version 0.9.2

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: localboot
 Type: Package
 Title: Local Bootstrap Methods for Various Networks
-Version: 0.9.1
-Date: 2023-12-18
+Version: 0.9.2
+Date: 2024-01-08
 Authors@R: c(
     person("Tianhai", "Zu", email = "zuti@mail.uc.edu", role = c("aut", "cre")),
     person("Yichen", "Qin", email = "qinyn@ucmail.uc.edu", role = c("aut","ctb"))
@@ -21,9 +21,9 @@ LinkingTo: Rcpp (>= 1.0.11), RcppEigen
 Encoding: UTF-8
 RoxygenNote: 7.2.3
 NeedsCompilation: yes
-Packaged: 2023-12-21 06:21:26 UTC; tianhaizu
+Packaged: 2024-01-09 23:36:45 UTC; tianhaizu
 Author: Tianhai Zu [aut, cre],
   Yichen Qin [aut, ctb]
 Maintainer: Tianhai Zu <zuti@mail.uc.edu>
 Repository: CRAN
-Date/Publication: 2023-12-21 16:30:02 UTC
+Date/Publication: 2024-01-10 11:33:21 UTC

MD5

@@ -1,17 +1,21 @@
-b3ff1e6fb2563796e33807e5fb5277e1 *DESCRIPTION
+a947509da42eac0e8ca8cad900e25ede *DESCRIPTION
 34b2759e632634bd546f0f996c90462d *NAMESPACE
+c2e388d5404970730871cb513d70b668 *NEWS.md
 2de21dbbe9981853ed8044136e4bfac7 *R/RcppExports.R
-3f12e430a5c85fc62a93fa4a46566c42 *R/generate_network.R
+faec646538a6580729f9787c8a2e238f *R/generate_network.R
 dbfa3d9aadd2c86f34d882814708dc99 *R/localboot-package.R
 2561a8d9d6edf4d3e1031010b9f1a7a0 *R/localboot.R
 a27164ba5703eb3ac36f0d4ff2fb8673 *R/plot_utils.R
-7db4f5555abf5afff49ac74d6b1b7aee *inst/sim/Fit_local_boot.R
+b35837be1bcc3a6f0fcdf6c82b39d056 *README.md
+59af8258a14eb1539b9bef66a61ee019 *inst/rds/email_Eu_core_adj.RDS
+a215b98595c9f13cbf8c97ee1b351cdd *inst/rds/rattus_norvegicus_brain_3_adj.RDS
+2cd7d660e71005f6248b683fab854f8f *inst/sim/Fit_local_boot.R
 3297eecf83620025ab244fc3042be725 *inst/sim/Generate_various_networks.R
-cee90d493ca0b4fef38062105123af52 *inst/sim/Optimal_local_size.R
-4c91a053d9937e9a6d05a82697b114ac *inst/sim/Sim1_estimate_others.R
-ecbd16a807885cfd9f774444c9333efc *inst/sim/Sim1_estimates_local.R
-6c19806713660c3fae228f51e2d72e2c *inst/sim/Sim1_truese.R
-7aeb7398c9f8ef60a0931772f320086d *inst/sim/test_localcpp.R
+5e01e394a9b195b58347a409a1a8afec *inst/sim/Optimal_local_size.R
+54176d96b0c35fdcd3bbaa251c121c02 *inst/sim/Sim1_estimate_others.R
+2640bffdcfbecf49fd8cb732fcaac6b6 *inst/sim/Sim1_estimates_local.R
+f1b36c42327c09ed28aded29e4338aec *inst/sim/Sim1_truese.R
+c66d0b124086ce00b9a3454de557ee50 *inst/sim/sup_funcs_sim.R
 c6bd637748ae88df554ced68e6771e5f *man/generate_graphon.Rd
 d4a8f4bc1d08552a82ce03853a80b001 *man/generate_network_P.Rd
 29713984eab34fbaf668b7aeb31a0947 *man/localboot-package.Rd
@@ -21,4 +25,4 @@ d4a8f4bc1d08552a82ce03853a80b001 *man/generate_network_P.Rd
 b4f0b014ec53404e843dbc718fabf57e *src/Makevars
 b4f0b014ec53404e843dbc718fabf57e *src/Makevars.win
 60ca2ca032d1a414ce63a92635ac1453 *src/RcppExports.cpp
-7fb7f7de7cc0aa9792b3ae46a8f87cde *src/localboot.cpp
+fc267719bb49cff524fa60eca14e7116 *src/localboot.cpp

NEWS.md

@@ -0,0 +1,15 @@
+# localboot 0.9.2 (12/29/2023)
+
+## New Features
+- Added new simulation scenarios.
+- Expanded `generate_graphon()` with more network types.
+- Added simulation scripts in `inst` folder.
+
+## Improvements
+- Updated documentation with examples for new features.
+- Optimized performance and improved error handling.
+
+## Installation
+```R
+install.packages("localboot")
+```

