OpenMx (version 2.7.9)

mxFitFunctionML: Create MxFitFunctionML Object

Description

This function creates a new MxFitFunctionML object.

Usage

mxFitFunctionML(vector = FALSE, rowDiagnostics = FALSE, ..., fellner =
  as.logical(NA), verbose=0L, profileOut=c(),
  rowwiseParallel=as.logical(NA), jointConditionOn = c("auto", "ordinal", "continuous"))

Arguments

vector

A logical value indicating whether the objective function result is the likelihood vector.

rowDiagnostics

A logical value indicating whether the row-wise results of the objective function should be returned as an attribute of the fit function.

...

Not used. Forces remaining arguments to be specified by name.

fellner

Whether to fully expand the covariance matrix for maximum flexibility.

verbose

Level of diagnostic output

profileOut

Character vector naming constant coefficients to profile out of the likelihood (sometimes known as REML)

rowwiseParallel

For raw data only, whether to use OpenMP to parallelize the evaluation of rows

jointConditionOn

The evaluation strategy when both continuous and ordinal data are present.

Value

Returns a new MxFitFunctionML object. One and only one MxFitFunctionML object should be included in each model along with an associated mxExpectationNormal or mxExpectationRAM object.

Details

Fit functions are functions for which free parameter values are optimized such that the value of a cost function is minimized. The mxFitFunctionML function computes -2*(log likelihood) of the data given the current values of the free parameters and the expectation function (e.g., mxExpectationNormal or mxExpectationRAM) selected for the model. The 'vector' argument is either TRUE or FALSE, and determines whether the objective function returns a column vector of the likelihoods, or a single -2*(log likelihood) value. The 'rowDiagnostics' argument is either TRUE or FALSE, and determines whether the row likelihoods are returned as an attribute of the fit function. It is sometimes useful to inspect the likelihoods for outliers, diagnostics, or other anomalies. When vector=FALSE and rowDiagnostics=TRUE, fitfunction can be referenced in the model and included in algebras as a scalar. The row likelihoods are an attribute of the fit function but are not accessible in the model during optimization. The row likelihoods are accessible to the user after the model has been run. By default, jointConditionOn='auto' and a heuristic will be used to select the fastest algorithm. Conditioning the continuous data on ordinal will be superior when there are relatively few unique ordinal patterns. Otherwise, conditioning the ordinal data on continuous will perform better when there are relatively many ordinal patterns. Usage Notes: The results of the optimization can be reported using the summary function, or accessed directly in the 'output' slot of the resulting model (i.e., modelName$output). Components of the output may be referenced using the Extract functionality.

References

The OpenMx User's guide can be found at http://openmx.ssri.psu.edu/documentation.

See Also

Other fit functions: mxFitFunctionMultigroup, mxFitFunctionWLS, mxFitFunctionAlgebra, mxFitFunctionGREML, mxFitFunctionR, mxFitFunctionRow More information about the OpenMx package may be found here.

Examples

# Create and fit a model using mxMatrix, mxAlgebra, mxExpectationNormal, and mxFitFunctionML

library(OpenMx)

# Simulate some data

x=rnorm(1000, mean=0, sd=1)
y= 0.5*x + rnorm(1000, mean=0, sd=1)
tmpFrame <- data.frame(x, y)
tmpNames <- names(tmpFrame)

# Define the matrices

M <- mxMatrix(type = "Full", nrow = 1, ncol = 2, values=c(0,0), 
              free=c(TRUE,TRUE), labels=c("Mx", "My"), name = "M")
S <- mxMatrix(type = "Full", nrow = 2, ncol = 2, values=c(1,0,0,1), 
              free=c(TRUE,FALSE,FALSE,TRUE), labels=c("Vx", NA, NA, "Vy"), name = "S")
A <- mxMatrix(type = "Full", nrow = 2, ncol = 2, values=c(0,1,0,0), 
              free=c(FALSE,TRUE,FALSE,FALSE), labels=c(NA, "b", NA, NA), name = "A")
I <- mxMatrix(type="Iden", nrow=2, ncol=2, name="I")

# Define the expectation

expCov <- mxAlgebra(solve(I-A) %*% S %*% t(solve(I-A)), name="expCov")
expFunction <- mxExpectationNormal(covariance="expCov", means="M", dimnames=tmpNames)

# Choose a fit function

fitFunction <- mxFitFunctionML(rowDiagnostics=TRUE)
# also return row likelihoods, even though the fit function
#  value is still 1x1

# Define the model

tmpModel <- mxModel(model="exampleModel", M, S, A, I, expCov, expFunction, fitFunction, 
                    mxData(observed=tmpFrame, type="raw"))

# Fit the model and print a summary

tmpModelOut <- mxRun(tmpModel)
summary(tmpModelOut)

fitResOnly <- mxEval(fitfunction, tmpModelOut)
attributes(fitResOnly) <- NULL
fitResOnly

# Look at the row likelihoods alone
fitLikeOnly <- attr(mxEval(fitfunction, tmpModelOut), 'likelihoods')
head(fitLikeOnly)