Structural Equation Modeling and Twin Modeling in R
Print a money object
Convert Degrees to Degrees
dl_from_dropbox
Extract AIC from MxModel
Compute the future value and gain of an investment
Compute the value of a principal & annual deposits at a compound inter...
Justified P/E Ratio
Compute the net present value of a future income stream
Compute NI given annual Earnings.
Compute the percent change needed to return to the original value afte...
Open a ticker in yahoo finance.
Work the valuation of a company
Fishers Method of combining p-values.
Geometric Mean
Add a fit statistic to a ggplot
Harmonic Mean
Install OpenMx, with choice of builds
load libraries
Extract factor loadings from an EFA (factor analysis).
loadings Generic loadings function to extract factor loadings from exp...
Succinctly select complete rows from a dataframe
Compute odds ratio (OR)
Create and display a graphical path diagram for a LISREL model.
Create and display a graphical path diagram for a model.
Create and display a graphical path diagram for a path-based twin mode...
Plot a percent change graph
Test the power of an ACE model to detect paths of interest.
Print a scale "oddsratio" object
Print a percent object
Print a scale "reliability" object
Print a RMSEA object
Clean up a prolific file for sharing by removing anonymity-compromisin...
Return PIDs in df
Read and optionally merge demographics file from prolific academic
qm
Convert Radians to Degrees
Report coefficient alpha (reliability)
Get residuals from an MxModel
RMSEA function for MxModels
Generic RMSEA function
RMSEA function for MxModel summary
Compute an SE from a beta and p value
Graphical display of genotypic effects.
Test if a factor model is identified
Show matrices of models in a easy-to-learn-from format.
Show matrices of RAM models in a easy-to-learn-from format.
Show matrices of models in a easy-to-learn-from format.
Convenient formula-based cross-tabs & built-in summary functions
Round p-values according to APA guidelines
umx_apply
Like the php array_shift function: shifts an item off the beginning of...
umx_as_numeric
Check for required features in an OpenMx.
Check if a request name exists in a dataframe or related object
umx_check_OS
Check if OpenMx is using OpenMP, test cores, and get timings
umx_check
umx_cont_2_quantiles
Report correlations and their p-values
Break twin variable names (BMI_T1, BMI_T2) into base variable names (B...
Explode a string (Like the php function explode)
Read in files from pseudocons.
umx_find_object
Summarizing functions used in umx_aggregate and for umxAPA
Get the alpha text
Get bracket-style addresses from an mxMatrix
Get or set checkpointing for a model
Display umx options
Search for text
umx_has_been_run
umx_has_CIs
umx_has_means
Check if a label contains square brackets
Check if variables in a dataframe are in a list of classes.
umx_is_cov
List endogenous variables in a model
umx_is_exogenous
Check if an object is an mxData object
umx_is_MxMatrix
umx_is_MxModel
Check if variables in a dataframe are numeric
Test if one or more variables in a dataframe are ordered
umx_is_RAM
Take a long twin-data file and make it wide (one family per row)
Get values from lower triangle of a matrix
Convert lower-only matrix data to full (or enforce symmetry on a full ...
umx_make_fake_data
Simulate Mendelian Randomization data
Turn a cov matrix into raw data
Convert an excel spreadsheet in a text file on sql statements.
Convert a twin dataset into umx standard format.
Simulate twin data with control over A, C, and E parameters, as well a...
"make" the umx package using devtools: release to CRAN etc.
umx_means
umx_merge_randomized_columns
Move files
Print the name and compact contents of variable.
umx_names
Open the CRAN page for a package
Open a file or folder
Pad an Object with NAs
Concatenate base variable names with suffixes to create wide-format va...
FIML-based polychoric, polyserial, and Pearson correlations
FIML-based Pairwise polychoric, polyserial, and Pearson correlations
FIML-based trio-based polychoric, polyserial, and Pearson correlations
Print tables in a range of formats (markdown default, see `umx_set_tab...
Test the difference between correlations for significance.
Read lower-triangle of data matrix from console or file
Rename files
umx_rename
Reorder or drop variables from a correlation/covariance matrix.
