Binary variable in 1.2 beta vs. 1.1.2
Mike Cheung
Joined: 10/08/2009
I am fitting a model with one binary variable and one latent variable. The goal was to estimate the threshold (and then the proportion) of the binary variable. The following syntax worked in OpenMx 1.1.2 but failed in OpenMx 1.2 beta. Attached are the output.
Any suggestions? Thanks in advance.
Mike
######### Fitting a binary variable
library(OpenMx)
## Create n=100 binary data with p=.6
my.df <- data.frame(x=c(rep(0,each=40),rep(1,each=60)))
## Starting value for the threshold
st <- qnorm(colMeans(my.df))
my.df$x <- mxFactor(my.df$x, levels=c(0,1))
prop.Model <- mxModel("Binary variable", mxData(my.df, type="raw"),
mxMatrix(type="Full", nrow=1, ncol=2, values=c(0,1), free=FALSE, name="A"),
mxMatrix(type="Diag", nrow=2, ncol=2, values=c(1,1), free=FALSE, name="S"),
mxMatrix(type="Full", nrow=1, ncol=2, values=c(1,0), free=FALSE, name="F"),
mxMatrix(type="Full", nrow=1, ncol=2, values=c(0,0), free=FALSE, name="M"),
mxMatrix(type="Full", nrow=1, ncol=1, free=TRUE, values=st, labels="th1", name="thresh"),
mxRAMObjective("A", "S", "F", "M", dimnames=c("x","f1"),
thresholds="thresh", threshnames=c("x"))
)
prop.fit <- mxRun(prop.Model)
summary(prop.fit)
######### OpenMx version (1.2 beta): "999.0.0-1876"
> prop.fit <- mxRun(prop.Model)
Running Binary variable
Error in runHelper(model, frontendStart, intervals, silent, suppressWarnings, :
BLAS/LAPACK routine 'OMXUNS' gave error code -10
######### OpenMx version: "1.1.2-1818"
data:
$`Binary variable.data`
x
0:40
1:60
free parameters:
name matrix row col Estimate Std.Error lbound ubound
1 th1 thresh 1 x -0.3583366 0.1793284
observed statistics: 100
estimated parameters: 1
degrees of freedom: 99
-2 log likelihood: 134.6023
saturated -2 log likelihood: NA
number of observations: 100
chi-square: NA
p: NA
Information Criteria:
df Penalty Parameters Penalty Sample-Size Adjusted
AIC -63.39767 136.6023 NA
BIC -321.30951 139.2075 136.0493
CFI: NA
TLI: NA
RMSEA: NA
timestamp: 2011-12-28 22:30:14
frontend time: 0.1774709 secs
backend time: 0.002981901 secs
independent submodels time: 0.0001196861 secs
wall clock time: 0.1805725 secs
cpu time: 0.1805725 secs
openmx version number: 1.1.2-1818
I don't know what the problem
I don't know what the problem is thus far, but we're looking into it, Mike.
ryne
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Script Error + OpenMx Error
This looks like a combination of a script error and a bug in OpenMx error checking.
The script error (and therefore your quick fix) is that your A matrix is non-conformable to the operation. The A matrix should be of the same order as the S matrix (in this case, 2x2), and you'll want to add two more zeros appropriately. I changed it to:
mxMatrix(type="Full", nrow=2, ncol=2, values=c(0,0,1,0), free=FALSE, name="A"),
and got the same threshold estimates, std. errors, and -2 log likelihood as your listed version 1.1.2 output.
The second problem, of course, is that users should never be getting a BLAS/LAPACK error directly--OpenMx should be noticing the error condition and giving you an error message that makes more sense in your context. We'll make sure to fix this for future releases.
Thanks for your help in hunting bugs! Do you mind if we keep a modified version of this script in our test bank for the future?
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In reply to Script Error + OpenMx Error by tbrick
Thanks, Timothy. It works
Thanks, Timothy. It works fine.
Feel free to use the script.
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In reply to Thanks, Timothy. It works by Mike Cheung
Oops. I committed a patch to
Oops. I committed a patch to the OpenMx 1.1 and 1.2 repositories that issues the error message:
Thanks for bringing this to our attention!
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