sim: Simulate Observed or Full Data from 'DAG' Object

Description Usage Arguments Value Forward Imputation References See Also Examples

View source: R/simulation.r

Description

This function simulates full data based on a list of intervention DAGs, returning a list of data.frames. See the vignette for examples and detailed description.

Usage

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sim(DAG, actions, n, wide = TRUE, LTCF = NULL, rndseed = NULL,
  rndseed.reset.node = NULL, verbose = getOption("simcausal.verbose"))

Arguments

DAG

A DAG objects that has been locked with set.DAG(DAG). Observed data from this DAG will be simulated if actions argument is omitted.

actions

Character vector of action names which will be extracted from the DAG object. Alternatively, this can be a list of action DAGs selected with A(DAG) function, in which case the argument DAG is unused. When actions is omitted, the function returns simulated observed data (see simobs).

n

Number of observations to sample.

wide

A logical, if TRUE the output data is generated in wide format, if FALSE, the output longitudinal data in generated in long format

LTCF

If forward imputation is desired for the missing variable values, this argument should be set to the name of the node that indicates the end of follow-up event.

rndseed

Seed for the random number generator.

rndseed.reset.node

When rndseed is specified, use this argument to specify the name of the DAG node at which the random number generator seed is reset back to NULL (simulation function will call set.seed(NULL)). Can be useful if one wishes to simulate data using the set seed rndseed only for the first K nodes of the DAG and use an entirely random sample when simulating the rest of the nodes starting at K+1 and on. The name of such (K+1)th order DAG node should be then specified with this argument.

verbose

Set to TRUE to print messages on status and information to the console. Turn this off by default using options(simcausal.verbose=FALSE).

Value

If actions argument is missing a simulated data.frame is returned, otherwise the function returns a named list of action-specific simulated data.frames with action names giving names to corresponding list items.

Forward Imputation

By default, when LTCF is left unspecified, all variables that follow after any end of follow-up (EFU) event are set to missing (NA). The end of follow-up event occurs when a binary node of type EFU=TRUE is equal to 1, indicating a failing or right-censoring event. To forward impute the values of the time-varying nodes after the occurrence of the EFU event, set the LTCF argument to a name of the EFU node representing this event. For additional details and examples see the vignette and doLTCF function.

References

Sofrygin O, van der Laan MJ, Neugebauer R (2017). "simcausal R Package: Conducting Transparent and Reproducible Simulation Studies of Causal Effect Estimation with Complex Longitudinal Data." Journal of Statistical Software, 81(2), 1-47. doi: 10.18637/jss.v081.i02.

See Also

simobs - a wrapper function for simulating observed data only; simfull - a wrapper function for simulating full data only; doLTCF - forward imputation of the missing values in already simulating data; DF.to.long, DF.to.longDT - converting longitudinal data from wide to long formats.

Other simulation functions: simfull, simobs

Examples

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t_end <- 10
lDAG <- DAG.empty()
lDAG <- lDAG +
	node(name = "L2", t = 0, distr = "rconst", const = 0) +
	node(name = "A1", t = 0, distr = "rconst", const = 0) +
	node(name = "L2", t = 1:t_end, distr = "rbern",
 	prob = ifelse(A1[t - 1]  ==  1, 0.1,
 			ifelse(L2[t-1] == 1, 0.9,
        min(1,0.1 + t/t_end)))) +
	node(name = "A1", t = 1:t_end, distr = "rbern",
 	prob = ifelse(A1[t - 1]  ==  1, 1,
 			 ifelse(L2[0] == 0, 0.3,
			  ifelse(L2[0] == 0, 0.1,
			   ifelse(L2[0] == 1, 0.7, 0.5))))) +
	node(name = "Y", t = 1:t_end, distr = "rbern",
 	prob = plogis(-6.5 + 4 * L2[t] + 0.05 * sum(I(L2[0:t] == rep(0,(t + 1))))),
 	EFU = TRUE)
lDAG <- set.DAG(lDAG)
#---------------------------------------------------------------------------------------
# EXAMPLE 1. No forward imputation.
#---------------------------------------------------------------------------------------
Odat.wide <- sim(DAG = lDAG, n = 1000, rndseed = 123)
Odat.wide[c(21,47), 1:18]
Odat.wideLTCF <- sim(DAG = lDAG, n = 1000, LTCF = "Y", rndseed = 123)
Odat.wideLTCF[c(21,47), 1:18]
#---------------------------------------------------------------------------------------
# EXAMPLE 2. With forward imputation.
#---------------------------------------------------------------------------------------
Odat.wideLTCF2 <- doLTCF(data = Odat.wide, LTCF = "Y")
Odat.wideLTCF2[c(21,47), 1:18]
# all.equal(Odat.wideLTCF, Odat.wideLTCF2)

osofr/simcausal documentation built on Jan. 6, 2019, 3:05 a.m.