ernm (version 1.0.4)

createCppSampler: Create a C++ MCMC sampler

Description

Create a C++ MCMC sampler

Usage

createCppSampler(
  formula,
  modelArgs = list(modelClass = "Model"),
  dyadToggle = NULL,
  dyadArgs = list(),
  vertexToggle = NULL,
  vertexArgs = list(),
  nodeSamplingPercentage = 0.2,
  ignoreMnar = TRUE,
  theta = NULL,
  ...
)

Value

a MetropolisHastings object

Arguments

formula

the model formula (see ernm-formula)

modelArgs

additional arguments for the model, e.g. tapering parameters

dyadToggle

the method of sampling to use. Defaults to alternating between nodal-tie-dyad and neighborhood toggling.

dyadArgs

list of args for dyad

vertexToggle

the method of vertex attribute sampling to use.

vertexArgs

list of args for vertex

nodeSamplingPercentage

how often the nodes should be toggled

ignoreMnar

ignore missing not at random offsets

theta

parameter values

...

additional parameters to be passed to createCppModel

Details

Available dyad toggles are:

'RandomDyad' : chooses a dyad randomly to toggle

'TieDyad' : chooses a dyad randomly with probability .5 and a random edge with probability .5

'NodeTieDyad' : chooses a random vertex and then chooses an out dyad from that vertex with probability .5 and an out edge with probability .5

'Neighborhood' : The neighborhood proposal starts by choosing a random vertex (a) and then selecting two random neighbors (b and c) Then a random non-a neighbor of b is also selected (d). The neighborhood toggle selects the dyad b- for toggling with probability 50% and the dyad d-c otherwise.

'Compound_NodeTieDyad_Neighborhood' : chooses 'NodeTieDyad' with probability .5 and 'Neighborhood' otherwise. This is the default proposal.

'Tetrad' : A toggle that preserves network degrees. This is useful when degrees are considered fixed.

'RandomMissingDyad' : RandomDyad, but restricted to missing dyads.

'NodeTieDyadMissing' : NodeTieDyad, but restricted to missing dyads.

'NeighborhoodMissing' : Neighborhood, but restricted to missing dyads.

'Compound_NodeTieDyadMissing_NeighborhoodMissing' : Compound_NodeTieDyad_Neighborhood, but restricted to missing dyads.

Available vertex toggles are:

'DefaultVertex' : The default toggle.

'DefaultVertexMissing' : DefaultVertex, but restricted to missing values.

Examples

if (FALSE) {
edge_list <- matrix(numeric(),ncol=2)
net <- new(UndirectedNet,edge_list,5)
net[["group"]] <- c("a","b","a","b","a")

# create a simple ernm model sampler
sampler <- createCppSampler(net ~ edges() + nodeCount("group") | group, theta = c(0,0))

# generate network statistics for 10 networks with a burn in of 100 steps and 200 steps between them
sampler$generateSampleStatistics(100,200,10)

# generate a network a further 100 steps later
sampler$generateSample(0,100,1)[[1]]

# make a sampler using Tie-Dyad proposals for the graph
td_sampler <- createCppSampler(net ~ edges() + nodeCount("group") | group,
  theta = c(0,0),
  dyadToggle = "TieDyad")
td_sampler$generateSampleStatistics(100,200,10)
}