ergm_MCMC_sample: Internal Function to Sample Networks and Network Statistics

In ergm: Fit, Simulate and Diagnose Exponential-Family Models for Networks

Internal Function to Sample Networks and Network Statistics

Description

This is an internal function, not normally called directly by the user. The ergm_MCMC_sample function samples networks and network statistics using an MCMC algorithm via MCMC_wrapper and is capable of running in multiple threads using ergm_MCMC_slave.

The ergm_MCMC_slave function calls the actual C routine and does minimal preprocessing.

Usage

ergm_MCMC_sample(
  state,
  control,
  theta = NULL,
  verbose = FALSE,
  ...,
  eta = ergm.eta(theta, (if (is.ergm_state(state)) as.ergm_model(state) else
    as.ergm_model(state[[1]]))$etamap)
)

ergm_MCMC_slave(
  state,
  eta,
  control,
  verbose,
  ...,
  burnin = NULL,
  samplesize = NULL,
  interval = NULL
)

Arguments

state	an ergm_state representing the sampler state, containing information about the network, the model, the proposal, and (optionally) initial statistics, or a list thereof.
control	A list of control parameters for algorithm tuning, typically constructed with control.ergm(), control.simulate.ergm(), etc., which have different defaults. Their documentation gives the the list of recognized control parameters and their meaning. The more generic utility snctrl() (StatNet ConTRoL) also provides argument completion for the available control functions and limited argument name checking.
theta	the (possibly curved) parameters of the model.
verbose	A logical or an integer to control the amount of progress and diagnostic information to be printed. FALSE/0 produces minimal output, with higher values producing more detail. Note that very high values (5+) may significantly slow down processing.
...	additional arugments.
eta	the natural parameters of the model; by default constructed from theta.
burnin, samplesize, interval	MCMC paramters that can be used to temporarily override those in the control list.

Value

ergm_MCMC_sample returns a list containing:

stats	an mcmc.list with sampled statistics.
networks	a list of final sampled networks, one for each thread.
status	status code, propagated from ergm_MCMC_slave().
final.interval	adaptively determined MCMC interval.
final.effectiveSize	adaptively determined target ESS (non-trivial if control$MCMC.effectiveSize is specified via a matrix).
sampnetworks	If control$MCMC.save_networks is set and is TRUE, a list of lists of ergm_states corresponding to the sampled networks.

ergm_MCMC_slave returns the MCMC sample as a list of the following:

s	the matrix of statistics.
state	an ergm_state object for the new network.
status	success or failure code: 0 is success, 1 for too many edges, and 2 for a Metropolis-Hastings proposal failing, -1 for ergm_model or ergm_proposal not passed and missing from the cache.

Note

ergm_MCMC_sample and ergm_MCMC_slave replace ergm.getMCMCsample and ergm.mcmcslave respectively. They differ slightly in their argument names and in their return formats. For example, ergm_MCMC_sample expects ergm_state rather than network/model/proposal, and theta or eta rather than eta0; and it does not return statsmatrix or newnetwork elements. Rather, if parallel processing is not in effect, stats is an mcmc.list with one chain and networks is a list with one element.

Note that unless stats is a part of the ergm_state, the returned stats will be relative to the original network, i.e., the calling function must shift the statistics if required.

At this time, repeated calls to ergm_MCMC_sample will not produce the same sequence of networks as a single long call, even with the same starting seeds. This is because the network sampling algorithms rely on the internal state of the network representation in C, which may not be reconstructed exactly the same way when "resuming". This behaviour may change in the future.

Examples

# This example illustrates constructing "ingredients" for calling
# ergm_MCMC_sample() from calls to simulate.ergm(). One can also
# construct an ergm_state object directly from ergm_model(),
# ergm_proposal(), etc., but the approach shown here is likely to
# be the least error-prone and the most robust to future API
# changes.
#
# The regular simulate() call hierarchy is
#
# simulate_formula.network(formula) ->
#   simulate.ergm_model(ergm_model) ->
#     simulate.ergm_state_full(ergm_state)
#
# They take an argument, return.args=, that will interrupt the call
# and have it return its arguments. We can use it to obtain
# low-level inputs robustly.

data(florentine)
control <- control.simulate(MCMC.burnin = 2, MCMC.interval = 1)


# FYI: Obtain input for simulate.ergm_model():
sim.mod <- simulate(flomarriage~absdiff("wealth"), constraints=~edges,
                    coef = NULL, nsim=3, control=control,
                    return.args="ergm_model")
names(sim.mod)
str(sim.mod$object,1) # ergm_model

# Obtain input for simulate.ergm_state_full():
sim.state <- simulate(flomarriage~absdiff("wealth"), constraints=~edges,
                      coef = NULL, nsim=3, control=control,
                      return.args="ergm_state")
names(sim.state)
str(sim.state$object, 1) # ergm_state

# This control parameter would be set by nsim in the regular
# simulate() call:
control$MCMC.samplesize <- 3

# Capture intermediate networks; can also be left NULL for just the
# statistics:
control$MCMC.save_networks <- TRUE

# Simulate starting from this state:
out <- ergm_MCMC_sample(sim.state$object, control, theta = -1, verbose=6)
names(out)
out$stats # Sampled statistics
str(out$networks, 1) # Updated ergm_state (one per thread)
# List (an element per thread) of lists of captured ergm_states,
# one for each sampled network:
str(out$sampnetworks, 2)
lapply(out$sampnetworks[[1]], as.network) # Converted to networks.

# One more, picking up where the previous sampler left off, but see Note:
control$MCMC.samplesize <- 1
str(ergm_MCMC_sample(out$networks, control, theta = -1, verbose=6), 2)

ergm documentation built on Oct. 7, 2024, 5:08 p.m.