umx v1.9.1

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Structural Equation Modeling in R with 'OpenMx'

Quickly create, run, and report structural equation and twin models. See '?umx' to learn more.

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umx

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CRAN status

umx is a structural equation modeling package designed to make SEM easier to build, modify, and report.

It includes high-level functions for complex models such as multi-group twin models, as well as for graphical model output.

Grab it from CRAN with

install.packages("umx")
library(umx)
?umx

The best way to learn what is on offer is to use the help ('?umx' works) and the online tutorial: tbates.github.io

umx stands for "user" OpenMx functions. It provides over 100 functions from high-level umxRAM and umxPath functions that make Structural Equation Modeling in R straightforward, to low-level functions to automate activities such as labelling, setting start values etc.,

Some highlights include:

  1. Building Path Models
    • umxRAM() # mxModel with smart data = parameter, no need to specify type = "RAM", + auto-discovery of manifests and latents from the paths you write
    • umxPath() # mxPath on steroids: one-word settings to set var , mean cov, fixedAt 'v.m.' = and more. Great time-saver!
  2. Reporting output
    • umxSummary(model) # A model fit designed for journal reporting (Χ², p, CFI, TLI, & RMSEA). Optionally show the path loadings
    • plot(model, std=T, digits = 3, file = "name") # Graphical, editable output of model in your browser!
  3. Modify models
    • umxModify() # Modify and run a model. You can add objects, drop or add paths, including by regular-expression label matching), re-name the model, re-run, and even return the comparison. All in 1 line
    • umxParameters(m1, "below", .1, pattern="_to_")) # A powerful assistant to get labels from a model (e.g. all 'to' params, below .1 in value)
  4. Twin modeling!
    • umxACE() # Twin ACE modeling with aplomb paths are labeled! Works with plot() and umxSummary!
    • umxCP(), umxIP(), umxGxE(), umxCP()
    • umxACE
  5. Easy-to-remember options
    • umx_set_cores()
    • umx_set_optimizer()
  6. Many more miscellaneous helpers e.g.
    • umx_time(model) # Report the time taken by a model in a compact programable format
    • umxHcor(data, use = "pairwise.complete.obs") # Compute appropriate pair-wise correlations for mixed data types.
    • Dozens more (?umx to see them all). Check out the "family links" in any help file also!

Feel free to use, and submit code and requests via Github. Tell your friends! Publish more good science :-)

For thrill-seekers and collaborators only: the bleeding-edge development version is here:

install.packages("devtools")
library("devtools")
install_github("tbates/umx")
library("umx")
?umx

