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ergm (version 4.5.0)

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

6,396

Version

4.5.0

License

GPL-3 + file LICENSE

Maintainer

Pavel N. Krivitsky

Last Published

May 28th, 2023

Functions in ergm (4.5.0)

Wrap binary terms for use in valued models

CondInDegreeDist-ergmProposal

MHp for idegreedist constraints

CondDegreeMix-ergmProposal

MHp for degree mix constraints

CondDegreeDist-ergmProposal

MHp for degreedist constraints

DiscUnif-ergmReference

Discrete Uniform reference

Take a natural logarithm of a network's statistic

DiscUnif-ergmProposal

NodematchFilter-ergmTerm

Filtering on nodematch

Modify terms' coefficient names

DiscUnifNonObserved-ergmProposal

HammingTNT-ergmProposal

DiscUnif2-ergmProposal

A for operator for terms

HammingConstantEdges-ergmProposal

CondOutDegree-ergmProposal

MHp for odegree constraints

absdiff-ergmTerm

Absolute difference in nodal attribute

CondOutDegreeDist-ergmProposal

MHp for odegreedist constraints

absdiffcat-ergmTerm

Categorical absolute difference in nodal attribute

altkstar-ergmTerm

Alternating \(k\)-star

DistRLE-ergmProposal

UnifNonObserved-ergmProposal

Symmetrize-ergmTerm

Evaluation on symmetrized (undirected) network

Filtering on arbitrary one-term model

Evaluation on an induced subgraph

Exponentiate a network's statistic

Dyads-ergmConstraint

Constrain fixed or varying dyad-independent terms

atmost-ergmTerm

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

Unif-ergmReference

Continuous Uniform reference

attrcov-ergmTerm

Edge covariate by attribute pairing

StdNormal-ergmProposal

Unif-ergmProposal

b1concurrent-ergmTerm

Concurrent node count for the first mode in a bipartite network

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

TNT-ergmProposal

Default MH algorithm

b1degrange-ergmTerm

Degree range for the first mode in a bipartite network

b1degree-ergmTerm

Degree for the first mode in a bipartite network

ConstantEdges-ergmProposal

MHp for edges constraints

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

Dyadwise shared partners for dyads in the second bipartition

b2factor-ergmTerm

Factor attribute effect for the second mode in a bipartite network

b1degrees-ergmConstraint

Preserve the actor degree for bipartite networks

b2starmix-ergmTerm

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

b2degrange-ergmTerm

Degree range for the second mode in a bipartite network

blockdiag-ergmConstraint

Block-diagonal structure constraint

blocks-ergmConstraint

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

b2twostar-ergmTerm

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

StdNormal-ergmReference

Standard Normal reference

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

Dyadwise shared partners for dyads in the first bipartition

Impose a curved structure on term parameters

Offset-ergmTerm

Terms with fixed coefficients

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

b1twostar-ergmTerm

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

b2concurrent-ergmTerm

Concurrent node count for the second mode in a bipartite network

coincidence-ergmTerm

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

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

approx.hotelling.diff.test

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

ANOVA for ERGM Fits

b2sociality-ergmTerm

concurrent-ergmTerm

Concurrent node count

concurrentties-ergmTerm

Concurrent tie count

b2star-ergmTerm

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

as.network.numeric

Create a Simple Random network of a Given Size

control.ergm.godfather

Control parameters for ergm.godfather().

Auxiliary for Controlling ERGM Goodness-of-Fit Evaluation

control.ergm.bridge

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

Auxiliary for Controlling ERGM Fitting

degreedist-ergmConstraint

Preserve the degree distribution of the given network

ctriple-ergmTerm

degree1.5-ergmTerm

Degree to the 3/2 power

Auxiliary for Controlling SAN

as.rlebdm.ergm_conlist

Extract dyad-level ERGM constraint information into an rlebdm object

dyadnoise-ergmConstraint

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

b1factor-ergmTerm

Factor attribute effect for the first mode in a bipartite network

asymmetric-ergmTerm

Asymmetric dyads

atleast-ergmTerm

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

Two versions of an E. Coli network dataset

edgecov-ergmTerm

dyadnoise-ergmProposal

degrange-ergmTerm

b1nodematch-ergmTerm

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

b1mindegree-ergmTerm

Minimum degree for the first mode in a bipartite network

b1sociality-ergmTerm

Computes and Returns the Degree Distribution Information for a Given Network

control.simulate.ergm

Auxiliary for Controlling ERGM Simulation

b1star-ergmTerm

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

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

ergm.bridge.llr

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

degrees-ergmConstraint

Preserve the degree of each vertex of the given network

Operations to map curved ergm() parameters onto canonical parameters

Compute the Sample Estimating Function Values of an ERGM.

