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ergm (version 4.6.0)

Fit, Simulate and Diagnose Exponential-Family Models for Networks

Description

An integrated set of tools to analyze and simulate networks based on exponential-family random graph models (ERGMs). 'ergm' is a part of the Statnet suite of packages for network analysis. See Hunter, Handcock, Butts, Goodreau, and Morris (2008) and Krivitsky, Hunter, Morris, and Klumb (2023) .

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Install

install.packages('ergm')

Monthly Downloads

8,222

Version

4.6.0

License

GPL-3 + file LICENSE

Maintainer

Pavel N. Krivitsky

Last Published

December 18th, 2023

Functions in ergm (4.6.0)

DiscUnif-ergmProposal

ConstantEdges-ergmProposal

MHp for edges constraints

DiscUnif2-ergmProposal

CondOutDegree-ergmProposal

MHp for odegree constraints

DiscUnif-ergmReference

Discrete Uniform reference

DiscUnifNonObserved-ergmProposal

Impose a curved structure on term parameters

A for operator for terms

Dyads-ergmConstraint

Constrain fixed or varying dyad-independent terms

DistRLE-ergmProposal

Offset-ergmTerm

Terms with fixed coefficients

HammingConstantEdges-ergmProposal

Take a natural logarithm of a network's statistic

CondOutDegreeDist-ergmProposal

MHp for odegreedist constraints

A sum (or an arbitrary linear combination) of one or more formulas

StdNormal-ergmReference

Standard Normal reference

HammingTNT-ergmProposal

Modify terms' coefficient names

A product (or an arbitrary power combination) of one or more formulas

altkstar-ergmTerm

Alternating \(k\)-star

NodematchFilter-ergmTerm

Filtering on nodematch

absdiffcat-ergmTerm

Categorical absolute difference in nodal attribute

absdiff-ergmTerm

Absolute difference in nodal attribute

UnifNonObserved-ergmProposal

Evaluation on an induced subgraph

atmost-ergmTerm

Number of dyads with values less than or equal to a threshold

StdNormal-ergmProposal

attrcov-ergmTerm

Edge covariate by attribute pairing

ANOVA for ERGM Fits

Exponentiate a network's statistic

Symmetrize-ergmTerm

Evaluation on symmetrized (undirected) network

TNT-ergmProposal

Default MH algorithm

Filtering on arbitrary one-term model

as.network.numeric

Create a Simple Random network of a Given Size

Unif-ergmReference

Continuous Uniform reference

atleast-ergmTerm

Number of dyads with values greater than or equal to a threshold

asymmetric-ergmTerm

Asymmetric dyads

Unif-ergmProposal

approx.hotelling.diff.test

Approximate Hotelling T^2-Test for One or Two Population Means

b1star-ergmTerm

\(k\)-stars for the first mode in a bipartite network

b1starmix-ergmTerm

Mixing matrix for \(k\)-stars centered on the first mode of a bipartite network

b1nodematch-ergmTerm

Nodal attribute-based homophily effect for the first mode in a bipartite network

blockdiag-ergmConstraint

Block-diagonal structure constraint

b1degrees-ergmConstraint

Preserve the actor degree for bipartite networks

b2sociality-ergmTerm

as.rlebdm.ergm_conlist

Extract dyad-level ERGM constraint information into an rlebdm object

bd-ergmConstraint

Constrain maximum and minimum vertex degree

b1sociality-ergmTerm

b1factor-ergmTerm

Factor attribute effect for the first mode in a bipartite network

b2degrees-ergmConstraint

Preserve the receiver degree for bipartite networks

Dyadwise shared partners for dyads in the first bipartition

b1mindegree-ergmTerm

Minimum degree for the first mode in a bipartite network

b2degree-ergmTerm

Degree for the second mode in a bipartite network

balance-ergmTerm

Balanced triads

b1degrange-ergmTerm

Degree range for the first mode in a bipartite network

b1degree-ergmTerm

Degree for the first mode in a bipartite network

blocks-ergmConstraint

Constrain blocks of dyads defined by mixing type on a vertex attribute.

Dyadwise shared partners for dyads in the second bipartition

Target statistics and model fit to a hypothetical 50,000-node network population with 50,000 nodes based on egocent

Main effect of a covariate for the second mode in a bipartite network

Locate and call an ERGM term initialization function.

