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ergm (version 4.3.1)

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 (2021) .

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Install

install.packages('ergm')

Monthly Downloads

6,854

Version

4.3.1

License

GPL-3 + file LICENSE

Maintainer

Pavel N. Krivitsky

Last Published

November 7th, 2022

Functions in ergm (4.3.1)

CondInDegreeDist-ergmProposal

MHp for idegreedist constraints

Wrap binary terms for use in valued models

CondDegreeDist-ergmProposal

MHp for degreedist constraints

CondB1Degree-ergmProposal

MHp for b1degree constraints

CondInDegree-ergmProposal

MHp for idegree constraints

CondDegree-ergmProposal

MHp for degree constraints

Bernoulli-ergmReference

Bernoulli reference

BDStratTNT-ergmProposal

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

CondDegreeMix-ergmProposal

MHp for degree mix constraints

CondB2Degree-ergmProposal

MHp for b2degree constraints

Impose a curved structure on term parameters

DistRLE-ergmProposal

DiscUnifNonObserved-ergmProposal

ConstantEdges-ergmProposal

MHp for edges constraints

DiscUnif2-ergmProposal

CondOutDegreeDist-ergmProposal

MHp for odegreedist constraints

CondOutDegree-ergmProposal

MHp for odegree constraints

Dyads-ergmConstraint

Constrain fixed or varying dyad-independent terms

DiscUnif-ergmReference

Discrete Uniform reference

DiscUnif-ergmProposal

NodematchFilter-ergmTerm

Filtering on nodematch

A for operator for terms

Take a natural logarithm of a network's statistic

Exponentiate a network's statistic

Modify terms' coefficient names

HammingTNT-ergmProposal

Filtering on arbitrary one-term model

Offset-ergmTerm

Terms with fixed coefficients

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

HammingConstantEdges-ergmProposal

UnifNonObserved-ergmProposal

Symmetrize-ergmTerm

Evaluation on symmetrized (undirected) network

TNT-ergmProposal

Default MH algorithm

Evaluation on an induced subgraph

StdNormal-ergmProposal

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

StdNormal-ergmReference

Standard Normal reference

Unif-ergmProposal

Unif-ergmReference

Continuous Uniform reference

absdiff-ergmTerm

Absolute difference in nodal attribute

approx.hotelling.diff.test

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

Extract dyad-level ERGM constraint information from an ergm fit into an rlebdm object

atmost-ergmTerm

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

altkstar-ergmTerm

Alternating \(k\)-star

absdiffcat-ergmTerm

Categorical absolute difference in nodal attribute

asymmetric-ergmTerm

Asymmetric dyads

atleast-ergmTerm

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

as.network.numeric

Create a Simple Random network of a Given Size

as.rlebdm.ergm_conlist

Extract dyad-level ERGM constraint information into an rlebdm object

b1mindegree-ergmTerm

Minimum degree for the first mode in a bipartite network

b1degree-ergmTerm

Degree for the first mode in a bipartite network

b1degrange-ergmTerm

Degree range for the first mode in a bipartite network

ANOVA for ERGM Fits

b1degrees-ergmConstraint

Preserve the actor degree for bipartite networks

b1nodematch-ergmTerm

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

attrcov-ergmTerm

Edge covariate by attribute pairing

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

Dyadwise shared partners for dyads in the first bipartition

b1concurrent-ergmTerm

Concurrent node count for the first mode in a bipartite network

b1factor-ergmTerm

Factor attribute effect for the first mode in a bipartite network

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

b1star-ergmTerm

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

b2degrees-ergmConstraint

Preserve the receiver degree for bipartite networks

b1starmix-ergmTerm

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

b1twostar-ergmTerm

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

Dyadwise shared partners for dyads in the second bipartition

b2concurrent-ergmTerm

Concurrent node count for the second mode in a bipartite network

b1sociality-ergmTerm

b2degrange-ergmTerm

Degree range for the second mode in a bipartite network

b2degree-ergmTerm

Degree for the second mode in a bipartite network

balance-ergmTerm

Balanced triads

b2twostar-ergmTerm

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

blockdiag-ergmConstraint

Block-diagonal structure constraint

b2mindegree-ergmTerm

Minimum degree for the second mode in a bipartite network

b2star-ergmTerm

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

bd-ergmConstraint

Constrain maximum and minimum vertex degree

b2nodematch-ergmTerm

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

b2starmix-ergmTerm

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

b2factor-ergmTerm

Factor attribute effect for the second mode in a bipartite network

b2sociality-ergmTerm

blocks-ergmConstraint

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

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

concurrentties-ergmTerm

Concurrent tie count

concurrent-ergmTerm

Concurrent node count

Locate and call an ERGM term initialization function.