b1starmix-ergmTerm

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

degree-ergmTerm

balance-ergmTerm

Balanced triads

Calculate the exact loglikelihood for an ERGM

b2mindegree-ergmTerm

Minimum degree for the second mode in a bipartite network

b2degrees-ergmConstraint

Preserve the receiver degree for bipartite networks

bd-ergmConstraint

Constrain maximum and minimum vertex degree

Parallel Processing in the ergm Package

b2degree-ergmTerm

Degree for the second mode in a bipartite network

Fit, Simulate and Diagnose Exponential-Family Models for Networks

Locate and call an ERGM term initialization function.

Ensures an Ergm Term and its Arguments Meet Appropriate Conditions

equalto-ergmTerm

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

ergm.geodistdist

Calculate geodesic distance distribution for a network or edgelist

enformulate.curved-deprecated

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

egocentric-ergmConstraint

Preserve values of dyads incident on vertices with given attribute

Internal representation of an ergm network model

b2nodematch-ergmTerm

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

ergm_plot.mcmc.list

Plot MCMC list using lattice package graphics

MCMC Hints for Exponential-Family Random Graph Models

Functions that have been removed from this package

Keywords defined for Exponential-Family Random Graph Models

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

Exponential-Family Random Graph Models

ergm_Cstate_clear

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

Reference Measures for Exponential-Family Random Graph Models

Directed edgewise shared partners

faux.desert.high

Faux desert High School as a network object

Curved settings for geometric weights for the gw* terms

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

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

ergm_dyadgen_select

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

Initializes the parameters to bound degree during sampling

ergm_edgecov_args

A common pattern for obtaining an edge covariate

Terms used in Exponential Family Random Graph Models

degcor-ergmTerm

Degree Correlation

degcrossprod-ergmTerm

Degree Cross-Product

ergm_cutoff_message

Helper function for constructing gw* cutoff error messages

density-ergmTerm

gwdegree-ergmTerm

Geometrically weighted degree distribution

Functions to initialize the ergm_proposal object

cyclicalties-ergmTerm

Geometrically weighted edgewise shared partner distribution

Geometrically weighted dyadwise shared partner distribution

gwidegree-ergmTerm

Geometrically weighted in-degree distribution

Goodreau's Faux Mesa High School as a network object

idegree1.5-ergmTerm

In-degree to the 3/2 power

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

ergm_proposal_table

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

greaterthan-ergmTerm

Number of dyads with values strictly greater than a threshold

ininterval-ergmTerm

Number of dyads whose values are in an interval

idegrees-ergmConstraint

Preserve indegree for directed networks

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

idegreedist-ergmConstraint

Preserve the indegree distribution

cyclicalweights-ergmTerm

Cyclical weights

A logLik method for ergm fits.

