Working with Custom Attributes and Summary Statistics in EpiModel

Accessing Attributes

The EpiModel::get_attr function will extract the vector of a given attribute. In its simplest form, we can pull a complete attribute vector from dat like so:

active <- EpiModel::get_attr(dat, "active")

The above call will pull from dat the active attribute for all nodes. active is a vector of size current number of nodes. With values being either 1 or 0 depending on whether a node is active or not.

Trying to extract an attribute that does not exist will cause EpiModel::get_attr to throw an error.

Modifying Attributes

In custom extension modules, we usually want to modify some of the attributes. Below is a minimal module that increments the age of all the nodes by 1.

aging_module <- function(dat, at) {

  # Extract current attribute
  age <- EpiModel::get_attr(dat, "age")

  # Aging process
  new_age <- age + 1

  # Output updated attributes
  dat <- EpiModel::set_attr(dat, "age", new_age)

  return(dat)
}

Let’s break down this very simple yet perfectly valid module.

1. Pull the age attribute vector as we did in the previous section.
2. Create a vector new_age incrementing all ages by one.
3. Update the dat object with the EpiModel::set_attr function.
4. Return the Updated dat object.

We can see that EpiModel::set_attr takes as arguments:

• The dat object to update.
• The name of the attribute vector of interest (here “age”).
• The new values for this vector (here new_age).

When using EpiModel::set_attr, there are several things to note:

• The function does not modify the dat object, it merely returns a modified version of it to be assigned back to dat. (Nicely, this does not cause performance issues due to the way R handles shallow copies since version 3.1)
• If new_age size is not equal to the number of nodes in the network, the function will throw an error.

Summary

The above example describes the recommended way to work with attribute:

1. Extract the attributes into local vectors.
2. Modify the local vectors with some dynamic process (like aging).
3. Update the dat object with the revised local vectors.
4. Return the dat object at the end of the function.

These functions have other arguments that are described in the documentation: see help("net-accessor", package = "EpiModel") for further details.

Recording Attribute Histories

The following is a module that records the viral load of infected nodes every 10 time steps. We assume that this module is part of a model that defines and updates two attributes over time:

• status with possible values being “infected” or “susceptible”.
• viral_load as a continuous number for “infected” nodes and NA otherwise.

viral_load_logger_module <- function(dat, at) {

  # Run every 10 time steps
  if (at %% 10 == 0) {

    # Attributes
    status <- EpiModel::get_attr(dat, "status")
    viral_load <- EpiModel::get_attr(dat, "viral_load")

    infected <- which(status == "infected")

    dat <- EpiModel::record_attr_history(
      dat, at,
      "viral_load",
      infected,
      viral_load[infected]
    )
  }

  # Output
  return(dat)
}

The steps in the code are as follows:

1. Check that the current time step is a multiple of ten. If yes, go to step 2, otherwise skip to step 5.
2. Pull the 2 attribute vectors of interest (“status” and “viral_load”).
3. Store in infected the posit_ids of the infected nodes.
4. Record the viral_load of infected nodes at time at under the label “viral_load”.
5. Return the dat object.

EpiModel::record_attr_history takes five arguments:

1. The dat object.
2. The time step to be associated with the recording (here at, the current time-step).
3. The label to be used for the attribute (here “viral_load”).
4. A vector of posit_ids referring to the nodes of interest (here infected).
5. The values to be recorded for those IDs (here viral_load[infected])

Note that EpiModel::record_attr_history requires a set of posit_ids. Internally, the function will convert them to unique_ids so the Attribute History will not be affected by nodes entering or leaving the population over time.

When recording some attribute histories, one must ensure that we record as many values as there are posit_ids. Otherwise, the function will throw an error. It however possible to use only one value for that attribute even if we record a value for multiple nodes. This last situation actually uses less RAM. In any case, we would want to record attribute histories sparingly as the storage can be large, especially for open population models with many nodes that run over many time steps.

