OpenMx Structural Equation Modeling
Parameter contraints across subgroups
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Empirical Underidentification with a bifactor type model
resVars <- mxPath( from=mylabels, arrows=2,
free=TRUE, values=rep(1,12),
labelatVars <- mxPath( from=c("X1","X2"), arrows=2, connect="unique.pairs",
free=c(TRUE,FALSE,TRUE), values=c(1,0,1), labels=c("varX1","cov","varX2") )
LISREL Simulation
I am trying to simulate data using the endogenous variables only LISREL model as seen on page 133 of the OpenMx.pdf help documentation. I was able to simulate data from a state space model using the example in the help documentation on page 174. Now I am modifying that piece of code for a LISREL model. However I am running into an error. Below is my code.
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multilevel path/structural equation models in OpenMx
Is it possible to estimate multilevel path/structural equation models with OpenMx?
If it is possible, is there an example code for multilevel mediation (path) model?
Attached files are the example of multilevel path model using Mplus.
Source: Heck, R. H., & Thomas, S. L. (2015). An introduction to multilevel modeling techniques: MLM and SEM approaches using Mplus. Routledge.
Hope I can do the same analysis using OpenMx.
Thank you in advance.
Soyoung.
Optimization issues - binary with low prevalence
I work with OpenMx using a bit different data than most others; often data comes from a full population and has quite many rows (up to 3 million). A common type of analysis is for relatives with one or more binary variables, e.g. observed disease diagnosis, where the prevalence is low, e.g. 1% to 0.05%. The complexity of the models vary from simple 2x2 covariance matrices without any definition variables to 8x8 covariance matrices with several definition variables adjusting the means/thresholds.
Wierd estimate of mean in a simple model
I've met a weird issue with means running a simple model.
The data:
Cov<-matrix(
c(10,3.0,6.5,
3.0,10,6.5,
6.5,6.5,10),ncol=3,nrow=3)
library('mvtnorm')
data<-as.data.frame(rmvnorm(1000,mean=rep(100,3),sigma=Cov))
names(data)<-c('X','Y','Z')
The covariance matrix corresponds the model:
X -> Z = 0.5
Y -> Z = 0.5
X <-> Y = 3
X <-> X = 10
Y <-> Y = 10
Z <-> Z = 3.5
All means are 100
The model:
aModel<-mxModel(type='RAM',name='Phenotypic model',
manifestVars=c('X','Y','Z'),
mxPath(from=c('X','Y'),to='Z',connect='single',
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Interpreting Output from mxTryHardOrdinal
Begin fit attempt 21 of at maximum 21 tries
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Constrain Total Variance instead of Residual Variance in Ordinal Threshold Path Mdel
Simplex models with thresholds - CIs?
I have fitted a simplex model with six time points. It's a threshold model with 2 thresholds. I fixed the thresholds and freely estimated the means. I used the CSOLNP optimizer.
I get stable estimates, they are in accordance with what I would expect based on the univariate results, and the gradients look ok.
As a next step, I wanted to calculate confidence intervals, but I only get this:
confidence intervals:
lbound estimate ubound note
atm21 NA 0.4871751 NA !!!
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Joint Ordinal-Continuous Model
I am trying to run a joint ordinal-continuous model.
In my model I have a continuous variable (varA) and an ordinal variable with 1 threshold (varB).
There are 5 zygosity groups (MZM, DZM, MZF, DZF, DOS) and a covariate age which
I modeled separately for men and women.
The model is actually running perfectly fine (no errors) and the estimates for the thresholds for varB
look good and are what I would have expected.
However, the estimates for the means are all way too low when I compare them with the raw data.
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