Calculate the null model likelihood

edges-ergmConstraint

Preserve the edge count of the given network

Number of edges in the network

mutual-ergmTerm

Synthetic network with 20 nodes and 28 edges

idegree-ergmTerm

idegrange-ergmTerm

In-degree range

Directed dyadwise shared partners

dyadcov-ergmTerm

Dyadic covariate

localtriangle-ergmTerm

Triangles within neighborhoods

nodeofactor-ergmTerm

Factor attribute effect for out-edges

nodecov-ergmTerm

Main effect of a covariate

nodecovar-ergmTerm

Covariance of undirected dyad values incident on each actor

fixallbut-ergmConstraint

Preserve the dyad status in all but the given edges

fixedas-ergmConstraint

Preserve and preclude edges

dyadnoiseTNT-ergmProposal

faux.dixon.high

Faux dixon High School as a network object

faux.magnolia.high

Goodreau's Faux Magnolia High School as a network object

Geometrically weighted non-edgewise shared partner distribution

gwodegree-ergmTerm

Geometrically weighted out-degree distribution

meandeg-ergmTerm

Mean vertex degree

Mixing matrix cells and margins

ergm-deprecated

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

nodefactor-ergmTerm

Factor attribute effect

odegreedist-ergmConstraint

Preserve the outdegree distribution

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

ergm.getnetwork

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

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

Sensible error and warning messages by ergm initializers

nodeicovar-ergmTerm

Covariance of in-dyad values incident on each actor

is.dyad.independent

Testing for dyad-independence

.dyads-ergmConstraint

A meta-constraint indicating handling of arbitrary dyadic constraints

ergm_MCMC_sample

Internal Function to Sample Networks and Network Statistics

nodeicov-ergmTerm

Main effect of a covariate for in-edges

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

nvattr.copy.network

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

Directed non-edgewise shared partners

Internal Function to Perform Simulated Annealing

Internal ergm Objects

odegrees-ergmConstraint

Preserve outdegree for directed networks

isolatededges-ergmTerm

receiver-ergmTerm

Receiver effect

RLE-Compressed Boolean Dyad Matrix

Global options and term options for the ergm package

randomtoggle-ergmProposal

Propose a randomly selected dyad to toggle

isolates-ergmTerm

nearsimmelian-ergmTerm

Near simmelian triads

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

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

nodeifactor-ergmTerm

Factor attribute effect for in-edges

observed-ergmConstraint

Preserve the observed dyads of the given network

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

Statnet Control

Dynamic ERGM keyword registry

sender-ergmTerm

Find a maximizer to the psuedolikelihood function

odegrange-ergmTerm

Out-degree range

ergm_mk_std_op_namewrap

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

Sample Space Constraints for Exponential-Family Random Graph Models

Generate networks with a given set of network statistics

A lack-of-fit test for ERGMs

smallerthan-ergmTerm

Number of dyads with values strictly smaller than a threshold

smalldiff-ergmTerm

Number of ties between actors with similar attribute values

A Representation of ERGM state

sociality-ergmTerm

Undirected degree

ERGM Predictors and response for logistic regression calculation of MPLE

search.ergmTerms

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

summary_formula

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

ergm_state_cache

A rudimentary cache for large objects

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

summary.formula

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

simmelian-ergmTerm

Simmelian triads

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.

simmelianties-ergmTerm

Ties in simmelian triads

sparse-ergmHint

Update the edges in a network based on a matrix

Weighted Median

Metropolis-Hastings Proposal Methods for ERGM MCMC

ergm_preprocess_response

Update the network and the response argument.

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

triangle-ergmTerm

tripercent-ergmTerm

Triangle percentage

gwb1degree-ergmTerm

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

gwb1dsp-ergmTerm

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

hamming-ergmConstraint

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

hamming-ergmTerm

Hamming distance

Stratify Proposed Toggles by Mixing Type on a Vertex Attribute

transitive-ergmTerm

Transitive triads

Sum of dyad values (optionally taken to a power)

transitiveties-ergmTerm

Transitive ties

ergm_propagate_ext.encode

Extended states for submodels

m2star-ergmTerm

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

nodal_attributes

Specifying nodal attributes and their levels

mcmc.diagnostics

Conduct MCMC diagnostics on a model fit

ergm_symmetrize

Return a symmetrized version of a binary network

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

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

nodal_attributes-API

Helper functions for specifying nodal attribute levels

nodematch-ergmTerm

Uniform homophily and differential homophily

gwb2degree-ergmTerm

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

nodemix-ergmTerm

Nodal attribute mixing

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

gwb2dsp-ergmTerm

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

odegree1.5-ergmTerm

Out-degree to the 3/2 power

odegree-ergmTerm

simulate.formula

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

Draw from the distribution of an Exponential Family Random Graph Model

intransitive-ergmTerm

Intransitive triads

Summarizing ERGM Model Fits

summary.ergm_model

Evaluate network summary statistics from an initialized ergm model

ttriple-ergmTerm

Transitive triples

Testing for curved exponential family

opentriad-ergmTerm

Kapferer's tailor shop data

nodeocovar-ergmTerm

Covariance of out-dyad values incident on each actor

nodeocov-ergmTerm

Main effect of a covariate for out-edges

twopath-ergmTerm

Names of the parameters associated with an object.

predict.formula

ERGM-based tie probabilities

threetrail-ergmTerm

triadcensus-ergmTerm

to_ergm_Cdouble.network

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

transitiveweights-ergmTerm

Transitive weights

Bernoulli-ergmReference

Bernoulli reference

CondB2Degree-ergmProposal

MHp for b2degree constraints

CondB1Degree-ergmProposal

MHp for b1degree constraints

CondInDegree-ergmProposal

MHp for idegree constraints

BDStratTNT-ergmProposal

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

CondDegree-ergmProposal

MHp for degree constraints