Ensures an Ergm Term and its Arguments Meet Appropriate Conditions

b1concurrent-ergmTerm

Concurrent node count for the first mode in a bipartite network

b2concurrent-ergmTerm

Concurrent node count for the second mode in a bipartite network

control.ergm.godfather

Control parameters for ergm.godfather().

Main effect of a covariate for the first mode in a bipartite network

b1twostar-ergmTerm

Two-star census for central nodes centered on the first mode of a bipartite network

b2nodematch-ergmTerm

Nodal attribute-based homophily effect for the second mode in a bipartite network

b2degrange-ergmTerm

Degree range for the second mode in a bipartite network

cyclicalties-ergmTerm

b2mindegree-ergmTerm

Minimum degree for the second mode in a bipartite network

degree-ergmTerm

degrange-ergmTerm

cyclicalweights-ergmTerm

Cyclical weights

dyadcov-ergmTerm

Dyadic covariate

Directed dyadwise shared partners

coincidence-ergmTerm

Coincident node count for the second mode in a bipartite (aka two-mode) network

b2star-ergmTerm

\(k\)-stars for the second mode in a bipartite network

ctriple-ergmTerm

concurrentties-ergmTerm

Concurrent tie count

concurrent-ergmTerm

Concurrent node count

degcor-ergmTerm

Degree Correlation

degcrossprod-ergmTerm

Degree Cross-Product

degree1.5-ergmTerm

Degree to the 3/2 power

b2factor-ergmTerm

Factor attribute effect for the second mode in a bipartite network

dyadnoiseTNT-ergmProposal

.dyads-ergmConstraint

A meta-constraint indicating handling of arbitrary dyadic constraints

b2starmix-ergmTerm

Mixing matrix for \(k\)-stars centered on the second mode of a bipartite network

degreedist-ergmConstraint

Preserve the degree distribution of the given network

egocentric-ergmConstraint

Preserve values of dyads incident on vertices with given attribute

b2twostar-ergmTerm

Two-star census for central nodes centered on the second mode of a bipartite network

density-ergmTerm

Functions that have been removed from this package

control.ergm.bridge

Auxiliaries for Controlling ergm.bridge.llr() and logLik.ergm()

Auxiliary for Controlling ERGM Fitting

Auxiliary for Controlling ERGM Goodness-of-Fit Evaluation

Obtain the set of informative dyads based on the network structure.

equalto-ergmTerm

Number of dyads with values equal to a specific value (within tolerance)

ergm.bridge.llr

Bridge sampling to evaluate ERGM log-likelihoods and log-likelihood ratios

enformulate.curved-deprecated

Convert a curved ERGM into a form suitable as initial values for the same ergm. Deprecated in 4.0.0.

Auxiliary for Controlling SAN

edgecov-ergmTerm

Two versions of an E. Coli network dataset

Parallel Processing in the ergm Package

Find a maximizer to the psuedolikelihood function

Reference Measures for Exponential-Family Random Graph Models

Sample Space Constraints for Exponential-Family Random Graph Models

Fit, Simulate and Diagnose Exponential-Family Models for Networks

Compute the Sample Estimating Function Values of an ERGM.

ergm_dyadgen_select

A helper function to select and construct a dyad generator for C.

Operations to map curved ergm() parameters onto canonical parameters

ergm_Cstate_clear

Deallocate the C data structures corresponding to an ergm_state left over from a .Call() run.

Calculate all possible vectors of statistics on a network for an ERGM

MCMC Hints for Exponential-Family Random Graph Models

Exponential-Family Random Graph Models

dyadnoise-ergmConstraint

A soft constraint to adjust the sampled distribution for dyad-level noise with known perturbation probabilities

dyadnoise-ergmProposal

ergm_edgecov_args

A common pattern for obtaining an edge covariate

control.simulate.ergm

Auxiliary for Controlling ERGM Simulation

ergm_plot.mcmc.list

Plot MCMC list using lattice package graphics

Terms used in Exponential Family Random Graph Models

Internal representation of an ergm network model

degrees-ergmConstraint

Preserve the degree of each vertex of the given network

Computes and Returns the Degree Distribution Information for a Given Network

edges-ergmConstraint

Preserve the edge count of the given network

ergm_symmetrize

Return a symmetrized version of a binary network

Keywords defined for Exponential-Family Random Graph Models

Curved settings for geometric weights for the gw* terms

Internal ergm Objects

Global options and term options for the ergm package

ergm.getnetwork

Acquire and verify the network from the LHS of an ergm formula and verify that it is a valid network.

