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Bates ", "License": "GPL-3", "Language": "en-US", "Encoding": "UTF-8", "URL": "https://github.com/tbates/umx#readme", "Description": "Quickly create, run, and report structural equation\nmodels, and twin models. See '?umx' for help, and\numx_open_CRAN_page(\"umx\") for NEWS. Timothy C. Bates, Michael\nC. Neale, Hermine H. Maes, (2019). umx: A library for\nStructural Equation and Twin Modelling in R. Twin Research and\nHuman Genetics, 22, 27-41. . Luis F.S.\nCastro-de-Araujo, Nathan A. Gillespie, Michael C. Neale, and\nTimothy Charles Bates (2026). umx version 4.5: Extending Twin\nand Path-Based SEM in R with CLPM, MR-DoC, Definition\nVariables, Onyx Integration, and Censored Distributions. 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"object": "iqdat", "class": [ "data.frame" ], "fields": [ "zygosity", "IQ_age1_T1", "IQ_age2_T1", "IQ_age3_T1", "IQ_age4_T1", "IQ_age1_T2", "IQ_age2_T2", "IQ_age3_T2", "IQ_age4_T2" ], "rows": 562, "table": true, "tojson": true }, { "name": "us_skinfold_data", "title": "Anthropometric data on twins", "object": "us_skinfold_data", "class": [ "data.frame" ], "fields": [ "fan", "zyg", "ht_T1", "wt_T1", "bmi_T1", "bml_T1", "bic_T1", "caf_T1", "ssc_T1", "sil_T1", "tri_T1", "ht_T2", "wt_T2", "bmi_T2", "bml_T2", "bic_T2", "caf_T2", "ssc_T2", "sil_T2", "tri_T2" ], "rows": 395, "table": true, "tojson": true } ], "_help": [ { "page": "bucks", "title": "Print a money object", "topics": [ "bucks", "print" ] }, { "page": "deg2rad", "title": "Convert Degrees to Degrees", "concept": [ "Miscellaneous Functions" ], "topics": [ "deg2rad" ] }, { "page": "dl_from_dropbox", "title": "dl_from_dropbox", "concept": [ "File Functions" ], "topics": [ "dl_from_dropbox" ] }, { "page": "docData", "title": "Twin data for Direction of causation modelling", "concept": [ "datasets" ], "topics": [ "docData" ] }, { "page": "extractAIC.MxModel", "title": "Extract AIC from MxModel", "concept": [ "Reporting functions" ], "topics": [ "extractAIC.MxModel" ] }, { "page": "fin_CAGR", "title": "Calculate Compound Annual Growth Rate (CAGR)", "concept": [ "financial functions" ], "topics": [ "fin_CAGR" ] }, { "page": "fin_carryCost", "title": "Work the carry cost of a house", "concept": [ "financial functions" ], "topics": [ "fin_carryCost" ] }, { "page": "fin_Greeks", "title": "Black-Scholes Call Option Price and Greeks Calculator", "concept": [ "financial functions" ], "topics": [ "fin_Greeks" ] }, { "page": "fin_interest", "title": "Compute the value of a principal & annual deposits at a compound interest over a number of years", "concept": [ "financial functions" ], "topics": [ "fin_interest" ] }, { "page": "fin_LeapSimulateRoll", "title": "Simulate and Compare LEAP Extrinsic Premium Decay", "concept": [ "financial functions" ], "topics": [ "fin_LeapSimulateRoll" ] }, { "page": "fin_net_present_value", "title": "Compute the net present value of a future income stream", "concept": [ "financial functions" ], "topics": [ "fin_net_present_value" ] }, { "page": "fin_percent", "title": "Compute the percent change needed to return to the original value after percent off (or on).", "concept": [ "financial functions" ], "topics": [ "fin_percent" ] }, { "page": "fin_plotGreekCurves", "title": "Plot Option Delta and Gamma Curves", "concept": [ "financial functions" ], "topics": [ "fin_plotGreekCurves" ] }, { "page": "fin_resolveVolatility", "title": "Resolve Option Implied Volatility from Ticker", "topics": [ "fin_resolveVolatility" ] }, { "page": "fin_stock_CAGR", "title": "Compute the CAGR of a stock", "concept": [ "financial functions" ], "topics": [ "fin_stock_CAGR" ] }, { "page": "fin_stock_justifiedPE", "title": "Justified P/E Ratio", "concept": [ "financial functions" ], "topics": [ "fin_stock_justifiedPE" ] }, { "page": "fin_stock_option", "title": "Teaching function for options", "concept": [ "financial functions" ], "topics": [ "fin_stock_option" ] }, { "page": "fin_stock_target", "title": "Compute the future value and gain of an investment", "concept": [ "financial functions" ], "topics": [ "fin_stock_target" ] }, { "page": "fin_stock_ticker", "title": "Open a ticker in yahoo finance.", "concept": [ "financial functions" ], "topics": [ "fin_stock_ticker" ] }, { "page": "fin_stock_valuation", "title": "Work the valuation of a company", "concept": [ "financial functions" ], "topics": [ "fin_stock_valuation" ] }, { "page": "fin_tax_FIF", "title": "NZ FIF Tax Offset & NAV Neutrality Calculator", "concept": [ "financial functions" ], "topics": [ "fin_tax_FIF" ] }, { "page": "fin_tax_NI", "title": "Compute UK NI given annual Earnings.", "concept": [ "financial functions" ], "topics": [ "fin_tax_NI" ] }, { "page": "Fischbein_wt", "title": "Weight data across time.", "concept": [ "datasets" ], "topics": [ "Fischbein_wt" ] }, { "page": "FishersMethod", "title": "Fishers Method of combining p-values.", "concept": [ "Miscellaneous Stats Functions" ], "topics": [ "FishersMethod" ] }, { "page": "geometric_mean", "title": "Geometric Mean", "concept": [ "Miscellaneous Stats Functions" ], "topics": [ "geometric_mean" ] }, { "page": "GFF", "title": "Twin data: General Family Functioning, divorce, and well-being.", "concept": [ "datasets" ], "topics": [ "GFF" ] }, { "page": "ggAddR", "title": "Add a fit statistic to a ggplot", "concept": [ "Plotting functions" ], "topics": [ "ggAddR" ] }, { "page": "harmonic_mean", "title": "Harmonic