Functions in umx

Name Description
dl_from_dropbox dl_from_dropbox
extractAIC.MxModel Extract AIC from MxModel
qm qm
reliability reliability
umxCF_SexLim umxCF_SexLim
umxCI Add (and, optionally, run) confidence intervals to a structural model.
umxDiagnose Diagnose problems in a model - this is a work in progress.
umxDrop1 umxDrop1: Unfinished function to mimic drop1 in OpenMx
umxJiggle umxJiggle
umxLabel umxLabel: Add labels to a RAM model, matrix, or path
umxLatent umxLatent: Helper to ease making formative and reflective latent variables
umxMI Report modifications which would improve fit.
umxRun umxRun: Run an mxModel
umxSetParameters umxSetParameters: Set parameters in an mxModel
umxSummaryGxE umxSummaryGxE
umxSummaryIP Present the results of an independent-pathway twin model in table and graphical form
umx_add_variances umx_add_variances
umx_aggregate Convenient formula-based cross-tabs & built-in summary functions
umx_cor umx_cor
umx_cov2raw Turn a cov matrix into raw data with umx_cov2raw
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_is_class Check if variables in a dataframe are in a list of classes.
umx_is_cov umx_is_cov
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_move_file Move files
umx_msg Print the name and compact contents of variable.
umx_read_lower Read lower-triangle of data matrix from console or file
umx_rename umx_rename
umx_round umx_round
umx_scale Scale data columns, skipping non-scalable columns
umx_set_optimizer umx_set_optimizer
umx_set_plot_file_suffix Set output suffix used in umx plot (structural diagrams) files to disk
umx_write_to_clipboard umx_write_to_clipboard
us_skinfold_data Anthropometric data on twins
xmuHasSquareBrackets xmuHasSquareBrackets
xmuLabel_MATRIX_Model xmuLabel_MATRIX_Model (not a user function)
xmu_check_levels_identical xmu_check_levels_identical
xmu_dot_make_paths xmu_dot_make_paths (not for end users)
RMSEA Generic RMSEA function
RMSEA.summary.mxmodel RMSEA function for MxModels
umx-deprecated Deprecated. May already stop() code and ask to be updated. May be dropped entirely in future.
umx Helper Functions for Structural Equation Modelling in OpenMx
umxCI_boot umxCI_boot
umxCP umxCP: Build and run a Common pathway twin model
umxExpMeans Extract the expected means matrix from an mxModel
umxFactor umxFactor
umxGxE umxGxE: Implements ACE models with moderation of paths, e.g. by SES.
umxGxE_window Implement the moving-window form of GxE analysis.
umxMatrix umxMatrix: labeled mxMatrix, with name in the first place
umxModel Catches users typing umxModel instead of umxRAM
umxPlotCP Draw a graphical figure for a Common Pathway model
umxPlotGxE Plot the results of a GxE univariate test for moderation of ACE components.
umxSummary.MxModel Shows a compact, publication-style, summary of a RAM model
umxSummary Shows a compact, publication-style, summary of umx models
umx_apply umx_apply
umx_as_numeric umx_as_numeric
umx_check_model umx_check_model
umx_check_names umx_check_names
umx_fix_latents umx_fix_latents
umx_fun_mean_sd umx_fun
umx_is_MxModel umx_is_MxModel
umx_is_RAM umx_is_RAM
umx_make_TwinData Simulate twin data with control over A, C, and E parameters, as well as moderation of A.
umx_make_bin_cont_pair_data Make pairs of bin & continuous columns to represent censored data
umx_means umx_means
umx_merge_CIs umx_merge_CIs
umx_rename_file umx_rename_file
umx_reorder Reorder or drop variables from a correlation/covariance matrix.
umx_set_condensed_slots umx_set_condensed_slots
umx_set_cores umx_set_cores
umx_standardize_ACEv Standardize an ACE variance components model (ACEv)
umxEFA umxEFA
umxEquate umxEquate: Equate two or more paths
umxFactorScores Return factor scores from a model as an easily consumable dataframe.
umxFitIndices Get additional fit-indices for a model with umxFitIndices
umx_standardize_CP umx_standardize_CP
umx_string_to_algebra Convert a string to an OpenMx algebra
umx_swap_a_block umx_swap_a_block
xmuMakeTwoHeadedPathsFromPathList xmuMakeTwoHeadedPathsFromPathList
xmuMaxLevels xmuMaxLevels
xmu_dot_make_residuals xmu_dot_make_residuals (not for end users)
umxReduceACE Reduce an ACE model.
umxReduceGxE Reduce a GxE model.
umxValues umxValues: Set values in RAM model, matrix, or path
xmu_dot_maker Internal umx function to help plotting graphviz
umxVersion Get or print the version of umx, along with detail from OpenMx and general system info.
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_scale_wide_twin_data umx_scale_wide_twin_data
umx_set_auto_plot umx_set_auto_plot
umx_standardize_IP umx_standardize_IP
umx_standardize_RAM Return a standardized version of a Structural Model
GFF Twin data: General Family Functioning, divorce, and wellbeing.
RMSEA.MxModel RMSEA function for MxModels
umxACE Build and run a 2-group Cholesky twin model (uni-variate or multi-variate)
umxACESexLim umxACESexLim: Build and run a sex-limitation twin model (not working yet)
umxAdd1 umxAdd1
umxBrownie A recipe Easter-egg for umx
umxCov2cor Convert a covariance matrix into a correlation matrix
umxCovData Convert a dataframe into a cov mxData object
umxPath Easier (and powerful) specification of paths in SEM.
umxPlotACE umxPlotACE
