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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