umx v4.0.0
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Functions in umx
| Name | Description | |
| SE_from_p | Compute an SE from a beta and p value | |
| plot.MxLISRELModel | Create and display a graphical path diagram for a LISREL model. | |
| power.ACE.test | Test the power of an ACE model to detect paths of interest. | |
| plot.MxModelTwinMaker | Create and display a graphical path diagram for a path-based twin model. | |
| oddsratio | Compute odds ratio (OR) | |
| loadings | loadings Generic loadings function to extract factor loadings from exploratory or confirmatory factor analyses. | |
| install.OpenMx | Install OpenMx, with choice of builds | |
| tmx_genotypic_effect | Graphical display of genotypic effects. | |
| tmx_is.identified | Test if a factor model is identified | |
| extractAIC.MxModel | Extract AIC from MxModel | |
| print.reliability | Print a scale "reliability" object | |
| print.oddsratio | Print a scale "oddsratio" object | |
| iqdat | Twin data: IQ measured longitudinally across 4 ages. | |
| tmx_show | Show matrices of RAM models in a easy-to-learn-from format. | |
| umx-deprecated | Deprecated. May already stop() code and ask to be updated. May be dropped entirely in future. | |
| plot.MxModel | Create and display a graphical path diagram for a model. | |
| qm | qm | |
| residuals.MxModel | Get residuals from an MxModel | |
| loadings.MxModel | Extract factor loadings from an EFA (factor analysis). | |
| reliability | Report coefficient alpha (reliability) | |
| rad2deg | Convert Radians to Degrees | |
| umxCI_boot | umxCI_boot | |
| umxBrownie | A recipe Easter-egg for umx | |
| umxACEcov | Run a Cholesky with covariates that are random (in the expected covariance matrix) | |
| umxAPA | Creates nicely formatted journal-style summaries of models, p-values, data-frames and much more. | |
| umxAlgebra | A simple wrapper for mxAlgebra with name as the first parameter for more readable compact code. | |
| umxACE | Build and run a 2-group Cholesky twin model (uni-variate or multi-variate) | |
| umx | Functions for Structural Equation Modeling in OpenMx | |
| umxCP | umxCP: Build and run a Common pathway twin model | |
| umxACEv | Build and run 2-group uni- or multi-variate ACE models based on VARIANCE (not paths). | |
| umxCI | Add (and, optionally, run) confidence intervals to a structural model. | |
| umxCov2cor | Convert a covariance matrix into a correlation matrix | |
| umxConfint | Get confidence intervals from a umx model | |
| umxEFA | FIML-based Exploratory Factor Analysis (EFA) | |
| umxExamples | Example code from Twin Research and Human Genetics Paper on umx | |
| umxCompare | Print a comparison table of one or more mxModel()s, formatted nicely. | |
| umxExpCov | Get the expected vcov matrix | |
| umxEquate | umxEquate: Equate two or more paths | |
| umxDiagnose | Diagnose problems in a model - this is a work in progress. | |
| umxFactor | umxFactor | |
| umxDoCp | Make a direction of causation model based on umxPath statements | |
| umxExpMeans | Extract the expected means matrix from an mxModel() | |
| umxDoC | Build and run a 2-group Direction of Causation twin models. | |
| umxGxEbiv | Purcell (2002) Bivariate GxE model: Suitable when twins differ on the moderator. | |
| umxGxE_window | Implement the moving-window form of GxE analysis. | |
| umxGxE | umxGxE: Implements ACE models with moderation of paths, e.g. by SES. | |
| umxHetCor | Create a matrix of correlations for variables of diverse types (binary, ordinal, continuous) | |
| umxFactorScores | Return factor scores from a model as an easily consumable dataframe. | |
| umxFitIndices | Get additional fit-indices for a model with umxFitIndices | |
