umxExamples: Example code from Twin Research and Human Genetics Paper on...

In tbates/umx: Structural Equation Modeling and Twin Modeling in R

Example code from Twin Research and Human Genetics Paper on umx

Description

This is the example code used in our Twin Research and Human Genetics Paper on umx

Usage

umxExamples()

References

• Bates, T. C., Neale, M. C., & Maes, H. H. (2019). umx: A library for Structural Equation and Twin Modelling in R. Twin Research and Human Genetics, 22, 27-41. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1017/thg.2019.2")}.

See Also

• umx()

Examples

## Not run: 

# ==========================================================================
# = Example code from Twin Research and Human Genetics Paper on umx(model) =
# ==========================================================================

# Installing umx can be done using the R-code:
install.packages("umx")
# load as usual
library("umx")

# The current package version can be shown with:
umxVersion("umx")

# Get the latest NPSOL and multi-core build of OpenMx
install.OpenMx("NPSOL")

# Bleeding edge version of OpenMx for MacOS
install.OpenMx("travis")

# ============
# = CFA Code =
# ============

# Load the umx library (this is assumed in subsequent examples
library("umx")

# Load demo data consisting of 5 correlated variables, x1:x5 
data(demoOneFactor)

# Create a list of the manifest variables for use in specifying the model
manifests = paste0("x", 1:5) # 'x1', 'x2', ...'x5'

# Create model cfa1, with name 'CFA', data demoOneFactor, and the CFA paths.

cfa1 = umxRAM("CFA", data = demoOneFactor,
	# Create latent variable 'G', with fixed variance of 1 and mean of 0
	umxPath(v1m0 = "G"),
	# Create 5 manifest variables, x1:x5, with free variance and mean
	umxPath(v.m. = manifests),
	# Create 1-headed paths from G to each of the manifests
	umxPath("G", to = manifests)
)

# ====================
# = Parameter labels =
# ====================

x = xmuLabel(mxMatrix(name="means", "Full", ncol = 2, nrow = 2))
x$labels

# ========
# = Plot =
# ========

plot(cfa1, means = FALSE, fixed = TRUE)
plot(cfa1, std = TRUE, digits = 3, resid= 'line')


m1 = umxRAM("play", data = c("A", "B", "C"),
	umxPath(unique.pairs = c("A", "B", "C"))
)

# ==============================================
# = Inspecting model parameters and residuals. =
# ==============================================

# Show parameters, below .1, with label containing `x2' 
parameters(cfa1, "above", .5, pattern= "x2")

residuals(cfa1, suppress = .005)

# ==================================
# = Modifying and comparing models =
# ==================================

# Variable names in the Duncan data
dimnames = c("RespOccAsp", "RespEduAsp", "RespParAsp", "RespIQ", "RespSES",
             "FrndOccAsp", "FrndEduAsp", "FrndParAsp", "FrndIQ", "FrndSES")
# lower-triangle of correlations among these variables
tmp = c(
	0.6247,
	0.2137, 0.2742,
	0.4105, 0.4043, 0.1839,
	0.3240, 0.4047, 0.0489, 0.2220,
	0.3269, 0.3669, 0.1124, 0.2903, 0.3054,
	0.4216, 0.3275, 0.0839, 0.2598, 0.2786, 0.6404,
	0.0760, 0.0702, 0.1147, 0.1021, 0.0931, 0.2784, 0.1988, 
	0.2995, 0.2863, 0.0782, 0.3355, 0.2302, 0.5191, 0.5007,  0.2087,
	0.2930, 0.2407, 0.0186, 0.1861, 0.2707, 0.4105, 0.3607, -0.0438, 0.2950
)

# Use the umx_lower2full function to create a full correlation matrix
duncanCov = umx_lower2full(tmp, diag = FALSE, dimnames = dimnames)

# Turn the duncan data into an mxData object for the model
duncanCov = mxData(duncanCov, type = "cov", numObs = 300)

respondentFormants   = c("RespSES", "FrndSES", "RespIQ", "RespParAsp")
friendFormants       = c("FrndSES", "RespSES", "FrndIQ", "FrndParAsp")
latentAspiration     = c("RespLatentAsp", "FrndLatentAsp")
respondentOutcomeAsp = c("RespOccAsp", "RespEduAsp")
friendOutcomeAsp     = c("FrndOccAsp", "FrndEduAsp")


duncan1 = umxRAM("Duncan", data = duncanCov,
	# Working from the left of the model, as laid out in the figure, to right...

