https://github.com/openmx/openmx
Repository for the OpenMx Structural Equation Modeling package
https://github.com/openmx/openmx
behavior-genetics c-plus-plus estimation graphical-models growth-curves item-response-theory multilevel-models openmx psychology r statistics structural-equation-modeling
Last synced: 6 months ago
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Repository for the OpenMx Structural Equation Modeling package
- Host: GitHub
- URL: https://github.com/openmx/openmx
- Owner: OpenMx
- Created: 2012-05-21T13:38:34.000Z (over 13 years ago)
- Default Branch: master
- Last Pushed: 2024-04-12T13:30:34.000Z (over 1 year ago)
- Last Synced: 2024-04-14T12:28:48.152Z (over 1 year ago)
- Topics: behavior-genetics, c-plus-plus, estimation, graphical-models, growth-curves, item-response-theory, multilevel-models, openmx, psychology, r, statistics, structural-equation-modeling
- Language: R
- Homepage: http://openmx.ssri.psu.edu
- Size: 33.2 MB
- Stars: 84
- Watchers: 14
- Forks: 33
- Open Issues: 105
-
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING
Awesome Lists containing this project
README
# OpenMx 
[](https://app.travis-ci.com/github/OpenMx/OpenMx)
[](https://app.codecov.io/gh/OpenMx/OpenMx?branch=master)
[](https://cran.r-project.org/package=OpenMx)
[](https://cranlogs.r-pkg.org/badges/OpenMx)
[](https://cranlogs.r-pkg.org/badges/grand-total/OpenMx)
[](https://doi.org/10.1007/s11336-014-9435-8)
> OpenMx is a [Structural Equation Modeling](https://en.wikipedia.org/wiki/Structural_equation_modeling)
package that encourages users to treat model specifications as something to be generated
and manipulated programmatically.
# TOC
- [Overview](#overview)
- [Installation](#installation)
* [Development versions](#development-versions)
- [Documentation](#documentation)
- [Quick usage examples](#quick-usage-examples)
* [Simple regression in path specification](#simple-regression-in-path-specification)
* [Simple regression using matrix algebra](#simple-regression-using-matrix-algebra)
- [Related work](#related-work)
- [Community and getting help](#community-and-getting-help)
* [Training](#training)
- [Contributing](#contributing)
# Overview
OpenMx is the next generation of the Mx structural equation modeling tool. It is an R package activelly maintained and supported with the work of developers around the globe. It is designed to allow the user the most freedom possible while specifying structural equation models, therefore providing minimal defaults. This helps the user know that each specification/optimization decision comes with their own assumptions and influences model interpretation.
# Installation
The package is on CRAN and should be installed with:
```r
install.packages("OpenMx")
```
## Development versions
Developers commit to the `master` branch. Intrepid users are encouraged to install the `master` branch. In order to install locally clone this repo and run:
```r
make cran-install # for the CRAN version
make install # for the version with the proprietary NPSOL optimizer
```
The `stable` branch can be considered our current alpha release.
The `stable` branch is updated automatically when all `models/passing`
and `models/nightly` tests pass along with `make cran-check`.
On macOS, this can be installed as a binary via travis:
```r
install.packages("https://vipbg.vcu.edu/vipbg/OpenMx2/software/bin/macosx/travis/OpenMx_latest.tgz")
```
# Documentation
OpenMx can fit everything from confirmatory factor analyses,
through multiple group, mixture distribution, categorical threshold,
modern test theory, differential equations, state space, and many others. Models may be specified as RAM or LISREL paths, or directly in matrix algebra. Fit functions include ML (summary and full information) and WLS.
The package manual can be accessed online in the [link](https://vipbg.vcu.edu/vipbg/OpenMx2/docs//OpenMx/latest/), and as a pdf from the [link](https://vipbg.vcu.edu/vipbg/OpenMx2/docs//OpenMx/latest/OpenMxUserGuide.pdf). The manual includes example models and scripts for the most common cases.