| umxMendelianRandomization | Build a SEM implementing the equivalent of 2-stage least squares regression | |
| umxModel | Catches users typing umxModel instead of umxRAM. | |
| umxParameters | Display path estimates from a model, filtering by name and value. | |
| umxModify | umxModify: Add, set, or drop model paths by label. | |
| umxFixAll | umxFixAll: Fix all free parameters | |
| umxIP | umxIP: Build and run an Independent pathway twin model | |
| umxGetParameters | Get parameters from a model, with support for pattern matching! | |
| umxJiggle | umxJiggle | |
| umxLabel | umxLabel: Add labels to a RAM model, matrix, or path | |
| umxLav2RAM | Convert lavaan string to a umxRAM model | |
| umxMatrix | Make a mxMatrix with automatic labels. Also takes name as the first parameter for more readable code. | |
| umxMI | Report modifications which would improve fit. | |
| umxPath | Easier (and powerful) specification of paths in SEM. | |
| umxPlotACE | Make a graphical display of an ACE model | |
| umxPlotACEv | Produce a graphical display of an ACE variance-components twin model | |
| umxPlotACEcov | Make a graphical display of an ACE model with covariates. | |
| umxPlotCP | Draw and display a graphical figure of Common Pathway model | |
| umxReduce | Reduce models, and report the results. | |
| umxPlotSimplex | Draw and display a graphical figure of a simplex model | |
| umxPlotDoC | Plot a Direction of Causation Model. | |
| umxPlotGxE | Plot the results of a GxE univariate test for moderation of ACE components. | |
| umxPlotIP | Draw a graphical figure for a Independent Pathway model | |
| umxPower | Test power to detect specified path values in a model. | |
| umxRAM | Easier path-based SEM modeling. | |
| umxPlotSexLim | Draw and display a graphical figure of a Sex limitation model | |
| umxRAM2Lav | Convert a RAM model to a lavaan string | |
| umxPlotGxEbiv | Plot the results of a GxE univariate test for moderation of ACE components. | |
| umxReduceGxE | Reduce a GxE model. | |
| umxSummary | Shows a compact, publication-style, summary of umx models | |
| umxSummarizeTwinData | Summarize twin data | |
| umxReduceACE | Reduce an ACE model. | |
| umxSummary.MxModel | Shows a compact, publication-style, summary of a RAM model | |
| umxRotate | Generic SEM factor model loading rotation function | |
| umxRotate.MxModelCP | Rotate a CP solution | |
| umx_cor | Report correlations and their p-values | |
| umx_cont_2_quantiles | umx_cont_2_quantiles | |
| umxSuperModel | Make a multi-group model | |
| umxSummarySimplex | Shows a compact, publication-style, summary of a Simplex model. | |
| umxRenameMatrix | Rename a umxMatrix (in a model) | |
| umxSexLim | Multivariate sex limitation twin model | |
| umxRun | umxRun: Run an mxModel | |
| umxSummaryIP | Present the results of an independent-pathway twin model in table and graphical form | |
| umxSetParameters | Change or fix parameters (e.g. their values, labels, bounds, ..) in a model. | |
| umxSimplex | Build and run a simplex twin model (not ready for use!) | |
| umx_get_checkpoint | Get or set checkpointing for a model | |
| umxSummarySexLim | Shows a compact, publication-style, summary of a umx Sex Limitation model | |
| umx_make_MR_data | Simulate Mendelian Randomization data | |
| umx_get_options | umx_get_options | |
| umx_is_cov | umx_is_cov | |
| umx_is_endogenous | List endogenous variables in a model | |
| umx_make_TwinData | Simulate twin data with control over A, C, and E parameters, as well as moderation of A. | |
| umx_polychoric | FIML-based polychoric, polyserial, and Pearson correlations | |
| umx_polypairwise | FIML-based Pairwise polychoric, polyserial, and Pearson correlations | |
| umx_set_optimizer | Set the optimizer in OpenMx | |
