| Type: | Package |
| Title: | Local Bootstrap Methods for Various Networks |
| Version: | 0.9.2 |
| Date: | 2024-01-08 |
| Description: | Network analysis usually requires estimating the uncertainty of graph statistics. Through this package, we provide tools to bootstrap various networks via local bootstrap procedure. Additionally, it includes functions for generating probability matrices, creating network adjacency matrices from probability matrices, and plotting network structures. The reference will be updated soon. |
| License: | GPL-3 |
| Depends: | R (≥ 3.5.0) |
| Imports: | graphics, viridis, Rcpp (≥ 1.0.11) |
| Suggests: | testthat (≥ 3.0.0) |
| LinkingTo: | Rcpp (≥ 1.0.11), RcppEigen |
| Encoding: | UTF-8 |
| RoxygenNote: | 7.2.3 |
| NeedsCompilation: | yes |
| 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: | 2024-01-10 11:33:21 UTC |
localboot: A Package for Local Bootstrap Methods for Various Networks
Description
Network analysis usually requires estimating the uncertainty of a graph statistics. Through this package, we provides tools to bootstrap various networks via local bootstrap procedure. Additionally, it includes functions for generating probability matrices, creating network adjacency matrices from probability matrices, and plotting network structures.
Author(s)
Maintainer: Tianhai Zu zuti@mail.uc.edu
Authors:
Yichen Qin qinyn@ucmail.uc.edu [contributor]
Generate a Graphon Probability Matrix
Description
This function generates a graphon probability matrix based on a specified graphon type. Users can control the generation process through various parameters.
Usage
generate_graphon(size, graph_num = 1, sampling_on_u = TRUE, u_input = NULL)
Arguments
size |
An integer specifying the size of the network. |
graph_num |
An integer (default is 1) indicating the graphon type to use. Acceptable values are from 1 to 6. |
sampling_on_u |
A logical value determining if uniform sampling should be used for 'u'. Defaults to TRUE. If FALSE, a regular sequence from 0 to 1 is used. |
u_input |
An optional numeric vector that provides specific values for 'u'. If NULL (default), 'u' is generated based on 'sampling_on_u'. |
Value
A matrix of probabilities is returned.
Examples
# Generate a graphon probability matrix of size 100 using graphon setting 1
P = generate_graphon(100, 1)
Generate Network Adjacency Matrix from Probability Matrix
Description
This function generates a network adjacency matrix from a given probability matrix. It checks if the input is a valid probability matrix and can produce either a single network or multiple replicates.
Usage
generate_network_P(P, replicate = 1, symmetric.out = TRUE, noloop = FALSE)
Arguments
P |
A square matrix representing the probability matrix, where each element is a probability (between 0 and 1) of an edge between nodes. |
replicate |
An integer indicating the number of network replicates to generate. Defaults to 1. |
symmetric.out |
A logical value indicating whether the output matrix should be symmetric. Defaults to TRUE. |
noloop |
A logical value indicating whether to include self-loops in the network. Defaults to FALSE. |
Value
If 'replicate' is 1, returns a single adjacency matrix. If 'replicate' is greater than 1, returns a list of adjacency matrices. Each matrix is a square binary matrix, where 1 indicates the presence of an edge and 0 indicates its absence.
Examples
P = generate_graphon(100, 1)
network = generate_network_P(P, replicate = 1, symmetric.out = TRUE)
Local Bootstrap for Network Data
Description
This function applies a local bootstrap method to network data, represented by an adjacency matrix. It offers various methods and options for bootstrapping, including handling weighted networks and custom distance functions.
Usage
localboot(
A,
B,
quantile_n = 0,
returns = "boot",
method = "own",
dist_func = get_dist_default_eigen,
kowning_u = NULL,
induced_sampling = TRUE,
weighted = FALSE,
getT = NULL,
user_blist = NULL,
fast = NULL,
...
)
Arguments
A |
A square adjacency matrix of the network. |
B |
The number of bootstrap samples to generate. |
quantile_n |
The quantile used for neighborhood selection in some methods. If set to 0 (default), it's calculated as (log(N) / N)^0.5. |
returns |
Specifies the type of output returned. Possible values are "boot" (default), "p_and_time", "p_and_boot", and "T". |
method |
The method used for bootstrapping. Options are "own" and "zhu". |
dist_func |
A function to compute the distance matrix. Default is 'get_dist_default_eigen'. |
kowning_u |
An optional known 'u' vector for distance calculation. |
induced_sampling |
A logical indicating whether to use induced sampling. Defaults to TRUE. |
weighted |
A logical indicating if the network is weighted. Defaults to FALSE. |
getT |
An optional function to apply to each bootstrapped sample. |
user_blist |
An optional user-provided bootstrap list. |
fast |
A logical indicating if a faster, approximate method should be used. Automatically set based on network size if NULL. |
... |
Additional arguments passed to other methods. |
Value
Depending on the 'returns' argument, this function can return various types of outputs including bootstrapped networks, estimated probabilities, computation times, and statistics from the 'getT' function.
Examples
# 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")
Plot Probability Matrix
Description
This function creates a filled contour plot of a probability matrix using the 'viridis' color palette. The plot is created using the 'ggplot2' and 'viridis' libraries.
Usage
plot_P(P)
Arguments
P |
A probability matrix to be plotted. |
Value
Generates a filled contour plot.
Examples
P_matrix <- matrix(runif(100), 10, 10)
plot_P(P_matrix)
Plot Adjacency Matrix
Description
This function creates a plot of an adjacency matrix, where the matrix is displayed as an image.
Usage
plot_adj(X, ...)
Arguments
X |
An adjacency matrix to be plotted. |
... |
Additional graphical parameters to pass to 'image'. |
Value
Generates a plot.
Examples
adj_matrix <- matrix(rbinom(100, 1, 0.5), 10, 10)
plot_adj(adj_matrix)