# Quick usage examples
Path specifications are matematically complete and is often considered an easier approach to teaching and analysis. The path below represents a simple regression:
## Simple regression in path specification
One can specify the above model using the following code:
```r
require(OpenMx)
data(myRegDataRaw) # load data
names(myRegDataRaw) # get names
SimpleDataRaw <- myRegDataRaw[,c("x","y")] # take only what is needed
dataRaw <- mxData( observed=SimpleDataRaw, type="raw" )
# variance paths
varPaths <- mxPath( from=c("x","y"), arrows=2,
free=TRUE, values = c(1,1), labels=c("varx","residual") )
# regression weights
regPaths <- mxPath( from="x", to="y", arrows=1,
free=TRUE, values=1, labels="beta1" )
# means and intercepts
means <- mxPath( from="one", to=c("x","y"), arrows=1,
free=TRUE, values=c(1,1), labels=c("meanx","beta0") )
uniRegModel <- mxModel(model="Simple Regression Path Specification", type="RAM",
dataRaw, manifestVars=c("x","y"), varPaths, regPaths, means)
uniRegFit <- mxRun(uniRegModel) # run it
summary(uniRegFit)
```
And the following output should appear in your R environment:
```
Summary of Simple Regression Path Specification
free parameters:
name matrix row col Estimate Std.Error A
1 beta1 A y x 0.48311962 0.07757687
2 varx S x x 1.10531952 0.15631652
3 residual S y y 0.66520320 0.09407411
4 meanx M 1 x 0.05415975 0.10513428
5 beta0 M 1 y 2.54776414 0.08166814
Model Statistics:
| Parameters | Degrees of Freedom | Fit (-2lnL units)
Model: 5 195 536.8226
Saturated: 5 195 NA
Independence: 4 196 NA
Number of observations/statistics: 100/200
Information Criteria:
| df Penalty | Parameters Penalty | Sample-Size Adjusted
AIC: 146.8226 546.8226 547.4609
BIC: -361.1856 559.8484 544.0572
CFI: NA
TLI: 1 (also known as NNFI)
RMSEA: 0 [95% CI (NA, NA)]
Prob(RMSEA <= 0.05): NA
To get additional fit indices, see help(mxRefModels)
timestamp: 2022-05-01 09:53:24
```
## Simple regression using matrix algebra
Since OpenMx is considered the specialist tool, you are probably more interested in the flexibility provided by the fact that you can build your own formulas. So going back to the simple regression, now in the formula (equivalent to the path specified in previous section):
It can be implemented with the following code:
```r
require(OpenMx)
data(myRegDataRaw) # load data
SimpleDataRaw <- myRegDataRaw[,c("x","y")] # take only what is needed
# create a data object
dataRaw <- mxData( observed=SimpleDataRaw, type="raw" )
# A matrix
matrA <- mxMatrix( type="Full", nrow=2, ncol=2,
free=c(F,F,T,F), values=c(0,0,1,0),
labels=c(NA,NA,"beta1",NA), byrow=TRUE, name="A" )
# S matrix
matrS <- mxMatrix( type="Symm", nrow=2, ncol=2,
free=c(T,F,F,T), values=c(1,0,0,1),
labels=c("varx",NA,NA,"residual"), byrow=TRUE, name="S" )
# Filter matrix
matrF <- mxMatrix( type="Iden", nrow=2, ncol=2, name="F" )
# M matrix
matrM <- mxMatrix( type="Full", nrow=1, ncol=2,
free=c(T,T), values=c(0,0),
labels=c("meanx","beta0"), name="M")
# Which expectation? RAM in this case
expRAM <- mxExpectationRAM("A","S","F","M", dimnames=c("x","y"))
# Run a maximum likelihood
funML <- mxFitFunctionML()
# Name it, pass the objects on to a final model object
uniRegModel <- mxModel("Simple Regression Matrix Specification",
dataRaw, matrA, matrS, matrF, matrM, expRAM, funML)
# Run it!
uniRegFit <- mxRun(uniRegModel)
summary(uniRegFit)
```
Now the output looks like:
```
Running Simple Regression Matrix Specification with 5 parameters
Summary of Simple Regression Matrix Specification
free parameters:
name matrix row col Estimate Std.Error A
1 beta1 A 2 1 0.48311963 0.07757699
2 varx S 1 1 1.10531937 0.15631498
3 residual S 2 2 0.66520312 0.09407369
4 meanx M 1 x 0.05416001 0.10513400
5 beta0 M 1 y 2.54776424 0.08166812
Model Statistics:
| Parameters | Degrees of Freedom | Fit (-2
Model: 5 195
Saturated: 5 195
Independence: 4 196
Number of observations/statistics: 100/200
Information Criteria:
| df Penalty | Parameters Penalty | Sample-Size Adju
AIC: 146.8226 546.8226 547.
BIC: -361.1856 559.8484 544.
CFI: NA
TLI: 1 (also known as NNFI)
RMSEA: 0 [95% CI (NA, NA)]
Prob(RMSEA <= 0.05): NA
To get additional fit indices, see help(mxRefModels)
timestamp: 2022-05-01 10:04:52
Wall clock time: 0.3507566 secs
optimizer: SLSQP
OpenMx version number: 2.19.6.6
Need help? See help(mxSummary)
```
# Related work
[umx()](https://github.com/tbates/umx) is a sister R package that bridges the gap between [lavaan](https://github.com/yrosseel/lavaan) and OpenMx. If you are coming from lavaan it is perhaps useful to check umx() too. [Onyx](https://onyx-sem.com/) is a software that allows you to design nice diagrams, and syncs (exports and imports) the diagrams with OpenMx code.
# Community and getting help
1. The support communication is centered around the OpenMx [forum](https://openmx.ssri.psu.edu/forums)
2. Also, but less often, at the StackOverflow OpenMx [tag](https://stackoverflow.com/questions/tagged/openmx).
## Training
We gather annually in beautiful [Boulder, CO](https://www.colorado.edu/ibg/workshop) for the international workshop for traning in behavioral genetics applications of OpenMx.
# Contributing
How can I contribute to this project?
OpenMx is maintained by a small team and all help is appreciated.
First read the team's conduct policy [here](https://github.com/OpenMx/OpenMx/blob/master/CONTRIBUTING). If you agree with it you can choose one of the below paths:
1. Do you have a well documented script (from one of our several workshops) that would make a great vignette? Great, because you don't even need to know how to use git. Simply go to the vignette folder and click in add file. This will automate the forking and uploading.
2. There are several issues that can be handled by new users. Go over to our oldest issues [here](https://github.com/OpenMx/OpenMx/issues?q=is%3Aissue+is%3Aopen+sort%3Acreated-asc), browse until something you find an issue you feel you can contribute to, and announce that you are planning to tackle it in the issue thread.
3. Have a completely new functionality that you want to discuss? Just create a PR and we will discuss whether it aligns with the package direction. In this case please add proper documentation for the new functionality. If you use RStudio there is a stub at File > New File > R Documentation. Also create a test unit in the tests/testthat folder, we currently use [testthat](https://testthat.r-lib.org/) to manage this.