| umx_trim | Trim whitespace surrounding a string. | |
| umx_set_mvn_optimization_options | Set options that affect optimization in OpenMx | |
| umx_rename_file | Rename files | |
| umx_rename | umx_rename | |
| umx_time | umx_time | |
| umxSummaryACEcov | Present results of a twin ACE-model with covariates in table and graphical forms. | |
| umxSummaryGxE | Summarize a GxE model | |
| umxSummaryGxEbiv | Summarize a bivariate GxE twin model | |
| xmuPropagateLabels | xmuPropagateLabels (not a user function) | |
| umxSummaryACE | Shows a compact, publication-style, summary of a umx Cholesky ACE model | |
| umxThresholdMatrix | Create the threshold matrix needed for modeling ordinal data. | |
| umxTwinMaker | Make a twin model from the model describing just one person | |
| umxValues | umxValues: Set values in RAM model, matrix, or path | |
| umx_file_load_pseudo | Read in files from pseudocons. | |
| umxUnexplainedCausalNexus | umxUnexplainedCausalNexus | |
| xmuRAM2Ordinal | xmuRAM2Ordinal | |
| umx_find_object | umx_find_object | |
| umx_fun_mean_sd | Summarizing functions used in umx_aggregate and for umxAPA | |
| umx_apply | umx_apply | |
| xmu_dot_maker | Internal umx function to help plotting graphviz | |
| xmu_dot_make_residuals | xmu_dot_make_residuals (not for end users) | |
| umx_check_names | Check if a request name exists in a dataframe or related object | |
| umxVersion | Get or print the version of umx, along with detail from OpenMx and general system info. | |
| umx_check_parallel | Check if OpenMx is using OpenMP, test cores, and get timings | |
| umxWeightedAIC | AIC weight-based conditional probabilities. | |
| umx_grep | Search for text | |
| umx_check_OS | umx_check_OS | |
| umx_array_shift | Like the php array_shift function: shifts an item off the beginning of a list | |
| umx_has_CIs | umx_has_CIs | |
| umx_check_model | Check for required features in an OpenMx. | |
| umx_make_twin_data_nice | Convert a twin dataset into umx standard format. | |
| umx_open | Open a file or folder | |
| umx_long2wide | Take a long twin-data file and make it wide (one family per row) | |
| umx_make_sql_from_excel | Convert an excel spreadsheet in a text file on sql statements. | |
| umx_is_ordered | Test if one or more variables in a dataframe are ordered | |
| umxSummaryACEv | Shows a compact, publication-style, summary of a variance-based Cholesky ACE model. | |
| umx_lower2full | Convert lower-only matrix data to full (or enforce symmetry on a full matrix) | |
| umx_get_bracket_addresses | Get bracket-style addresses from an mxMatrix | |
| umxSummaryCP | Present the results of a Common-pathway twin model in table and graphical form | |
| umxSummaryDoC | Shows a compact, publication-style, summary of a umx Direction of Causation model | |
| xmu_match.arg | Select first item in list of options, while being flexible about choices. | |
| umx_APA_pval | Round p-values according to APA guidelines | |
| umx_make | "make" the umx package using devtools: release to CRAN etc. | |
| umx_check | umx_check | |
| umx_as_numeric | umx_as_numeric | |
| umx_r_test | Test the difference between correlations for significance. | |
| umx_set_checkpoint | umx_set_checkpoint | |
| umx_pad | Pad an Object with NAs | |
| umx_read_lower | Read lower-triangle of data matrix from console or file | |
| umx_paste_names | Concatenate base variable names with suffixes to create wide-format variable names (i.e twin-format) | |
| umx_set_condensed_slots | umx_set_condensed_slots | |
| umx_set_table_format | umx_set_table_format | |
| umx_open_CRAN_page | Open the CRAN page for a package | |
| umx_stack | Stack data like stack() does, with more control. | |
| umx_has_square_brackets | Check if a label contains square brackets | |