Mean", "concept": [ "Miscellaneous Stats Functions" ], "topics": [ "harmonic_mean" ] }, { "page": "install.OpenMx", "title": "Install OpenMx, with choice of builds", "concept": [ "Miscellaneous Utility Functions" ], "topics": [ "install.OpenMx", "umx_update_OpenMx" ] }, { "page": "iqdat", "title": "Twin data: IQ measured longitudinally across 4 ages.", "concept": [ "datasets" ], "topics": [ "iqdat" ] }, { "page": "libs", "title": "load libraries", "concept": [ "Miscellaneous Utility Functions" ], "topics": [ "libs" ] }, { "page": "loadings", "title": "loadings Generic loadings function to extract factor loadings from exploratory or confirmatory factor analyses.", "concept": [ "Reporting functions" ], "topics": [ "loadings" ] }, { "page": "loadings.MxModel", "title": "Extract factor loadings from an EFA (factor analysis).", "concept": [ "Reporting functions" ], "topics": [ "loadings.MxModel" ] }, { "page": "noNAs", "title": "Succinctly select complete rows from a dataframe", "concept": [ "Data Functions" ], "topics": [ "noNAs" ] }, { "page": "oddsratio", "title": "Compute odds ratio (OR)", "concept": [ "Miscellaneous Stats Functions" ], "topics": [ "oddsratio" ] }, { "page": "plot.MxLISRELModel", "title": "Create and display a graphical path diagram for a LISREL model.", "concept": [ "Plotting functions", "umx S3 functions" ], "topics": [ "plot.MxLISRELModel" ] }, { "page": "plot.MxModel", "title": "Create and display a graphical path diagram for a model.", "concept": [ "Plotting functions" ], "topics": [ "plot", "plot.MxModel" ] }, { "page": "plot.MxModelTwinMaker", "title": "Create and display a graphical path diagram for a path-based twin model.", "concept": [ "Plotting functions" ], "topics": [ "plot.MxModelTwinMaker", "umxPlotMxModelTwinMaker" ] }, { "page": "plot.percent", "title": "Plot a percent change graph", "topics": [ "plot.percent" ] }, { "page": "power.ACE.test", "title": "Test the power of an ACE model to detect paths of interest.", "concept": [ "Twin Modeling Functions" ], "topics": [ "power.ACE.test" ] }, { "page": "print.oddsratio", "title": "Print a scale \"oddsratio\" object", "topics": [ "print.oddsratio" ] }, { "page": "print.percent", "title": "Print a percent object", "topics": [ "print.percent" ] }, { "page": "print.reliability", "title": "Print a scale \"reliability\" object", "topics": [ "print.reliability" ] }, { "page": "print.RMSEA", "title": "Print a RMSEA object", "topics": [ "print.RMSEA" ] }, { "page": "prolific_anonymize", "title": "Clean up a prolific file for sharing by removing anonymity-compromising columns.", "concept": [ "Data Functions" ], "topics": [ "prolific_anonymize" ] }, { "page": "prolific_check_ID", "title": "Return PIDs in df", "concept": [ "Data Functions" ], "topics": [ "prolific_check_ID" ] }, { "page": "prolific_read_demog", "title": "Read and optionally merge demographics file from prolific academic", "concept": [ "Data Functions" ], "topics": [ "prolific_read_demog" ] }, { "page": "qm", "title": "qm", "concept": [ "Miscellaneous Utility Functions" ], "topics": [ "qm" ] }, { "page": "rad2deg", "title": "Convert Radians to Degrees", "concept": [ "Miscellaneous Functions" ], "topics": [ "rad2deg" ] }, { "page": "reliability", "title": "Report coefficient alpha (reliability)", "concept": [ "Miscellaneous Stats Functions" ], "topics": [ "reliability" ] }, { "page": "residuals.MxModel", "title": "Get residuals from an MxModel", "concept": [ "Reporting functions" ], "topics": [ "residuals.MxModel" ] }, { "page": "RMSEA", "title": "Generic RMSEA function", "concept": [ "Reporting functions" ], "topics": [ "RMSEA" ] }, { "page": "RMSEA.MxModel", "title": "RMSEA function for MxModels", "concept": [ "Reporting functions" ], "topics": [ "RMSEA.MxModel" ] }, { "page": "RMSEA.summary.mxmodel", "title": "RMSEA function for MxModel summary", "concept": [ "Reporting functions" ], "topics": [ "RMSEA.summary.mxmodel" ] }, { "page": "SE_from_p", "title": "Compute an SE from a beta and p value", "concept": [ "Miscellaneous Stats Functions" ], "topics": [ "SE_from_p" ] }, { "page": "tmx_genotypic_effect", "title": "Graphical display of genotypic effects.", "concept": [ "Teaching and testing Functions" ], "topics": [ "tmx_genotypic_effect" ] }, { "page": "tmx_is.identified", "title": "Test if a factor model is identified", "concept": [ "Teaching and testing Functions" ], "topics": [ "tmx_is.identified" ] }, { "page": "tmx_show", "title": "Show matrices of models in a easy-to-learn-from format.", "concept": [ "Reporting functions" ], "topics": [ "tmx_show" ] }, { "page": "tmx_show.MxMatrix", "title": "Show matrices of models in a easy-to-learn-from format.", "concept": [ "Reporting functions" ], "topics": [ "tmx_show.MxMatrix" ] }, { "page": "tmx_show.MxModel", "title": "Show matrices of RAM models in a easy-to-learn-from format.", "concept": [ "Teaching and Testing functions" ], "topics": [ "tmx_show.MxModel" ] }, { "page": "umx", "title": "Functions for Structural Equation Modeling in OpenMx", "concept": [ "Advanced Model Building Functions", "Check or test", "Core Model Building Functions", "Data Functions", "File Functions", "Get and set", "Miscellaneous Stats Functions", "Miscellaneous Utility Functions", "Model Summary and Comparison", "Plotting functions", "Reporting Functions", "String Functions", "Super-easy helpers", "Teaching and testing Functions", "Twin Data functions", "Twin Modeling Functions", "datasets", "zAdvanced