# Structural Equation and Twin Modeling in R

## Documentation for package ‘umx’ version 2.10.0

- DESCRIPTION file.

## Help Pages

D E F G I L N P Q R S T U V X

umx-package | Functions for Structural Equation Modeling in OpenMx

## -- D --

dl_from_dropbox | dl_from_dropbox

## -- E --

extractAIC.MxModel | Extract AIC from MxModel

## -- F --

Fischbein_wt | Weight data across time.

## -- G --

GFF | Twin data: General Family Functioning, divorce, and well-being.

## -- I --

install.OpenMx | Install OpenMx, with choice of builds
iqdat | Twin data: IQ measured longitudinally

## -- L --

loadings | loadings Generic loadings function to extract factor loadings from exploratory or confirmatory factor analyses.
loadings.MxModel | Extract factor loadings from an EFA (factor analysis).

## -- N --

namez | umx_names

## -- P --

parameters | Display path estimates from a model, filtering by name and value.
plot | Create and display a graphical path diagram for a model.
plot.MxLISRELModel | Create and display a graphical path diagram for a LISREL model.
plot.MxModel | Create and display a graphical path diagram for a model.
plot.MxModelACE | umxPlotACE
plot.MxModelACEcov | Make a graphical display of an ACE model with covariates.
plot.MxModelACEv | Produce a graphical display of an ACE variance-components twin model
plot.MxModelCP | Draw and display a graphical figure of Common Pathway model
plot.MxModelGxE | Plot the results of a GxE univariate test for moderation of ACE components.
plot.MxModelGxEbiv | Plot the results of a GxE univariate test for moderation of ACE components.
plot.MxModelIP | Draw a graphical figure for a Independent Pathway model
plot.MxModelSimplex | Draw and display a graphical figure of a simplex model

## -- Q --

qm | qm

## -- R --

reliability | reliability
residuals.MxModel | Get residuals from an MxModel
RMSEA | Generic RMSEA function
RMSEA.MxModel | RMSEA function for MxModels
RMSEA.summary.mxmodel | RMSEA function for MxModels

## -- S --

summaryAPA | Creates nicely formatted journal style summaries of lm models, p-values, data-frames etc.

## -- T --

tmx_genotypic_effect | Graphical display of genotypic effects.
tmx_is.identified | Test if a factor model is identified
tmx_show | Show matrices of RAM models in a easy-to-learn-from format.
tvars | Concatenate base variable names with suffixes to create wide-format variable names (i.e twin-format)

