long2LGMM: Long data to wide latent growth mixture model

Description Usage Arguments Details Examples

View source: R/trainlgmm.R

Description

This function streamlines the process of converting long data into a format that Mplus can use for latent growth mixture models in wide form. It makes use of continuous time scores, and these time scores must be supplied as variables in the R dataset. For the conversion to wide form, it is assumed that although assessments may have happened in continuous time, a discrete number of assessments (likely ismilar for all participants) were collected.

Usage

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long2LGMM(data, idvar, assessmentvar, dv, timevars, misstrick = TRUE,
  k = 1L, title = "Trajectory Model", base = "trajmodel_",
  run = FALSE, processors = 1L, starts = "500 100", newdata,
  cov = c("un", "independent", "intercept", "zero"), model)

Arguments

data

A data frame in long format (i.e., multiple rows per ID).

idvar

A character string of the variable name in the dataset that is the ID variable.

assessmentvar

A character string of the variable name in the dataset that indicates the particular assessment point for each timepoint.

dv

A character string of the dependent variable name.

timevars

A character vector of the time variables. Can be a single variable or more than one. By allowing more than one variable, it is easy to include linear; linear and quadratic; it is also possible to calculate splines in R and pass these. The variable names should be 7 characters or fewer, each.

misstrick

A logical value whether to set values of the DV where a time variable is missing to missing as well. Defaults to TRUE.

k

An integer indicating the number of distinct classes to test. Currently must be greater than 0 and less than 10.

title

A character string giving a title for the model

base

A character string providing a base name for model outputs, that is combined with the number of classes.

run

A logical value whether or not to run the models or only create the data and input files, but not run them.

processors

An integer value indicating the number of processors to use.

starts

A character string passed to Mplus providing the number of random starts and iterations

newdata

A data frame of new values to use for generating predicted trajectories by class.

cov

A character string indicating the random covariance structure to use

model

An optional argument, can pass an existing model, the output from mplusModeler().

Details

One valuable feature of this function is that it makes it possible to feed any continuous time scores to Mplus for mixture modelling. For example, continuous linear time is straightforward, but so to are quadratic time models or piecewise models. Using facilities in R, spline models are also comparatively easy to specify.

Examples

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## Not run: 
## Simulate Some Data from 3 classes
library(MASS)
set.seed(1234)
allcoef <- rbind(
  cbind(1, mvrnorm(n = 200,
                   mu = c(0, 2, 0),
                   Sigma = diag(c(.2, .1, .01)),
                   empirical = TRUE)),
  cbind(2, mvrnorm(n = 200,
                   mu = c(-3.35, 2, 2),
                   Sigma = diag(c(.2, .1, .1)),
                   empirical = TRUE)),
  cbind(3, mvrnorm(n = 200,
                   mu = c(3.35, 2, -2),
                   Sigma = diag(c(.2, .1, .1)),
                   empirical = TRUE)))
allcoef <- as.data.frame(allcoef)
names(allcoef) <- c("Class", "I", "L", "Q")
allcoef$ID <- 1:nrow(allcoef)
d <- do.call(rbind, lapply(1:nrow(allcoef), function(i) {
  out <- data.frame(
    ID = allcoef$ID[i],
    Class = allcoef$Class[i],
    Assess = 1:11,
    x = sort(runif(n = 11, min = -2, max = 2)))
  out$y <- rnorm(11,
    mean = allcoef$I[i] + allcoef$L[i] * out$x + allcoef$Q[i] * out$x^2,
    sd = .1)
  return(out)
}))

## create splines
library(splines)
time_splines <- ns(d$x, df = 3, Boundary.knots = quantile(d$x, probs = c(.02, .98)))
d$t1 <- time_splines[, 1]
d$t2 <- time_splines[, 2]
d$t3 <- time_splines[, 3]
d$xq <- d$x^2

## create new data to be used for predictions
nd <- data.frame(ID = 1,
                 x = seq(from = -2, to = 2, by = .1))
nd.splines <- with(attributes(time_splines),
                   ns(nd$x, df = degree, knots = knots,
                      Boundary.knots = Boundary.knots))
nd$t1 <- nd.splines[, 1]
nd$t2 <- nd.splines[, 2]
nd$t3 <- nd.splines[, 3]
nd$xq <- nd$x^2

## create a tuning grid of models to try
## all possible combinations are created of different time trends
## different covariance structures of the random effects
## and different number of classes
tuneGrid <- expand.grid(
  dv = "y",
  timevars = list(c("t1", "t2", "t3"), "x", c("x", "xq")),
  starts = "2 1",
  cov = c("independent", "zero"),
  k = c(1L, 3L),
  processors = 1L, run = TRUE,
  misstrick = TRUE, stringsAsFactors = FALSE)
tuneGrid$title <- paste0(
  c("linear", "quad", "spline")[sapply(tuneGrid$timevars, length)],
  "_",
  sapply(tuneGrid$cov, function(x) if(nchar(x)==4) substr(x, 1, 4) else substr(x, 1, 3)),
  "_",
  tuneGrid$k)
tuneGrid$base <- paste0(
  c("linear", "quad", "spline")[sapply(tuneGrid$timevars, length)],
  "_",
  sapply(tuneGrid$cov, function(x) if(nchar(x)==4) substr(x, 1, 4) else substr(x, 1, 3)))

## example using long2LGMM to fit one model at a time
mres <- long2LGMM(
        data = d,
        idvar = "ID",
        assessmentvar = "Assess",
        dv = tuneGrid$dv[1],
        timevars = tuneGrid$timevars[[1]],
        misstrick = tuneGrid$misstrick[1],
        k = tuneGrid$k[1],
        title = paste0(tuneGrid$title[1], tuneGrid$k[1]),
        base = tuneGrid$base[1],
        run = tuneGrid$run[1],
        processors = tuneGrid$processors[1],
        starts = tuneGrid$starts[1],
        newdata = nd,
        cov = tuneGrid$cov[1])

rm(mres)

## End(Not run)

MplusAutomation documentation built on Nov. 25, 2018, 5:04 p.m.