make_one_dataset: Simulate time-varying covariates

In SimTimeVar: Simulate Longitudinal Dataset with Time-Varying Correlated Covariates

Description

Simulates a dataset with correlated time-varying covariates with an exchangeable correlation structure. Covariates can be normal or binary and can be static within a cluster or time-varying. Time-varying normal variables can optionally have linear trajectories within each cluster.

Usage

make_one_dataset(n, obs, n.TBins, pcor, wcor, parameters, cat.parameters)

Arguments

n	The number of clusters.
obs	The number of observations per cluster.
n.TBins	Number of time-varying binary variables.
pcor	The across-subject correlation matrix. See Details.
wcor	The within-subject correlation matrix. See Details.
parameters	A dataframe containing the general simulation parameters. See Details.
cat.parameters	A dataframe containing parameters for the categorical variables. See Details.

Details

SPECIFYING THE PARAMETERS MATRIX

The matrix parameters contains parameters required to generate all non-categorical variables. It must contain column names name, type, across.mean, across.SD, across.var, within.var, prop, and error.SD. (To see an example, use data(params).) Each variable to be generated requires either one or two rows in parameters, depending on the variable type.

The possible variable types and their corresponding specifications are:

• Static binary variables do not change over time within a cluster. For example, if clusters are subjects, sex would be a static binary variable. Generating such a variable requires a single row of type static.binary with prop corresponding to the proportion of clusters for which the variable equals 1 and all other columns set to NA. (The correct standard deviation will automatically be computed later.) For example, if the variable is an indicator for a subject's being male, then prop specifies the proportion of males to be generated.

• Time-varying binary variables can change within a cluster over time, as for an indicator for whether a subject is currently taking the study drug. These variables require two rows in parameters. The first row should be of type static.binary with prop representing the proportion of clusters for which the time-varying binary variable is 1 at least once (and all other columns set to NA). For example, this row in parameters could represent the proportion of subjects who ever take the study drug ("ever-users").

  The second row should be of type subject.prop with across.mean representing, for clusters that ever have a 1 for the binary variable, the proportion of observations within the cluster for which the variable is equal to 1. (All other columns should be set to NA.) For example, this this row in parameters could represent the proportion of observations for which an ever-user is currently taking the drug. To indicate which pair of variables go together, the subject.prop should have the same name as the static.binary variable, but with the suffix _s appended (for example, the former could be named drug_s and the latter drug).

• Normal variables are normally distributed within a cluster such that the within-cluster means are themselves also normally distributed in the population of clusters. Generating a normal variable requires specification of the population mean (across.mean) and standard deviation (across.SD) as well as of the within-cluster standard deviation (within.SD). To generate a static continuous variable, simply set within.SD to be extremely small (e.g., $1 * 10^-7$) and all corresponding correlations in matrix wcor to 0.

• Time-function variables are linear functions of time (with normal error) within each cluster such that the within-cluster baseline values are normally distributed in the population of clusters. Generating a time-function variable requires two entries. The first entry should be of type time.function and specifies the population mean (across.mean) and standard deviation (across.SD) of the within-cluster baseline values as well as the error standard deviation (error.SD). The second entry should be of type normal and should have the same name as the time.function entry, but with the "_s" suffix. This entry specifies the mean (across.mean) and standard deviation (across.SD) of the within-cluster slopes.

SPECIFYING THE CATEGORICAL PARAMETERS MATRIX

The matrix cat.parameters contains parameters required to generate the single categorical variable, if any. It must contain column names level, parameter, and beta. (To see an example, use data(cat.params).)

• The reference level: Each categorical variable must have exactly one "reference" level. The reference level should have one row in cat.parameters for which parameters is set to NA and beta is set to ref. For example, in the example file cat.params specifying parameters to generate a subject's race, the reference level is white.

• Other levels: Other levels of the categorical variable will have one or more rows. One row with parameter set to intercept and beta set to a numeric value represents the intercept term in the corresponding multinomial model. Any subsequent rows, with parameters set to names of other variables in the dataset and beta set to numeric values, represents other coefficients in the corresponding multinomial models.

SPECIFYING THE POPULATION CORRELATION MATRIX

Matrix pcor specifies the population (i.e., across-cluster) correlation matrix. It should have the same number of rows and columns as parameters as well as the same variable names and ordering of variables.

SPECIFYING THE WITHIN-CLUSTER CORRELATION MATRIX

Matrix wcor specifies the within-cluster correlation matrix. The order of the variables listed in this file should be consistent with the order in params and pcor. However, static.binary and subject.prop variables should not be included in wcor since they are static within a cluster. Static continuous variables should be included, but all the correlations should be set to zero.

Examples

data = make_one_dataset(n=10, obs=10, n.TBins=2, pcor=pcor, wcor=wcor, 
parameters=complete_parameters(params, n=10), cat.parameters=cat.params)$data

SimTimeVar documentation built on May 2, 2019, 8:31 a.m.