Helpers" ], "topics": [ "umx-package", "umx" ] }, { "page": "umx_aggregate", "title": "Convenient formula-based cross-tabs & built-in summary functions", "concept": [ "Reporting Functions" ], "topics": [ "umx_aggregate" ] }, { "page": "umx_APA_pval", "title": "Round p-values according to APA guidelines", "concept": [ "xmu internal not for end user" ], "topics": [ "umx_APA_pval" ] }, { "page": "umx_apply", "title": "umx_apply", "concept": [ "Miscellaneous Stats Functions" ], "topics": [ "umx_apply" ] }, { "page": "umx_array_shift", "title": "Like the php array_shift function: shifts an item off the beginning of a list", "concept": [ "Miscellaneous Utility Functions" ], "topics": [ "umx_array_shift" ] }, { "page": "umx_as_numeric", "title": "umx_as_numeric", "concept": [ "Data Functions" ], "topics": [ "umx_as_numeric" ] }, { "page": "umx_check", "title": "umx_check", "concept": [ "Test" ], "topics": [ "umx_check" ] }, { "page": "umx_check_model", "title": "Check for required features in an OpenMx.", "concept": [ "Test" ], "topics": [ "umx_check_model" ] }, { "page": "umx_check_names", "title": "Check if a request name exists in a dataframe or related object", "concept": [ "Check or test", "Test" ], "topics": [ "umx_check_names" ] }, { "page": "umx_check_OS", "title": "umx_check_OS", "concept": [ "Test" ], "topics": [ "umx_check_OS" ] }, { "page": "umx_check_parallel", "title": "Check if OpenMx is using OpenMP, test cores, and get timings", "concept": [ "Test" ], "topics": [ "umx_check_parallel" ] }, { "page": "umx_complete_dollar", "title": "umx_complete_dollar", "concept": [ "Miscellaneous Functions" ], "topics": [ "umx_complete_dollar" ] }, { "page": "umx_cont_2_quantiles", "title": "umx_cont_2_quantiles", "concept": [ "Data Functions" ], "topics": [ "umx2ord", "umx_cont_2_quantiles" ] }, { "page": "umx_cor", "title": "Report correlations and their p-values", "concept": [ "Miscellaneous Stats Functions" ], "topics": [ "umx_cor" ] }, { "page": "umx_explode", "title": "Explode a string (Like the php function 'explode')", "concept": [ "String Functions" ], "topics": [ "umx_explode" ] }, { "page": "umx_explode_twin_names", "title": "Break twin variable names (BMI_T1, BMI_T2) into base variable names (BMI, \"_T\", 1:2)", "concept": [ "String Functions" ], "topics": [ "umx_explode_twin_names" ] }, { "page": "umx_file_load_pseudo", "title": "Read in files from pseudocons.", "concept": [ "File Functions" ], "topics": [ "umx_file_load_pseudo" ] }, { "page": "umx_find_object", "title": "umx_find_object", "concept": [ "Miscellaneous Utility Functions" ], "topics": [ "umx_find_object" ] }, { "page": "umx_fun_mean_sd", "title": "Summarizing functions used in umx_aggregate and for umxAPA", "concept": [ "xmu internal not for end user" ], "topics": [ "umx_fun_mean_sd" ] }, { "page": "umx_get_alphas", "title": "Get the alpha text", "concept": [ "Get and set" ], "topics": [ "umx_get_alphas" ] }, { "page": "umx_get_bracket_addresses", "title": "Get bracket-style addresses from an mxMatrix", "concept": [ "xmu internal not for end user" ], "topics": [ "umx_get_bracket_addresses" ] }, { "page": "umx_get_checkpoint", "title": "Get or set checkpointing for a model", "concept": [ "Get and set" ], "topics": [ "umx_get_checkpoint" ] }, { "page": "umx_get_options", "title": "Display umx options", "concept": [ "Get and set" ], "topics": [ "umx_get_options" ] }, { "page": "umx_grep", "title": "Search for text", "concept": [ "String Functions" ], "topics": [ "umx_grep" ] }, { "page": "umx_has_been_run", "title": "umx_has_been_run", "concept": [ "Test" ], "topics": [ "umx_has_been_run" ] }, { "page": "umx_has_CIs", "title": "umx_has_CIs", "concept": [ "Test" ], "topics": [ "umx_has_CIs" ] }, { "page": "umx_has_means", "title": "umx_has_means", "concept": [ "Test" ], "topics": [ "umx_has_means" ] }, { "page": "umx_has_square_brackets", "title": "Check if a label contains square brackets", "concept": [ "Test" ], "topics": [ "umx_has_square_brackets" ] }, { "page": "umx_is_class", "title": "Check if variables in a dataframe are in a list of classes.", "concept": [ "Check or test" ], "topics": [ "umx_is_class" ] }, { "page": "umx_is_cov", "title": "umx_is_cov", "concept": [ "Test" ], "topics": [ "umx_is_cov" ] }, { "page": "umx_is_endogenous", "title": "List endogenous variables in a model", "concept": [ "Check or test" ], "topics": [ "umx_is_endogenous" ] }, { "page": "umx_is_exogenous", "title": "umx_is_exogenous", "concept": [ "Check or test" ], "topics": [ "umx_is_exogenous" ] }, { "page": "umx_is_LISREL", "title": "umx_is_LISREL", "concept": [ "Test" ], "topics": [ "umx_is_LISREL" ] }, { "page": "umx_is_MxData", "title": "Check if an object is an mxData object", "concept": [ "Test" ], "topics": [ "umx_is_MxData" ] }, { "page": "umx_is_MxMatrix", "title": "umx_is_MxMatrix", "concept": [ "Test" ], "topics": [ "umx_is_MxMatrix" ] }, { "page": "umx_is_MxModel", "title": "umx_is_MxModel", "concept": [ "Test" ], "topics": [ "umx_is_MxModel" ] }, { "page": "umx_is_numeric", "title": "Check if variables in a dataframe are numeric", "concept": [ "Check or test" ], "topics": [ "umx_is_numeric" ] }, { "page": "umx_is_ordered", "title": "Test if one or more variables in a dataframe are ordered", "concept": [ "Check or test" ], "topics": [ "umx_is_ordered" ] }, { "page": "umx_is_RAM", "title": "umx_is_RAM", "concept": [ "Test" ], "topics": [ "umx_is_RAM" ] }, { "page": "umx_log_wide_twin_data", "title": "Log-transform