## -- U --

umx | Functions for Structural Equation Modeling in OpenMx
umx-deprecated | Deprecated. May already stop() code and ask to be updated. May be dropped entirely in future.
umx2ord | umx_cont_2_quantiles
umxACE | Build and run a 2-group Cholesky twin model (uni-variate or multi-variate)
umxACEcov | Run a Cholesky with covariates, either fixed (def var in the means) or random (in the expected covariance matrix)
umxACEold | Build and run a 2-group Cholesky twin model (uni-variate or multi-variate)
umxACEv | Build and run 2-group uni- or multi-variate ACE models based on VARIANCE (not paths).
umxACE_cov_fixed | Run a Cholesky with covariates ("fixed" / definition variables in the means style)
umxAdd1 | umxAdd1
umxAlgebra | A simple wrapper for mxAlgebra with name as the first parameter for more readable compact code.
umxAPA | Creates nicely formatted journal style summaries of lm models, p-values, data-frames etc.
umxBrownie | A recipe Easter-egg for umx
umxCI | Add (and, optionally, run) confidence intervals to a structural model.
umxCI_boot | umxCI_boot
umxCompare | Print a comparison table of one or more 'mxModel's, formatted nicely.
umxConfint | Get confidence intervals from a umx model
umxCov2cor | Convert a covariance matrix into a correlation matrix
umxCovData | Convert a dataframe into a cov mxData object
umxCP | umxCP: Build and run a Common pathway twin model
umxCPold | umxCPold: Build and run a Common pathway twin model
umxDescribeDataWLS | Determine whether a dataset will have weights and summary statistics for the means if used with mxFitFunctionWLS
umxDiagnose | Diagnose problems in a model - this is a work in progress.
umxDrop1 | umxDrop1: Unfinished function to mimic drop1 in OpenMx
umxEFA | FIML-based Exploratory Factor Analysis (EFA)
umxEquate | umxEquate: Equate two or more paths
umxEval | umxEval
umxExampleCode_TRHGpaper | Example code from Twin Research and Human Genetics Paper on umx
umxExamples | Example code from Twin Research and Human Genetics Paper on umx
umxExpCov | Get the expected vcov matrix
umxExpMeans | Extract the expected means matrix from an 'mxModel'
umxFactanal | FIML-based Exploratory Factor Analysis (EFA)
umxFactor | umxFactor
umxFactorScores | Return factor scores from a model as an easily consumable dataframe.
umxFitIndices | Get additional fit-indices for a model with umxFitIndices
umxFixAll | umxFixAll: Fix all free parameters
umxGetParameters | Get parameters from a model, with support for pattern matching!
umxGxE | umxGxE: Implements ACE models with moderation of paths, e.g. by SES.
umxGxEbiv | Bivariate GxE models where twins differ on the moderator.
umxGxE_window | Implement the moving-window form of GxE analysis.
umxHetCor | Create a matrix of correlations for variables of diverse types (binary, ordinal, continuous)
umxIP | umxIP: Build and run an Independent pathway twin model
umxIPold | umxIPold: Build and run an Independent pathway twin model
umxJiggle | umxJiggle
umxLabel | umxLabel: Add labels to a RAM model, matrix, or path
umxLatent | umxLatent: Helper to ease making formative and reflective latent variables
umxLav2RAM | Convert a lavaan syntax 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.
umxModel | Catches users typing umxModel instead of umxRAM.
umxModify | umxModify: Add, set, or drop model paths by label.
umxPadAndPruneForDefVars | umxPadAndPruneForDefVars
umxParameters | Display path estimates from a model, filtering by name and value.
umxPath | Easier (and powerful) specification of paths in SEM.
umxPlot | Create and display a graphical path diagram for a model.
umxPlotACE | umxPlotACE
umxPlotACEcov | Make a graphical display of an ACE model with covariates.
umxPlotACEv | Produce a graphical display of an ACE variance-components twin model
umxPlotCP | Draw and display a graphical figure of Common Pathway model
umxPlotCPold | Draw and display a graphical figure of Common Pathway model
umxPlotGxE | Plot the results of a GxE univariate test for moderation of ACE components.
umxPlotGxEbiv | Plot the results of a GxE univariate test for moderation of ACE components.
umxPlotIP | Draw a graphical figure for a Independent Pathway model
umxPlotSexLim | Draw and display a graphical figure of a Sex limitation model
umxPlotSimplex | Draw and display a graphical figure of a simplex model
umxRAM | Easier path-based SEM modeling.
umxRAM2 | Make RAM model using lavaan syntax
umxRAM2Ordinal | umxRAM2Ordinal
umxReduce | Reduce models, and report the results.
umxReduceACE | Reduce an ACE model.
umxReduceGxE | Reduce a GxE model.
umxRun | umxRun: Run an mxModel
umxSetParameters | umxSetParameters: Set parameters in an mxModel
umxSexLim | Multivariate sex limitation twin model
umxSimplex | Build and run a simplex twin model (not ready for use!)
umxSummarizeTwinData | Summarize twin data
umxSummary | Shows a compact, publication-style, summary of umx models
umxSummary.MxModel | Shows a compact, publication-style, summary of a RAM model
umxSummary.MxModelACE | Shows a compact, publication-style, summary of a umx Cholesky ACE model
umxSummary.MxModelACEcov | Present results of a twin ACE-model with covariates in table and graphical forms.
umxSummary.MxModelACEv | Shows a compact, publication-style, summary of a variance-based Cholesky ACE model.
umxSummary.MxModelCP | Present the results of a Common-pathway twin model in table and graphical form
umxSummary.MxModelGxE | umxSummaryGxE
umxSummary.MxModelGxEbiv | Summarize a bivariate GxE twin model
umxSummary.MxModelIP | Present the results of an independent-pathway twin model in table and graphical form
umxSummary.MxModelSexLim | Shows a compact, publication-style, summary of a umx Sex Limitation model
umxSummary.MxModelSimplex | Shows a compact, publication-style, summary of a Simplex model.
umxSummaryACE | Shows a compact, publication-style, summary of a umx Cholesky ACE model
umxSummaryACEcov | Present results of a twin ACE-model with covariates in table and graphical forms.
umxSummaryACEv | Shows a compact, publication-style, summary of a variance-based Cholesky ACE model.
umxSummaryCP | Present the results of a Common-pathway twin model in table and graphical form
umxSummaryGxE | umxSummaryGxE
umxSummaryGxEbiv | Summarize a bivariate GxE twin model
umxSummaryIP | Present the results of an independent-pathway twin model in table and graphical form
umxSummarySexLim | Shows a compact, publication-style, summary of a umx Sex Limitation model