Easily residualize variables in long or wide dataframes, returning the...
Rotate a vector
umx_round
Scale wide twin data
Scale data columns, skipping non-scalable columns
Score a psychometric scale by summing normal and reversed items.
Update NA values in one column with valid entries from another
umx_set_auto_plot
Automatically run models?
umx_set_checkpoint
umx_set_condensed_slots
umx_set_cores
umx_set_data_variance_check
Set the symbol for money
Set options that affect optimization in OpenMx
Set the optimizer in OpenMx
Set output suffix used in umx SEM diagram files saved to disk.
Set output format of plots (structural diagrams) in umx
Set the separator
Turn off most console and summary output from umx
umx_set_table_format
Stack data like stack() does, with more control.
Return a standardized version of a Structural Model
Select desired characters from a string
Return variable name as a string
Convert a string to an OpenMx algebra
A wrapper to map columns of strings to numeric.
umx_time
Trim whitespace surrounding a string.
Get variances from a df that might contain some non-numeric columns
umx_wide2long
Change twin data from wide (2 twins per row) to long format.
Take a long dataframe and make it wide for repeated measures and multi...
umx_write_to_clipboard
Deprecated. May already stop() code and ask to be updated. May be drop...
Functions for Structural Equation Modeling in OpenMx
Build and run a 2-group Cholesky ACE twin model (univariate or multiva...
Run a Cholesky with covariates that are random (in the expected covari...
Build and run 2-group uni- or multi-variate ACE models based on VARIAN...
A simple wrapper for mxAlgebra with name as the first parameter for mo...
Creates nicely formatted journal-style summaries of models, p-values, ...
A recipe Easter-egg for umx
umxCI_boot
Add (and, optionally, run) confidence intervals to a structural model.
Runs cross-lagged panel models
Print a comparison table of one or more OpenMx::mxModel()s, formatte...
Get confidence intervals from a umx model
Convert a covariance matrix into a correlation matrix
umxCP: Build and run a Common Pathway twin model
Diagnose problems in a model - not working!
MZ differences method for testing evidence for causality.
Intra-pair association in MZ, DZ twin models. (ALPHA quality!)
Build and run a 2-group Direction of Causation twin models.
Make a direction of causation model based on umxPath statements
FIML-based Exploratory Factor Analysis (EFA)
umxEquate: Equate two or more paths
Example code from Twin Research and Human Genetics Paper on umx
Get the expected vcov matrix
Extract the expected means matrix from an OpenMx::mxModel()
umxFactor
Return factor scores from a model as an easily consumable dataframe.
Get additional fit-indices for a model with umxFitIndices
umxFixAll: Fix all free parameters
Get the latentVars from a RAM model
Get the manifestVars from a RAM model
Used to get a RAM submodel by name
Get parameters from a model, with support for pattern matching!
Implement the moving-window form of GxE analysis.
umxGxE: Implements ACE models with moderation of paths, e.g. by SES.
Purcell (2002) Bivariate GxE model: Suitable when twins differ on the ...
Create a matrix of correlations for variables of diverse types (binary...
umxIP: Build and run an Independent Pathway twin model
umxJiggle
Convert lavaan string to a umxRAM model
Make a mxMatrix with automatic labels. Also takes name as the first pa...
Sets labeled matrix cells to free
Report modifications which would improve fit.
Catches users typing umxModel instead of umxRAM.
Return names of models found within a model
umxModify: Add, set, or drop model paths by label.
Extends Mendelian randomization with the twin design to test evidence ...
Display path estimates from a model, filtering by name and value.
A wrapper to make paran easier to use. Just automates applying `comple...
Easier (and powerful) specification of paths in SEM.
Quickly plot y ~ x with a regression line and R^2, and nice labels.
Make a graphical display of an ACE model
Make a graphical display of an ACE model with covariates.
Produce a graphical display of an ACE variance-components twin model
Draw and display a graphical figure of Common Pathway model
Plot a Direction of Causation Model.
Easily plot functions in R
Plot the results of a GxE univariate test for moderation of ACE compon...
