net-accessor: Functions to Access and Edit the Main netsim_dat Object in...

In EpiModel: Mathematical Modeling of Infectious Disease Dynamics

Functions to Access and Edit the Main netsim_dat Object in Network Models

Description

These get_, set_, append_, and add_ functions allow a safe and efficient way to retrieve and mutate the main netsim_dat class object of network models (typical variable name dat).

Usage

get_attr_list(dat, item = NULL)

get_attr(dat, item, posit_ids = NULL, override.null.error = FALSE)

add_attr(dat, item)

set_attr(dat, item, value, posit_ids = NULL, override.length.check = FALSE)

append_attr(dat, item, value, n.new)

get_epi_list(dat, item = NULL)

get_epi(dat, item, at = NULL, override.null.error = FALSE)

add_epi(dat, item)

set_epi(dat, item, at, value)

get_param_list(dat, item = NULL)

get_param(dat, item, override.null.error = FALSE)

add_param(dat, item)

set_param(dat, item, value)

get_control_list(dat, item = NULL)

get_control(dat, item, override.null.error = FALSE)

get_network_control(dat, network, item, override.null.error = FALSE)

add_control(dat, item)

set_control(dat, item, value)

get_init_list(dat, item = NULL)

get_init(dat, item, override.null.error = FALSE)

add_init(dat, item)

set_init(dat, item, value)

append_core_attr(dat, at, n.new)

Arguments

dat	Main netsim_dat object containing a networkDynamic object and other initialization information passed from netsim.
item	A character vector containing the name of the element to access (for get_ functions), create (for add_ functions), or edit (for set_ and append_ functions). Can be of length > 1 for get_*_list functions.
posit_ids	For set_attr and get_attr, a numeric vector of posit_ids or a logical vector to subset the desired item.
override.null.error	If TRUE, get_ will return NULL if the item does not exist instead of throwing an error. (default = FALSE).
value	New value to be attributed in the set_ and append_ functions.
override.length.check	If TRUE, set_attr allows the modification of the item size. (default = FALSE).
n.new	For append_core_attr, the number of new nodes to initiate with core attributes; for append_attr, the number of new elements to append at the end of item.
at	For get_epi, the timestep at which to access the specified item; for set_epi, the timestep at which to add the new value for the epi output item; for append_core_attr, the current time step.
network	index of network for which to get control

Value

A vector or a list of vectors for get_ functions; the main list object for set_, append_, and add_ functions.

Core Attribute

The append_core_attr function initializes the attributes necessary for EpiModel to work (the four core attributes are: "active", "unique_id", "entrTime", and "exitTime"). These attributes are used in the initialization phase of the simulation, to create the nodes (see initialize.net); and also used when adding nodes during the simulation (see arrivals.net).

Mutability

The set_, append_, and add_ functions DO NOT modify the netsim_dat object in place. The result must be assigned back to dat in order to be registered: dat <- set_*(dat, item, value).

set_ and append_ vs add_

The set_ and append_ functions edit a pre-existing element or create a new one if it does not exist already by calling the add_ functions internally.

Examples

dat <- list(
  attr = list(
    active = rbinom(100, 1, 0.9)
  ),
  epi = list(),
  param = list(),
  init = list(),
  control = list(
    nsteps = 150
  )
)
class(dat) <- c("netsim_dat", class(dat))

dat <- add_attr(dat, "age")
dat <- set_attr(dat, "age", runif(100))
dat <- set_attr(dat, "status", rbinom(100, 1, 0.9))
dat <- set_attr(dat, "status", rep(1, 150), override.length.check = TRUE)
dat <- append_attr(dat, "status", 1, 10)
dat <- append_attr(dat, "age", NA, 10)
get_attr_list(dat)
get_attr_list(dat, c("age", "active"))
get_attr(dat, "status")
get_attr(dat, "status", c(1, 4))

dat <- add_epi(dat, "i.num")
dat <- set_epi(dat, "i.num", 150, 10)
dat <- set_epi(dat, "s.num", 150, 90)
get_epi_list(dat)
get_epi_list(dat, c("i.num", "s.num"))
get_epi(dat, "i.num")
get_epi(dat, "i.num", c(1, 4))
get_epi(dat, "i.num", rbinom(150, 1, 0.2) == 1)

dat <- add_param(dat, "x")
dat <- set_param(dat, "x", 0.4)
dat <- set_param(dat, "y", 0.8)
get_param_list(dat)
get_param_list(dat, c("x", "y"))
get_param(dat, "x")

dat <- add_init(dat, "x")
dat <- set_init(dat, "x", 0.4)
dat <- set_init(dat, "y", 0.8)
get_init_list(dat)
get_init_list(dat, c("x", "y"))
get_init(dat, "x")

dat <- add_control(dat, "x")
dat <- set_control(dat, "x", 0.4)
dat <- set_control(dat, "y", 0.8)
get_control_list(dat)
get_control_list(dat, c("x", "y"))
get_control(dat, "x")

EpiModel documentation built on July 9, 2023, 5:21 p.m.