NEWS file for the tergm package

Changes in version 4.2.2

C-LEVEL FACILITIES

• Update to work with ergm 4.9 ABI.

Changes in version 4.2.1

NEW FEATURES

• In TERGM simulation, space for toggle history is now dynamically allocated; this is mainly visible in more efficient memory usage.

BUG FIXES

• Calloc(), Realloc(), and Free() C calls now use their R_-prefixed counterparts.

• tergm() with CMLE for networkDynamic now stops with an informative error message if times= is not passed.

• Some corner cases in the discordant bounded-degree stratified TNT proposal have been fixed.

• General documentation fixes and improvements.

OTHER USER-VISIBLE CHANGES

• Error messages in TERGM MCMC sampling are now more informative.

Changes in version 4.2.0

NEW FEATURES

• Operators Form(), Persist(), Diss(), Cross(), and Change() can now specify time-varying network-level covariates using the syntax of N.

• tergm() now supports a basis= argument like ergm() does.

• tergm's functions now support networkLite objects in place of network objects.

BUG FIXES

• tergm()'s term options are now propagated correctly.

• tergm's simulate_formula.network() no longer propagates dynamic argument onto the ergm's back-end when dynamic=FALSE.

OTHER USER-VISIBLE CHANGES

• tergm now relies on ergm.multi for much of its back-end.

Changes in version 4.1.1

BUG FIXES

• networkDynamic now handles dimnames more consistently.

OTHER USER-VISIBLE CHANGES

• Documentation improvements.

• Terms edgecov.mean.age() and edgecov.ages() now handle their arguments more consistently with edgecov() and stop with error if the network does not have the specified attribute.

DEPRECATED & DEFUNCT

• stergm() and related facilities have been deprecated.

• Some vestigial files have been removed.

• Workaround storing ergm::simulate_formula() is no longer needed.

Changes in version 4.1.0

NEW FEATURES

• Term documentation has been ported to the ergm 4.2 documentation API.

• New term operator EdgeAges.

• Term and proposal keyword/concept durational is registered by tergm.

BUG FIXES

• Fixes to handling of networkDynamic objects.

• Fixes to documentation URLs.

OTHER USER-VISIBLE CHANGES

• Miscellaneous speed-ups.

• Documentation for some arguments and control parameters is now more standardized and detailed.

• Dissolution parameter estimation in the simple (EDApprox) case is a bit more accurate.

DEPRECATED & DEFUNCT

• stergm() has been deprecated in favor of [tergm()], whose special case it is. It, and its associated functions may be removed in a future release.

Changes in version 4.0.2

BUG FIXES

• Fixes to acommodate ergm's BDStratTNT API changes (which were not as backwards-compatible as hoped).

• Better error checking in simulate() calls.

• Some memory leaks fixed.

OTHER USER-VISIBLE CHANGES

• Cross() operator term now labels its coefficient names as such.

Changes in version 4.0.1

NEW FEATURES

• The package has undergone a major rewrite, making use of operator terms introduced in ergm 4.0 to facilitate model specification. See the “Conversions for tergm version 4.0” vignette for some examples.

• stergm has been superseded by tergm, which can fit non-separable discrete temporal ERGMs as well as separable.

• In temporal estimation and simulation, operator terms Form(), Persist(), and Diss() can be used to specify STERGMs, with Form() evaluating statistics on a post-formation network, Persist() on post-dissolution (i.e., persistence) network, and Diss() on the post-dissolution network, but with statistics negated for convenience. Change() and Cross() can be used to specify models for changes (i.e., a “virtual” network that has edges where the previous network differs from the current one) and models for cross-section.

• NetSeries() constructor can be used to specify network series for conditional estimation and simulation (though tergm does it automatically for appropriate input).

• Constraints applied via constraints= argument for tergm() and simulate.tergm() are now applied to the sampled or estimated networks rather than to formation and dissolution phases separately.

• Control parameters in tergm's functions can now be specified using snctrl().

DEPRECATED & DEFUNCT

• stergm and its family of functions has been deprecated.

Changes in version 3.7.0

BUG FIXES

• Durational terms edges.ageinterval (s_ function) and edgecov.mean.age (s_ and d_ functions) had bugs fixed.

• A bug involving assumptions based on the first entry of the lasttoggle vector has been corrected.

• A number of broken links has been fixed.

OTHER USER-VISIBLE CHANGES

• The package no longer (incorrectly) requires R 3.6.0 or the very-very latest version of nlme.

• Progress reports are now printed to stderr rather than stdout.

Changes in version 3.6.0

NEW FEATURES

• Compatibility with ergm 3.10 API changes.

• Optimizations to make use of ergm 3.10 APIs and parallel facilities.

• Improved utilization of san.

• stergm's eval.loglik= argument's default can now be controlled by a options-style option.

