| Print a money object | bucks print |
| Convert Degrees to Degrees | deg2rad |
| dl_from_dropbox | dl_from_dropbox |
| Twin data for Direction of causation modelling | docData |
| Extract AIC from MxModel | extractAIC.MxModel |
| Compute the value of a principal & annual deposits at a compound interest over a number of years | fin_interest |
| Justified P/E Ratio | fin_JustifiedPE |
| Compute NI given annual Earnings. | fin_NI |
| Compute the percent change needed to return to the original value after percent off (or on). | fin_percent |
| Open a ticker in yahoo finance. | fin_ticker |
| Work the valuation of a company | fin_valuation |
| Weight data across time. | Fischbein_wt |
| Fishers Method of combining p-values. | FishersMethod |
| Geometric Mean | geometric_mean |
| Twin data: General Family Functioning, divorce, and well-being. | GFF |
| Add a fit statistic to a ggplot | ggAddR |
| Harmonic Mean | harmonic_mean |
| Install OpenMx, with choice of builds | install.OpenMx umx_update_OpenMx |
| Twin data: IQ measured longitudinally across 4 ages. | iqdat |
| load libraries | libs |
| loadings Generic loadings function to extract factor loadings from exploratory or confirmatory factor analyses. | loadings |
| Extract factor loadings from an EFA (factor analysis). | loadings.MxModel |
| Succinctly select complete rows from a dataframe | noNAs |
| Compute odds ratio (OR) | oddsratio |
| Create and display a graphical path diagram for a LISREL model. | plot.MxLISRELModel |
| Create and display a graphical path diagram for a model. | plot plot.MxModel |
| Create and display a graphical path diagram for a path-based twin model. | plot.MxModelTwinMaker umxPlotMxModelTwinMaker |
| Plot a percent change graph | plot.percent |
| Test the power of an ACE model to detect paths of interest. | power.ACE.test |
| Print a scale "oddsratio" object | print.oddsratio |
| Print a percent object | print.percent |
| Print a scale "reliability" object | print.reliability |
| Print a RMSEA object | print.RMSEA |
| Clean up a prolific file for sharing by removing anonymity-compromising columns. | prolific_anonymize |
| Return PIDs in df | prolific_check_ID |
| Read and optionally merge demographics file from prolific academic | prolific_read_demog |
| qm | qm |
| Convert Radians to Degrees | rad2deg |
| Report coefficient alpha (reliability) | reliability |
| Get residuals from an MxModel | residuals.MxModel |
| Generic RMSEA function | RMSEA |
| RMSEA function for MxModels | RMSEA.MxModel |
| RMSEA function for MxModel summary | RMSEA.summary.mxmodel |
| Compute an SE from a beta and p value | SE_from_p |
| Graphical display of genotypic effects. | tmx_genotypic_effect |
| Test if a factor model is identified | tmx_is.identified |
| Show matrices of models in a easy-to-learn-from format. | tmx_show |
| Show matrices of models in a easy-to-learn-from format. | tmx_show.MxMatrix |
| Show matrices of RAM models in a easy-to-learn-from format. | tmx_show.MxModel |
| Functions for Structural Equation Modeling in OpenMx | umx-package umx |
| Convenient formula-based cross-tabs & built-in summary functions | umx_aggregate |
| Round p-values according to APA guidelines | umx_APA_pval |
| umx_apply | umx_apply |
| Like the php array_shift function: shifts an item off the beginning of a list | umx_array_shift |
| umx_as_numeric | umx_as_numeric |
| umx_check | umx_check |
| Check for required features in an OpenMx. | umx_check_model |
| Check if a request name exists in a dataframe or related object | umx_check_names |
| umx_check_OS | umx_check_OS |
| Check if OpenMx is using OpenMP, test cores, and get timings | umx_check_parallel |
| umx_cont_2_quantiles | umx2ord umx_cont_2_quantiles |
| Report correlations and their p-values | umx_cor |
| Explode a string (Like the php function 'explode') | umx_explode |
| Break twin variable names (BMI_T1, BMI_T2) into base variable names (BMI, "_T", 1:2) | umx_explode_twin_names |
| Read in files from pseudocons. | umx_file_load_pseudo |
| umx_find_object | umx_find_object |
| Summarizing functions used in umx_aggregate and for umxAPA | umx_fun_mean_sd |
| Get bracket-style addresses from an mxMatrix | umx_get_bracket_addresses |
| Get or set checkpointing for a model | umx_get_checkpoint |
| Display umx options | umx_get_options |
| Search for text | umx_grep |
