Package: ghypernet 1.1.1.1

ghypernet: Fit and Simulate Generalised Hypergeometric Ensembles of Graphs

Provides functions for model fitting and selection of generalised hypergeometric ensembles of random graphs (gHypEG). To learn how to use it, check the vignettes for a quick tutorial. Please reference its use as Casiraghi, G., Nanumyan, V. (2019) <doi:10.5281/zenodo.2555300> together with those relevant references from the one listed below. The package is based on the research developed at the Chair of Systems Design, ETH Zurich. Casiraghi, G., Nanumyan, V., Scholtes, I., Schweitzer, F. (2016) <arxiv:1607.02441>. Casiraghi, G., Nanumyan, V., Scholtes, I., Schweitzer, F. (2017) <doi:10.1007/978-3-319-67256-4_11>. Casiraghi, G., (2017) <arxiv:1702.02048> Brandenberger, L., Casiraghi, G., Nanumyan, V., Schweitzer, F. (2019) <doi:10.1145/3341161.3342926> Casiraghi, G. (2019) <doi:10.1007/s41109-019-0241-1>. Casiraghi, G., Nanumyan, V. (2021) <doi:10.1038/s41598-021-92519-y>. Casiraghi, G. (2021) <doi:10.1088/2632-072X/ac0493>.

Authors:Giona Casiraghi [aut, cre], Vahan Nanumyan [aut], Laurence Brandenberger [ctb], Giacomo Vaccario [ctb]

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ghypernet.pdf |ghypernet.html✨
ghypernet/json (API)
NEWS

# Install 'ghypernet' in R:

install.packages('ghypernet', repos = c('https://gi0na.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/gi0na/r-ghypernet/issues

Datasets:

adj_karate - Zachary's Karate Club graph
contacts.adj - Highschool contact network adjacency matrix
cospons_mat - Swiss MPs network adjacency matrix
dt - Swiss MPs attribute data frame.
dtcommittee - Swiss MPs committee affiliation data frame.
highschool.multiplex - Highschool contact network multiplex representation
highschool.predictors - Highschool contact network predictors
onlinesim_mat - Swiss MPs committee similarity matrix.
vertexlabels - Zachary's Karate Club vertex faction assignment

On CRAN:

data-mining data-science graphs network network-analysis random-graph-generation random-graphs

5.73 score 9 stars 20 scripts 231 downloads 41 exports 34 dependencies

Last updated 7 months agofrom:42935e73a1. Checks:OK: 1 NOTE: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 08 2024
R-4.5-win	NOTE	Oct 08 2024
R-4.5-linux	NOTE	Oct 08 2024
R-4.4-win	NOTE	Oct 08 2024
R-4.4-mac	NOTE	Oct 08 2024
R-4.3-win	NOTE	Oct 08 2024
R-4.3-mac	NOTE	Oct 08 2024

Exports:adj2el as.ghype bccm BootstrapProperty compute_xi ComputeXi conf.test coxsnellR2 create_predictors CreateIgGraphs createPredictors el2adj extract.nrm.cluster FitOmega get_zero_dummy ghype gof.test homophily_stat isNetwork link_significance linkSignificance logl loglratio lr.test mat2vec.ix mcfaddenR2 nr.ci nr.significance nrm nrm_choose nrm_selection nrmChoose nrmSelection reciprocity_stat regularm rghype RMSE RMSLE scm sharedPartner_stat vec2mat

Dependencies:askpass cli curl dplyr extraDistr fansi generics glue httr jsonlite lifecycle magrittr mime numbers openssl pbmcapply pillar pkgconfig plyr purrr R6 Rcpp reshape2 rlang rootSolve stringi stringr sys texreg tibble tidyselect utf8 vctrs withr

An introduction to generalized hypergeometric ensembles (gHypEG) regressions.

Giona Casiraghi, Laurence Brandenberger

Rendered fromTutorial_NRM.Rmdusingknitr::rmarkdownon Oct 08 2024.

