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

deg2radConvert Degrees to Degrees
dl_from_dropboxdl_from_dropbox
docDataTwin data for Direction of causation modelling
extractAIC.MxModelExtract AIC from MxModel
Fischbein_wtWeight data across time.
FishersMethodFishers Method of combining p-values.
GFFTwin data: General Family Functioning, divorce, and...
install.OpenMxInstall OpenMx, with choice of builds
iqdatTwin data: IQ measured longitudinally across 4 ages.
loadingsloadings Generic loadings function to extract factor loadings...
loadings.MxModelExtract factor loadings from an EFA (factor analysis).
oddsratioCompute odds ratio (OR)
plot.MxLISRELModelCreate and display a graphical path diagram for a LISREL...
plot.MxModelCreate and display a graphical path diagram for a model.
plot.MxModelTwinMakerCreate and display a graphical path diagram for a path-based...
power.ACE.testTest the power of an ACE model to detect paths of interest.
print.oddsratioPrint a scale "oddsratio" object
print.reliabilityPrint a scale "reliability" object
qmqm
rad2degConvert Radians to Degrees
reliabilityReport coefficient alpha (reliability)
residuals.MxModelGet residuals from an MxModel
RMSEAGeneric RMSEA function
RMSEA.MxModelRMSEA function for MxModels
RMSEA.summary.mxmodelRMSEA function for MxModels
SE_from_pCompute an SE from a beta and p value
tmx_genotypic_effectGraphical display of genotypic effects.
tmx_is.identifiedTest if a factor model is identified
tmx_showShow matrices of RAM models in a easy-to-learn-from format.
umxFunctions for Structural Equation Modeling 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...
umxACEvBuild and run 2-group uni- or multi-variate ACE models based...
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 models,...
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_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,...
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
umxCPumxCP: Build and run a Common pathway twin model
umx-deprecatedDeprecated. May already stop() code and ask to be updated....
umxDiagnoseDiagnose problems in a model - this is a work in progress.
umxDoCBuild and run a 2-group Direction of Causation twin models.
umxDoCpMake a direction of causation model based on umxPath...
umxEFAFIML-based Exploratory Factor Analysis (EFA)
umxEquateumxEquate: Equate two or more paths
umxExamplesExample code from Twin Research and Human Genetics Paper on...
umxExpCovGet the expected vcov matrix
umx_explodeExplode a string (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_file_load_pseudoRead in files from pseudocons.
umx_find_objectumx_find_object
umxFitIndicesGet additional fit-indices for a model with umxFitIndices
umxFixAllumxFixAll: Fix all free parameters
umx_fun_mean_sdumx_fun
umx_get_bracket_addressesGet bracket-style addresses from an mxMatrix
umx_get_checkpointGet or set checkpointing for a model
umx_get_optionsumx_get_options
umxGetParametersGet parameters from a model, with support for pattern...
umx_grepSearch for text
umxGxEumxGxE: Implements ACE models with moderation of paths, e.g....
umxGxEbivPurcell (2002) Bivariate GxE model: Suitable when twins...
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
umx_is_classCheck if variables in a dataframe are in a list of classes.
umx_is_covumx_is_cov
umx_is_endogenousList endogenous variables in a model
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
umxLav2RAMConvert lavaan string to a umxRAM model
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_fake_dataumx_make_fake_data
umx_make_MR_dataSimulate Mendelian Randomization data
umx_make_raw_from_covTurn a cov matrix into raw 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_make_twin_data_niceConvert a twin dataset into umx standard format.
umxMatrixMake a mxMatrix with automatic labels. Also takes name as the...
umx_meansumx_means
umxMendelianRandomizationBuild a SEM implementing the equivalent of 2-stage least...
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_openOpen a file or folder
umx_open_CRAN_pageOpen the CRAN page for a package
umx_padPad an Object with NAs
umxParametersDisplay 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.
umxPlotACEMake a graphical display of an ACE model
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
umxPlotDoCPlot a Direction of Causation 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
umxPlotSexLimDraw and display a graphical figure of a Sex limitation 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...
umxPowerTest power to detect specified path values in a model.
umx_printPrint tables in a range of formats (markdown default, see...
umxRAMEasier path-based SEM modeling.
umxRAM2LavConvert a RAM model to a lavaan string
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_fileRename files
umx_reorderReorder or drop variables from a correlation/covariance...
umx_residualizeEasily residualize variables in long or wide dataframes,...
umx_rotRotate a vector
umxRotateGeneric SEM factor model loading rotation function
umxRotate.MxModelCPRotate a CP solution
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_dataScale wide twin data
umx_score_scaleScore a psychometric scale by summing normal and reversed...
umx_select_validUpdate NA values in one column with valid entries from...