R/generate_network.R

@@ -1,29 +1,29 @@
 # Define the formula to generate p matrix of graphon1
-graphon1 <- function(u, size){
+graphon3 <- function(u, size){
   p_matrix = matrix(0,nrow=size,ncol=size)
   for(i in 1:size){
     for(j in 1:size){
-      p <- cos(pi*(u[i]-u[j]))/(2^3) + 0.5
+      p <- sin(((u[i]^2+u[j]^2)^(1/4))*0.01)/2 +0.5
       p_matrix[i,j] <- p    
     }
   }
   p_matrix
 }
 
 # Define the formula to generate p matrix of graphon2
-graphon2 <- function(u, size){
+graphon6 <- function(u, size){
   p_matrix = matrix(0,nrow=size,ncol=size)
   for(i in 1:size){
     for(j in 1:size){
-      p <- cos(pi*(u[i]-u[j]))/(2^3) + 0.5
+      p <- sin(((u[i]^2+u[j]^2)^(1/4))*10)/2 +0.5
       p_matrix[i,j] <- p    
     }
   }
   p_matrix
 }
 
 # Define the formula to generate p matrix of graphon3
-graphon3 <- function(u, size){
+graphon1 <- function(u, size){
   p_matrix = matrix(0,nrow=size,ncol=size)
   for(i in 1:size){
     for(j in 1:size){
@@ -38,44 +38,64 @@ graphon4 <- function(u, size){
   p_matrix = matrix(0,nrow=size,ncol=size)
   for(i in 1:size){
     for(j in 1:size){
-      p <- cos(pi*(u[i]-u[j]))/(2^3) + 0.5
+      p <- cos(pi*(u[i]-u[j]))/(2) + 0.5
       p_matrix[i,j] <- p    
     }
   }
   p_matrix
 }
 
 # Define the formula to generate p matrix of graphon5
-graphon5 <- function(u, size){
+graphon2 <- function(u, size){
   p_matrix = matrix(0,nrow=size,ncol=size)
+  s = 8
   for(i in 1:size){
     for(j in 1:size){
-      p <- cos(pi*(u[i]-u[j]))/(2^3) + 0.5
-      p_matrix[i,j] <- p    
+      if(u[i]>=u[j]){
+        p = sin((s*u[i]-s/2)*sin(s*u[j]-s/2))
+      }else{
+        p = sin((s*u[j]-s/2)*sin(s*u[i]-s/2))
+      }
+      p_matrix[i,j] <-  (p+1)/2
     }
   }
   p_matrix
 }
 
 # Define the formula to generate p matrix of graphon6
-graphon6 <- function(u, size){
+graphon5 <- function(u, size){
   p_matrix = matrix(0,nrow=size,ncol=size)
+  s = 10
   for(i in 1:size){
     for(j in 1:size){
-      p <- cos(pi*(u[i]-u[j]))/(2^3) + 0.5
-      p_matrix[i,j] <- p    
+      if(u[i]>=u[j]){
+        p = sin((s*u[i]-s/2)*sin(s*u[j]-s/2))
+      }else{
+        p = sin((s*u[j]-s/2)*sin(s*u[i]-s/2))
+      }
+      p_matrix[i,j] <- (p+1)/2
     }
   }
   p_matrix
 }
 
 # Function to generate sub-network from real network, labeled as 7
 graphon7 <- function(u,size){
+  #read real data
+  RDS_path <- system.file("rds", "rattus_norvegicus_brain_3_adj.RDS", package = "localboot")
+  P <- readRDS(RDS_path)
+  node_samples <- sample(1:NROW(P),size,replace = TRUE)
+  P[node_samples,node_samples]
 }
 
 
 # Function to generate sub-network from real network, labeled as 8
 graphon8 <- function(u,size){
+  #read real data
+  RDS_path <- system.file("rds", "email_Eu_core_adj.RDS", package = "localboot")
+  P <- readRDS(RDS_path)
+  node_samples <- sample(1:NROW(P),size,replace = TRUE)
+  P[node_samples,node_samples]
 }
 
 
@@ -118,6 +138,8 @@ generate_graphon <- function(size, graph_num = 1,sampling_on_u=TRUE,u_input=NULL
                            "4" = graphon4(u, size),
                            "5" = graphon5(u, size),
                            "6" = graphon6(u, size),
+                           "7" = graphon7(u, size),
+                           "8" = graphon8(u, size),
                            stop("Invalid graph_num: should be between 1 and 6"))
   return(p_matrix)
 

