Man pages for tbates/umx
Structural Equation and Twin Modeling in R

dl_from_dropboxdl_from_dropbox
extractAIC.MxModelExtract AIC from MxModel
GFFTwin data: General Family Functioning, divorce, and...
install.OpenMxInstall OpenMx, with choice of builds
iqdatTwin data: IQ measured longitudinally
loadingsloadings Generic loadings function to extract factor loadings...
loadings.MxModelExtract factor loadings from an EFA (factor analysis).
plot.MxModelCreate and display a graphical path diagram for a model.
qmqm
reliabilityreliability
residuals.MxModelGet residuals from an MxModel
RMSEAGeneric RMSEA function
RMSEA.MxModelRMSEA function for MxModels
RMSEA.summary.mxmodelRMSEA function for MxModels
tmx_genotypic_effectGraphical display of genotypic effects.
tmx_is.identifiedTest if a factor model is identified
umxHelper Functions for Structural Equation Modelling in OpenMx
umxACEBuild and run a 2-group Cholesky twin model (uni-variate or...
umxACEcovRun a Cholesky with covariates, either fixed (def var in the...
umxACE_cov_fixedRun a Cholesky with covariates ("fixed" / definition...
umxACEnewBuild and run a 2-group Cholesky twin model (uni-variate or...
umxACEvBuild and run 2-group uni- or multi-variate ACE models based...
umxAdd1umxAdd1
umx_add_variancesumx_add_variances
umx_aggregateConvenient formula-based cross-tabs & built-in summary...
umxAlgebraA simple wrapper for mxAlgebra with name as the first...
umxAPACreates nicely formatted journal style summaries of lm...
umx_APA_model_CIumx_APA_model_CI
umx_APA_pvalRound p-values according to APA guidelines
umx_applyumx_apply
umx_array_shiftLike the php array_shift function: shifts an item off the...
umx_as_numericumx_as_numeric
umxBrownieA recipe Easter-egg for umx
umx_cell_is_onReturn whether a cell is in a set location of a matrix
umx_checkumx_check
umx_check_modelCheck for required features in an OpenMx.
umx_check_namesumx_check_names
umx_check_OSumx_check_OS
umx_check_parallelCheck if OpenMx is using OpenMP, test cores, and get timings
umxCIAdd (and, optionally, run) confidence intervals to a...
umxCI_bootumxCI_boot
umxComparePrint a comparison table of one or more 'mxModel's, formatted...
umxConfintGet confidence intervals from a umx model
umx_cont_2_quantilesumx_cont_2_quantiles
umx_corReport correlations and their p-values
umxCov2corConvert a covariance matrix into a correlation matrix
umx_cov2rawTurn a cov matrix into raw data with umx_cov2raw
umxCovDataConvert a dataframe into a cov mxData object
umxCPumxCP: Build and run a Common pathway twin model
umxCPoldumxCP: Build and run a Common pathway twin model
umx_default_optionSelect first item in list of options, while being flexible...
umx-deprecatedDeprecated. May already stop() code and ask to be updated....
umxDiagnoseDiagnose problems in a model - this is a work in progress.
umxDrop1umxDrop1: Unfinished function to mimic drop1 in OpenMx
umx_drop_okumx_drop_ok
umxEFAFIML-based Exploratory Factor Analysis (EFA)
umxEquateumxEquate: Equate two or more paths
umxEvalumxEval
umxExpCovGet the expected vcov matrix
umx_explodeumx_explode - like the php function 'explode'
umx_explode_twin_namesBreak twin variable names (BMI_T1, BMI_T2) into base variable...
umxExpMeansExtract the expected means matrix from an 'mxModel'
umxFactorumxFactor
umxFactorScoresReturn factor scores from a model as an easily consumable...
umx_find_objectumx_find_object
umxFitIndicesGet additional fit-indices for a model with umxFitIndices
umxFixAllumxFixAll: Fix all free parameters
umx_fix_first_loadingsumx_fix_first_loadings
umx_fix_latentsumx_fix_latents
umx_fun_mean_sdumx_fun
umx_get_bracket_addressesget mat[r,c] style cell address from an mxMatrix
umx_get_checkpointumx_get_checkpoint
umx_get_optionsumx_get_options
umxGetParametersGet parameters from a model, with support for pattern...
umx_graphviz_rankHelper to make a graphviz rank string
umx_grepumx_grep
umxGxEumxGxE: Implements ACE models with moderation of paths, e.g....
umxGxEbivBivariate GxE models where twins differ on the moderator.
umxGxE_windowImplement the moving-window form of GxE analysis.