umxSummarySimplex | Shows a compact, publication-style, summary of a Simplex model.
umxSuperModel | Make a multi-group model
umxThresholdMatrix | Create the threshold matrix needed for modeling ordinal data.
umxTwoStage | umxTwoStage
umxUnexplainedCausalNexus | umxUnexplainedCausalNexus
umxValues | umxValues: Set values in RAM model, matrix, or path
umxVersion | Get or print the version of umx, along with detail from OpenMx and general system info.
umxWeightedAIC | AIC weight-based conditional probabilities.
umx_aggregate | Convenient formula-based cross-tabs & built-in summary functions
umx_APA_pval | Round p-values according to APA guidelines
umx_apply | umx_apply
umx_array_shift | Like the php array_shift function: shifts an item off the beginning of a list
umx_as_numeric | umx_as_numeric
umx_cell_is_on | Return whether a cell is in a set location of a matrix
umx_check | umx_check
umx_checkpoint | umx_set_checkpoint
umx_check_model | Check for required features in an OpenMx.
umx_check_names | umx_check_names
umx_check_OS | umx_check_OS
umx_check_parallel | Check if OpenMx is using OpenMP, test cores, and get timings
umx_cont_2_quantiles | umx_cont_2_quantiles
umx_cor | Report correlations and their p-values
umx_cov2raw | Turn a cov matrix into raw data with umx_cov2raw
umx_default_option | Select first item in list of options, while being flexible about choices.
umx_dot_define_shapes | Helper to make the list of vars and their shapes for a graphviz string
umx_dot_mat2dot | Return dot code for paths in a matrix
umx_dot_rank | Helper to make a graphviz rank string
umx_drop_ok | umx_drop_ok
umx_explode | umx_explode - like the php function 'explode'
umx_explode_twin_names | Break twin variable names (BMI_T1, BMI_T2) into base variable names (BMI, "_T", 1:2)
umx_factor | umxFactor
umx_find_object | umx_find_object
umx_fix_first_loadings | umx_fix_first_loadings
umx_fix_latents | umx_fix_latents
umx_fun_mean_sd | umx_fun
umx_get_bracket_addresses | Get mat[r,c] style cell address from an mxMatrix
umx_get_checkpoint | umx_get_checkpoint
umx_get_options | umx_get_options
umx_grep | umx_grep
umx_has_been_run | umx_has_been_run
umx_has_CIs | umx_has_CIs
umx_has_means | umx_has_means
umx_has_square_brackets | Check if a label contains square brackets
umx_is_class | Check if variables in a dataframe are in a list of classes.
umx_is_cov | umx_is_cov
umx_is_endogenous | umx_is_endogenous
umx_is_exogenous | umx_is_exogenous
umx_is_MxData | Check if an object is an mxData object
umx_is_MxMatrix | umx_is_MxMatrix
umx_is_MxModel | umx_is_MxModel
umx_is_numeric | Check if variables in a dataframe are numeric
umx_is_ordered | Test if one or more variables in a dataframe are ordered
umx_is_RAM | umx_is_RAM
umx_long2wide | Take a long twin-data file and make it wide (one family per row)
umx_lower2full | Convert lower-only matrix data to full (or enforce symmetry on a full matrix)
umx_make | "make" the umx package using devtools: release to CRAN etc.
umx_make_bin_cont_pair_data | Make pairs of bin & continuous columns to represent censored data
umx_make_fake_data | umx_make_fake_data
umx_make_MR_data | Simulate Mendelian Randomization data
umx_make_sql_from_excel | Convert an excel spreadsheet in a text file on sql statements.
umx_make_TwinData | Simulate twin data with control over A, C, and E parameters, as well as moderation of A.
umx_match.arg | Select first item in list of options, while being flexible about choices.
umx_means | umx_means
umx_merge_CIs | umx_merge_CIs
umx_move_file | Move files
umx_msg | Print the name and compact contents of variable.
umx_names | umx_names
umx_object_as_str | umx_object_as_str
umx_open | umx_open
umx_open_CRAN_page | Open the CRAN page for a package
umx_pad | Pad an Object with NAs
umx_parameters | Display path estimates from a model, filtering by name and value.
umx_paste_names | Concatenate base variable names with suffixes to create wide-format variable names (i.e twin-format)
umx_pb_note | umx_pb_note
umx_polychoric | FIML-based polychoric, polyserial, and Pearson correlations
umx_polypairwise | FIML-based Pairwise polychoric, polyserial, and Pearson correlations
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_read_lower | Read lower-triangle of data matrix from console or file
umx_rename | umx_rename
umx_rename_file | umx_rename_file
umx_reorder | Reorder or drop variables from a correlation/covariance matrix.
umx_residualize | Easily residualize variables in long or wide dataframes, returning them changed in-place.
umx_rot | umx_rot
umx_round | umx_round
umx_r_test | Test the difference between correlations for significance.
umx_scale | Scale data columns, skipping non-scalable columns
umx_scale_wide_twin_data | umx_scale_wide_twin_data
umx_score_scale | Score a psychometric scale by summing normal and reversed items
umx_set_auto_plot | umx_set_auto_plot
umx_set_auto_run | umx_set_auto_run
umx_set_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
umx_set_optimization_options | umx_set_optimization_options
umx_set_optimizer | umx_set_optimizer
umx_set_plot_file_suffix | Set output suffix used in umx plot (structural diagrams) files to disk
umx_set_plot_format | Set output format of plots (structural diagrams) in umx
umx_set_table_format | umx_set_table_format
umx_show_fit_or_comparison | Show model logLik of model or print comparison table
umx_stack | Stack data like stack() does, with more control.
umx_standardize | Return a standardized version of a Structural Model
umx_standardize_ACE | umx_standardize_ACE
umx_standardize_ACEcov | umx_standardize_ACEcov
umx_standardize_ACEv | Standardize an ACE variance components model (ACEv)
umx_standardize_CP | umx_standardize_CP
umx_standardize_IP | umx_standardize_IP
umx_standardize_RAM | Return a standardized version of a Structural Model
umx_standardize_SexLim | Standardize a SexLim model
umx_standardize_Simplex | Standardize a Simplex twin model
umx_stash_CIs | Stash the CI values of a model as strings in the values of the model
umx_string_to_algebra | Convert a string to an OpenMx algebra
umx_swap_a_block | umx_swap_a_block
umx_time | umx_time
umx_trim | Trim whitespace surrounding a string.
umx_update_OpenMx | Install OpenMx, with choice of builds
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.
umx_write_to_clipboard | umx_write_to_clipboard
us_skinfold_data | Anthropometric data on twins