wide twin data with a positive shift", "topics": [ "umx_log_wide_twin_data" ] }, { "page": "umx_long2wide", "title": "Take a long twin-data file and make it wide (one family per row)", "concept": [ "Twin Data functions" ], "topics": [ "umx_long2wide" ] }, { "page": "umx_lower.tri", "title": "Get values from lower triangle of a matrix", "concept": [ "Miscellaneous Utility Functions" ], "topics": [ "umx_lower.tri" ] }, { "page": "umx_lower2full", "title": "Convert lower-only matrix data to full (or enforce symmetry on a full matrix)", "concept": [ "Data Functions" ], "topics": [ "umx_lower2full" ] }, { "page": "umx_make", "title": "\"make\" the umx package using devtools: release to CRAN etc.", "concept": [ "xmu internal not for end user" ], "topics": [ "umx_make" ] }, { "page": "umx_make_fake_data", "title": "umx_make_fake_data", "concept": [ "Data Functions" ], "topics": [ "umx_make_fake_data" ] }, { "page": "umx_make_MR_data", "title": "Simulate Mendelian Randomization data", "concept": [ "Data Functions" ], "topics": [ "umx_make_MR_data" ] }, { "page": "umx_make_raw_from_cov", "title": "Turn a cov matrix into raw data", "concept": [ "Data Functions" ], "topics": [ "umx_make_raw_from_cov" ] }, { "page": "umx_make_sql_from_excel", "title": "Convert an excel spreadsheet in a text file on sql statements.", "concept": [ "File Functions" ], "topics": [ "umx_make_sql_from_excel" ] }, { "page": "umx_make_twin_data_nice", "title": "Convert a twin dataset into umx standard format.", "concept": [ "Twin Data functions" ], "topics": [ "umx_make_twin_data_nice" ] }, { "page": "umx_make_TwinData", "title": "Simulate twin data with control over A, C, and E parameters, as well as moderation of A.", "concept": [ "Data Functions", "Twin Data functions" ], "topics": [ "umx_make_TwinData" ] }, { "page": "umx_means", "title": "umx_means", "concept": [ "Miscellaneous Stats Functions" ], "topics": [ "umx_means" ] }, { "page": "umx_merge_randomized_columns", "title": "umx_merge_randomized_columns", "concept": [ "Data Functions" ], "topics": [ "umx_merge_randomized_columns" ] }, { "page": "umx_move_file", "title": "Move files", "concept": [ "File Functions" ], "topics": [ "umx_move_file" ] }, { "page": "umx_msg", "title": "Print the Name and Compact Contents of a Variable", "concept": [ "Miscellaneous Utility Functions" ], "topics": [ "umx_msg" ] }, { "page": "umx_names", "title": "umx_names", "concept": [ "String Functions" ], "topics": [ "namez", "umx_names" ] }, { "page": "umx_open", "title": "Open a file or folder", "concept": [ "File Functions" ], "topics": [ "umx_open" ] }, { "page": "umx_open_CRAN_page", "title": "Open the CRAN page for a package", "concept": [ "Miscellaneous Utility Functions" ], "topics": [ "umx_open_CRAN_page" ] }, { "page": "umx_pad", "title": "Pad an Object with NAs", "concept": [ "Miscellaneous Utility Functions" ], "topics": [ "umx_pad" ] }, { "page": "umx_paste_names", "title": "Concatenate base variable names with suffixes to create wide-format variable names (i.e twin-format)", "concept": [ "String Functions" ], "topics": [ "tvars", "umx_paste_names" ] }, { "page": "umx_polychoric", "title": "FIML-based polychoric, polyserial, and Pearson correlations", "concept": [ "Data Functions" ], "topics": [ "umx_polychoric" ] }, { "page": "umx_polypairwise", "title": "FIML-based Pairwise polychoric, polyserial, and Pearson correlations", "concept": [ "Data Functions" ], "topics": [ "umx_polypairwise" ] }, { "page": "umx_polytriowise", "title": "FIML-based trio-based polychoric, polyserial, and Pearson correlations", "concept": [ "Data Functions" ], "topics": [ "umx_polytriowise" ] }, { "page": "umx_print", "title": "Print tables in a range of formats (markdown default, see 'umx_set_table_format()' for other formats) or as a web browser table.", "concept": [ "Miscellaneous Utility Functions" ], "topics": [ "umx_print" ] }, { "page": "umx_r_test", "title": "Test the difference between correlations for significance.", "concept": [ "Miscellaneous Stats Functions" ], "topics": [ "umx_r_test" ] }, { "page": "umx_read_lower", "title": "Read lower-triangle of data matrix from console or file", "concept": [ "Data Functions" ], "topics": [ "umx_read_lower" ] }, { "page": "umx_rename", "title": "umx_rename", "concept": [ "Data Functions" ], "topics": [ "umx_rename" ] }, { "page": "umx_rename_file", "title": "Rename files", "concept": [ "File Functions" ], "topics": [ "umx_rename_file" ] }, { "page": "umx_reorder", "title": "Reorder or drop variables from a correlation/covariance matrix.", "concept": [ "Data Functions" ], "topics": [ "umx_reorder" ] }, { "page": "umx_residualize", "title": "Easily residualize variables in long or wide dataframes, returning them changed in-place.", "concept": [ "Twin Data functions" ], "topics": [ "umx_residualize" ] }, { "page": "umx_rot", "title": "Rotate a vector", "concept": [ "String Functions" ], "topics": [ "umx_rot" ] }, { "page": "umx_round", "title": "umx_round", "concept": [ "Miscellaneous Stats Functions" ], "topics": [ "umx_round" ] }, { "page": "umx_scale", "title": "Scale data columns, skipping non-scalable columns", "concept": [ "Miscellaneous Stats Functions" ], "topics": [ "umx_scale" ] }, { "page": "umx_scale_wide_twin_data", "title": "Scale wide twin data", "concept": [ "Twin Data functions" ], "topics": [ "umx_scale_wide_twin_data" ] }, { "page": "umx_score_scale", "title": "Score a psychometric scale by summing normal and