ergm Termsoptions(rmarkdown.html_vignette.check_title = FALSE)This document seeks to be the most up-to-date API documentation for ergm terms. Note that it is not intended to be a tutorial as much as a description of what inputs and outputs different parts of the system expect.
The storage API defines two types of storage: private storage, which is attached the ModelTerm structure and is specific to each ergm term, and public storage, which is attached to the Model and can be accessed by all terms.
A statistic is a familiar ergm term like “edges” or “nodefactor”: it adds at least one sufficient statistic to the model. Every statistic can have private storage, and it can read from public storage, but it cannot write to public storage.
An auxiliary in an ergm term but not an ERGM term in the mathematical sense: it adds no statistics to the model and exists only to initialize and maintain public storage to be used by statistics. It may not be specified on an ergm formula by the end-user, but only requested by a statistic.
An auxiliary can rely on another auxiliary’s public storage. Note that circular dependencies are not checked.
For the purposes of this overview, the following information is relevant, and is elaborated formally later:
void *mtp->storage to private storagevoid **mtp->aux_storage. (The pointer is to the same location for all terms of a model.)i_), updaters (u_), change stats (c_), difference stats (d_), finalizers (f_), writers (w_), and “eXtended” functions (x_).InitErgmTerm. function’s output list can have an additional element, auxiliaries, a one-sided formula.ergm, summary, etc.); this formula may only have statistics.ergm_model() is called.
InitErgmTerm.<NAME>() functions in turn (or InitWtErgmTerm.<NAME>() for valued ERGMs), adding their output to the model term list. Some terms include auxiliaries formulas in their list.call.ErgmTerm() when it finds that a term has requested auxiliaries, attaches an attribute attr(., "aux.slots") containing an integer vector for the model’s own and/or requested auxiliaries’ positions on the aux_storage vector.ergm.auxstorage() with the complete model.
auxiliaries element for a one-sided formula listing their requested auxiliaries.auxiliaries elements of auxiliary terms and initialises those, etc..model$terms and the index (in the unique list) of the auxiliary requested by each statistic in the aux.slots of the requesting statistic.aux.slots is set to the position of the auxiliary itself.ergm_state is constructed from an edgelist (state$el), an empty network (state$nw0), a model (state$model), and (optionally) a proposal (state$proposal) and a statistics vector (state$stats).update.ergm_state() is called.
term$ext.encode() (if defined) to construct a vector state$ext.state. state$ext.flag is set to reconciled.ergm_state is passed to the C code.Redgelist2Network() initializes the network.ModelInitialize() is called:
ModelInitialize() initializes all terms (statistic and auxiliaries), also counting up the number of auxiliaries (distinguished by having no c_, d_, or s_ functions). A term can export both a c_ function and a d_ function. In that case, it is responsible for deleting one of them when its i_ function is called.void *s, one for each auxiliary. The mtp->aux_storage pointer for each term is set to point to that (one) array.attr(model$terms[[i]], "aux.slotes") to mtp->aux_slots.ergm_model SEXP to model->R, in case it’s needed.ergm_model$terms[[i]] SEXP to mtp->R, in case it’s needed.InitStats() is called, calling the initializer (i_ function) of each term or, if not found, an updater (u_ function) with invalid input (i.e., toggle \((0,0)\)) is called in case the term developer prefers a one-function implementation.ChangeStats() is called.
d_ functions, for those terms for which they are initialized.c_ functions.u_ functions with the toggle (if more to come).u_ function is called, and network is updated for each toggle.ModelDestroy() is called:
DestroyStats() is called, iterating through the terms.
f_) function is called, if defined.mtp->storage is not NULL, it is freed.mtp->aux_storage if not NULL.ErgmStateRSave() is called:
Network2Redgelist() is called, returning a SEXP with the state.w_ function) is called if defined, returning a SEXP with the extended state.state$ext.state. Element state$ext.flag is set to signal that a change was made on the C side.NetworkDestroy() is called.update.ergm_state() is called.
term$ext.decode() (if defined) to update state$nw0 or other aspects of the network. state$ext.flag is set to reconciled.void *mtp->storage: A pointer to private storage.
void **mtp->aux_storage: An array of pointers to public storage, referring to the same memory location for all terms in the model.
R sideUnchanged.
C sidec_, d_, and s_ functionsd_ functions are the original difference statistics. c_ functions are new, while s_ functions have been around for a long time, but never formally documented.
