Package: SBMSplitMerge 1.1.1

Matthew Ludkin

SBMSplitMerge: Inference for a Generalised SBM with a Split Merge Sampler

Inference in a Bayesian framework for a generalised stochastic block model. The generalised stochastic block model (SBM) can capture group structure in network data without requiring conjugate priors on the edge-states. Two sampling methods are provided to perform inference on edge parameters and block structure: a split-merge Markov chain Monte Carlo algorithm and a Dirichlet process sampler. Green, Richardson (2001) <doi:10.1111/1467-9469.00242>; Neal (2000) <doi:10.1080/10618600.2000.10474879>; Ludkin (2019) <arxiv:1909.09421>.

Authors:Matthew Ludkin [aut, cre, cph]

SBMSplitMerge_1.1.1.tar.gz
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SBMSplitMerge_1.1.1.tgz(r-4.4-any)SBMSplitMerge_1.1.1.tgz(r-4.3-any)
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SBMSplitMerge.pdf |SBMSplitMerge.html✨
SBMSplitMerge/json (API)
NEWS

# Install 'SBMSplitMerge' in R:
install.packages('SBMSplitMerge', repos = c('https://ludkinm.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:
  • Enron - The Enron data set as extracted from 'igraph' using the script in data-raw
  • Macaque - The Macaque data set as extracted from 'igraph' using the script in data-raw
  • StackOverflow - The Stack-Overflow data set as extracted from 'igraph' using the script in data-raw Extracted on 27/8/2019 from Kaggle (login required) using: 'library(rvest)' 'read_html("https://www.kaggle.com/stackoverflow/stack-overflow-tag-network/downloads/stack_network_links.csv/1")'

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

2.70 score 3 scripts 128 downloads 40 exports 33 dependencies

Last updated 4 years agofrom:85c1a1bd92. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 13 2024
R-4.5-winOKNov 13 2024
R-4.5-linuxOKNov 13 2024
R-4.4-winOKNov 13 2024
R-4.4-macOKNov 13 2024
R-4.3-winOKNov 13 2024
R-4.3-macOKNov 13 2024

Exports:ARIblockmodblocksblocktracecrpddirichletdedgesdmaedgemodedgesedges_bernedges_nbinedges_normedges_poiseval_plotsis.sbmmarglike_bernmarglike_normmarglike_poismodeblocksmultinomnumblockstraceparam_betaparam_gammaparam_nbinparam_normparammodparamsparamtracercatrdirichletredgessamplersampler.conjsampler.dpsampler.gibbssampler.rjsbmsbmmodvmeasure

Dependencies:clicolorspacefansifarverggplot2gluegtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigplyrR6RColorBrewerRcppreshape2rlangscalesstringistringrtibbleutf8vctrsviridisLitewithr

Weibull edges

Rendered fromWeibull-edges.Rmdusingknitr::rmarkdownon Nov 13 2024.

Last update: 2020-06-04
Started: 2020-06-04

Readme and manuals

Help Manual

Help pageTopics
accept 'propsbm' with the acceptance probability alphaaccept
Add a block moveaddblock
Adjusted Rand IndexARI
Block matrixblockmat
Block matrixblockmat.blocks
Block matrixblockmat.factor blockmat.numeric
Block matrixblockmat.sbm
Block Modelblockmod
Blocks objectblocks
plot a trace of the blocks from MCMC samplesblocktrace
Chinese Restaurant Processcrp
Dirichlet distributionddirichlet
Density of edgesdedges
likelihood of edgesdedges.numeric
Density of edgesdedges.sbm
Delete a block movedelblock
Dirichlet Multinomial Allocationdma
Draw block membershipdrawblock.dp
Gibbs-like reassignment of nodes to the current set of blocksdrawblock.gibbs
Draw block membershipsdrawblocks.dp
Gibbs-like reassignment of nodes to the current set of blocksdrawblocks.gibbs
Metropolis updates by drawing parametersdrawparams
Class for edge modelsedgemod
Class for edge dataedges
Bernoulli edge modeledges_bern
Negative-Binomial edge modeledges_nbin
Normal edge modeledges_norm
Poisson edge modeledges_pois
The Enron data set as extracted from 'igraph' using the script in data-rawEnron
get a set of evaluation plots from MCMC sampleseval_plots
is.sbmis.sbm
The Macaque data set as extracted from 'igraph' using the script in data-rawMacaque
Marginal likelihood model for Bernoulli distributed edgesmarglike_bern
Marginal likelihood model for Normal distributed edgesmarglike_norm
Marginal likelihood model for Poisson distributed edgesmarglike_pois
Merge blocksmergeavg
merge move block mergingmergeblocks
merge parametersmergeparams
Merge step: parametersmergeparams.default
Merge step - parameter mergingmergeparams.numeric
modal block assignments from MCMC samplesmodeblocks
Multinomial block assignmentmultinom
Likelihood of node assignmentnodelike
plot a trace of the number of blocks from MCMC samplesnumblockstrace
Beta parameter modelparam_beta
Gamma parameter modelparam_gamma
Parameter model for Negative Binomialparam_nbin
Parameter model for Normal Modelparam_norm
Parameter Matrixparammat
Parameter Matrixparammat.blocks
Parameter Matrixparammat.matrix
Parameter Matrixparammat.params
Parameter Matrixparammat.sbm
Parameter Modelparammod
'params' S3 objectparams
plot a trace of parameter values from MCMC samplesparamtrace
Plot blocksimage.blocks plot.blocks
Plotimage.edges plot.edges
Plot for 'sbm' objectimage.sbm plot.sbm
helper function for trace plotsplotpostpairs
mean proportion of times two nodes were in the same block under MCMC samplespostpairs
Draw draw Categorical distributionrcat
Dirichlet distributionrdirichlet
Simulate edgesredges
Random Walkrw
top level sampler functionsampler
Conjugate model samplersampler.conj
Dirichlet process samplersampler.dp
Gibbs sampling for node assignmentssampler.gibbs
reversible jump Markov chain Monte Carlo split-merge samplersampler.rj
Class 'sbm'sbm
Stochastic block model objectsbmmod
split move using average to merge parameterssplitavg
split move: blockssplitblocks
split move: parameterssplitparams
split move: 'params'splitparams.numeric
split move: 'params'splitparams.params
The Stack-Overflow data set as extracted from 'igraph' using the script in data-raw Extracted on 27/8/2019 from Kaggle (login required) using: 'library(rvest)' 'read_html("https://www.kaggle.com/stackoverflow/stack-overflow-tag-network/downloads/stack_network_links.csv/1")'StackOverflow
Update the block assignment of a nodeupdateblock
Update the block assignment of a nodeupdateblock.blocks
Update the block assignment of a nodeupdateblock.sbm
V-measurevmeasure