reversed items.", "concept": [ "Data Functions" ], "topics": [ "umx_score_scale" ] }, { "page": "umx_select_valid", "title": "Update NA values in one column with valid entries from another", "concept": [ "Data Functions" ], "topics": [ "umx_select_valid" ] }, { "page": "umx_set_auto_plot", "title": "umx_set_auto_plot", "concept": [ "Get and set" ], "topics": [ "umx_set_auto_plot" ] }, { "page": "umx_set_auto_run", "title": "Automatically run models?", "concept": [ "Get and set" ], "topics": [ "umx_set_auto_run" ] }, { "page": "umx_set_checkpoint", "title": "umx_set_checkpoint", "concept": [ "Get and set" ], "topics": [ "umx_checkpoint", "umx_set_checkpoint" ] }, { "page": "umx_set_condensed_slots", "title": "umx_set_condensed_slots", "concept": [ "Get and set" ], "topics": [ "umx_set_condensed_slots" ] }, { "page": "umx_set_cores", "title": "umx_set_cores", "concept": [ "Get and set" ], "topics": [ "umx_set_cores" ] }, { "page": "umx_set_data_variance_check", "title": "umx_set_data_variance_check", "concept": [ "Get and set" ], "topics": [ "umx_set_data_variance_check" ] }, { "page": "umx_set_dollar_symbol", "title": "Set the symbol for money", "concept": [ "Get and set" ], "topics": [ "umx_set_dollar_symbol" ] }, { "page": "umx_set_optimization_options", "title": "Set options that affect optimization in OpenMx", "concept": [ "Get and set" ], "topics": [ "umx_set_optimization_options" ] }, { "page": "umx_set_optimizer", "title": "Set the optimizer in OpenMx", "concept": [ "Get and set" ], "topics": [ "umx_set_optimizer" ] }, { "page": "umx_set_plot_file_suffix", "title": "Set output suffix used in umx SEM diagram files saved to disk.", "concept": [ "Get and set" ], "topics": [ "umx_set_plot_file_suffix" ] }, { "page": "umx_set_plot_format", "title": "Set output format of plots (structural diagrams) in umx", "concept": [ "Get and set" ], "topics": [ "umx_set_plot_format" ] }, { "page": "umx_set_separator", "title": "Set the separator", "concept": [ "Get and set" ], "topics": [ "umx_set_separator" ] }, { "page": "umx_set_silent", "title": "Turn off most console and summary output from umx", "concept": [ "Get and set" ], "topics": [ "umx_set_silent" ] }, { "page": "umx_set_table_format", "title": "umx_set_table_format", "concept": [ "Get and set" ], "topics": [ "umx_set_table_format" ] }, { "page": "umx_stack", "title": "Stack data like stack() does, with more control.", "concept": [ "Data Functions" ], "topics": [ "umx_stack" ] }, { "page": "umx_standardize", "title": "Return a standardized version of a Structural Model", "concept": [ "xmu internal not for end user" ], "topics": [ "umx_standardize" ] }, { "page": "umx_str_chars", "title": "Select desired characters from a string", "concept": [ "String Functions" ], "topics": [ "umx_str_chars" ] }, { "page": "umx_str_from_object", "title": "Return variable name as a string", "concept": [ "String Functions" ], "topics": [ "umx_str_from_object" ] }, { "page": "umx_string_to_algebra", "title": "Convert a string to an OpenMx algebra", "concept": [ "xmu internal not for end user" ], "topics": [ "umx_string_to_algebra" ] }, { "page": "umx_strings2numeric", "title": "A wrapper to map columns of strings to numeric.", "concept": [ "Data Functions" ], "topics": [ "umx_strings2numeric" ] }, { "page": "umx_time", "title": "umx_time", "concept": [ "Reporting Functions" ], "topics": [ "umx_time" ] }, { "page": "umx_trim", "title": "Trim whitespace surrounding a string.", "concept": [ "String Functions" ], "topics": [ "umx_trim" ] }, { "page": "umx_var", "title": "Get variances from a df that might contain some non-numeric columns", "concept": [ "Miscellaneous Stats Functions" ], "topics": [ "umx_var" ] }, { "page": "umx_wide2long", "title": "umx_wide2long", "concept": [ "Miscellaneous Utility Functions" ], "topics": [ "umx_wide2long" ] }, { "page": "umx_wide2longTwinData", "title": "Change twin data from wide (2 twins per row) to long format.", "concept": [ "Twin Data functions" ], "topics": [ "umx_wide2longTwinData" ] }, { "page": "umx_wide4lmer", "title": "Take a long dataframe and make it wide for repeated measures and multi-level analysis", "concept": [ "Miscellaneous Utility Functions" ], "topics": [ "umx_wide4lmer" ] }, { "page": "umx_write_to_clipboard", "title": "umx_write_to_clipboard", "concept": [ "File Functions" ], "topics": [ "umx_write_to_clipboard" ] }, { "page": "umx_yj_wide_twin_data", "title": "Yeo-Johnson transform wide twin data (Non-destructive)", "concept": [ "Twin Data functions" ], "topics": [ "umx_yj_wide_twin_data" ] }, { "page": "umx-deprecated", "title": "Deprecated. May already stop() code and ask to be updated. May be dropped entirely in future.", "concept": [ "umx deprecated" ], "topics": [ "umx-deprecated" ] }, { "page": "umxACE", "title": "Build and run a 2-group Cholesky ACE twin model (univariate or multivariate)", "concept": [ "Twin Modeling Functions" ], "topics": [ "umxACE" ] }, { "page": "umxACE_DE", "title": "Build a Double-Entry Censored Data ACE twin model", "concept": [ "Twin Modeling Functions" ], "topics": [ "umxACE_DE" ] }, { "page": "umxACEcov", "title": "Run a Cholesky with covariates that are random (in the expected covariance matrix)", "concept": [ "Twin Modeling Functions" ], "topics": [ "umxACEcov" ] }, { "page": "umxACEv", "title": "Build and run 2-group uni- or multi-variate ACE models based on VARIANCE (not paths).", "concept": [ "Twin Modeling Functions" ], "topics": [ "umxACEv" ] }, { "page": "umxAlgebra", "title": "A simple wrapper for mxAlgebra with name as the first parameter for more readable compact code.", "concept": [ "Advanced Model Building Functions" ], "topics": [ "umxAlgebra" ] }, { "page": "umxAPA", "title": "Creates nicely formatted journal-style summaries of models, p-values, data-frames and much more.", "concept": [ "Reporting Functions" ], "topics": [ "summaryAPA", "umxAPA" ] }, { "page": "umxBrownie", "title": "A recipe Easter-egg for umx", "concept": [ "Miscellaneous Functions" ], "topics": [ "umxBrownie" ] }, { "page": "umxCI", "title": "Add (and, optionally, run) confidence intervals to a structural model.", "concept": [ "Reporting functions" ], "topics": [ "umxCI" ] }, { "page": "umxCI_boot", "title": "umxCI_boot", "concept": [ "Reporting functions" ], "topics": [ "umxCI_boot" ] }, { "page": "umxCLPM", "title": "Runs cross-lagged panel models", "concept": [ "CLPM Functions" ], "topics": [ "umxCLPM" ] }, { "page": "umxCompare", "title": "Print a comparison table of one or more 'OpenMx::mxModel()'s, formatted nicely.", "concept": [ "Model Summary and Comparison" ], "topics": [ "umxCompare" ] }, { "page": "umxConfint", "title": "Get confidence intervals from a umx model", "concept": [ "Reporting functions" ], "topics": [ "umxConfint" ] }, { "page": "umxCov2cor", "title": "Convert a covariance matrix into a correlation matrix", "concept": [ "Miscellaneous Stats Functions" ], "topics": [ "umxCov2cor" ] }, { "page": "umxCP", "title": "umxCP: Build and run a Common Pathway twin model", "concept": [ "Twin Modeling Functions" ], "topics": [ "umxCP" ] }, { "page": "umxDiagnose", "title": "Diagnose problems in a model - not working!", "concept": [ "Teaching and Testing functions" ], "topics": [ "umxDiagnose" ] }, { "page": "umxDiffMZ", "title": "MZ differences method for testing evidence for causality.", "concept": [ "Twin Modeling Functions" ], "topics": [ "umxDiffMZ" ] }, { "page": "umxDiscTwin", "title": "Intra-pair association in MZ, DZ twin models. (ALPHA quality!)", "concept": [ "Twin Modeling Functions" ], "topics": [ "umxDiscTwin" ] }, { "page": "umxDoC", "title": "Build and run a 2-group Direction of Causation twin models.", "concept": [ "Twin Modeling Functions" ], "topics": [ "umxDoC" ] }, { "page": "umxDoCp", "title": "Make a direction of causation model based on umxPath statements", "concept": [ "Twin Modeling Functions" ], "topics": [ "umxDoCp" ] }, { "page": "umxEFA", "title": "FIML-based Exploratory Factor Analysis (EFA)", "concept": [ "Super-easy helpers" ], "topics": [ "umxEFA", "umxFactanal" ] }, { "page": "umxEquate", "title": "umxEquate: Equate two or more paths", "concept": [ "Model Summary and Comparison" ], "topics": [ "umxEquate" ] }, { "page": "umxExamples", "title": "Example code from Twin Research and Human Genetics Paper on umx", "topics": [ "umxExampleCode_TRHGpaper", "umxExamples" ] }, { "page": "umxExpCov", "title": "Get the expected vcov matrix", "concept": [ "Reporting functions" ], "topics": [ "umxExpCov", "vcov.MxModel" ] }, { "page": "umxExpMeans", "title": "Extract the expected means matrix from an 'OpenMx::mxModel()'", "concept": [ "Reporting functions" ], "topics": [ "umxExpMeans" ] }, { "page": "umxFactor", "title": "umxFactor", "concept": [ "Data Functions" ], "topics": [ "umxFactor", "umx_factor" ] }, { "page": "umxFactorScores", "title": "Return factor scores from a model as an easily consumable dataframe.", "concept": [ "Reporting Functions" ], "topics": [ "umxFactorScores" ] }, { "page": "umxFitIndices", "title": "Get additional fit-indices for a model with umxFitIndices", "concept": [ "Reporting functions" ], "topics": [ "umxFitIndices" ] }, { "page": "umxFixAll", "title": "umxFixAll: Fix all free parameters", "concept": [ "Advanced Model Building Functions" ], "topics": [ "umxFixAll" ] }, { "page": "umxGetLatents", "title": "Get the latentVars from a RAM model", "concept": [ "Reporting Functions" ], "topics": [ "umxGetLatents" ] }, { "page": "umxGetManifests", "title": "Get the manifestVars from a RAM model", "concept": [ "Reporting Functions" ], "topics": [ "umxGetManifests" ] }, { "page": "umxGetModel", "title": "Used to get a RAM submodel by name", "concept": [ "Reporting Functions" ], "topics": [ "umxGetModel" ] }, { "page": "umxGetParameters", "title": "Get parameters from a model, with support for pattern matching!", "concept": [ "Reporting Functions" ], "topics": [ "umxGetParameters" ] }, { "page": "umxGxE", "title": "umxGxE: Implements ACE models with moderation of paths, e.g. by SES.", "concept": [ "Twin Modeling Functions" ], "topics": [ "umxGxE" ] }, { "page": "umxGxE_window", "title": "Implement the moving-window form of GxE analysis.", "concept": [ "Twin Modeling Functions" ], "topics": [ "umxGxE_window" ] }, { "page": "umxGxEbiv", "title": "Purcell (2002) Bivariate GxE model: Suitable when twins differ on the moderator.", "concept": [ "Twin Modeling Functions" ], "topics": [ "umxGxEbiv" ] }, { "page": "umxHetCor", "title": "Create a matrix of correlations for variables of diverse types (binary, ordinal, continuous)", "concept": [ "Data Functions", "Miscellaneous Stats Functions" ], "topics": [ "umxHetCor" ] }, { "page": "umxIP", "title": "umxIP: Build and run an Independent Pathway twin model", "concept": [ "Twin Modeling Functions" ], "topics": [ "umxIP" ] }, { "page": "umxJiggle", "title": "umxJiggle", "concept": [ "Advanced Model Building Functions" ], "topics": [ "umxJiggle" ] }, { "page": "umxLav2RAM", "title": "Convert lavaan string to a umxRAM model", "concept": [ "Miscellaneous Utility Functions" ], "topics": [ "umxLav2RAM" ] }, { "page": "umxLISREL", "title": "Make a LISREL model analogous to umxRAM", "concept": [ "Core Model Building Functions" ], "topics": [ "umxLISREL" ] }, { "page": "umxMatrix", "title": "Make a mxMatrix with automatic labels. Also takes name as the first parameter for more readable code.", "concept": [ "Core Model Building Functions" ], "topics": [ "umxMatrix" ] }, { "page": "umxMatrixFree", "title": "Sets labeled matrix cells to free", "topics": [ "umxMatrixFree" ] }, { "page": "umxMeasurementInvariance", "title": "Test measurement invariance of a confirmatory factor analysis model", "concept": [ "Model Comparison" ], "topics": [ "umxMeasurementInvariance" ] }, { "page": "umxMI", "title": "Report modifications which would improve fit.", "concept": [ "Model Summary and Comparison" ], "topics": [ "umxMI" ] }, { "page": "umxModel", "title": "Catches users typing umxModel instead of umxRAM.", "concept": [ "xmu internal not for end user" ], "topics": [ "umxModel" ] }, { "page": "umxModelNames", "title": "Return names of models found within a model", "concept": [ "Miscellaneous Utility Functions" ], "topics": [ "umxModelNames" ] }, { "page": "umxModify", "title": "umxModify: Add, set, or drop model paths by label.", "concept": [ "Core Model Building Functions" ], "topics": [ "umxModify" ] }, { "page": "umxMRDoC", "title": "Extends Mendelian randomization with the twin design to test evidence of causality", "concept": [ "Twin Modeling Functions" ], "topics": [ "umxMRDoC" ] }, { "page": "umxParameters", "title": "Display path estimates from a model, filtering by name and value.", "concept": [ "Reporting Functions" ], "topics": [ "parameters", "umxParameters" ] }, { "page": "umxParan", "title": "A wrapper to make paran easier to use. Just automates applying 'complete.cases()'", "concept": [ "Miscellaneous Stats Functions" ], "topics": [ "umxParan" ] }, { "page": "umxPath", "title": "Easier (and powerful) specification of paths in SEM.", "concept": [ "Core Model Building Functions" ], "topics": [ "umxPath" ] }, { "page": "umxPlot", "title": "Quickly plot y ~ x with a regression line and R^2, and nice labels.", "concept": [ "Plotting functions" ], "topics": [ "umxPlot" ] }, { "page": "umxPlotACE", "title": "Make a graphical display of an ACE model", "concept": [ "Plotting functions" ], "topics": [ "plot.MxModelACE", "umxPlotACE" ] }, { "page": "umxPlotACEcov", "title": "Make a graphical display of an ACE model with covariates.", "concept": [ "Plotting functions" ], "topics": [ "plot.MxModelACEcov", "umxPlotACEcov" ] }, { "page": "umxPlotACEv", "title": "Produce a graphical display of an ACE variance-components twin model", "concept": [ "Plotting functions" ], "topics": [ "plot.MxModelACEv", "umxPlotACEv" ] }, { "page": "umxPlotCP", "title": "Draw and display a graphical figure of Common Pathway model", "concept": [ "Plotting functions" ], "topics": [ "plot.MxModelCP", "umxPlotCP" ] }, { "page": "umxPlotDoC", "title": "Plot a Direction of Causation Model.", "concept": [ "Plotting functions" ], "topics": [ "plot.MxModelDoC", "umxPlotDoC" ] }, { "page": "umxPlotFun", "title": "Easily plot functions in R", "concept": [ "Plotting functions" ], "topics": [ "umxPlotFun" ] }, { "page": "umxPlotGxE", "title": "Plot the results of a GxE univariate test for moderation of ACE components.", "concept": [ "Plotting functions" ], "topics": [ "plot.MxModelGxE", "umxPlotGxE" ] }, { "page": "umxPlotGxEbiv", "title": "Plot the results of a GxE univariate test for moderation of ACE components.", "concept": [ "Plotting functions" ], "topics": [ "plot.MxModelGxEbiv", "umxPlotGxEbiv" ] }, { "page": "umxPlotIP", "title": "Draw a graphical figure for a Independent Pathway model", "concept": [ "Plotting functions" ], "topics": [ "plot.MxModelIP", "umxPlotIP" ] }, { "page": "umxPlotPredict", "title": "'umxPlotPredict' Take a model and plot the y against predicted(y)", "concept": [ "Plotting functions" ], "topics": [ "umxPlotPredict" ] }, { "page": "umxPlotSexLim", "title": "Draw and display a graphical figure of a Sex limitation model", "concept": [ "Plotting functions" ], "topics": [ "plot.MxModelSexLim", "umxPlotSexLim" ] }, { "page": "umxPlotSimplex", "title": "Draw and display a graphical figure of a simplex model", "concept": [ "Plotting functions" ], "topics": [ "plot.MxModelSimplex", "umxPlotSimplex" ] }, { "page": "umxPower", "title": "Test power to detect specified path values in a model.", "concept": [ "Teaching and Testing functions" ], "topics": [ "umxPower" ] }, { "page": "umxRAM", "title": "Build and run path-based SEM models", "concept": [ "Core Model Building Functions" ], "topics": [ "umxRAM" ] }, { "page": "umxRAM2Lav", "title": "Convert a RAM model to a lavaan string", "concept": [ "Miscellaneous Utility Functions" ], "topics": [ "umxRAM2Lav" ] }, { "page": "umxReduce", "title": "Reduce models, and report the results.", "concept": [ "Model Summary and Comparison", "Twin Modeling Functions" ], "topics": [ "umxReduce" ] }, { "page": "umxReduceACE", "title": "Reduce an ACE model.", "concept": [ "Twin Modeling Functions" ], "topics": [ "umxReduceACE" ] }, { "page": "umxReduceGxE", "title": "Reduce a GxE model.", "concept": [ "Twin Modeling Functions" ], "topics": [ "umxReduceGxE" ] }, { "page": "umxRenameMatrix", "title": "Rename