OpenMxReferenceSeptember 2010Wednesday, September 29, 2010Wednesday, September 29, 2010OpenMx DocumentationWednesday, September 29, 2010Pass-by-Value•variables•values stored in variables•the only way to update a variable in a function call is to capture the result of the function callWednesday, September 29, 2010Functions vs ClassesfunctionmxModelmxMatrixmxPathmxAlgebramxBoundsmxConstraintmxDataclassMxModelMxMatrixMxPathMxAlgebraMxBoundsMxConstraintMxDataFunctions create objects of specific classWednesday, September 29, 2010OpenMx ProcessmxModel( name="myModelName" ) testModelmxRun( )mxMatrix(),mxMatrix(),mxConstraint(),mxAlgebra(),mxModel(),mxMatrix(),mxData(),mxObjective(), testModel testFitmxEval( algebra, ) testFitoutputMxModel R ObjectsR ObjectstestSummsummary( ) testFitWednesday, September 29, 2010Key Features•mxRun•mxModel•mxMatrix•mxPath•mxAlgebra•mxAlgebra-Objective•mxBounds•mxConstraints•mxData•mxOption•mxEval•mxRAM/R/ML/FIMLObjectiveWednesday, September 29, 2010mxModelmodel....manifestVarslatentVarsremoveindependenttypenameoptionalmxModel or stringarbitrary number of entities, data sources, Mx.... objectslist of manifest variableslist of latent variableslogical. TRUE= remove elements, else addlogical. TRUE= model is independentcharacter vector. name of model typeoptional character vector. name of objectlist of MxMatrix, MxAlgebra, MxModel, MxConstraint, MxBounds,MxData, MxObjective. MxOptions objectsmxModel( model = NA, ...., manifestVars = NA, latentVars = NA, remove = FALSE, independent = NA, type = NA, name = NA)Wednesday, September 29, 2010mxRunmxModel any mxModelmxRun( mxModel)Wednesday, September 29, 2010mxMatrixtypenrowncolfreevalueslabelslbounduboundbyrowdimnamesnamecharacter string for matrix type: Full Diag Iden Lower sDiag Stnd Symm Unit Zerodesired number of rowsdesired number of columnslogical. TRUE=free, FALSE=fixedvector/matrix of numeric start valuesvector/matrix of character labelsvector/matrix of numeric upper boundsvector/matrix of numeric lower boundslogical. TRUE=by row, FALSE=by columnlist of length 2 for row&column namesoptional character string. name of objectmxMatrix( type = "Full", nrow = NA, ncol = NA, free = FALSE, values = NA, labels = NA, lbound = NA, ubound = NA, byrow = getOption('mxByrow'), dimnames = NA, name = NA)Wednesday, September 29, 2010mxAlgebraexpressionnamedimnamesR expression of matrix operators & matrix functionsoptional character string. name of objectlist (length=2) for row & column namesmxAlgebra( expression, name = NA, dimnames = NA)Wednesday, September 29, 2010R Matrix operatorsR (OpenMx)solve()t()+-%*%*/%x%%&%cbind()rbind()inversiontranspositionadditionsubtractionmatrix multiplicationelement or dot productelement divisionKronecker productquadratic producthorizontal adhesionvertical adhesionpowerMx~‘+-*.%@&|_^Wednesday, September 29, 2010R Matrix operatorsR (OpenMx)tr()det()sum()max(), min()abs()exp()log()sqrt()diag2vec()c(t())c()vech()cov2cor()Re(eigen(A..Im(eigen(A..colMeans()var()tracedeterminantsummaximum, minimumabsolute valueexponentnatural logarithmsquare rootdiagonal 2 vector, v2dmatrix 2 vector (byRow)matrix 2 vector (byCol)lower triangular 2 vectorstandardize matrixreal eigenvalues/vectorsimaginary eigenvalues/vectorsmeans of columnscovariance of columns Mx\trace()\det()\sum()\max(), \min()\abs()\exp()\ln()\sqrt()\d2v()\m2v()\vec() \vech()\stnd()\eval(), \evec()\ival(),\ivec()\mean()\cov()sin(), sinh(), cos(), cosh(), tan(), tanh() also available\prod(), \pchi(), \pdfnor(), \mnor(), \moment(), \allint(), \cumnor(), \aorder(), \dorder(),\sortr(), \sortc(), \rprod(), \cprod(), \incrow(), \part(), \chol() not implemented yetWednesday, September 29, 2010mxEvalexpressionmodelcomputeshowarbitrary R expressionmodel in which to evaluate expressionlogical: TRUE= compute value of algebra expressionlogical: TRUE= print translated expressionmxEval( expression, model, compute, show)Wednesday, September 29, 2010mxDataobservedtypemeansnumObsmatrix or data.frame of datacharacter string. type of data: raw cov cor sscpoptional vector or means (when type = cov or cor)number of observations in data (required unless type = raw)mxData( observed, type = NA, means = NA, numObs = NA)Wednesday, September 29, 2010mxFIMLObjectivecovariancemeansdimnamesthresholdscharacter string of name of expected covariance matrix/algebraoptional character string of name of expected means vector/algebraoptional character vector to assign to dimnames of covariance and meansoptional character string of name of expected thresholds matrix/algebramxMLObjective( covariance, means, dimnames, thresholds)mxFIMLObjective( covariance, means, dimnames, thresholds)Wednesday, September 29, 2010mxPathfromtoallarrowsfreevalueslabelslbounduboundcharacter vector. sources of pathscharacter vector. sinks of pathslogical. TRUE=connect all sources-sinksnumeric value. 1=single, 2=doublelogical. TRUE=free, FALSE=fixedvector/matrix of numeric start valuesvector/matrix of character labelsvector/matrix of numeric upper boundsvector/matrix of numeric lower boundsmxPath( from = NA, to = NA, all = FALSE, arrows = 1, free = TRUE, values = NA, labels = NA, lbound = NA, ubound = NA)Wednesday, September 29, 2010mxRAMObjectiveASFMthresholdscharacter string of name of A matrix (of asymmetric paths) character string of name of S matrix (of symmetric paths)character string of name of F matrix (of filter matrix)optional character string of name of M matrix of expected means vectoroptional character string of name of expected thresholds matrix/algebramxRAMObjective( A, S, F, M = NA, thresholds = NA)Wednesday, September 29, 2010mxBoundsparametersminmaxcharacter vectors of names of parameters on which to apply boundnumberic value for lower boundnumberic value for upper boundmxBounds( parameters, min = NA, max = NA)Wednesday, September 29, 2010mxConstraintexpressionnameR expression of matrix operators and matrix functionsoptional character stringmxBounds( alg1, relation, alg2, name = NA)Wednesday, September 29, 2010mxOptionmodelkeyvalueresetmxModel objectname of optionvalue of optionTRUE=reset all options to defaultsgetOption(‘mxOptimizerOptions’) for default optimizer optionsmxOption( model, key, value, reset = FALSE)Wednesday, September 29, 2010mxAlgebraObjectivealgebra character string of name of MxMatrix or MxAlgebra objectto use for optimizationmxAlgebraObjective( algebra)Wednesday, September 29,
View Full Document
Unlocking...