Change statistic (binary): void c_<NAME>(Vertex tail, Vertex head, Model *mtp, Network *nwp, Rboolean edgestate)
Change statistic (valued): void c_<NAME>(Vertex tail, Vertex head, double weight, WtModel *mtp, WtNetwork *nwp, double edgestate)
Difference statistic (binary): void d_<NAME>(Vertex *tails, Vertex *heads, Model *mtp, Network *nwp)
Difference statistic (valued): void d_<NAME>(Vertex *tails, Vertex *heads, double *weights, WtModel *mtp, WtNetwork *nwp)
Summary statistic (binary): void s_<NAME>(Model *mtp, Network *nwp)
Summary statistic (valued): void s_<NAME>(WtModel *mtp, WtNetwork *nwp)
Edge ntgoggles: Number of edges to be toggled or updated.
Vertex tail: Tail of (1) dyad to be toggled or updated.
Vertex *tails: An array of tails of the dyads to be toggled or updated.
Vertex head: Head of (1) dyad to be toggled or updated.
Vertex *heads: An array of heads of the dyads to be toggled or updated.
double weight: New weight for (1) dyad.
double *weights: An array of new weights for the dyads to be toggled or updated.
Model *mtp: A pointer to a Model of interest.
Network *nwp: A pointer to the Network of interest before any toggles are applied.
Rboolean edgestate: An indicator of whether edge (tail,head) is in the network nwp pre-toggle.
double edgestate: The weight of dyad (tail,head) in the network nwp pre-update.
All functions except for s_ expect any storage they need to be initialized and up to date (consistent with nwp). In particular, if their statistic requested \(k\) auxiliary terms, the \(k\) (mtp->n_aux) elements of its mtp->aux_slots vector will be the indexes of mtp->aux_storage where they can find the respective objects.
It is worth noting that macros defined for d_ functions that refer to a specific toggle, such as TAIL, HEAD, etc. might not be usable in a c_ function, but it’s made up for by c_ function’s reduced need for bookkeeping: tail, head, etc. can be used directly.
These functions overwrite mtp->dstats (often aliased as CHANGE_STAT) with the following:
c_ and d_ functions: change of the value of the statistic they implement relative to nwp due to the toggles.s_ the value of the statistic it implements.Every ergm term has private storage, found at void *mtp->storage, which allows it to store arbitrary information about the state of the network, as well as precalculated values of variables, preallocated memory it needs for its calculations, or any other use. It does so by specifying an updating function (and, optionally, an initialization and a finalization function). This updating function is called every time the network is about to change. The API for these functions is defined below.
Public storage is found at void **mtp->aux_storage. Each auxiliary term gets assigned a slot (i.e., void *nwp->mtp->aux_storage[i]) to manage; its slot number is the first element of its input vector, and terms requesting it are told which slot to look in in a similar fashion. An auxiliary term that requests other auxiliaries will have its own slot as the first input and the slots of auxiliaries it requests as subsequent inputs.
R sideA statistic that only references its private storage or is an auxiliary itself does not need to do anything special on the R side.
To request an auxiliary, a term’s InitErgmTerm call’s output list must include an auxiliaries element containing a one-sided ergm-style formula listing the auxiliary terms it wishes to use separated by the + operator.
C side: Modifying Storagei_ functions: Initializer/ConstructorThis function is optional for using storage: if it’s not provided, the model code will call the u_ function with an invalid toggle first, signaling for it to initialize.
Binary: void i_<NAME>(Model *mtp, Network *nwp)
Valued: void i_<NAME>(WtModel *mtp, WtNetwork *nwp)
In general, i_ function expects to be called after ModelInitialize() and NetworkInitialize(), before any c_ or d_ functions. That is, the network must be populated with the ties of its initial state and have mtp->aux_storage vector allocated.
Network populated with initial ties and initialized model.
The first element of mtp->aux_slots is the index of the element of mtp->aux_storage to be managed by this auxiliary. That is mtp->aux_storage[mtp->aux_slots[0]] is a void * to point to the data to be public.
The other data passed from the InitErgmTerm. are shifted over to make room for it.
Allocates memory for the information to be stored and overwrites mtp->storage with a pointer to it, then updates the stored information to be consistent with *nwp.
Public storage
Allocates memory for the information to be stored and overwrites mtp->aux_storage[mtp->aux_slots[0]] with a pointer to it, then updates the stored information to be consistent with *nwp.
An auxiliary can also use its private storage as needed.
u_ functions: UpdaterBinary: void u_<NAME>(Vertex tail, Vertex head, Model *mtp, Network *nwp, Rboolean edgestate)
Valued: void u_<NAME>(Vertex tail, Vertex head, double weight, Model *mtp, Network *nwp, double edgestate)
Initialized network. If no i_ function was provided, to be called with a \((0,0)\) toggle as a signal to initialize; otherwise, initialized storage. Any statistic or auxiliary can rely on its auxiliaries having been initialized before it.