Accessing the Attribute Histories

The Attribute History is meant to be accessed once the netsim simulation is complete. At that point, we can use the EpiModel::get_attr_history function to access the histories that we have recorded, like so:

sim <- netsim(est, param, init, control)
attr_history <- EpiModel::get_attr_history(sim)

The attr_history object is a list of data.frames. One for each attribute history that was recorded (we use this flexible list structure because each history may be of different dimension). Assume that we were running two simulations, using the module defined above and another one (not shown) recording when a node switched from infected to recovered.

get_attr_history(sim)

# $viral_load
#    sim step attribute    uids values
# 1  1   10   viral_load   1001   2000
# 2  1   10   viral_load   1002   1878
# 3  1   20   viral_load   1001   1500
# 4  1   20   viral_load   1002    300
# 5  2   10   viral_load    401   2500
# 6  2   10   viral_load    402   1378
# 7  2   20   viral_load    401   1200
# 8  2   20   viral_load    402    100
# ...
#
# $status
#    sim step attribute      uids     values
# 1  1   22   status  1001   infected
# 2  1   64   status  1002   infected
# 3  1  110   status  1001  recovered
# 4  1  220   status  1002  recovered
# 5  2    7   status   401   infected
# 6  2   15   status   402   infected
# 7  2   20   status   401  recovered
# 8  2  120   status   402  recovered
# ...

We would get a named list of two data.frame’s:

• “viral_load” with the value column being the viral loads.
• “status” with the value column being whether the node became “infected” or “recovered” at the given time-step.

Writing Tracker Functions

We call a tracker function a function that takes dat as arguments and outputs a scalar value. Every tracker function is run by EpiModel::netsim at each time step.

epi_s_num <- function(dat) {
  needed_attributes <- c("status")
  output <- with(get_attr_list(dat, needed_attributes), {
    sum(status == "s", na.rm = TRUE)
  })
  return(output)
}

The epi_s_num function defined above is a tracker function. It calculates at each time step the number of susceptible nodes in the network.

The next example is a tracker function that calculates the proportion of the population infected at each time step. Let’s look what each element does:

epi_prop_infected <- function(dat) {
  # we need two attributes for our calculation: `status` and `active`
  needed_attributes <- c("status", "active")
  # we use `with` to simplify code
  output <- with(EpiModel::get_attr_list(dat, needed_attributes), {
    pop <- active == 1    # we only look at active nodes
    cond <- status == "i" # which are infected

    # how many are `infected` among the `active`
    sum(cond & pop, na.rm = TRUE) / sum(pop, na.rm = TRUE)
  })
  return(output)
}

We recommend that you write your tracker functions using this format:

1. Define a needed_attributes variable containing a vector of attribute names: in this example: “status” and “active”.
2. Use with and EpiModel::get_attr_list(dat, needed_attributes) to work in an environment with only the objects you need. This helps clarify what the tracker does and simplify any debugging. We save the result of this call into output.
3. The last statement in the with expression is what will be stored in output. This must be a scalar.
4. return(output), what was calculated inside the with construct.

Using custom tracker functions

This functionality is enabled by passing the tracker functions as a named list in control.net: .tracker.list. Let’s make a simple SI epidemic model with some added trackers:

# Create the `tracker.list` list
some.trackers <- list(
  prop_infected = epi_prop_infected,
  s_num         = epi_s_num
)

control <- EpiModel::control.net(
  type = "SI",
  nsims = 1,
  nsteps = 50,
  verbose = FALSE,
  .tracker.list = some.trackers
)

param <- EpiModel::param.net(
  inf.prob = 0.3,
  act.rate = 0.1
)

nw <- network_initialize(n = 50)
nw <- set_vertex_attribute(nw, "race", rbinom(50, 1, 0.5))
est <- EpiModel::netest(
  nw,
  formation = ~edges,
  target.stats = 25,
  coef.diss = dissolution_coefs(~offset(edges), 10, 0),
  verbose = FALSE
)
#> Starting maximum pseudolikelihood estimation (MPLE):
#> Obtaining the responsible dyads.
#> Evaluating the predictor and response matrix.
#> Maximizing the pseudolikelihood.
#> Finished MPLE.

init <- EpiModel::init.net(i.num = 10)
sim <- EpiModel::netsim(est, param, init, control)

d <- as.data.frame(sim)

knitr::kable(tail(d, n = 15))

Each function must be named in the .tracker.list list. The name given there will be used to identify the tracker function in the epi list and will be the name of the corresponding column of the data.frame produced by as.data.frame(sim) where sim is a netsim object.

Note: in the some.trackers list, we put epi_prop_infected and epi_s_num without parentheses at the end. This is because we store the function and not the result of calling the function.

Important: The trackers are Always run at the end of a simulation step. The value outputted reflect the state of the simulation after all the modules performed their tasks.