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

bucksPrint a money object
deg2radConvert Degrees to Degrees
dl_from_dropboxdl_from_dropbox
docDataTwin data for Direction of causation modelling
extractAIC.MxModelExtract AIC from MxModel
fin_interestCompute the value of a principal & annual deposits at a...
fin_JustifiedPEJustified P/E Ratio
fin_NICompute NI given annual Earnings.
fin_percentCompute the percent change needed to return to the original...
fin_tickerOpen a ticker in yahoo finance.
fin_valuationWork the valuation of a company
Fischbein_wtWeight data across time.
FishersMethodFishers Method of combining p-values.
geometric_meanGeometric Mean
GFFTwin data: General Family Functioning, divorce, and...
ggAddRAdd a fit statistic to a ggplot
harmonic_meanHarmonic Mean
install.OpenMxInstall OpenMx, with choice of builds
iqdatTwin data: IQ measured longitudinally across 4 ages.
libsload libraries
loadingsloadings Generic loadings function to extract factor loadings...
loadings.MxModelExtract factor loadings from an EFA (factor analysis).
noNAsSuccinctly select complete rows from a dataframe
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...
plot.percentPlot a percent change graph
power.ACE.testTest the power of an ACE model to detect paths of interest.
print.oddsratioPrint a scale "oddsratio" object
print.percentPrint a percent object
print.reliabilityPrint a scale "reliability" object
print.RMSEAPrint a RMSEA object
prolific_anonymizeClean up a prolific file for sharing by removing...
prolific_check_IDReturn PIDs in df
prolific_read_demogRead and optionally merge demographics file from prolific...
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 MxModel summary
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 models in a easy-to-learn-from format.
tmx_show.MxMatrixShow matrices of models in a easy-to-learn-from format.
tmx_show.MxModelShow 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 ACE twin model (univariate...
umxACEcovRun a Cholesky with covariates that are random (in the...
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_namesCheck if a request name exists in a dataframe or related...
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
umxCLPMRuns cross-lagged panel models
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.
umxDiffMZMZ differences method for testing evidence for causality.
umxDiscTwinIntra-pair association in MZ, DZ twin models. (ALPHA...
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_sdSummarizing functions used in umx_aggregate and for umxAPA
umx_get_bracket_addressesGet bracket-style addresses from an mxMatrix
umx_get_checkpointGet or set checkpointing for a model
umxGetLatentsGet the latentVars from a RAM model
umxGetManifestsGet the manifestVars from a RAM model
umxGetModelUsed to get a RAM submodel by name
umx_get_optionsDisplay umx 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
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_lower.triGet values from lower triangle of a matrix
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...
umxMatrixFreeSets labeled matrix cells to free
umx_meansumx_means
umx_merge_randomized_columnsumx_merge_randomized_columns
umxMIReport modifications which would improve fit.
umxModelCatches users typing umxModel instead of umxRAM.
umxModelNamesReturn names of models found within a model
umxModifyumxModify: Add, set, or drop model paths by label.
umx_move_fileMove files
umxMRDoCExtends Mendelian randomization with the twin design to test...
umx_msgPrint the name and compact contents of variable.
umx_namesumx_names
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...
umxParanA wrapper to make paran easier to use. Just automates...
umx_paste_namesConcatenate base variable names with suffixes to create...
umxPathEasier (and powerful) specification of paths in SEM.
umxPlotQuickly plot y ~ x with a regression line and R^2, and nice...
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.
umxPlotFunEasily plot functions in R
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...
umxRAMBuild and run path-based SEM models
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
umxRenameMatrixRename a umxMatrix (even in a model)
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_runAutomatically run models?
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_dollar_symbolSet the symbol for money
umx_set_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 SEM diagram files saved to...
umx_set_plot_formatSet output format of plots (structural diagrams) in umx
umx_set_plot_use_hrbrthemesSet theme system to use for plots.
umx_set_separatorSet the separator
umx_set_silentTurn off most console and summary output from umx
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_str_charsSelect desired characters from a string
umx_str_from_objectReturn variable name as a string
umx_strings2numericA wrapper to map columns of strings to numeric.
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...
umxSummaryMRDoCPresent the results of a Mendelian Randomization Direction of...
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.
umxTwinMakerMake a twin model from the model describing just one person
umxTwoStageBuild a SEM implementing the instrumental variable design
umxUnexplainedCausalNexusumxUnexplainedCausalNexus
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_bracket_address2rclabelConvert a bracket address into an A_rXcX-style label.
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_missingDrop rows with missing definition variables
xmu_data_swap_a_blockData helper function to swap blocks of data from one set of...
xmu_describe_data_WLSDetermine if a dataset will need statistics for the means if...
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_extract_columnGet one or more columns from mzData or regular data.frame
xmu_get_CILook up and report CIs for free parameters
xmuHasSquareBracketsxmuHasSquareBrackets
xmuLabelxmuLabel: Add labels to a RAM model, matrix, or path
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_TwinSuperModelHelper 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)
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
xmu_print_algebrasPrint algebras from a umx model
xmuPropagateLabelsxmuPropagateLabels (not a user function)
xmuRAM2OrdinalxmuRAM2Ordinal
xmu_rclabel_2_bracket_addressConvert an "A_r1c1"-style label to a bracket address.
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 boilerplate start values for means and...
xmu_start_value_listMake start values
xmu_summary_RAM_group_parametersOrder and group the parameters in a RAM summary
xmu_twin_add_WeightMatricesAdd weight matrices to twin models.
xmu_twin_checkCheck basic aspects of input for twin models.
xmu_twin_get_var_namesNot for user: pull variable names from a twin model
xmu_twin_make_def_means_mats_and_algMake the matrices and algebras for definition-based means...
xmuTwinSuper_ContinuousCreate core of twin model for all-continuous data.
xmuTwinSuper_NoBinaryxmuTwinSuper_NoBinary
xmuTwinUpgradeMeansToCovariateModelNot for end-users: Add a means model with covariates to a...
xmu_twin_upgrade_selDvs2SelVarsUpgrade selDVs to selVars
xmuValuesxmuValues: Set values in RAM model, matrix, or path
tbates/umx documentation built on March 16, 2024, 4:26 a.m.