Last update: 2022-12-05
Started: 2019-09-02

Finding Significant Links with gHypEGs

Giona CasiraghI

Rendered fromSignificantlinks.Rmdusingknitr::rmarkdownon Oct 08 2024.

Last update: 2021-10-15
Started: 2019-01-15

ghypernet Tutorial

Giona Casiraghi

Rendered fromtutorial.Rmdusingknitr::rmarkdownon Oct 08 2024.

Last update: 2019-02-01
Started: 2019-02-01

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Zachary's Karate Club graph	adj_karate
Maps adjacency matrix to edgelist	adj2el
Map list to ghype object	as.ghype as.ghype.list as.ghype.nrm
Fitting bccm models	bccm print.bccm
BootstrapProperty computes igraph analytics function on ensemble	BootstrapProperty
Check graph input type (for whether it's a graph or a edgelist).	checkGraphtype
Extraction method for coefficients of models of class ''nrm''.	coef.nrm
Auxiliary function. Computes combinatorial matrix.	ComputeXi compute_xi
Test regular (gnp) vs configuration model	conf.test
Highschool contact network adjacency matrix	contacts.adj
Swiss MPs network adjacency matrix	cospons_mat
Computes Cox and Snell pseudo R-squared for nrm models.	coxsnellR2
Create a nrmpredictor object from passed argument	createPredictors create_predictors
Create a nrmpredictor object from list	create_predictors.list
Convert a list of adjacency matrices to a list of igraph graphs.	CreateIgGraphs
Swiss MPs attribute data frame.	dt
Swiss MPs committee affiliation data frame.	dtcommittee
Maps edgelist to adjacency matrix	el2adj
Extract details from statistical models for table construction. The function has methods for a range of statistical models.	extract.nrm.cluster
Fit propensity matrix for full model	FitOmega
Create a dummy variable to encode zero values of another variable.	get_zero_dummy
Fitting gHypEG models	ghype ghype.default ghype.igraph ghype.matrix print.ghype
Perform a goodness-of-fit test	gof.test
Highschool contact network multiplex representation	highschool.multiplex
Highschool contact network predictors	highschool.predictors
Calculate homophily in multi-edge graphs.	homophily_stat
Test null model vs full ghype.	isNetwork
Fisher Information matrix for estimators in block models.	JnBlock
Estimate statistical deviations from ghype model	linkSignificance link_significance
General method to compute log-likelihood for ghype models.	logl logl.ghype logl.matrix
Extract Log-Likelihood	logLik.ghype
Compute log-likelihood ratio for ghype models.	loglratio
Perform likelihood ratio test between two ghype models.	lr.test
Auxiliary function, gives mask for matrix for directed, undirected etc.	mat2vec.ix
Computes Mc Fadden pseudo R-squared.	mcfaddenR2
Confidence intervals for nrm models.	nr.ci
Computes the significance of more complex model against a simpler model by means of a likelihood ratio test.	nr.significance
Fitting gHypEG regression models for multi-edge networks.	nrm nrm.default print.nrm
Selects the best set of predictors among the given sets by means of AIC.	nrmChoose nrm_choose
Perform AIC forward selection for nrm.	nrmSelection nrm_selection nrm_selection.default nrm_selection.nrmpredictor print.nrm_selection
Swiss MPs committee similarity matrix.	onlinesim_mat
Method to predict the expected values of a nrm model	predict.nrm
Calculate weighted reciprocity change statistics for multi-edge graphs.	reciprocity_stat
Fit the gnm model	regularm
Method to compute residuals of nrm models	residuals.nrm
Generate random realisations from ghype model.	rghype
Computes the Root Mean Squared Error	RMSE
Computes the Root Mean Squared Logged Error	RMSLE
Fit the Soft-Configuration Model	scm
Calculate (un-)weighted shared partner change statistics for multi-edge graphs.	sharedPartner_stat
Summary method for elements of class ''nrm''.	print.summary.nrm summary.nrm
Summary method for elements of class ''nrm_selection''.	print.summary.nrm_selection summary.nrm_selection
Auxiliary function, produces matrix from vector	vec2mat
Zachary's Karate Club vertex faction assignment	vertexlabels