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_data_variance_checkumx_set_data_variance_check
umx_set_mvn_optimization_optionsSet options that affect optimization in OpenMx
umx_set_optimizerSet the optimizer in OpenMx
umxSetParametersChange or fix parameters (e.g. their values, labels, bounds,...
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_separatorSet the separator
umx_set_silentPrint anything when running a model?
umx_set_table_formatumx_set_table_format
umxSexLimMultivariate sex limitation twin model
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_string_to_algebraConvert a string to an OpenMx algebra
umxSummarizeTwinDataSummarize twin data
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...
umxSummaryDoCShows a compact, publication-style, summary of a umx...
umxSummaryGxESummarize a GxE model
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
umxThresholdMatrixCreate the threshold matrix needed for modeling ordinal data.
umx_timeumx_time
umx_trimTrim whitespace surrounding a string.
umxTwinAddMeansModelAdd a means model to a twin model
umxTwinMakerMake a twin model from the model describing just one person
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_cell_is_onReturn whether a cell is in a set location of a matrix
xmu_check_levels_identicalxmu_check_levels_identical
xmu_check_needs_meansCheck data to see if model needs means.
xmu_check_varianceCheck the minimum variance in data frame
xmu_CI_mergexmu_CI_merge
xmu_CI_stashStash the CI values of a model as strings in the values of...
xmu_clean_labelRemove illegal characters from labels
xmu_data_swap_a_blockData helper function to swap blocks of data from one set of...
xmuDefBetasNot for end-users: Create matrices "Mean" and "betaDef" in...
xmuDefMeanNot for end-users: Create matrices and algebra for means in...
xmu_describe_data_WLSDetermine whether a dataset will need weights and summary...
xmu_DF_to_mxData_TypeCovConvert a dataframe into a cov mxData object
xmu_dot_define_shapesHelper to make the list of vars and their shapes for a...
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)
xmu_dot_mat2dotReturn dot code for paths in a matrix
xmu_dot_move_ranksxmu_dot_move_ranks (not for end users)
xmu_dot_rankHelper to make a graphviz rank string
xmu_dot_rank_strxmu_dot_rank_str (not for end users)
xmu_get_CILook up and report CIs for free parameters
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)
xmu_lavaan_process_groupProcess table of paths to model
xmu_make_bin_cont_pair_dataMake pairs of bin & continuous columns to represent censored...
xmuMakeDeviationThresholdsMatricesMake a deviation-based mxRAMObjective for ordinal models.
xmu_make_mxDataUpgrade a dataframe to an mxData type.
xmuMakeOneHeadedPathsFromPathListxmuMakeOneHeadedPathsFromPathList
xmu_make_top_twinHelper to make a basic top, MZ, and DZ model.
xmuMakeTwoHeadedPathsFromPathListxmuMakeTwoHeadedPathsFromPathList
xmu_match.argSelect first item in list of options, while being flexible...
xmuMaxLevelsxmuMaxLevels
xmuMIxmuMI (not for end users - you want umxMI! )
xmuMinLevelsxmuMinLevels
xmu_name_from_lavaan_strFind name for model
xmu_PadAndPruneForDefVarsWhere all data are missing for a twin, add default values for...
xmu_path2twinRe-name variables in umxPaths to twin versions
xmu_path_regexRe-name variables umxPaths to twin versions
xmuPropagateLabelsxmuPropagateLabels (not a user function)
xmuRAM2OrdinalxmuRAM2Ordinal
xmu_safe_run_summarySafely run and summarize a model
xmu_set_sep_from_suffixJust a helper to cope with deprecated suffix lying around.
xmu_show_fit_or_comparisonShow model logLik of model or print comparison table
xmu_simplex_cornerInternal function to help building simplex models
xmu_standardize_ACExmu_standardize_ACE
xmu_standardize_ACEcovxmu_standardize_ACEcov
xmu_standardize_ACEvStandardize an ACE variance components model (ACEv)
xmu_standardize_CPFunction to standardize a common pathway model
xmu_standardize_IPnon-user: Standardize an IP model
xmu_standardize_RAMStandardize a Structural Model (not for end users)
xmu_standardize_SexLimStandardize a SexLim model
xmu_standardize_SimplexStandardize a Simplex twin model
xmu_startsHelper providing twin models with boilerplate means and...
xmu_start_value_listMake start values
xmu_twin_checkCheck basic aspects of input for twin models.
tbates/umx documentation built on March 30, 2020, 7:56 a.m.