## -- V --

vcov.MxModel | Get the expected vcov matrix

## -- X --

xmuHasSquareBrackets | xmuHasSquareBrackets
xmuLabel_Matrix | xmuLabel_Matrix (not a user function)
xmuLabel_MATRIX_Model | xmuLabel_MATRIX_Model (not a user function)
xmuLabel_RAM_Model | xmuLabel_RAM_Model (not a user function)
xmuMakeDeviationThresholdsMatrices | Make a deviation-based mxRAMObjective for ordinal models.
xmuMakeOneHeadedPathsFromPathList | xmuMakeOneHeadedPathsFromPathList
xmuMakeTwoHeadedPathsFromPathList | xmuMakeTwoHeadedPathsFromPathList
xmuMaxLevels | xmuMaxLevels
xmuMI | xmuMI
xmuMinLevels | xmuMinLevels
xmuPropagateLabels | xmuPropagateLabels (not a user function)
xmu_assemble_twin_supermodel | Assemble top, MZ and DZ into a supermodel
xmu_check_levels_identical | xmu_check_levels_identical
xmu_check_variance | Check the minimum variance in data frame
xmu_clean_label | Remove illegal characters from labels
xmu_dot_maker | Internal umx function to help plotting graphviz
xmu_dot_make_paths | xmu_dot_make_paths (not for end users)
xmu_dot_make_residuals | xmu_dot_make_residuals (not for end users)
xmu_dot_move_ranks | xmu_dot_move_ranks (not for end users)
xmu_dot_rank_str | xmu_dot_rank_str (not for end users)
xmu_get_CI | xmu_get_CI
xmu_lavaan_process_group | lavaan parameter table rows to model
xmu_make_mxData | Upgrade a dataframe to an mxData type.
xmu_make_top_twin | Helper to make a basic top, MZ, and DZ model.
xmu_model_needs_means | Check data to see if model needs means.
xmu_safe_run_summary | Safely run and summarize a model
xmu_set_sep_from_suffix | Just a helper to cope with deprecated suffix lying around.
xmu_simplex_corner | Internal function to help building simplex models
xmu_starts | Helper providing twin models with boilerplate means and variance start values
xmu_start_value_list | Make start values
xmu_twin_check | Check basic aspects of input for twin models.