umxRAM2Ordinal umxRAM2Ordinal
umxReduce Reduce models, and report the results.
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
umx_check umx_check
umx_check_OS umx_check_OS
umx_find_object umx_find_object
umx_fix_first_loadings umx_fix_first_loadings
umx_has_means umx_has_means
umx_has_square_brackets Check if a label contains square brackets
umx_is_exogenous umx_is_exogenous
umx_is_endogenous umx_is_endogenous
umx_make_fake_data umx_make_fake_data
umx_make_sql_from_excel umx_make_sql_from_excel
umx_pad Pad an Object with NAs
umx_parameters Display path estimates from a model, filtering by name and value.
umx_residualize Easily residualize variables in long or wide dataframes, returning them changed in-place.
umx_rot umx_rot
umx_standardize_ACE umx_standardize_ACE
umx_standardize_ACEcov umx_standardize_ACEcov
xmuMakeOneHeadedPathsFromPathList xmuMakeOneHeadedPathsFromPathList
xmuMakeThresholdsMatrices xmuMakeThresholdsMatrices (not a user function)
loadings loadings Generic loadings function to extract factor loadings from exploratory or confirmatory factor analyses.
plot.MxModel Create and display a graphical path diagram for a model.
residuals.MxModel Get residuals from an MxModel
tmx_is.identified Test if a factor model is identified
umxACEv Build and run a 2-group Cholesky twin model (uni-variate or multi-variate) with variance estimates.
umxAPA Creates nicely formatted journal style summaries of lm models, p-values, data-frames etc.
umxEval umxEval
umxExpCov Get the expected vcov matrix
umxFixAll umxFixAll: Fix all free parameters
umxGetParameters umxGetParameters: Get parameters from a model
umxACE_cov_fixed Run a Cholesky with covariates ("fixed" / definition variables in the means style)
umxACEcov Run a Cholesky with covariates, either fixed (def var in the means) or random (in the expected covariance matrix)
umxHetCor Create a matrix of correlations for variables of diverse types (binary, ordinal, continuous)
umxIP umxIP: Build and run an Independent pathway twin model
umxModify umxModify: Add, set, or drop model paths by label.
umxPadAndPruneForDefVars umxPadAndPruneForDefVars
umxPlotACEcov Make a graphical display of an ACE model with covariates.
umxPlotACEv Produce a graphical display of an ACE variance-components twin model
umxPlotIP Draw a graphical figure for a Independent Pathway model
umxRAM Easy-to-use RAM model maker.
umxSuperModel Make a multi-group model
umxThresholdMatrix Create the threshold matrix needed for modeling ordinal data.
umxTwoStage umxTwoStage
umxUnexplainedCausalNexus umxUnexplainedCausalNexus
umx_default_option Select first item in list of options, while being flexible about choices.
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.
umx_APA_model_CI umx_APA_model_CI
umx_APA_pval Round p-values according to APA guidelines
umx_get_options umx_get_options
umx_drop_ok umx_drop_ok
umx_grep umx_grep
umx_is_MxData Check if an object is an mxData object
umx_is_MxMatrix umx_is_MxMatrix
umx_has_CIs umx_has_CIs
umx_has_been_run umx_has_been_run
umx_open umx_open
umx_open_CRAN_page Open the CRAN page for a package
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_r_test Test the difference between correlations for significance.
umx_show umx_show
umx_standardize Return a standardized version of a Structural Model
umx_make umx_make umx using devtools
umx_make_MR_data Simulate Mendelian Randomization data
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_var Get variances from a df that might contain some non-numeric columns
umx_wide2long Change data 2-twin family data from wide to long format.
umx_set_plot_format Set output format of plots (structural diagrams) in umx
umx_set_table_format umx_set_table_format
umx_time umx_time
umx_trim Trim whitespace surrounding a string.
xmu_start_value_list Make start values
xmu_twin_check Check basic aspects of input for twin models
xmuLabel_Matrix xmuLabel_Matrix (not a user function)
xmuLabel_RAM_Model xmuLabel_RAM_Model (not a user function)
xmuMinLevels xmuMinLevels
xmuPropagateLabels xmuPropagateLabels (not a user function)
umxCompare Print a comparison table of one or more mxModels, formatted nicely.
umxConfint Get confidence intervals from an MxModel
umx_check_parallel Check if OpenMx is using OpenMP, test cores, and get timings
umx_cont_2_quantiles umx_cont_2_quantiles
xmuMI xmuMI
xmuMakeDeviationThresholdsMatrices Make a deviation-based mxRAMObjective for ordinal models.
install.OpenMx Easily install the latest parallel/NPSOL enabled build of OpenMx.
loadings.MxModel Extract factor loadings from an EFA (factor analysis).
umx_set_auto_run umx_set_auto_run
umx_set_checkpoint umx_set_checkpoint
umx_get_bracket_addresses get mat[r,c] style cell address from an mxMatrix
umx_get_checkpoint umx_get_checkpoint
umx_names umx_names
umx_object_as_str umx_object_as_str
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Date 2017-11-02
License GPL-3
Encoding UTF-8
URL http://github.com/tbates/umx
BugReports http://github.com/tbates/umx/issues
LazyData true
RoxygenNote 6.0.1
NeedsCompilation no
Packaged 2017-11-02 15:08:09 UTC; tim
Repository CRAN
Date/Publication 2017-11-02 15:28:10 UTC

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