BUG FIXES

• Miscellaneous compiler warnings fixed.

Changes in version 3.5.2

NEW FEATURES

• Compatibility with ergm 3.9 API changes.

BUG FIXES

• Documentation fixes.

• A number of methods are no longer called directly but through generics.

DEPRECATED & DEFUNCT

• stergm.getMCMCsample and stergm.mcmcslave have been deprecatedin favor of stergm_MCMC_sample and stergm_MCMC_slave, respectively.

Changes in version 3.4.1

NEW FEATURES

• Development has been migrated to GitHub.

BUG FIXES

• Constraint violations in dynamic MCMC are now handled correctly.

• Native C routine registration has been added.

OTHER USER-VISIBLE CHANGES

• By request from Sam Jennes, stergm.getMCMCsample.slave has been split out of stergm.getMCMCsample and exported.

Changes in version 3.4.0

BUG FIXES

• Miscellaneous bugfixes.

• The list of functions exported is now explicitly defined.

• robust.inverse has been replaced by ginv.

Changes in version 3.3.1

NEW FEATURES

• STERGM conditional MLE can now be fit to series of more than two bipartite networks. (Previously, for bipartite networks, only a series of two (i.e., one transition) could be fit.)

BUG FIXES

• Miscellaneous CMLE bug fixes.

• Some low-priority warnings are no longer printed by default.

• A bug in formation TNT proposals has been fixed. The only analyses that may be affected are those on tiny (about 8 nodes) or extremely dense (i.e., high probability of a complete graph) networks.

Changes in version 3.3

NEW FEATURES

• A new control parameter, SA.par.eff.pow, now controls the degree to which the magnitude of the gradient afects the rescaling of the estimating functions (see help): higher means that "stronger" parameters effectively get lower gain, making the optimization more stable.

• Running with verbose=TRUE now prints gc output periodically.

• Most durational functions can now take a binary option log=, which will result in them using log-ages instead of raw ages. (In a discrete-time model, there are no 0-age ties, so log transformation is safe.)

• tergm.godfather example now tests for a few more terms, degrange ages in particular.

• Implemented reference to MH_listTNT in applicable constraints in tergm as well.

• Durational statistics can now take NULL as their "role", disabling role testing.

BUG FIXES

• Running STERGM EGMME with parallel > 0 no longer causes it to eat up all the memory.

• Namespace prefixing has been added to some functions called from external packages to deal with CRAN check warnings, replaced require and library calls with requireNamespace()

• Updated CITATION file to deal with CRAN check warnings (packageDescription is no longer used).

• Added S3 method registration in NAMESPACE for all S3 functions.

• Handling of networkDynamic inputs has been improved.

OTHER USER-VISIBLE CHANGES

• Changed CMLE MCMC default parameters to match those of ergm.

• Additions and corrections to documentation

• Most formerly undocumented 'internal' functions have been made internal by the NAMESPACE. As far as we know, this avoids functions in use by reverse-Depending packages. These currently appear as commented items in the NAMESPACE file.

Changes in version 3.2.4

BUG FIXES

• Some potential memory issues revealed by Valgrind have been fixed.

Changes in version 3.2

NEW FEATURES

• Speed improvements. Internal data handling has been modified to avoid allocating (and passing around) a large matrix of tie ages unless the formula/model explicitly requires tie duration information. This increases speed of model initialization, which is especially helpful when simulating a network where the model must be re-initialized at each timestep (i.e. models with vital dynamics).

• Simplified specification of offset values in formation model, when using stergm.EGMME with target statistics. Edges dissolution approximation is used to initialize the coefficients for estimation when there is an offset. See https://statnet.org/Workshops/tergm_tutorial.html for examples.

• Offset terms in the target formula are automatically removed. This includes the case where the target is set equal to formation: targets = "formation"

• The simulate.networkDynamic and related function now make use of networkDynamics persistant id (PID) functionality. If the network does not have any persistent.ids defined for vertices, a vertex.pid will be attached in a vertex attribute named 'tergm_pid' to facilitate 'bookkeeping' between the networkDynamic argument and the simulated network time step.

• Parallel functionality: tergm can take user-created clusters as the control.stergm(parallel) control parameter. This is the recommended method for using tergm on a high-performance computing cluster. See ergm-parallel. Functionality is now implemented via the parallel package, direct dependence on snow package is removed

• Addition of bipartite formation and dissolution Metropolis-Hastings proposals

• Addition of a TNT dissolution proposal constraint

• Inclusion of a Stergm vignette

• -Inf offsets are recoded to a large negative number to be compatible with C code. The fitted coefficients will show the large negative number instead of the -Inf offset.

