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Error Meesage from mxGenerateData from Documentation Example Code

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rabil's picture
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Joined: 01/14/2010 - 16:47
Error Meesage from mxGenerateData from Documentation Example Code

I included "facLoads" in the mxModel arguments so I could get estimates of the factor loadings. (It was missing from code in the on-line documentation.)

When I try to use mxGenerateData, it gives an error.

http://openmx.psyc.virginia.edu/docs/OpenMx/2.6.7/_static/demo/OneFactorJoint_PathRaw.R

#
#   Copyright 2007-2012 The OpenMx Project
#
#   Licensed under the Apache License, Version 2.0 (the "License");
#   you may not use this file except in compliance with the License.
#   You may obtain a copy of the License at
# 
#        http://www.apache.org/licenses/LICENSE-2.0
# 
#   Unless required by applicable law or agreed to in writing, software
#   distributed under the License is distributed on an "AS IS" BASIS,
#   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
#   See the License for the specific language governing permissions and
#   limitations under the License.
 
 
# -----------------------------------------------------------------------------
# Program: OneFactorJoint_PathRaw.R  
# Author: Ryne Estabrook
# Date: 2014.05.09 
#
# ModelType: Factor
# DataType: Ordinal
# Field: None
#
# Purpose:
#      One Factor model to estimate factor loadings, residual variances, means and thresholds
#      Path style model input - Raw data input
#
# RevisionHistory:
#      Hermine Maes -- 2014.11.02 piecewise specification
# -----------------------------------------------------------------------------
 
require(OpenMx)
# Load Library
# -----------------------------------------------------------------------------
 
data(myFADataRaw)
 
oneFactorJoint <- myFADataRaw[,c("x1","x2","x3","z1","z2","z3")]
 
oneFactorJoint$z1 <- mxFactor(oneFactorJoint$z1, levels=c(0, 1))
oneFactorJoint$z2 <- mxFactor(oneFactorJoint$z2, levels=c(0, 1))
oneFactorJoint$z3 <- mxFactor(oneFactorJoint$z3, levels=c(0, 1, 2))
 
# Prepare Data
# -----------------------------------------------------------------------------
 
dataRaw      <- mxData( observed=oneFactorJoint, type="raw" )
# residual variances
resVars      <- mxPath( from=c("x1","x2","x3","z1","z2","z3"), arrows=2,
                        free=c(TRUE, TRUE, TRUE, FALSE, FALSE, FALSE),
                        values=1, labels=c("e1","e2","e3","e4","e5","e6") )
# latent variance
latVar       <- mxPath( from="F1", arrows=2,
                        free=FALSE, values=1, labels ="varF1" )
# factor loadings
facLoads     <- mxPath( from="F1", to=c("x1","x2","x3","z1","z2","z3"), arrows=1,
                        free=TRUE, values=1, labels=c("l1","l2","l3","l4","l5","l6") )
# means
means        <- mxPath( from="one", to=c("x1","x2","x3","z1","z2","z3","F1"), arrows=1,
                        free=c(TRUE,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE), values=0,
                        labels=c("meanx1","meanx2","meanx3","meanz1","meanz2","meanz3","meanF") )
# thresholds
thresholds   <- mxThreshold(vars=c("z1","z2","z3"), nThresh=c(1,1,2),
                        free=TRUE, values=c(-1, 0, -.5, 1.2),
                        labels=c("var1_th1","var2_th1","var3_th1","var3_th2") )
 
oneFactorJointModel <- mxModel("Common Factor Model Path Specification", type="RAM",
                        manifestVars=c("x1","x2","x3","z1","z2","z3"), latentVars="F1",
                        dataRaw, resVars, latVar, means, thresholds, facLoads)
 
# Create an MxModel object
# -----------------------------------------------------------------------------
 
oneFactorJointFit <- mxRun(oneFactorJointModel,intervals=TRUE)
# Fit the model with mxRun
# -----------------------------------------------------------------------------
 
summary(oneFactorJointFit)
oneFactorJointFit$output$estimate
# Print a summary of the results
# -----------------------------------------------------------------------------
 
mxGenerateData(oneFactorJointModel,100)
> mxGenerateData(oneFactorJointModel,100)
Error in cut.default(as.vector(data[, avar]), c(-Inf, delthr, Inf), labels = levthr) : 
  'breaks' are not unique

How can I fix this?

AdminHunter's picture
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Joined: 03/01/2013 - 11:03
mxVersion?

Strange. It works fine on my Windows machine. What's your mxVersion? Mine is

> mxVersion()
OpenMx version: 2.6.8.192 [GIT v2.6.8-192-g550639d]
R version: R version 3.2.4 Revised (2016-03-16 r70336)
Platform: x86_64-w64-mingw32
Default optimiser: CSOLNP
rabil's picture
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Joined: 01/14/2010 - 16:47
mxVersion

> mxVersion()
OpenMx version: 2.6.9 [GIT v2.6.9]
R version: R version 3.3.1 (2016-06-21)
Platform: x86_64-pc-linux-gnu
Default optimiser: SLSQP

Any thoughts?

AdminHunter's picture
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Joined: 03/01/2013 - 11:03
Inspecting the change log

Inspecting the change log, it looks like a few changes have occurred since 2.6.9 that alter the data generation ... apparently for the better. The latest version on GitHub (v2.6.8-255-g096de3b), works fine for this case, but the the older version on CRAN that you have failed. I replicated the failure you found on the CRAN version. The older version couldn't handle joint ordinal and continuous data generation. This works in the next release!

rabil's picture
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Joined: 01/14/2010 - 16:47
So if I install the stable

So if I install the stable version on GitHub it will work?

jpritikin's picture
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Joined: 05/24/2012 - 00:35
stable

Yes.

rabil's picture
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Joined: 01/14/2010 - 16:47
I tried to install, but I get

I tried to install, but I get an error:

> require(devtools)
Loading required package: devtools
> install_github("OpenMx/OpenMx", ref="stable")
Downloading GitHub repo OpenMx/OpenMx@stable
from URL https://api.github.com/repos/OpenMx/OpenMx/zipball/stable
Error: Does not appear to be an R package (no DESCRIPTION)

rabil's picture
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Joined: 01/14/2010 - 16:47
The directions here for

The directions here for installing from github also do not seem to work:

http://openmx.psyc.virginia.edu/wiki/howto-build-openmx-source-repository

git clone git@github.com:OpenMx/OpenMx.git
Cloning into 'OpenMx'...
The authenticity of host 'github.com (192.30.253.113)' can't be established.
RSA key fingerprint is SHA256:nThbg6kXUpJWGl7E1IGOCspRomTxdCARLviKw6E5SY8.
Are you sure you want to continue connecting (yes/no)? yes
Warning: Permanently added 'github.com,192.30.253.113' (RSA) to the list of known hosts.
Permission denied (publickey).
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.

This was also suggested but does not work:

git clone https://github.com:OpenMx/OpenMx.git
Cloning into 'OpenMx'...
fatal: repository 'https://github.com:OpenMx/OpenMx.git/' not found

rabil's picture
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Joined: 01/14/2010 - 16:47
After changing the code shown

After changing the code shown on the web pages, I was able to install the stable version of GitHub.

jpritikin's picture
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Joined: 05/24/2012 - 00:35
what changed?

Oh, did you update the instructions to what worked for you?

tbates's picture
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Joined: 07/31/2009 - 14:25
let us know what you wish changed

let me know here, or email, or just edit the wiki page if the instructions can be improved and you have some suggested edits.

t

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