| umx_has_been_run | umx_has_been_run |
| umx_has_CIs | umx_has_CIs |
| umx_has_means | umx_has_means |
| Check if a label contains square brackets | umx_has_square_brackets |
| Check if variables in a dataframe are in a list of classes. | umx_is_class |
| umx_is_cov | umx_is_cov |
| List endogenous variables in a model | umx_is_endogenous |
| umx_is_exogenous | umx_is_exogenous |
| Check if an object is an mxData object | umx_is_MxData |
| umx_is_MxMatrix | umx_is_MxMatrix |
| umx_is_MxModel | umx_is_MxModel |
| Check if variables in a dataframe are numeric | umx_is_numeric |
| Test if one or more variables in a dataframe are ordered | umx_is_ordered |
| umx_is_RAM | umx_is_RAM |
| Take a long twin-data file and make it wide (one family per row) | umx_long2wide |
| Get values from lower triangle of a matrix | umx_lower.tri |
| Convert lower-only matrix data to full (or enforce symmetry on a full matrix) | umx_lower2full |
| "make" the umx package using devtools: release to CRAN etc. | umx_make |
| umx_make_fake_data | umx_make_fake_data |
| Simulate Mendelian Randomization data | umx_make_MR_data |
| Turn a cov matrix into raw data | umx_make_raw_from_cov |
| Convert an excel spreadsheet in a text file on sql statements. | umx_make_sql_from_excel |
| Convert a twin dataset into umx standard format. | umx_make_twin_data_nice |
| Simulate twin data with control over A, C, and E parameters, as well as moderation of A. | umx_make_TwinData |
| umx_means | umx_means |
| umx_merge_randomized_columns | umx_merge_randomized_columns |
| Move files | umx_move_file |
| Print the name and compact contents of variable. | umx_msg |
| umx_names | namez umx_names |
| Open a file or folder | umx_open |
| Open the CRAN page for a package | umx_open_CRAN_page |
| Pad an Object with NAs | umx_pad |
| Concatenate base variable names with suffixes to create wide-format variable names (i.e twin-format) | tvars umx_paste_names |
| FIML-based polychoric, polyserial, and Pearson correlations | umx_polychoric |
| FIML-based Pairwise polychoric, polyserial, and Pearson correlations | umx_polypairwise |
| FIML-based trio-based polychoric, polyserial, and Pearson correlations | umx_polytriowise |
| Print tables in a range of formats (markdown default, see 'umx_set_table_format()' for other formats) or as a web browser table. | umx_print |
| Test the difference between correlations for significance. | umx_r_test |
| Read lower-triangle of data matrix from console or file | umx_read_lower |
| umx_rename | umx_rename |
| Rename files | umx_rename_file |
| Reorder or drop variables from a correlation/covariance matrix. | umx_reorder |
| Easily residualize variables in long or wide dataframes, returning them changed in-place. | umx_residualize |
| Rotate a vector | umx_rot |
| umx_round | umx_round |
| Scale data columns, skipping non-scalable columns | umx_scale |
| Scale wide twin data | umx_scale_wide_twin_data |
| Score a psychometric scale by summing normal and reversed items. | umx_score_scale |
| Update NA values in one column with valid entries from another | umx_select_valid |
| umx_set_auto_plot | umx_set_auto_plot |
| Automatically run models? | umx_set_auto_run |
| umx_set_checkpoint | umx_checkpoint umx_set_checkpoint |
| umx_set_condensed_slots | umx_set_condensed_slots |
| umx_set_cores | umx_set_cores |
| umx_set_data_variance_check | umx_set_data_variance_check |
| Set the symbol for money | umx_set_dollar_symbol |
| Set options that affect optimization in OpenMx | umx_set_optimization_options |
| Set the optimizer in OpenMx | umx_set_optimizer |
| Set output suffix used in umx SEM diagram files saved to disk. | umx_set_plot_file_suffix |
| Set output format of plots (structural diagrams) in umx | umx_set_plot_format |
| Set theme system to use for plots. | umx_set_plot_use_hrbrthemes |
| Set the separator | umx_set_separator |
| Turn off most console and summary output from umx | umx_set_silent |
| umx_set_table_format | umx_set_table_format |
| Stack data like stack() does, with more control. | umx_stack |
| Return a standardized version of a Structural Model | umx_standardize |
| Select desired characters from a string | umx_str_chars |
| Return variable name as a string | umx_str_from_object |
| Convert a string to an OpenMx algebra | umx_string_to_algebra |
