggets_cluster)
plot(df,xlab="p",ylab="Biggest Cluster")

We can choose how many cores we want to use in registerDoParallel argument. we recommend using at most detectCores()-1 cores. Remenber stop the parallel process with stopImplicitCluster() when you finish your calculations.

If we want see how many clusters there are after several iterations we must do:

library(foreach)
library(doParallel)
library(RandomClustering)
iterations<-50
n<-100
prob_vec<-seq(.01,.9,.01)
#------------Progress bar------------------
l<-length(prob_vec)
pb <- txtProgressBar(0,l, style = 3)
#------------------------------------------
registerDoParallel(detectCores()-2)
biggets_cluster<-unlist(complete_clusterNumberPar(n, prob_vec,iterations,l,pb))
stopImplicitCluster()
df<-data.frame(prob_vec,biggets_cluster)
plot(df,xlab="p",ylab="Clusters number")

Please cite this work with:

citation("RandomClustering")

or in bibtex format

toBibtex(citation("RandomClustering"))

FrankBaut/RandomClustering documentation built on Feb. 19, 2020, 2:07 a.m.