umxACEcov: Run a Cholesky with covariates that are random (in the expected covariance matrix)

Description

Often, researchers include covariates in 2-group Cholesky umxACE() twin models. The umxACEcov 'random' option models the covariates in the expected covariance matrix, thus allowing all data to be preserved. The downside is that this method has a strong assumption of multivariate normality. Covariates like age, which are perfectly correlated in twins cannot be used. Covariates like sex, which are ordinal, violate the normality assumption.

Usage

umxACEcov(
  name = "ACEcov",
  selDVs,
  selCovs,
  dzData,
  mzData,
  sep = NULL,
  type = c("Auto", "FIML", "cov", "cor", "WLS", "DWLS", "ULS"),
  allContinuousMethod = c("cumulants", "marginals"),
  dzAr = 0.5,
  dzCr = 1,
  addStd = TRUE,
  addCI = TRUE,
  boundDiag = 0,
  equateMeans = TRUE,
  bVector = FALSE,
  autoRun = getOption("umx_auto_run"),
  tryHard = c("no", "yes", "ordinal", "search"),
  optimizer = NULL
)

Arguments

name

The name of the model (defaults to"ACE").

selDVs

The variables to include from the data (do not include sep).

selCovs

The covariates to include from the data (do not include sep).

dzData

The DZ dataframe.

mzData

The MZ dataframe.

sep

Separator text between basename for twin variable names. Often "_T". Used to expand selDVs into full column names, i.e., "dep" --> c("dep_T1", "dep_T2").

type

Analysis method one of c("Auto", "FIML", "cov", "cor", "WLS", "DWLS", "ULS")

allContinuousMethod

"cumulants" or "marginals". Used in all-continuous WLS data to determine if a means model needed.

dzAr

The DZ genetic correlation (defaults to .5, vary to examine assortative mating).

dzCr

The DZ "C" correlation (defaults to 1: set to .25 to make an ADE model).

addStd

Whether to add the algebras to compute a std model (defaults to TRUE).

addCI

Whether to add intervals to compute CIs (defaults to TRUE).

boundDiag

= Whether to bound the diagonal of the a, c, and e matrices.

equateMeans

Whether to equate the means across twins (defaults to TRUE).

bVector

Whether to compute row-wise likelihoods (defaults to FALSE).

autoRun

Whether to run the model (default), or just to create it and return without running.

tryHard

Default ('no') uses normal mxRun. "yes" uses mxTryHard. Other options: "ordinal", "search"

optimizer

optionally set the optimizer. Default (NULL) does nothing.

Value

mxModel() of subclass mxModel.ACEcov

Details

The following figure shows how the ACE model with random covariates appears as a path diagram:

Figure: ACEcovVarianceModel.png

References

Neale, M. C., & Martin, N. G. (1989). The effects of age, sex, and genotype on self-report drunkenness following a challenge dose of alcohol. Behavior Genetics, 19, 63-78. doi:https://doi.org/10.1007/BF01065884.

Schwabe, I., Boomsma, D. I., Zeeuw, E. L., & Berg, S. M. (2015). A New Approach to Handle Missing Covariate Data in Twin Research : With an Application to Educational Achievement Data. Behavior Genetics, 46, 583-95. doi:https://doi.org/10.1007/s10519-015-9771-1.

Examples

Run this code

# NOT RUN {
# ============================================
# = BMI, can't use Age as a random covariate =
# ============================================
require(umx)
data(twinData)
# Replicate age to age1 & age2
twinData$age1 = twinData$age2 = twinData$age
mzData = subset(twinData, zygosity == "MZFF")
dzData = subset(twinData, zygosity == "DZFF")

# =====================================================================
# = Trying to use identical var (like age) as a random cov is ILLEGAL =
# =====================================================================
m1 = umxACEcov(selDVs = "bmi", selCovs = "age", dzData = dzData, mzData = mzData, sep = "")

# ========================================================
# = Use an lm-based age-residualisation approach instead =
# ========================================================

resid_data = umx_residualize("bmi", "age", suffixes = 1:2, twinData)
mzData = subset(resid_data, zygosity == "MZFF")
dzData = subset(resid_data, zygosity == "DZFF")
m2     = umxACE("resid", selDVs = "bmi", dzData = dzData, mzData = mzData, sep = "")

# Univariate BMI without covariate of age for comparison
mzData = subset(twinData, zygosity == "MZFF")
dzData = subset(twinData, zygosity == "DZFF")
m3 = umxACE("raw_bmi", selDVs = "bmi", dzData = dzData, mzData = mzData, sep = "")

# ===========================================================================
# = A bivariate example (need a dataset with a VIABLE COVARIATE to do this) =
# ===========================================================================
selDVs  = c("ht", "wt") # Set the DV
selCovs = c("income") # Set the COV
selVars = umx_paste_names(selDVs, covNames = selCovs, sep = "", sep = 1:2)
# 80 rows so example runs fast on CRAN
mzData = subset(twinData, zygosity == "MZFF", selVars)[1:80, ]
dzData = subset(twinData, zygosity == "DZFF", selVars)[1:80, ]
m1 = umxACEcov(selDVs = selDVs, selCovs = selCovs,
   dzData = dzData, mzData = mzData, sep = "", autoRun = TRUE
)
# }

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