| A wrapper to map columns of strings to numeric. | umx_strings2numeric |
| umx_time | umx_time |
| Trim whitespace surrounding a string. | umx_trim |
| Get variances from a df that might contain some non-numeric columns | umx_var |
| Change data family data from wide (2 twins per row) to long format. | umx_wide2long |
| umx_write_to_clipboard | umx_write_to_clipboard |
| Deprecated. May already stop() code and ask to be updated. May be dropped entirely in future. | umx-deprecated |
| Build and run a 2-group Cholesky ACE twin model (univariate or multivariate) | umxACE |
| Run a Cholesky with covariates that are random (in the expected covariance matrix) | umxACEcov |
| Build and run 2-group uni- or multi-variate ACE models based on VARIANCE (not paths). | umxACEv |
| A simple wrapper for mxAlgebra with name as the first parameter for more readable compact code. | umxAlgebra |
| Creates nicely formatted journal-style summaries of models, p-values, data-frames and much more. | summaryAPA umxAPA |
| A recipe Easter-egg for umx | umxBrownie |
| Add (and, optionally, run) confidence intervals to a structural model. | umxCI |
| umxCI_boot | umxCI_boot |
| Runs cross-lagged panel models | umxCLPM |
| Print a comparison table of one or more 'OpenMx::mxModel()'s, formatted nicely. | umxCompare |
| Get confidence intervals from a umx model | umxConfint |
| Convert a covariance matrix into a correlation matrix | umxCov2cor |
| umxCP: Build and run a Common Pathway twin model | umxCP |
| Diagnose problems in a model - not working! | umxDiagnose |
| MZ differences method for testing evidence for causality. | umxDiffMZ |
| Intra-pair association in MZ, DZ twin models. (ALPHA quality!) | umxDiscTwin |
| Build and run a 2-group Direction of Causation twin models. | umxDoC |
| Make a direction of causation model based on umxPath statements | umxDoCp |
| FIML-based Exploratory Factor Analysis (EFA) | umxEFA umxFactanal |
| umxEquate: Equate two or more paths | umxEquate |
| Example code from Twin Research and Human Genetics Paper on umx | umxExampleCode_TRHGpaper umxExamples |
| Get the expected vcov matrix | umxExpCov vcov.MxModel |
| Extract the expected means matrix from an 'OpenMx::mxModel()' | umxExpMeans |
| umxFactor | umxFactor umx_factor |
| Return factor scores from a model as an easily consumable dataframe. | umxFactorScores |
| Get additional fit-indices for a model with umxFitIndices | umxFitIndices |
| umxFixAll: Fix all free parameters | umxFixAll |
| Get the latentVars from a RAM model | umxGetLatents |
| Get the manifestVars from a RAM model | umxGetManifests |
| Used to get a RAM submodel by name | umxGetModel |
| Get parameters from a model, with support for pattern matching! | umxGetParameters |
| umxGxE: Implements ACE models with moderation of paths, e.g. by SES. | umxGxE |
| Implement the moving-window form of GxE analysis. | umxGxE_window |
| Purcell (2002) Bivariate GxE model: Suitable when twins differ on the moderator. | umxGxEbiv |
| Create a matrix of correlations for variables of diverse types (binary, ordinal, continuous) | umxHetCor |
| umxIP: Build and run an Independent Pathway twin model | umxIP |
| umxJiggle | umxJiggle |
| Convert lavaan string to a umxRAM model | umxLav2RAM |
| Make a mxMatrix with automatic labels. Also takes name as the first parameter for more readable code. | umxMatrix |
| Sets labeled matrix cells to free | umxMatrixFree |
| Report modifications which would improve fit. | umxMI |
| Catches users typing umxModel instead of umxRAM. | umxModel |
| Return names of models found within a model | umxModelNames |
| umxModify: Add, set, or drop model paths by label. | umxModify |
| Extends Mendelian randomization with the twin design to test evidence of causality | umxMRDoC |
| Display path estimates from a model, filtering by name and value. | parameters umxParameters |
| A wrapper to make paran easier to use. Just automates applying 'complete.cases()' | umxParan |
| Easier (and powerful) specification of paths in SEM. | umxPath |
| Quickly plot y ~ x with a regression line and R^2, and nice labels. | umxPlot |
| Make a graphical display of an ACE model | plot.MxModelACE umxPlotACE |
| Make a graphical display of an ACE model with covariates. | plot.MxModelACEcov umxPlotACEcov |
| Produce a graphical display of an ACE variance-components twin model | plot.MxModelACEv umxPlotACEv |