	# 1. Add all distinct paths between variables to allow the 
	# exogenous manifests to covary with each other.
	umxPath(unique.bivariate = c(friendFormants, respondentFormants)),

	# 2. Add variances for the exogenous manifests,
	# These are assumed to be error-free in this model,
	# and are fixed at their known value).
	umxPath(var = c(friendFormants, respondentFormants), fixedAt = 1),

	# 3. Paths from IQ, SES, and parental aspiration 
	# to latent aspiration for Respondents:
	umxPath(respondentFormants, to = "RespLatentAsp"),
	# And same for friends
	umxPath(friendFormants,     to = "FrndLatentAsp"),

	# 4. Add residual variance for the two aspiration latent traits.
	umxPath(var = latentAspiration),

	# 5. Allow the latent traits each influence the other.
	# This is done using fromEach, and the values are 
	# bounded to improve stability.
	# note: Using one-label would equate these 2 influences
	umxPath(fromEach = latentAspiration, lbound = 0, ubound = 1), 

	# 6. Allow latent aspiration to affect respondent's
	# occupational & educational aspiration.
	# note: firstAt = 1 is used to provide scale to the latent variables.
	umxPath("RespLatentAsp", to = respondentOutcomeAsp, firstAt = 1),

	# And their friends
	umxPath("FrndLatentAsp", to = friendOutcomeAsp, firstAt = 1),
	
	# 7. Finally, on the right hand side of figure, we add
	# residual variance for the endogenous manifests.
	umxPath(var = c(respondentOutcomeAsp, friendOutcomeAsp))
)

# ====================
# = Modifying models =
# ====================

# Collect a list of paths to drop
pathList = c("RespLatentAsp_to_FrndLatentAsp", "FrndLatentAsp_to_RespLatentAsp")

# Modify the model duncan1, requesting a comparison table:
duncan2 = umxModify(duncan1, update = pathList, name = "No_influence", comparison = TRUE)

# An example using regex, to drop all paths beginning "G_to_"
cfa2 = umxModify(cfa1, regex = "^G_to.*")

# ====================
# = Comparing models =
# ====================

umxCompare(duncan1, duncan2, report = "inline")

# To open the output as an html table in a browser, say:
umxCompare(duncan1, duncan2, report = "html")

# =============================
# = Equating model parameters =
# =============================

parameters(duncan1, pattern = "IQ_to_")


duncan3 = umxModify(duncan1, name = "Equate IQ effect", comparison = TRUE,
	master = "RespIQ_to_RespLatentAsp", 
	update = "FrndIQ_to_FrndLatentAsp" 
)

# ================
# = ACE examples =
# ================

require(umx); 
# open the built in dataset of Australian height and weight twin data
data("twinData")
selDVs = c("wt")
dz = twinData[twinData$zygosity == "DZFF", ]
mz = twinData[twinData$zygosity == "MZFF", ]

ACE1 = umxACE(selDVs = selDVs, dzData = dz, mzData = mz, sep = "")
ACE2 = umxModify(ACE1, update = "c_r1c1", name = "dropC")
umxSummary(ACE1, std = FALSE, report = 'html', digits = 3, comparison = ACE2)
parameters(ACE1)

ACE2 = umxModify(ACE1, update = "c_r1c1", name = "dropC")

# ================================
# = Example Common Pathway model =
# ================================

# load twin data built into umx
data("twinData")

# Selecting the 'ht' and 'wt' variables
selDVs = c("ht", "wt")
mzData = subset(twinData, zygosity == "MZFF",)
dzData = subset(twinData, zygosity == "DZFF",)

# Run and report a common-pathway model
CP1 = umxCP(selDVs = selDVs, dzData = dzData, mzData = mzData, suffix = "")

paths = c("c_cp_r1c1", "cs_r1c1", "cs_r2c2")
CP2 = umxModify(CP1, update = paths, name = "dropC", comparison = TRUE)

CP2 = umxModify(CP1, regex = "(^cs_)|(^c_cp_)", name = "dropC")
umxSummary(CP2, comparison = CP1)

# ====================================
# = Example Gene x environment model =
# ====================================

data("twinData")
twinData$age1 = twinData$age2 = twinData$age
# Define the DV and definition variables
selDVs  = c("bmi1", "bmi2")
selDefs = c("age1", "age2")
selVars = c(selDVs, selDefs)

# Create datasets
mzData  = subset(twinData, zygosity == "MZFF")
dzData  = subset(twinData, zygosity == "DZFF")

# Build, run and report the GxE model using selected DV and moderator
# umxGxE will remove and report rows with missing data in definition variables.
GE1 = umxGxE(selDVs = selDVs, selDefs = selDefs, 
  dzData = dzData, mzData = mzData,  dropMissingDef = TRUE)

# Shift the legend to the top right
umxSummary(GE1, location = "topright")

# plot standardized and raw output in separate graphs
umxSummary(GE1, separateGraphs = TRUE)

GE2 = umxModify(GE1, update = "am_r1c1", comparison = TRUE)
umxReduce(GE1)

# =================================
# = Example GxE windowed analysis =
# =================================

require(umx);
data("twinData") 
mod     = "age"
selDVs  = c("bmi1", "bmi2")

# select the younger cohort of twins
tmpTwin = twinData[twinData$cohort == "younger", ]
# Drop twins with missing moderator
tmpTwin = tmpTwin[!is.na(tmpTwin[mod]), ]
mzData  = subset(tmpTwin, zygosity == "MZFF", c(selDVs, mod))
dzData  = subset(tmpTwin, zygosity == "DZFF", c(selDVs, mod))
# toggle autoplot off, so we don't plot every level of the moderator
umx_set_auto_plot(FALSE)
umxGxE_window(selDVs = selDVs, moderator = mod, mzData = mzData, dzData = dzData)
umx_set_auto_plot(TRUE)


## End(Not run)

tbates/umx documentation built on Dec. 14, 2024, 11:28 a.m.