umx_has_been_runumx_has_been_run
umx_has_CIsumx_has_CIs
umx_has_meansumx_has_means
umx_has_square_bracketsCheck if a label contains square brackets
umxHetCorCreate a matrix of correlations for variables of diverse...
umxIPumxIP: Build and run an Independent pathway twin model
umxIPnewumxIP: Build and run an Independent pathway twin model
umx_is_classCheck if variables in a dataframe are in a list of classes.
umx_is_covumx_is_cov
umx_is_endogenousumx_is_endogenous
umx_is_exogenousumx_is_exogenous
umx_is_MxDataCheck if an object is an mxData object
umx_is_MxMatrixumx_is_MxMatrix
umx_is_MxModelumx_is_MxModel
umx_is_numericCheck if variables in a dataframe are numeric
umx_is_orderedTest if one or more variables in a dataframe are ordered
umx_is_RAMumx_is_RAM
umxJiggleumxJiggle
umxLabelumxLabel: Add labels to a RAM model, matrix, or path
umxLatentumxLatent: Helper to ease making formative and reflective...
umx_long2wideTake a long twin-data file and make it wide (one family per...
umx_lower2fullConvert lower-only matrix data to full (or enforce symmetry...
umx_make"make" the umx package using devtools: release to CRAN etc.
umx_make_bin_cont_pair_dataMake pairs of bin & continuous columns to represent censored...
umx_make_fake_dataumx_make_fake_data
umx_make_MR_dataSimulate Mendelian Randomization data
umx_make_sql_from_excelConvert an excel spreadsheet in a text file on sql...
umx_make_TwinDataSimulate twin data with control over A, C, and E parameters,...
umx_mat2dotReturn dot code for paths in a matrix
umxMatrixMake a mxMatrix with automatic labels. Also takes name as the...
umx_meansumx_means
umx_merge_CIsumx_merge_CIs
umxMIReport modifications which would improve fit.
umxModelCatches users typing umxModel instead of umxRAM.
umxModifyumxModify: Add, set, or drop model paths by label.
umx_move_fileMove files
umx_msgPrint the name and compact contents of variable.
umx_namesumx_names
umx_object_as_strumx_object_as_str
umx_openumx_open
umx_open_CRAN_pageOpen the CRAN page for a package
umx_padPad an Object with NAs
umxPadAndPruneForDefVarsumxPadAndPruneForDefVars
umx_parametersDisplay path estimates from a model, filtering by name and...
umx_paste_namesConcatenate base variable names with suffixes to create...
umxPathEasier (and powerful) specification of paths in SEM.
umx_pb_noteumx_pb_note
umxPlotACEumxPlotACE
umxPlotACEcovMake a graphical display of an ACE model with covariates.
umxPlotACEvProduce a graphical display of an ACE variance-components...
umxPlotCPDraw and display a graphical figure of Common Pathway model
umxPlotCPnewDraw and display a graphical figure of Common Pathway model
umxPlotGxEPlot the results of a GxE univariate test for moderation of...
umxPlotGxEbivPlot the results of a GxE univariate test for moderation of...
umxPlotIPDraw a graphical figure for a Independent Pathway model
umxPlotSimplexDraw and display a graphical figure of a simplex model
umx_polychoricFIML-based polychoric, polyserial, and Pearson correlations
umx_polypairwiseFIML-based Pairwise polychoric, polyserial, and Pearson...
umx_polytriowiseFIML-based trio-based polychoric, polyserial, and Pearson...
umx_printPrint tables in a range of formats (markdown default, see...
umxRAMEasy-to-use RAM model maker.
umx_read_lowerRead lower-triangle of data matrix from console or file
umxReduceReduce models, and report the results.
umxReduceACEReduce an ACE model.
umxReduceGxEReduce a GxE model.
umx_renameumx_rename
umx_rename_fileumx_rename_file
umx_reorderReorder or drop variables from a correlation/covariance...
umx_residualizeEasily residualize variables in long or wide dataframes,...
umx_rotumx_rot
umx_roundumx_round
umx_r_testTest the difference between correlations for significance.
umxRunumxRun: Run an mxModel
umx_scaleScale data columns, skipping non-scalable columns
umx_scale_wide_twin_dataumx_scale_wide_twin_data
umx_score_scaleScore a scale by summing normal and reversed items
umx_set_auto_plotumx_set_auto_plot
umx_set_auto_runumx_set_auto_run
umx_set_checkpointumx_set_checkpoint
umx_set_condensed_slotsumx_set_condensed_slots
umx_set_coresumx_set_cores
umx_set_optimization_optionsumx_set_optimization_options
umx_set_optimizerumx_set_optimizer
umxSetParametersumxSetParameters: Set parameters in an mxModel
umx_set_plot_file_suffixSet output suffix used in umx plot (structural diagrams)...