| umx_is_MxMatrix | umx_is_MxMatrix | |
| umx_is_MxData | Check if an object is an mxData object | |
| umx_scale | Scale data columns, skipping non-scalable columns | |
| umx_str_from_object | Return variable name as a string | |
| xmuMaxLevels | xmuMaxLevels | |
| umx_string_to_algebra | Convert a string to an OpenMx algebra | |
| umx_scale_wide_twin_data | Scale wide twin data | |
| xmuMinLevels | xmuMinLevels | |
| xmu_name_from_lavaan_str | Find name for model | |
| xmu_standardize_ACEv | Standardize an ACE variance components model (ACEv) | |
| umx_is_MxModel | umx_is_MxModel | |
| umx_var | Get variances from a df that might contain some non-numeric columns | |
| umx_wide2long | Change data family data from wide (2 twins per row) to long format. | |
| xmu_standardize_CP | Function to standardize a common pathway model | |
| xmu_twin_add_WeightMatrices | Add weight matrices to twin models. | |
| xmu_twin_check | Check basic aspects of input for twin models. | |
| xmuTwinSuper_Continuous | Create core of twin model for all-continuous data. | |
| xmu_cell_is_on | Return whether a cell is in a set location of a matrix | |
| xmu_make_bin_cont_pair_data | Make pairs of bin & continuous columns to represent censored data | |
| xmu_check_levels_identical | xmu_check_levels_identical | |
| xmu_dot_rank | Helper to make a graphviz rank string | |
| xmu_dot_rank_str | xmu_dot_rank_str (not for end users) | |
| xmu_make_mxData | Upgrade a dataframe to an mxData type. | |
| umx_aggregate | Convenient formula-based cross-tabs & built-in summary functions | |
| umx_explode | Explode a string (Like the php function explode) | |
| umx_has_been_run | umx_has_been_run | |
| umx_names | umx_names | |
| umx_msg | Print the name and compact contents of variable. | |
| umx_has_means | umx_has_means | |
| umx_residualize | Easily residualize variables in long or wide dataframes, returning them changed in-place. | |
| umx_set_data_variance_check | umx_set_data_variance_check | |
| umx_set_cores | umx_set_cores | |
| umx_set_plot_file_suffix | Set output suffix used in umx plot (structural diagrams) files to disk | |
| umx_reorder | Reorder or drop variables from a correlation/covariance matrix. | |
| xmuHasSquareBrackets | xmuHasSquareBrackets | |
| umx_set_plot_format | Set output format of plots (structural diagrams) in umx | |
| umx_explode_twin_names | Break twin variable names (BMI_T1, BMI_T2) into base variable names (BMI, "_T", 1:2) | |
| xmu_clean_label | Remove illegal characters from labels | |
| xmuTwinUpgradeMeansToCovariateModel | Not for end-users: Add a means model with covariates to a twin model | |
| xmu_standardize_IP | non-user: Standardize an IP model | |
| umx_is_exogenous | umx_is_exogenous | |
| xmuMakeTwoHeadedPathsFromPathList | xmuMakeTwoHeadedPathsFromPathList | |
| xmuLabel_MATRIX_Model | xmuLabel_MATRIX_Model (not a user function) | |
| xmu_DF_to_mxData_TypeCov | Convert a dataframe into a cov mxData object | |
| xmuMakeOneHeadedPathsFromPathList | xmuMakeOneHeadedPathsFromPathList | |
| xmu_PadAndPruneForDefVars | Where all data are missing for a twin, add default values for definition variables, allowing the row to be kept | |
| umx_is_numeric | Check if variables in a dataframe are numeric | |
| xmu_data_swap_a_block | Data helper function to swap blocks of data from one set of columns to another. | |
| xmu_extract_column | Get on or more columns from mzData or regular data.frame | |
| xmu_get_CI | Look up and report CIs for free parameters | |
| xmu_describe_data_WLS | Determine whether a dataset will need weights and summary statistics for the means if used with mxFitFunctionWLS | |
| umx_is_RAM | umx_is_RAM | |