If called with an a toggle (0,0) and uninitialized storage, initialize. This will never be done if an i_ function is defined for the term.
Update the state of its storage (mtp->storage and/or mtp->aux_storage[mtp->aux_slots[0]]) to match what the state of *nwp would be after the given dyad had been toggled.
f_ functions: Finalizer/DestructorThis function is optional for using storage: if it’s not provided, the model code will free any pointers to mtp->aux_storage and mtp->storage that are not NULL.
Binary: void f_<NAME>(Model *mtp, Network *nwp)
Valued: void f_<NAME>(WtModel *mtp, WtNetwork *nwp)
Network and a model.
Deallocates its storage (mtp->storage and/or mtp->aux_storage[mtp->aux_slots[0]]) and sets its pointers to NULL.
C side: Accessing Storagec_, d_, and s_ functions can read from, but not write to, their private storage. c_ and d_ functions can rely on initialization having been called before.
Auxilaries must not implement c_, d_, and s_ functions.
Terms requesting one or more auxiliaries will be passed the indices of the element of mtp->aux_storage by inserting them at the start of mtp->aux_slots. That is mtp->aux_storage[mtp->aux_slots[0]] is a void * to point to the data public by the first auxiliary term on the auxiliaries formula, mtp->aux_storage[mtp->aux_slots[1]] is the second, etc..
x_ functions: eXtensionsThis interface is intended to be used by packages extending ergm to send arbitrary signals to statistics and auxiliaries. For example, for temporal ERGMs, it may be used to signal to the statistic that the clock is about to advance. It is the responsibility of the extension writer to ensure that everything behaves sensibly.
Binary: void x_<NAME>(unsigned int type, void *data, Model *mtp, Network *nwp)
Valued: void x_<NAME>(unsigned int type, void *data, Model *mtp, Network *nwp)
type: a magic constant identifying the type of signal being sent. Based on it, the function can ignore the signal, or determine how to interpret data.
data: arbitrary data to be sent to the function; it is up to the extension writer to determine how it is formatted and interpreted.
There are no restrictions on side-effects. It is up to the extension writer to ensure that everything works.
The following helper macros have been defined to date, and can be found in storage.h.
These functions are defined in ergm_storage.h and exported.
ALLOC_STORAGE(nmemb, stored_type, store_into): Allocate a vector of nmemb elements of type stored_type, save its pointer to private storage and also to a stored_type *store_into which is also declared. Should be used by the i_ function, but may also be used by the u_ function.
GET_STORAGE(stored_type, store_into): Declare stored_type *store_into and assign the pointer to private storage to it. Can be used by all functions.
ALLOC_AUX_STORAGE(nmemb, stored_type, store_into): Allocate a vector of nmemb elements of type stored_type, and save it to the auxiliary storage slot belonging to the calling auxiliary and into a stored_type *store_into which is also declared. Can be used by the i_ function, but may also be used by the u_ function.
GET_AUX_STORAGE(stored_type, store_into): Declare stored_type *store_into and assign the pointer to the auxiliary storage (either for a statistic or for the auxiliary). Can bn used by all functions.
GET_AUX_STORAGE_NUM(stored_type, store_into, ind): Declare stored_type *store_into and assign the pointer to the indth auxiliary). Can be used by clients of auxiliaries.
ALLOC_AUX_SOCIOMATRIX(stored_type, store_into): Allocate an array of appropriate dimension with elements of type stored_type, save it to auxiliary storage, and into **store_type, so that store_into[i][j] returns the value associated with dyad \((i,j)\), with vertices indexed from 1. For bipartite and undirected networks, as little space as possible (resp. a rectangle or a triangle) is allocated.
Note that this term assumes that the private and the public storage of the calling term are not used in any other way.
FREE_AUX_SOCIOMATRIX: Frees the sociomatrix allocated by ALLOC_AUX_SOCIOMATRIX.
MHproposals may also request auxiliary terms. An InitErgmProposal.<NAME>() or InitWtErgmProposal.<NAME>()with an auxiliaries formula will similarly receive the positions of its auxiliaries’ slots in the network. However, this appears to have a slight cost in speed and a potentially significant cost in memory, since the auxiliary may need to duplicate the information in the MH_ function.
Functions prefixed with Mi_, Mu_, and, Mf_ serve as respectively the initializers, the updaters, and the finalizers of the MHproposal storage, though the old-style call with MHp->ntoggles==0 is also supported. Macros in the MHstorage.h header file can be used to access storage the same way as for the statistics.
The function called to generate the proposal can have a prefix of either MH_ (for backwards compatibility) or Mp_ for consistency.
One important difference is that Mp_ function is permitted to write to its private storage. This may be useful if, say, a systematic sample is desired.