README.md

@@ -0,0 +1,86 @@
+# localboot
+
+## Overview
+
+`localboot` is an R package that offers tools for bootstrapping various networks through a local bootstrap procedure. It's particularly useful in network analysis for estimating the uncertainty of graph statistics. The package also includes utility functions that generating probability matrices, creating network adjacency matrices, and plotting network.
+
+## Installation
+
+To install the latest version of `localboot` from CRAN:
+
+```R
+install.packages("localboot")
+```
+
+To install the development version from GitHub:
+
+```R
+# install.packages("devtools")
+devtools::install_github("zzz1990771/localboot")
+```
+
+## Features
+
+- Local bootstrap methods for network analysis.
+- Tools for generating probability matrices and network adjacency matrices.
+- Functions for plotting network structures.
+- Several simulation scripts included in the `inst\sim` folder for advanced analysis.
+
+## Usage
+
+After installing the `localboot` package, you can load it into your R session:
+
+```R
+library(localboot)
+?localboot
+```
+
+Example usage:
+
+```R
+# Example usage
+P = generate_graphon(100, 1)
+A = generate_network_P(P, replicate = 1, symmetric.out = TRUE)
+result <- localboot(A = A, B = 100, returns = "boot")
+```
+
+### Included Simulation Scripts
+
+The localboot package comes with several simulation scripts located in the `inst\sim` folder. These scripts can be loaded and used for various simulations and analyses:
+
+- `Fit_local_boot.R`: Demonstrates the application of local bootstrap procedures to networks. It generates random networks by `generate_graphon()` and `generate_network_P()` and fit local boostrap procedures on it using the main function `localboot()`.
+
+- `Generate_various_networks.R`: Generates a variety of synthetic networks for testing network analysis algorithms.
+
+- `Sim1_truese.R`: Obtains true simulated standard errors for graph statistics in various network simulations.
+
+- `Sim1_estimates_local.R`: Generates various simulated networks and obtains estimated standard errors for different graph statistics by applying local bootstrap procedure.
+
+- `Sim1_estimate_others.R`: Generates various simulated networks and obtains estimated standard errors for different graph statistics by applying other alternative procedures.
+
+- `sup_funcs_sim.R`: Support functions for simulations in `Sim1_estimate_others.R`.
+
+- `Optimal_local_size.R`: Generates plots to visualize the optimal neighbor set size of local bootstrap procedure for standard error estimation in relation to the number of blocks (K) in a Stochastic Block Model (SBM). 
+
+
+To load a script, use the `system.file()` function to find its path and then load it with `file.edit()`. For example:
+
+```R
+scriptPath <- system.file("sim/Generate_various_networks.R", package = "localboot")
+file.edit(scriptPath)
+```
+
+## Results from Paper XXX
+
+This package, along with the scripts `Sim1_truese.R`, `Sim1_estimates_local.R`, and `Sim1_estimate_others.R`, can be used to replicate the results presented in Paper XXX. Detailed instructions and data required for replication are provided within each script, ensuring a comprehensive understanding of the proposed local boostrap procedure.
+
+
+## License
+
+This package is free and open source software, licensed under GPL-3.
+
+## Authors
+
+-Tianhai Zu (zuti@mail.uc.edu)
+
+-Yichen Qin (qinyn@ucmail.uc.edu)

inst/sim/Fit_local_boot.R

@@ -26,14 +26,9 @@
 
 # Library Imports
 library(igraph)
-#library(localboot) #currently commented out
+library(localboot)
 library(ggplot2)
 
-#temp source, will be deleted after the package is finished.
-source("./R/generate_network.R")
-source("./R/localboot.R")
-source("./R/plot_utils.R")
-
 # -------------------------------------------------------------------
 # Script Starts Here
 # -------------------------------------------------------------------
@@ -42,7 +37,7 @@ source("./R/plot_utils.R")
 n = 400
 
 # Generate network adjacency matrix
-P <- graphon3(size = n)
+P <- generate_graphon(n,1) 
 adj.matrix <- generate_network_P(P)
 
 # Let's assume we are investigating:
@@ -59,12 +54,5 @@ getT <- function(adj.matrix){
 getT(adj.matrix)
 
 # Use local bootstrap to estimate standard error of certain graph statistics
-local_boot_res = local_boot(adj.matrix,0.1,100,returns = "T",fast=1)
+local_boot_res = localboot(adj.matrix,200,returns = "T",getT=getT)
 local_boot_res$se #should be around 0.003 to 0.0036.
-
-local_boot_old(adj.matrix,0.1,100,returns = "T",fast=1)$se
-
-
-system.time(local_boot(adj.matrix,0.1,100,fast=1))
-
-system.time(local_boot_old(adj.matrix,0.1,100,fast=1))

inst/sim/Optimal_local_size.R

@@ -21,12 +21,12 @@
 #
 # Author: Tianhai Zu
 # Affiliation: University of Texas at San Antonio
-# Created on: 12/05/2023
+# Created on: 01/08/2024
 #
 # Requirements:
 # The script requires the following R packages:
 # - igraph (for basic network generation and manipulation)
-# - [Any other packages needed for specific models or patterns]
+# - localboot (this package)
 # Install these packages using install.packages() if not already installed.
 
 # Library Imports