| xmu_set_sep_from_suffix | Just a helper to cope with deprecated suffix lying around. | |
| xmu_safe_run_summary | Safely run and summarize a model | |
| xmu_data_missing | Drop rows with missing definition variables | |
| umx_is_class | Check if variables in a dataframe are in a list of classes. | |
| xmu_standardize_SexLim | Standardize a SexLim model | |
| xmu_standardize_Simplex | Standardize a Simplex twin model | |
| xmu_standardize_RAM | Standardize a Structural Model (not for end users) | |
| umx_round | umx_round | |
| umx_rot | Rotate a vector | |
| umx_select_valid | Update NA values in one column with valid entries from another | |
| umx_means | umx_means | |
| umx_score_scale | Score a psychometric scale by summing normal and reversed items. | |
| umx_move_file | Move files | |
| xmu_start_value_list | Make start values | |
| umx_set_silent | Print anything when running a model? | |
| umx_set_separator | Set the separator | |
| xmu_starts | Helper providing boilerplate start values for means and variance in twin models | |
| umx_make_fake_data | umx_make_fake_data | |
| xmu_simplex_corner | Internal function to help building simplex models | |
| xmu_show_fit_or_comparison | Show model logLik of model or print comparison table | |
| xmuLabel_RAM_Model | xmuLabel_RAM_Model (not a user function) | |
| xmuLabel_Matrix | xmuLabel_Matrix (not a user function) | |
| umx_make_raw_from_cov | Turn a cov matrix into raw data | |
| xmuMakeDeviationThresholdsMatrices | Make a deviation-based mxRAMObjective for ordinal models. | |
| xmuMI | xmuMI (not for end users) | |
| xmu_twin_get_var_names | Not for user: pull variable names from a twin model | |
| xmu_twin_upgrade_selDvs2SelVars | Upgrade selDvs to SelVars | |
| umx_polytriowise | FIML-based trio-based polychoric, polyserial, and Pearson correlations | |
| umx_print | Print tables in a range of formats (markdown default, see umx_set_table_format() for other formats) or as a web browser table. | |
| umx_set_auto_plot | umx_set_auto_plot | |
| umx_set_auto_run | umx_set_auto_run | |
| umx_standardize | Return a standardized version of a Structural Model | |
| xmu_CI_merge | xmu_CI_merge | |
| umx_str_chars | Select desired characters from a string | |
| umx_write_to_clipboard | umx_write_to_clipboard | |
| xmu_check_needs_means | Check data to see if model needs means. | |
| xmu_check_variance | Check the minimum variance in data frame | |
| xmu_path2twin | Re-name variables in umxPaths to twin versions | |
| xmu_dot_mat2dot | Return dot code for paths in a matrix | |
| us_skinfold_data | Anthropometric data on twins | |
| xmu_path_regex | Re-name variables umxPaths to twin versions | |
| xmu_dot_move_ranks | xmu_dot_move_ranks (not for end users) | |
| xmu_CI_stash | Stash the CI values of a model as strings in the values of the model | |
| xmu_dot_define_shapes | Helper to make the list of vars and their shapes for a graphviz string | |
| xmu_dot_make_paths | xmu_dot_make_paths (not for end users) | |
| xmu_standardize_ACE | xmu_standardize_ACE | |
| xmu_standardize_ACEcov | xmu_standardize_ACEcov | |
| xmu_lavaan_process_group | Process table of paths to model | |
| xmu_make_TwinSuperModel | Helper to make a basic top, MZ, and DZ model. | |
| dl_from_dropbox | dl_from_dropbox | |
| docData | Twin data for Direction of causation modelling | |
| RMSEA | Generic RMSEA function | |
| RMSEA.summary.mxmodel | RMSEA function for MxModels | |
| RMSEA.MxModel | RMSEA function for MxModels | |
| GFF | Twin data: General Family Functioning, divorce, and well-being. | |
| FishersMethod | Fishers Method of combining p-values. | |
| Fischbein_wt | Weight data across time. | |
| deg2rad | Convert Degrees to Degrees | |
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