BUG FIXES

• Namespace prefixing has been added to some functions called from external packages to deal with CRAN check warnings

• Bug fix where stergm constraints were not being passed from all the way down into san

OTHER USER-VISIBLE CHANGES

• Changes to control.stergm parameters:

  • init.method If NULL (the default), the initial values are computed using the edges dissolution approximation (Carnegie et al.) when appropriate. If set to "zeros", the initial values are set to zeros.

  • SA.oh.memory = 100000 Absolute maximum number of data points per thread to store in the full optimization history.

• Changes to simulate.stergm parameters: addition of duration.dependent parameter to control whether the model terms in formula or model are duration dependent. E.g., if a duration-dependent term is used in estimation/simulation model, the probability of forming or dissolving a tie may dependent on the age the dyad status.

Changes in version 3.1.3

BUG FIXES

• Some Metropolis-Hastings proposal functions would sometimes return incorrect acceptance probabilities when combined with the bd constraint. This has been fixed.

• In simulate.networkDynamic, an error in which vertices were queried and updated in the simulation has been fixed.

OTHER USER-VISIBLE CHANGES

• simulate.networkDynamic and simulate.network functions now take an additional argument, time.offset. See help for those functions for details.

Changes in version 3.1.2

NEW FEATURES

• The Tie-NonTie (TNT) proposal has been implemented for dissolution phase models. This should improve mixing and inference for these models.

• stergm and simulate.stergm now determine the number of Metropolis-Hastings steps per time step adaptively, stopping when the formation/dissolution process appears to have converged.

DEPRECATED & DEFUNCT

• The previously deprecated start and end attr values attached to networks returned by simulate.network and simulate.networkDynamic have been removed and replaced with observation spells recorded as a net.obs.period network attribute.

• MCMC.burnin and MCMC.interval arguments to control.stergm, control.simulate.network, and control.simulate.stergm have been replaced by a different mechanism. See the help for the respective control functions for more information.

BUG FIXES

• No longer generates deprecation warnings about start and end attrs when various internal functions use as.data.frame. Resolved by replacing start and end with a net.obs.period object.

• A bug in the check for whether terms were amenable to being fit using STERGM CMLE for multiple transitions has been fixed.

• Some minor documentation typos have been fixed.

Changes in version 3.1.1

• Version 3.1.1 has been skipped to ease upgrading for those using a preview release.

Changes in version 3.1

THIS IS AN INITIAL RELEASE

• This package consists of the dynamic network modeling code that has been split out of the ergm package.

• Changes listed in the following sections are relative to ergm version 3.0.

NEW FEATURES

• Although fitting the EGMME for dissolution was possible before, it was impractical due to nonidentifiability: for example, one cannot fit both edges formation and edges dissolution with only one edges target statistic. Four new statistics have been added and documented that focus on targeting observed and hazard: mean.age, edgecov.mean.age, degree.mean.age, degrange.mean.age, edge.ages, edgecov.ages, and edges.ageinterval. This allow jointly fitting formation and dissolution.

• In addition to the progress plot, EGMME fitting routines can now plot the estimated gradient matrix and the matrix of correlations among the target statistics.

• EGMME fitting is now more adaptive when determining when to stop the optimization and return the result.

• EGMME fitting can now take advantage of multiple CPUs, cores, or cluster nodes for faster and more robust fitting.

• EGMME and CMLE fitting can now accommodate a constraints argument. However, note that the constraints apply to post-formation (y^+=y^0\cup\y^1) and post-dissolution (y^-=y^0\cap\y^1) networks, not to the final network (y^1). This may change in the future.

• CMLE can now be fit to more than two networks. (Not all ERGM terms and constraints can be used in this mode, however.)

• A new (sort of) function, tergm.godfather has been fixed and documented; it can be used to apply a specific set of changes to a network, returning statistics of interest as it evolves. In particular, it can be used to “retrace” the evolution of a networkDynamic, calculating statistics at discrete time points along the way.

• tergm now implements a formula-based summary method for networkDynamic LHS, to compute dynamic network statistics at specified time points.

• Fitting CMLE to network series with transitioned-from networks having missing dyads is now possible, using automatic imputation. See impute.network.list and control.tergm.

  STERGM simulate can now be used for CMLE fits, takes a number of new arguments, and can be used to “resume” a simulation from a networkDynamic object.

  gof methods have been implemented for CMLE fits.

OTHER USER-VISIBLE CHANGES

• stergm EGMME initial fitting code has been vastly improved.

• The EGMME fitting algorithm has been vastly improved and is now a lot more adaptive and able to recover from problems. Many bugs have also been fixed.

DEPRECATED & DEFUNCT

• A number of control.stergm parameters had been renamed and otherwise changed.

• Argument statsonly to the simulate.stergm and related functions has been deprecated in favor of output.

BUG FIXES

• The conditional MPLE (CMPLE) for formation and dissolution is now fit correctly. This also means that the starting values for the CMLE are much better.

• Bugs in EGMME code related to handling of bipartite networks have been fixed.