R: Using Discrete-Time Simulation to Generate Complex Data from...

sim_discrete_time {simDAG}

R Documentation

Using Discrete-Time Simulation to Generate Complex Data from a Given DAG and Node Information

Description

Similar to the sim_from_dag function, this function can be used to generate data from a given DAG. In contrast to the sim_from_dag function, this function utilizes a discrete-time simulation approach. This is not an "off-the-shelves" simulation function, it should rather be seen as a "framework-function", making it easier to create discrete-time-simulations. It usually requires custom functions written by the user. See details.

Usage

sim_discrete_time(dag, n_sim=NULL, t0_sort_dag=TRUE,
                  t0_data=NULL, t0_transform_fun=NULL,
                  t0_transform_args=list(), max_t,
                  tx_nodes_order=NULL, tx_transform_fun=NULL,
                  tx_transform_args=list(),
                  save_states="last", save_states_at=NULL,
                  verbose=FALSE, check_inputs=TRUE)

Arguments

`dag`	A `DAG` object created using the `empty_dag` function with `node_td` calls added to it (see details and examples). If the `dag` contains root nodes and child nodes which are time-fixed (those who were added using `node` calls), data according to this DAG will be generated for time = 0. That data will then be used as starting data for the following simulation. Alternatively, the user can specify the `t0_data` argument directly. In either case, the supplied `dag` needs to contain at least one time-dependent node added using the `node_td` function.
`n_sim`	A single number specifying how many observations should be generated. If a `data.table` is supplied to the `t0_data` argument, this argument is ignored. The sample size will then correspond to the number of rows in `t0_data`.
`t0_sort_dag`	Corresponds to the `sort_dag` argument in the `sim_from_dag` function. Ignored if `t0_data` is specified.
`t0_data`	An optional `data.table` like object (also accepts a `data.frame`, `tibble` etc.) containing values for all relevant variables at `t = 0`. This dataset will then be transformed over time according to the node functions specified in `tx_nodes`. Alternatively, data for `t = 0` may be generated automatically by this function if standard `node` calls were added to the `dag`.
`t0_transform_fun`	An optional function that takes the data created at `t = 0` as the first argument. The function will be applied to the starting data and its output will replace the `data.table`. Can be used to perform arbitrary data transformations after the starting data was created. Set to `NULL` (default) to not use this functionality.
`t0_transform_args`	A named list of additional arguments passed to the `t0_transform_fun`. Ignored if `t0_transform_fun=NULL`.
`max_t`	A single integer specifying the final point in time to which the simulation should be carried out. The simulation will start at `t = 1` (after creating the starting data with the arguments above) and will continue with until `max_t` by increasing the time by one unit at every step.
`tx_nodes_order`	A numeric vector specifying the order in which the time-dependent nodes added to the `dag` object using the `node_td` function should be executed at each time step. If `NULL` (default), the nodes will be generated in the order in which they were originally added.
`tx_transform_fun`	An optional function that takes the data created after every point in time `t > 0` as the first argument and the simulation time as the second argument. The function will be applied to that data after all node functions at that point in time have been executed and its output will replace the previous `data.table`. Can be used to perform arbitrary data transformations at every point in time. Set to `NULL` (default) to not use this functionality.
`tx_transform_args`	A named list of additional arguments passed to the `tx_transform_fun`. Ignored if `tx_transform_fun=NULL`.
`save_states`	Specifies the amount of simulation states that should be saved in the output object. Has to be one of `"all"`, `"at_t"` or `"last"` (default). If set to `"all"`, a list of containing the `data.table` after every point in time will be added to the output object. If `"at_t"`, only the states at specific points in time specified by the `save_states_at` argument will be saved (plus the final state). If `"last"`, only the final state of the `data.table` is added to the output.
`save_states_at`	The specific points in time at which the simulated `data.table` should be saved. Ignored if `save_states!="at_t"`.
`verbose`	If `TRUE` prints one line at every point in time before a node function is executed. This can be useful when debugging custom node functions. Defaults to `FALSE`.
`check_inputs`	Whether to perform plausibility checks for the user input or not. Is set to `TRUE` by default, but can be set to `FALSE` in order to speed things up when using this function in a simulation study or something similar.

Details

Sometimes it is necessary to simulate complex data that cannot be described easily with a single DAG and node information. This may be the case if the desired data should contain multiple time-dependent variables or time-to-event variables in which the event has time-dependent effects on other events. An example for this is data on vaccinations and their effects on the occurrence of adverse events (see vignette). Discrete-Time Simulation can be an effective tool to generate these kinds of datasets.

What is Discrete-Time Simulation?:

In a discrete-time simulation, there are entities who have certain states associated with them that only change at discrete points in time. For example, the entities could be people and the state could be alive or dead. In this example we could generate 100 people with some covariates such as age, sex etc.. We then start by increasing the simulation time by one day. For each person we now check if the person has died using a bernoulli trial, where the probability of dying is generated at each point in time based on some of the covariates. The simulation time is then increased again and the process is repeated until we reach max_t.

