mixmetaSim: Simulating Responses for mixmeta Models

In mixmeta: An Extended Mixed-Effects Framework for Meta-Analysis

Description

These functions simulate sets of responses (either univariate or multivariate) for a group of units, in terms of their mean (expected) values and within and between-group (co)variances. These sets of outcomes can be used in meta-analytical models for simulation purposes.

Usage

mixmetaSim(y, S, Psi, random, data, nsim=1, seed=NULL, ...)

## S3 method for class 'mixmeta'
simulate(object, nsim=1, seed=NULL, ...)

Arguments

In order to simulate k outcomes for n units:

y	a n-dimensional vector (for simulating univariate responses) or m x k matrix (for simulating multivariate responses) of mean (expected) outcomes.
S	series of within-unit variances (or (co)variance matrices for multivariate models) of the estimated outcome(s). For the list of accepted format, see the argument with the same name in mixmeta. Covariances or more complex error structures can be passed through additional arguments. See Details below.
Psi	the random-effects (co)variance matrix (or a list of matrices for multilevel models) of the outcomes. Dimension must be consistent with the specification of the random-effects structure in random.
random	a one-sided formula (or a list of formulae for multilevel models) offering a symbolic description of the linear predictor(s) and grouping structure for the random-effects part of the model. See the argument with the same name in mixmeta.
data	an optional data frame, list or environment (or object coercible by as.data.frame to a data frame), optionally containing the variables in y, S, and random.
nsim	number of simulation sets.
seed	an object specifying if and how the random number generator should be initialized.
object	an object of class "mixmeta".
...	further optional arguments.

Details

The set(s) of responses can be simulated either from a fitted model, using the method function simulate for objects of class "mixmeta", or directly through the function mixmetaSim. In the former case, the fitted values from the model are used as mean (expected) outcomes, together with the within-unit and estimated random-effects (co)variance structure. In the latter option, this information need to be provided by the user in the correct dimensions and forms.

Additional arguments can be passed in '...'. Specifically, arguments Scor and addSlist can be added to input missing within-unit error covariances, or to specify more complex within-unit error structures, respectively. Another argument can be checkPD (logical), that checks the semi-positive definiteness of the matrices). See mixmeta.control for details.

The functions simulate the responses for each study separately from a marginal multivariate normal distribution with mean equal to the expected values and (co)variance equal to the sum of the within-unit errors and random-effects components. The computation is identical to that implemented in the function mvrnorm of the package MASS, involving a eigen decomposition of the marginal (co)variance matrix. Numerical negative definiteness is checked, and positive semi-definiteness then forced by truncating the eigenvalues at a value close to zero (see control).

Value

If nsim=1, a matrix or vector of simulated k outcomes for the n units. If more simulation sets are required (nsim higher than 1), a list of matrices or vectors.

Note

Studies with missing values in the fitted values or in the components of the within (co)variances are excluded by simulate. Missing values are instead not accepted in metaSim.

Author(s)

Antonio Gasparrini <[e-mail]> and Francesco Sera <[e-mail]>

References

Sera F, Armstrong B, Blangiardo M, Gasparrini A (2019). An extended mixed-effects framework for meta-analysis.Statistics in Medicine. 2019;38(29):5429-5444. [Freely available here].

See Also

See simulate for the general method function. See inputcov for inputting correlations. See mixmeta-package for an overview of the package and modelling framework.

Examples

# RUN A MODEL
model <- mixmeta(cbind(PD,AL) ~ pubyear, S=berkey98[5:7], data=berkey98)

# SIMULATE A NEW SET OF OUTCOMES
simulate(model)

# SIMULATE FROM SCRATCH: 3 OUTCOMES, 8 STUDIES
(y <- matrix(0, 8, 3))
(S <- inputcov(matrix(runif(8*3, 0.1, 2), 8, 3, dimnames=list(NULL,
  c("V1","V2","V3"))), cor=c(0,0.5,0.7)))
(Psi <- inputcov(1:3, cor=0.3))
mixmetaSim(y, S, Psi)

# 2 SIMULATION SETS
mixmetaSim(y, S, Psi, nsim=2)

mixmeta documentation built on Oct. 16, 2021, 5:09 p.m.