| Draw and display a graphical figure of Common Pathway model | plot.MxModelCP umxPlotCP |
| Plot a Direction of Causation Model. | plot.MxModelDoC umxPlotDoC |
| Easily plot functions in R | umxPlotFun |
| Plot the results of a GxE univariate test for moderation of ACE components. | plot.MxModelGxE umxPlotGxE |
| Plot the results of a GxE univariate test for moderation of ACE components. | plot.MxModelGxEbiv umxPlotGxEbiv |
| Draw a graphical figure for a Independent Pathway model | plot.MxModelIP umxPlotIP |
| Draw and display a graphical figure of a Sex limitation model | plot.MxModelSexLim umxPlotSexLim |
| Draw and display a graphical figure of a simplex model | plot.MxModelSimplex umxPlotSimplex |
| Test power to detect specified path values in a model. | umxPower |
| Build and run path-based SEM models | umxRAM |
| Convert a RAM model to a lavaan string | umxRAM2Lav |
| Reduce models, and report the results. | umxReduce |
| Reduce an ACE model. | umxReduceACE |
| Reduce a GxE model. | umxReduceGxE |
| Rename a umxMatrix (even in a model) | umxRenameMatrix |
| Generic SEM factor model loading rotation function | umxRotate |
| Rotate a CP solution | umxRotate.MxModelCP |
| umxRun: Run an mxModel | umxRun |
| Change or fix parameters (e.g. their values, labels, bounds, ..) in a model. | umxSetParameters |
| Multivariate sex limitation twin model | umxSexLim |
| Build and run a simplex twin model (not ready for use!) | umxSimplex |
| Summarize twin data | umxSummarizeTwinData |
| Shows a compact, publication-style, summary of umx models | umxSummary |
| Shows a compact, publication-style, summary of a RAM model | umxSummary.MxModel umxSummary.MxRAMModel |
| Shows a compact, publication-style, summary of a umx Cholesky ACE model | umxSummary.MxModelACE umxSummaryACE |
| Present results of a twin ACE-model with covariates in table and graphical forms. | umxSummary.MxModelACEcov umxSummaryACEcov |
| Shows a compact, publication-style, summary of a variance-based Cholesky ACE model. | umxSummary.MxModelACEv umxSummaryACEv |
| Present the results of a Common-pathway twin model in table and graphical form | umxSummary.MxModelCP umxSummaryCP |
| Shows a compact, publication-style, summary of a umx Direction of Causation model | umxSummary.MxModelDoC umxSummaryDoC |
| Summarize a GxE model | umxSummary.MxModelGxE umxSummaryGxE |
| Summarize a bivariate GxE twin model | umxSummary.MxModelGxEbiv umxSummaryGxEbiv |
| Present the results of an independent-pathway twin model in table and graphical form | umxSummary.MxModelIP umxSummaryIP |
| Present the results of a Mendelian Randomization Direction of Causation Model in a table | umxSummary.MxModelMRDoC umxSummaryMRDoC |
| Shows a compact, publication-style, summary of a umx Sex Limitation model | umxSummary.MxModelSexLim umxSummarySexLim |
| Shows a compact, publication-style, summary of a Simplex model. | umxSummary.MxModelSimplex umxSummarySimplex |
| Make a multi-group model | umxSuperModel |
| Create the threshold matrix needed for modeling ordinal data. | umxThresholdMatrix |
| Make a twin model from the model describing just one person | umxTwinMaker |
| Build a SEM implementing the instrumental variable design | umxMR umxTwoStage |
| umxUnexplainedCausalNexus | umxUnexplainedCausalNexus |
| Get or print the version of umx, along with detail from OpenMx and general system info. | umxVersion |
| AIC weight-based conditional probabilities. | umxWeightedAIC |
| Anthropometric data on twins | us_skinfold_data |
| Convert a bracket address into an A_rXcX-style label. | xmu_bracket_address2rclabel |
| Return whether a cell is in a set location of a matrix | xmu_cell_is_on |
| xmu_check_levels_identical | xmu_check_levels_identical |
| Check data to see if model needs means. | xmu_check_needs_means |
| Check the minimum variance in data frame | xmu_check_variance |
| xmu_CI_merge | xmu_CI_merge |
| Stash the CI values of a model as strings in the values of the model | xmu_CI_stash |
| Remove illegal characters from labels | xmu_clean_label |
| Drop rows with missing definition variables | xmu_data_missing |
| Data helper function to swap blocks of data from one set of columns to another. | xmu_data_swap_a_block |
| Determine if a dataset will need statistics for the means if used in a WLS model. | xmu_describe_data_WLS |