Due to the iterative process it is very easy to simulate arbitrarily complex data. The covariates may change over time in arbitrary ways, the event probability can have any functional relationship with the covariates and so on. If we want to model an event type that is not terminal, such as occurrence of cardiovascular disease, events can easily be simulated to be dependent on the timing and number of previous events. Since Discrete-Time Simulation is a special case of Discrete-Event Simulation, introductory textbooks on the latter can be of great help in getting a better understanding of the former.

How it Works:

Internally, this function works by first simulating data using the sim_from_dag function. Alternatively, the user can supply a custom data.table using the t0_data argument. This data defines the state of all entities at t = 0. Afterwards, the simulation time is increased by one unit and the data is transformed in place by calling each node function defined by the time-dependent nodes which were added to the dag using the node_td function (either in the order in which they were added to the dag object or by the order defined by the tx_nodes_order argument). Usually, each transformation changes the state of the entities in some way. For example if there is an age variable, we would probably increase the age of each person by one time unit at every step. Once max_t is reached, the resulting data.table will be returned. It contains the state of all entities at the last step with additional information of when they experienced some events (if node_time_to_event was used as time-dependent node). Multiple in-depth examples can be found in the vignettes of this package.

Specifying the dag argument:

The dag argument should be specified as described in the node documentation page. More examples specific to discrete-time simulations can be found in the vignettes and the examples. The only difference to specifying a dag for the sim_from_dag function is that the dag here should contain at least one time-dependent node added using the node_td function.

Speed Considerations:

All functions in this package rely on the data.table backend in order to make them more memory efficient and faster. It is however important to note that the time to simulate a dataset increases non-linearly with an increasing max_t value and additional time-dependent nodes. This is usually not a concern for smaller datasets, but if n_sim is very large (say > 1 million) this function will get rather slow.

What do I do with the output?:

This function outputs a simDT object, not a data.table. To obtain an actual dataset from the output of this function, users should use the sim2data function to transform it into the desired format. Currently, the long-format, the wide-format and the start-stop format are supported. See sim2data for more information.

A Few Words of Caution:

In most cases it will be necessary for the user to write their own functions in order to actually use the sim_discrete_time function. Unlike the sim_from_dag function, in which many popular node types can be implemented in a re-usable way, discrete-time simulation will always require some custom input by the user. This is the price users have to pay for the almost unlimited flexibility offered by this simulation methodology.

Value

Returns a simDT object, containing some general information about the simulated data as well as the final state of the simulated dataset (and more states, depending on the specification of the save_states argument). In particular, it includes the following objects:

past_states: A list containing the generated data at the specified points in time.
save_states: The value of the save_states argument supplied by the user.
data: The data at time max_t.
tte_past_events: A list storing the times at which events happened in variables of type "time_to_event", if specified.
ce_past_events: A list storing the times at which events happened in variables of type "competing_events", if specified.
ce_past_causes: A list storing the types of events which happened at in variables of type "competing_events", if specified.
tx_nodes: A list of all time-varying nodes, as specified in the supplied dag object.
max_t: The value of max_t, as supplied by the user.
t0_var_names: A character vector containing the names of all variable names that do not vary over time.

To obtain a single dataset from this function that can be processed further, please use the sim2data function.

Author(s)

Robin Denz, Katharina Meiszl

References

Tang, Jiangjun, George Leu, und Hussein A. Abbass. 2020. Simulation and Computational Red Teaming for Problem Solving. Hoboken: IEEE Press.

Banks, Jerry, John S. Carson II, Barry L. Nelson, and David M. Nicol (2014). Discrete-Event System Simulation. Vol. 5. Edinburgh Gate: Pearson Education Limited.

Examples

library(simDAG)

set.seed(454236)

## simulating death dependent on age, sex, bmi
## NOTE: this example is explained in detail in one of the vignettes

# initializing a DAG with nodes for generating data at t0
dag <- empty_dag() +
  node("age", type="rnorm", mean=50, sd=4) +
  node("sex", type="rbernoulli", p=0.5) +
  node("bmi", type="gaussian", parents=c("sex", "age"),
       betas=c(1.1, 0.4), intercept=12, error=2)

# a function that increases age as time goes on
node_advance_age <- function(data) {
  return(data$age + 1/365)
}

# a function to calculate the probability of death as a
# linear combination of age, sex and bmi on the log scale
prob_death <- function(data, beta_age, beta_sex, beta_bmi, intercept) {
  prob <- intercept + data$age*beta_age + data$sex*beta_sex + data$bmi*beta_bmi
  prob <- 1/(1 + exp(-prob))
  return(prob)
}

# adding time-dependent nodes to the dag
dag <- dag +
  node_td("age", type="advance_age", parents="age") +
  node_td("death", type="time_to_event", parents=c("age", "sex", "bmi"),
          prob_fun=prob_death, beta_age=0.1, beta_bmi=0.3, beta_sex=-0.2,
          intercept=-20, event_duration=Inf, save_past_events=FALSE)

# run simulation for 100 people, 50 days long
sim_dt <- sim_discrete_time(n_sim=100,
                            dag=dag,
                            max_t=50,
                            verbose=FALSE)

[Package simDAG version 0.1.1 Index]