A function to apply a given series of changes to a network.

ergm_MCMC_sample

Internal Function to Sample Networks and Network Statistics

Internal Function to Perform Simulated Annealing

ergm_state_cache

A rudimentary cache for large objects

Functions to initialize the ergm_proposal object

ergm_mk_std_op_namewrap

Combine an operator term's and a subterm's name in a standard fashion.

Metropolis-Hastings Proposal Methods for ERGM MCMC

faux.dixon.high

Faux dixon High School as a network object

ERGM Predictors and response for logistic regression calculation of MPLE

Conduct Goodness-of-Fit Diagnostics on a Exponential Family Random Graph Model

Dynamic ERGM keyword registry

A Representation of ERGM state

gwb1degree-ergmTerm

Geometrically weighted degree distribution for the first mode in a bipartite network

An API for specifying aspects of an ergm model in the LHS/basis network.

ergm_proposal_table

Table mapping reference,constraints, etc. to ERGM Metropolis-Hastings proposals

gwb1dsp-ergmTerm

Geometrically weighted dyadwise shared partner distribution for dyads in the first bipartition

faux.magnolia.high

Goodreau's Faux Magnolia High School as a network object

Retrieve and check assumptions about vertex attributes (nodal covariates) in a network

greaterthan-ergmTerm

Number of dyads with values strictly greater than a threshold

intransitive-ergmTerm

Intransitive triads

Testing for curved exponential family

Directed edgewise shared partners

faux.desert.high

Faux desert High School as a network object

Number of edges in the network

hamming-ergmTerm

Hamming distance

idegrees-ergmConstraint

Preserve indegree for directed networks

ininterval-ergmTerm

Number of dyads whose values are in an interval

isolatededges-ergmTerm

hamming-ergmConstraint

Preserve the hamming distance to the given network (BROKEN: Do NOT Use)

Multivariate version of coda's coda::geweke.diag().

Florentine Family Marriage and Business Ties Data as a "network" object

isolates-ergmTerm

gwb2dsp-ergmTerm

Geometrically weighted dyadwise shared partner distribution for dyads in the second bipartition

gwb2degree-ergmTerm

Geometrically weighted degree distribution for the second mode in a bipartite network

idegrange-ergmTerm

In-degree range

Goodreau's four node network as a "network" object

nearsimmelian-ergmTerm

Near simmelian triads

ergm-deprecated

Functions that will no longer be supported in future releases of the package

A convenience container for a list of network objects, output by simulate.ergm among others.

meandeg-ergmTerm

Mean vertex degree

idegree-ergmTerm

Kapferer's tailor shop data

Geometrically weighted non-edgewise shared partner distribution

Mixing matrix cells and margins

nodeocov-ergmTerm

Main effect of a covariate for out-edges

nodefactor-ergmTerm

Factor attribute effect

Calculate the exact loglikelihood for an ERGM

nodeicov-ergmTerm

Main effect of a covariate for in-edges

Sensible error and warning messages by ergm initializers

ergm_cutoff_message

Helper function for constructing gw* cutoff error messages

Initializes the parameters to bound degree during sampling

ergm.geodistdist

Calculate geodesic distance distribution for a network or edgelist

nvattr.copy.network

Copy network- and vertex-level attributes between two network objects

nodeocovar-ergmTerm

Covariance of out-dyad values incident on each actor

Directed non-edgewise shared partners

gwodegree-ergmTerm

Geometrically weighted out-degree distribution

is.dyad.independent

Testing for dyad-independence

localtriangle-ergmTerm

Triangles within neighborhoods

ergm_preprocess_response

Update the network and the response argument.

nodecov-ergmTerm

Main effect of a covariate

ergm_propagate_ext.encode

Extended states for submodels

fixallbut-ergmConstraint

Preserve the dyad status in all but the given edges

Goodreau's Faux Mesa High School as a network object

gwidegree-ergmTerm

Geometrically weighted in-degree distribution

Geometrically weighted edgewise shared partner distribution

idegree1.5-ergmTerm

In-degree to the 3/2 power

gwdegree-ergmTerm

Geometrically weighted degree distribution

fixedas-ergmConstraint

Preserve and preclude edges

Convert a curved ERGM into a corresponding "fixed" ERGM.