umx_set_plot_formatSet output format of plots (structural diagrams) in umx
umx_set_table_formatumx_set_table_format
umxSexLimMultivariate twin analysis with sex limitation
umx_showumx_show
umx_show_fit_or_comparisonShow model logLik of model or print comparison table
umxSimplexBuild and run a simplex twin model (not ready for use!)
umx_stackStack data like stack() does, with more control.
umx_standardizeReturn a standardized version of a Structural Model
umx_standardize_ACEumx_standardize_ACE
umx_standardize_ACEcovumx_standardize_ACEcov
umx_standardize_ACEvStandardize an ACE variance components model (ACEv)
umx_standardize_CPumx_standardize_CP
umx_standardize_IPumx_standardize_IP
umx_standardize_RAMReturn a standardized version of a Structural Model
umx_standardize_SimplexStandardize a Simplex twin model
umx_stash_CIsStash the CI values of a model as strings in the values of...
umx_string_to_algebraConvert a string to an OpenMx algebra
umxSummaryShows a compact, publication-style, summary of umx models
umxSummaryACEShows a compact, publication-style, summary of a umx Cholesky...
umxSummaryACEcovPresent results of a twin ACE-model with covariates in table...
umxSummaryACEvShows a compact, publication-style, summary of a...
umxSummaryCPPresent the results of a Common-pathway twin model in table...
umxSummaryGxEumxSummaryGxE
umxSummaryGxEbivSummarize a bivariate GxE twin model
umxSummaryIPPresent the results of an independent-pathway twin model in...
umxSummary.MxModelShows a compact, publication-style, summary of a RAM model
umxSummarySexLimShows a compact, publication-style, summary of a umx Sex...
umxSummarySimplexShows a compact, publication-style, summary of a Simplex...
umxSuperModelMake a multi-group model
umx_swap_a_blockumx_swap_a_block
umxThresholdMatrixCreate the threshold matrix needed for modeling ordinal data.
umx_timeumx_time
umx_trimTrim whitespace surrounding a string.
umxTwoStageumxTwoStage
umxUnexplainedCausalNexusumxUnexplainedCausalNexus
umxValuesumxValues: Set values in RAM model, matrix, or path
umx_varGet variances from a df that might contain some non-numeric...
umxVersionGet or print the version of umx, along with detail from...
umxWeightedAICAIC weight-based conditional probabilities.
umx_wide2longChange data family data from wide (2 twins per row) to long...
umx_write_to_clipboardumx_write_to_clipboard
us_skinfold_dataAnthropometric data on twins
xmu_assemble_twin_supermodelAssemble top, MZ and DZ into a supermodel
xmu_check_levels_identicalxmu_check_levels_identical
xmu_dot_make_pathsxmu_dot_make_paths (not for end users)
xmu_dot_makerInternal umx function to help plotting graphviz
xmu_dot_make_residualsxmu_dot_make_residuals (not for end users)
xmuHasSquareBracketsxmuHasSquareBrackets
xmuLabel_MatrixxmuLabel_Matrix (not a user function)
xmuLabel_MATRIX_ModelxmuLabel_MATRIX_Model (not a user function)
xmuLabel_RAM_ModelxmuLabel_RAM_Model (not a user function)
xmuMakeDeviationThresholdsMatricesMake a deviation-based mxRAMObjective for ordinal models.
xmu_make_mxDataUpgrade a dataframe to an mxData type.
xmuMakeOneHeadedPathsFromPathListxmuMakeOneHeadedPathsFromPathList
xmuMakeThresholdsMatricesxmuMakeThresholdsMatrices (not a user function)
xmu_make_top_twin_modelsHelper to make a basic top, MZ, and DZ model.
xmuMakeTwoHeadedPathsFromPathListxmuMakeTwoHeadedPathsFromPathList
xmuMaxLevelsxmuMaxLevels
xmu_mean_var_startsHelper for boilerplate means and variance start values for...
xmuMIxmuMI
xmuMinLevelsxmuMinLevels
xmuPropagateLabelsxmuPropagateLabels (not a user function)
xmu_safe_run_summarySafely try to run and summarize a model
xmu_set_sep_from_suffixJust a helper to cope with deprecated suffix lying around.
xmu_simplex_cornerInternal function to help building simplex models
xmu_start_value_listMake start values
xmu_twin_checkCheck basic aspects of input for twin models.
tbates/umx documentation built on Nov. 10, 2018, 2:25 p.m.