control.ergm.godfather

Control parameters for ergm.godfather().

coincidence-ergmTerm

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

Ensures an Ergm Term and its Arguments Meet Appropriate Conditions

control.ergm.bridge

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

Auxiliary for Controlling ERGM Fitting

degcrossprod-ergmTerm

Degree Cross-Product

ctriple-ergmTerm

Auxiliary for Controlling SAN

cyclicalties-ergmTerm

cyclicalweights-ergmTerm

Cyclical weights

Directed dyadwise shared partners

degcor-ergmTerm

Degree Correlation

Auxiliary for Controlling ERGM Goodness-of-Fit Evaluation

control.simulate.ergm

Auxiliary for Controlling ERGM Simulation

degree1.5-ergmTerm

Degree to the 3/2 power

degrange-ergmTerm

dgwdsp-ergmTerm

Geometrically weighted dyadwise shared partner distribution

dgwesp-ergmTerm

Geometrically weighted edgewise shared partner distribution

degrees-ergmConstraint

Preserve the degree of each vertex of the given network

degreedist-ergmConstraint

Preserve the degree distribution of the given network

Directed edgewise shared partners

Computes and Returns the Degree Distribution Information for a Given Network

density-ergmTerm

degree-ergmTerm

dyadnoise-ergmProposal

Directed non-edgewise shared partners

dyadnoise-ergmConstraint

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

Dyadwise shared partners

dyadcov-ergmTerm

Dyadic covariate

dyadnoiseTNT-ergmProposal

Two versions of an E. Coli network dataset

dgwnsp-ergmTerm

Geometrically weighted non-edgewise shared partner distribution

.dyads-ergmConstraint

A meta-constraint indicating handling of arbitrary dyadic constraints

Number of edges in the network

egocentric-ergmConstraint

Preserve values of dyads incident on vertices with given attribute

ergm-deprecated

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

edgecov-ergmTerm

edges-ergmConstraint

Preserve the edge count of the given network

Internal ergm Objects

Sensible error and warning messages by ergm initializers

equalto-ergmTerm

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

enformulate.curved-deprecated

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

Functions that have been removed from this package

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

Fit, Simulate and Diagnose Exponential-Family Models for Networks

Global options and term options for the ergm package

Parallel Processing in the ergm Package

Calculate the exact loglikelihood for an ERGM

ergm.bridge.llr

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

Operations to map curved ergm() parameters onto canonical parameters

Exponential-Family Random Graph Models

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

Compute the Sample Estimating Function Values of an ERGM.

Sample Space Constraints for Exponential-Family Random Graph Models

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.

Metropolis-Hastings Proposal Methods for ERGM MCMC

ergm.geodistdist

Calculate geodesic distance distribution for a network or edgelist

Reference Measures for Exponential-Family Random Graph Models

MCMC Hints for Exponential-Family Random Graph Models

Keywords defined for Exponential-Family Random Graph Models

Find a maximizer to the psuedolikelihood function

ERGM Predictors and response for logistic regression calculation of MPLE

Terms used in Exponential Family Random Graph Models

Curved settings for geometric weights for the gw* terms

ergm_mk_std_op_namewrap

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

Initializes the parameters to bound degree during sampling

ergm_MCMC_sample

Internal Function to Sample Networks and Network Statistics

ergm_Cstate_clear

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

Internal Function to Perform Simulated Annealing

ergm_dyadgen_select

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

ergm_edgecov_args

A common pattern for obtaining an edge covariate

Dynamic ERGM keyword registry

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

ergm_symmetrize

Return a symmetrized version of a binary network

ergm_plot.mcmc.list

Plot MCMC list using lattice package graphics

ergm_state_cache

A rudimentary cache for large objects

ergm_propagate_ext.encode

Extended states for submodels

ergm_preprocess_response

Update the network and the response argument.