| Convert a dataframe into a cov mxData object | xmu_DF_to_mxData_TypeCov |
| Helper to make the list of vars and their shapes for a graphviz string | xmu_dot_define_shapes |
| xmu_dot_make_paths (not for end users) | xmu_dot_make_paths |
| xmu_dot_make_residuals (not for end users) | xmu_dot_make_residuals |
| Internal umx function to help plotting graphviz | xmu_dot_maker |
| Return dot code for paths in a matrix | xmu_dot_mat2dot |
| xmu_dot_move_ranks (not for end users) | xmu_dot_move_ranks |
| Helper to make a graphviz rank string | xmu_dot_rank |
| xmu_dot_rank_str (not for end users) | xmu_dot_rank_str |
| Equate Threshold Values Across Columns in a Model | xmu_equate_threshold_values |
| Get one or more columns from mzData or regular data.frame | xmu_extract_column |
| Look up and report CIs for free parameters | xmu_get_CI |
| Process table of paths to model | xmu_lavaan_process_group |
| Make pairs of bin & continuous columns to represent censored data | xmu_make_bin_cont_pair_data |
| Upgrade a dataframe to an mxData type. | xmu_make_mxData |
| Helper to make a basic top, MZ, and DZ model. | xmu_make_TwinSuperModel |
| Select first item in list of options, while being flexible about choices. | xmu_match.arg |
| Find name for model | xmu_name_from_lavaan_str |
| Where all data are missing for a twin, add default values for definition variables, allowing the row to be kept | xmu_PadAndPruneForDefVars |
| Re-name variables umxPaths to twin versions | xmu_path_regex |
| Re-name variables in umxPaths to twin versions | xmu_path2twin |
| Print algebras from a umx model | xmu_print_algebras |
| Convert an "A_r1c1"-style label to a bracket address. | xmu_rclabel_2_bracket_address |
| Relabel Factor Columns in a Data Frame | xmu_relevel_factors |
| Safely run and summarize a model | xmu_safe_run_summary |
| Scale Wide Data Function | xmu_scale_wide_data |
| Just a helper to cope with deprecated suffix lying around. | xmu_set_sep_from_suffix |
| Show model logLik of model or print comparison table | xmu_show_fit_or_comparison |
| Internal function to help building simplex models | xmu_simplex_corner |
| xmu_standardize_ACE | xmu_standardize_ACE |
| xmu_standardize_ACEcov | xmu_standardize_ACEcov |
| Standardize an ACE variance components model (ACEv) | xmu_standardize_ACEv |
| Function to standardize a common pathway model | xmu_standardize_CP |
| non-user: Standardize an IP model | xmu_standardize_IP |
| Standardize a Structural Model (not for end users) | xmu_standardize_RAM |
| Standardize a SexLim model | xmu_standardize_SexLim |
| Standardize a Simplex twin model | xmu_standardize_Simplex |
| Make start values | xmu_start_value_list |
| Helper providing boilerplate start values for means and variance in twin models | xmu_starts |
| Order and group the parameters in a RAM summary | xmu_summary_RAM_group_parameters |
| Add weight matrices to twin models. | xmu_twin_add_WeightMatrices |
| Check basic aspects of input for twin models. | xmu_twin_check |
| Not for user: pull variable names from a twin model | xmu_twin_get_var_names |
| Make the matrices and algebras for definition-based means models | xmu_twin_make_def_means_mats_and_alg |
| Upgrade selDVs to selVars | xmu_twin_upgrade_selDvs2SelVars |
| xmuHasSquareBrackets | xmuHasSquareBrackets |
| xmuLabel: Add labels to a RAM model, matrix, or path | xmuLabel |
| xmuLabel_Matrix (not a user function) | xmuLabel_Matrix |
| xmuLabel_MATRIX_Model (not a user function) | xmuLabel_MATRIX_Model |
| xmuLabel_RAM_Model (not a user function) | xmuLabel_RAM_Model |
| Make a deviation-based mxRAMObjective for ordinal models. | xmuMakeDeviationThresholdsMatrices |
| xmuMakeOneHeadedPathsFromPathList | xmuMakeOneHeadedPathsFromPathList |
| xmuMakeTwoHeadedPathsFromPathList | xmuMakeTwoHeadedPathsFromPathList |
| xmuMaxLevels | xmuMaxLevels |
| xmuMI (not for end users) | xmuMI |
| xmuMinLevels | xmuMinLevels |
| xmuPropagateLabels (not a user function) | xmuPropagateLabels |
| xmuRAM2Ordinal | xmuRAM2Ordinal |
| Create core of twin model for all-continuous data. | xmuTwinSuper_Continuous |
| xmuTwinSuper_NoBinary | xmuTwinSuper_NoBinary |
| Not for end-users: Add a means model with covariates to a twin model | xmuTwinUpgradeMeansToCovariateModel |
| xmuValues: Set values in RAM model, matrix, or path | xmuValues |