idegreedist-ergmConstraint

Preserve the indegree distribution

nodecovar-ergmTerm

Covariance of undirected dyad values incident on each actor

nodematch-ergmTerm

Uniform homophily and differential homophily

nodemix-ergmTerm

Nodal attribute mixing

odegree-ergmTerm

nodal_attributes-API

Helper functions for specifying nodal attribute levels

Geometrically weighted dyadwise shared partner distribution

nodal_attributes

Specifying nodal attributes and their levels

search.ergmTerms

Search ERGM terms, constraints, references, hints, and proposals

Generate networks with a given set of network statistics

Function to check whether an ERGM fit or some aspect of it is valued

mutual-ergmTerm

Synthetic network with 20 nodes and 28 edges

m2star-ergmTerm

Mixed 2-stars, a.k.a 2-paths

odegreedist-ergmConstraint

Preserve the outdegree distribution

mcmc.diagnostics

Conduct MCMC diagnostics on a model fit

nodeicovar-ergmTerm

Covariance of in-dyad values incident on each actor

nodeifactor-ergmTerm

Factor attribute effect for in-edges

Calculate the null model likelihood

A logLik method for ergm fits.

summary.ergm_model

Evaluate network summary statistics from an initialized ergm model

Summarizing ERGM Model Fits

Longitudinal networks of positive affection within a monastery as a "network" object

odegree1.5-ergmTerm

Out-degree to the 3/2 power

opentriad-ergmTerm

odegrees-ergmConstraint

Preserve outdegree for directed networks

Draw from the distribution of an Exponential Family Random Graph Model

simulate.formula

A simulate Method for formula objects that dispatches based on the Left-Hand Side

receiver-ergmTerm

Receiver effect

observed-ergmConstraint

Preserve the observed dyads of the given network

Length of the parameter vector associated with an object or with its terms.

nodeofactor-ergmTerm

Factor attribute effect for out-edges

odegrange-ergmTerm

Out-degree range

RLE-Compressed Boolean Dyad Matrix

A lack-of-fit test for ERGMs

smallerthan-ergmTerm

Number of dyads with values strictly smaller than a threshold

randomtoggle-ergmProposal

Propose a randomly selected dyad to toggle

smalldiff-ergmTerm

Number of ties between actors with similar attribute values

Cumulative network of positive affection within a monastery as a "network" object

Names of the parameters associated with an object.

predict.formula

ERGM-based tie probabilities

simmelian-ergmTerm

Simmelian triads

Statnet Control

summary_formula

Dispatching a summary function based on the class of the LHS of a formula.

Stratify Proposed Toggles by Mixing Type on a Vertex Attribute

triangle-ergmTerm

tripercent-ergmTerm

Triangle percentage

sociality-ergmTerm

Undirected degree

summary.formula

Calculation of network or graph statistics or other attributes specified on a formula

threetrail-ergmTerm

simmelianties-ergmTerm

Ties in simmelian triads

to_ergm_Cdouble.network

Methods to serialize objects into numeric vectors for passing to the C side.

ttriple-ergmTerm

Transitive triples

twopath-ergmTerm

Sum of dyad values (optionally taken to a power)

sender-ergmTerm

Identify the position of a point relative to the convex hull of a set of points

transitiveweights-ergmTerm

Transitive weights

sparse-ergmHint

triadcensus-ergmTerm

Multivariate version of coda's spectrum0.ar().

wrap.ergm_model

Wrap a submodel's curved, empty network statistics, and extended state (read-only) specification (if present) for output from an InitErgmTerm or InitWtErgmTerm.

transitive-ergmTerm

Transitive triads

transitiveties-ergmTerm

Transitive ties

Update the edges in a network based on a matrix

Weighted Median

Bernoulli-ergmReference

Bernoulli reference

CondB2Degree-ergmProposal

MHp for b2degree constraints

Wrap binary terms for use in valued models

BDStratTNT-ergmProposal

TNT proposal with degree bounds, stratification, and a blocks constraint

CondInDegree-ergmProposal

MHp for idegree constraints

CondDegree-ergmProposal

MHp for degree constraints

CondDegreeMix-ergmProposal

MHp for degree mix constraints

CondDegreeDist-ergmProposal

MHp for degreedist constraints

CondB1Degree-ergmProposal

MHp for b1degree constraints

CondInDegreeDist-ergmProposal

MHp for idegreedist constraints