Wildly different results using combined data vs dzData and mzData for umxACE?
hampusgronvall
Joined: 05/24/2023
When I run umxACE on the same data-set using either the data argument versus dzData and mzData arguments, I get wildly different results. I noticed this when working on my own data that I unfortunately can not share, but it's also replicated in the twinData sample set. Is there something I'm misunderstanding here?
Thanks!
Hampus
Code:
> data(twinData)
> twinData[, c("ht1", "ht2")] <- twinData[, c("ht1", "ht2")] * 10
>
> # Extract only FF DZ and MZ twins
> twinData <- twinData[twinData$zygosity %in% c("MZFF", "DZFF"),]
> twinData$zygosity <- gsub("MZFF", "MZ", twinData$zygosity)
> twinData$zygosity <- gsub("DZFF", "DZ", twinData$zygosity)
>
> # Make separate dfs for MZ and DZ
> mzData <- twinData[twinData$zygosity %in% "MZ", ]
> dzData <- twinData[twinData$zygosity %in% "DZ", ]
>
> # Do the umxACE-stuff
> ACE_split <- umxACE(selDVs = "ht", selCovs = "age", sep = "", dzData = dzData, mzData = mzData)
1 row(s) dropped from 'data' due to missing definition variable(s)
Running ACE with 5 parameters
ACE -2 × log(Likelihood) = 5944.831
Table: Standardized parameter estimates from a 1-factor Cholesky ACE model. A: additive genetic; C: common environment; E: unique environment.
| | a1| c1| e1|
|:--|-----:|-----:|----:|
|ht | 0.929| 0.082| 0.36|
Table: Means and (raw) betas from model$top$intercept and model$top$meansBetas
| | ht1| ht2|
|:---------|------:|------:|
|intercept | 16.446| 16.446|
|age | -0.005| -0.005|
?umxPlotACE options: std=T/F, means=T/F, digits=n, strip_zero=T/F, file=, min=, max =
> ACE_merged <- umxACE(data = twinData, selDVs = "ht", selCovs = "age", sep = "")
1 row(s) dropped from 'data' due to missing definition variable(s)
1 row(s) dropped from 'data' due to missing definition variable(s)
Running ACE with 5 parameters
ACE -2 × log(Likelihood) = 5655.484
Table: Standardized parameter estimates from a 1-factor Cholesky ACE model. A: additive genetic; C: common environment; E: unique environment.
| | a1| c1| e1|
|:--|-----:|-----:|-----:|
|ht | 0.004| 0.667| 0.745|
Table: Means and (raw) betas from model$top$intercept and model$top$meansBetas
| | ht1| ht2|
|:---------|------:|------:|
|intercept | 16.496| 16.496|
|age | -0.006| -0.006|
?umxPlotACE options: std=T/F, means=T/F, digits=n, strip_zero=T/F, file=, min=, max =