a umxMatrix (even in a model)", "concept": [ "xmu internal not for end user" ], "topics": [ "umxRenameMatrix" ] }, { "page": "umxRotate", "title": "Generic SEM factor model loading rotation function", "concept": [ "Reporting functions" ], "topics": [ "umxRotate" ] }, { "page": "umxRotate.MxModelCP", "title": "Rotate a CP solution", "concept": [ "Twin Modeling Functions" ], "topics": [ "umxRotate.MxModelCP" ] }, { "page": "umxRun", "title": "umxRun: Run an mxModel", "concept": [ "Advanced Model Building Functions" ], "topics": [ "umxRun" ] }, { "page": "umxSetParameters", "title": "Change or fix parameters (e.g. their values, labels, bounds, ..) in a model.", "concept": [ "Model Summary and Comparison" ], "topics": [ "umxSetParameters" ] }, { "page": "umxSexLim", "title": "Multivariate sex limitation twin model", "concept": [ "Twin Modeling Functions" ], "topics": [ "umxSexLim" ] }, { "page": "umxSimplex", "title": "Build and run a simplex twin model (not ready for use!)", "concept": [ "Twin Modeling Functions" ], "topics": [ "umxSimplex" ] }, { "page": "umxSummarizeTwinData", "title": "Summarize twin data", "concept": [ "Twin Modeling Functions" ], "topics": [ "umxSummarizeTwinData" ] }, { "page": "umxSummary", "title": "Shows a compact, publication-style, summary of umx models", "concept": [ "Model Summary and Comparison" ], "topics": [ "umxSummary" ] }, { "page": "umxSummary.MxLISRELModel", "title": "umxSummary.MxLISRELModel", "concept": [ "Model Summary" ], "topics": [ "umxSummary.MxLISRELModel" ] }, { "page": "umxSummary.MxModel", "title": "Shows a compact, publication-style, summary of a RAM model", "concept": [ "Summary functions" ], "topics": [ "umxSummary.MxModel", "umxSummary.MxRAMModel" ] }, { "page": "umxSummaryACE", "title": "Shows a compact, publication-style, summary of a umx Cholesky ACE model", "concept": [ "Twin Modeling Functions" ], "topics": [ "umxSummary.MxModelACE", "umxSummaryACE" ] }, { "page": "umxSummaryACEcov", "title": "Present results of a twin ACE-model with covariates in table and graphical forms.", "concept": [ "Summary functions" ], "topics": [ "umxSummary.MxModelACEcov", "umxSummaryACEcov" ] }, { "page": "umxSummaryACEv", "title": "Shows a compact, publication-style, summary of a variance-based Cholesky ACE model.", "concept": [ "Twin Modeling Functions" ], "topics": [ "umxSummary.MxModelACEv", "umxSummaryACEv" ] }, { "page": "umxSummaryCP", "title": "Present the results of a Common-pathway twin model in table and graphical form", "concept": [ "Summary functions" ], "topics": [ "umxSummary.MxModelCP", "umxSummaryCP" ] }, { "page": "umxSummaryDoC", "title": "Shows a compact, publication-style, summary of a umx Direction of Causation model", "concept": [ "Twin Modeling Functions" ], "topics": [ "umxSummary.MxModelDoC", "umxSummaryDoC" ] }, { "page": "umxSummaryGxE", "title": "Summarize a GxE model", "concept": [ "Summary functions" ], "topics": [ "umxSummary.MxModelGxE", "umxSummaryGxE" ] }, { "page": "umxSummaryGxEbiv", "title": "Summarize a bivariate GxE twin model", "concept": [ "Twin Modeling Functions" ], "topics": [ "umxSummary.MxModelGxEbiv", "umxSummaryGxEbiv" ] }, { "page": "umxSummaryIP", "title": "Present the results of an independent-pathway twin model in table and graphical form", "concept": [ "Summary functions" ], "topics": [ "umxSummary.MxModelIP", "umxSummaryIP" ] }, { "page": "umxSummaryMRDoC", "title": "Present the results of a Mendelian Randomization Direction of Causation Model in a table", "concept": [ "Summary functions" ], "topics": [ "umxSummary.MxModelMRDoC", "umxSummaryMRDoC" ] }, { "page": "umxSummarySexLim", "title": "Shows a compact, publication-style, summary of a umx Sex Limitation model", "concept": [ "Twin Modeling Functions" ], "topics": [ "umxSummary.MxModelSexLim", "umxSummarySexLim" ] }, { "page": "umxSummarySimplex", "title": "Shows a compact, publication-style, summary of a Simplex model.", "concept": [ "Twin Modeling Functions" ], "topics": [ "umxSummary.MxModelSimplex", "umxSummarySimplex" ] }, { "page": "umxSuperModel", "title": "Make a multi-group model", "concept": [ "Core Model Building Functions" ], "topics": [ "umxSuperModel" ] }, { "page": "umxThresholdMatrix", "title": "Create the threshold matrix needed for modeling ordinal data.", "concept": [ "Advanced Model Building Functions" ], "topics": [ "umxThresholdMatrix" ] }, { "page": "umxTwinMaker", "title": "Make a twin model from the model describing just one person", "concept": [ "Twin Modeling Functions" ], "topics": [ "umxTwinMaker" ] }, { "page": "umxTwoStage", "title": "Build a SEM implementing the instrumental variable design", "concept": [ "Super-easy helpers" ], "topics": [ "umxMR", "umxTwoStage" ] }, { "page": "umxUnexplainedCausalNexus", "title": "umxUnexplainedCausalNexus", "concept": [ "Advanced Model Building Functions" ], "topics": [ "umxUnexplainedCausalNexus" ] }, { "page": "umxVersion", "title": "Get or print the version of umx, along with detail from OpenMx and general system info.", "concept": [ "Miscellaneous Utility Functions" ], "topics": [ "umxVersion" ] }, { "page": "umxWeightedAIC", "title": "AIC weight-based conditional probabilities.", "concept": [ "Miscellaneous Stats Functions" ], "topics": [ "umxWeightedAIC" ] }, { "page": "us_skinfold_data", "title": "Anthropometric data on twins", "concept": [ "datasets" ], "topics": [ "us_skinfold_data" ] }, { 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