Internal representation of an ergm network model

ergm_proposal_table

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

A Representation of ERGM state

Functions to initialize the ergm_proposal object

faux.dixon.high

Faux dixon High School as a network object

fixallbut-ergmConstraint

Preserve the dyad status in all but the given edges

fixedas-ergmConstraint

Preserve and preclude edges

Edgewise shared partners

faux.desert.high

Faux desert High School as a network object

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

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

faux.magnolia.high

Goodreau's Faux Magnolia High School as a network object

Goodreau's Faux Mesa High School as a network object

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

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

greaterthan-ergmTerm

Number of dyads with values strictly greater than a threshold

gwb2dsp-ergmTerm

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

gwdegree-ergmTerm

Geometrically weighted degree distribution

gwb2degree-ergmTerm

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

Geometrically weighted dyadwise shared partner distribution

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

gwb1dsp-ergmTerm

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

gwb1degree-ergmTerm

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

gwidegree-ergmTerm

Geometrically weighted in-degree distribution

idegreedist-ergmConstraint

Preserve the indegree distribution

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

Geometrically weighted edgewise shared partner distribution

hamming-ergmTerm

Hamming distance

idegree1.5-ergmTerm

In-degree to the 3/2 power

hamming-ergmConstraint

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

idegree-ergmTerm

idegrange-ergmTerm

In-degree range

Geometrically weighted nonedgewise shared partner distribution

intransitive-ergmTerm

Intransitive triads

gwodegree-ergmTerm

Geometrically weighted out-degree distribution

idegrees-ergmConstraint

Preserve indegree for directed networks

isolatededges-ergmTerm

isolates-ergmTerm

ininterval-ergmTerm

Number of dyads whose values are in an interval

Testing for curved exponential family

Kapferer's tailor shop data

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

is.dyad.independent

Testing for dyad-independence

mutual-ergmTerm

Synthetic network with 20 nodes and 28 edges

m2star-ergmTerm

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

localtriangle-ergmTerm

Triangles within neighborhoods

Calculate the null model likelihood

meandeg-ergmTerm

Mean vertex degree

Mixing matrix cells and margins

mcmc.diagnostics

Conduct MCMC diagnostics on a model fit

A logLik method for ergm fits.

nodecovar-ergmTerm

Covariance of undirected dyad values incident on each actor

nodecov-ergmTerm

Main effect of a covariate

nodeicovar-ergmTerm

Covariance of in-dyad values incident on each actor

nodal_attributes

Specifying nodal attributes and their levels

nodeicov-ergmTerm

Main effect of a covariate for in-edges

nodeifactor-ergmTerm

Factor attribute effect for in-edges

nearsimmelian-ergmTerm

Near simmelian triads

nodal_attributes-API

Helper functions for specifying nodal attribute levels

nodefactor-ergmTerm

Factor attribute effect

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

odegrange-ergmTerm

Out-degree range

Nonedgewise shared partners

nodematch-ergmTerm

Uniform homophily and differential homophily

observed-ergmConstraint

Preserve the observed dyads of the given network

nodeocov-ergmTerm

Main effect of a covariate for out-edges

nvattr.copy.network

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

nodeofactor-ergmTerm

Factor attribute effect for out-edges

nodemix-ergmTerm

Nodal attribute mixing

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

nodeocovar-ergmTerm

Covariance of out-dyad values incident on each actor

odegree-ergmTerm

Names of the parameters associated with an object.

odegreedist-ergmConstraint

Preserve the outdegree distribution

odegrees-ergmConstraint

Preserve outdegree for directed networks

odegree1.5-ergmTerm

Out-degree to the 3/2 power

predict.formula

ERGM-based tie probabilities

opentriad-ergmTerm

randomtoggle-ergmProposal

Propose a randomly selected dyad to toggle

A lack-of-fit test for ERGMs

sender-ergmTerm

Generate networks with a given set of network statistics

simmelianties-ergmTerm

Ties in simmelian triads

simmelian-ergmTerm

Simmelian triads

search.ergmTerms

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

receiver-ergmTerm

Receiver effect

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

RLE-Compressed Boolean Dyad Matrix

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

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

Stratify Proposed Toggles by Mixing Type on a Vertex Attribute

smalldiff-ergmTerm

Number of ties between actors with similar attribute values

sparse-ergmHint

smallerthan-ergmTerm

Number of dyads with values strictly smaller than a threshold

Sum of dyad values (optionally taken to a power)

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

Statnet Control

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

sociality-ergmTerm

Undirected degree

threetrail-ergmTerm

transitive-ergmTerm

Transitive triads

summary.formula

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

transitiveties-ergmTerm

Transitive ties

transitiveweights-ergmTerm

Transitive weights

triadcensus-ergmTerm

summary_formula

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

summary.ergm_model

Evaluate network summary statistics from an initialized ergm model

Summarizing ERGM Model Fits

to_ergm_Cdouble.network

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

triangle-ergmTerm

ttriple-ergmTerm

Transitive triples

Update the edges in a network based on a matrix

Weighted Median

tripercent-ergmTerm

Triangle percentage

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.

twopath-ergmTerm