Plot the results of a GxE univariate test for moderation of ACE compon...
Draw a graphical figure for a Independent Pathway model
umxPlotPredict Take a model and plot the y against predicted(y)
Draw and display a graphical figure of a Sex limitation model
Draw and display a graphical figure of a simplex model
Test power to detect specified path values in a model.
Build and run path-based SEM models
Convert a RAM model to a lavaan string
Reduce models, and report the results.
Reduce an ACE model.
Reduce a GxE model.
Rename a umxMatrix (even in a model)
Rotate a CP solution
Generic SEM factor model loading rotation function
umxRun: Run an mxModel
Change or fix parameters (e.g. their values, labels, bounds, ..) in a ...
Multivariate sex limitation twin model
Build and run a simplex twin model (not ready for use!)
Summarize twin data
Shows a compact, publication-style, summary of a RAM model
Shows a compact, publication-style, summary of umx models
Shows a compact, publication-style, summary of a umx Cholesky ACE mode...
Present results of a twin ACE-model with covariates in table and graph...
Shows a compact, publication-style, summary of a variance-based Choles...
Present the results of a Common-pathway twin model in table and graphi...
Shows a compact, publication-style, summary of a umx Direction of Caus...
Summarize a GxE model
Summarize a bivariate GxE twin model
Present the results of an independent-pathway twin model in table and ...
Present the results of a Mendelian Randomization Direction of Causatio...
Shows a compact, publication-style, summary of a umx Sex Limitation mo...
Shows a compact, publication-style, summary of a Simplex model.
Make a multi-group model
Create the threshold matrix needed for modeling ordinal data.
Make a twin model from the model describing just one person
Build a SEM implementing the instrumental variable design
umxUnexplainedCausalNexus
Get or print the version of umx, along with detail from OpenMx and gen...
AIC weight-based conditional probabilities.
Convert a bracket address into an A_rXcX-style label.
Return whether a cell is in a set location of a matrix
xmu_check_levels_identical
Check data to see if model needs means.
Check the minimum variance in data frame
xmu_CI_merge
Stash the CI values of a model as strings in the values of the model
Remove illegal characters from labels
Drop rows with missing definition variables
Data helper function to swap blocks of data from one set of columns to...
Determine if a dataset will need statistics for the means if used in a...
Convert a dataframe into a cov mxData object
Helper to make the list of vars and their shapes for a graphviz string
xmu_dot_make_paths (not for end users)
xmu_dot_make_residuals (not for end users)
Internal umx function to help plotting graphviz
Return dot code for paths in a matrix
xmu_dot_move_ranks (not for end users)
xmu_dot_rank_str (not for end users)
Helper to make a graphviz rank string
Equate Threshold Values Across Columns in a Model
Get one or more columns from mzData or regular data.frame
Look up and report CIs for free parameters
Process table of paths to model
Make pairs of bin & continuous columns to represent censored data
Upgrade a dataframe to an mxData type.
Helper to make a basic top, MZ, and DZ model.
Select first item in list of options, while being flexible about choic...
Find name for model
Where all data are missing for a twin, add default values for definiti...
Re-name variables umxPaths to twin versions
Re-name variables in umxPaths to twin versions
Print algebras from a umx model
Convert an "A_r1c1"-style label to a bracket address.
Relabel Factor Columns in a Data Frame
Safely run and summarize a model
Just a helper to cope with deprecated suffix lying around.
Show model logLik of model or print comparison table
Internal function to help building simplex models
xmu_standardize_ACE
xmu_standardize_ACEcov
Standardize an ACE variance components model (ACEv)
Function to standardize a common pathway model
non-user: Standardize an IP model
Standardize a Structural Model (not for end users)
Standardize a SexLim model
Standardize a Simplex twin model
Make start values
Helper providing boilerplate start values for means and variance in tw...
Order and group the parameters in a RAM summary
Add weight matrices to twin models.
Check basic aspects of input for twin models.
Not for user: pull variable names from a twin model
Make the matrices and algebras for definition-based means models
Upgrade selDVs to selVars
Update covariates in twin data sets to 99999 if missing and correspond...
xmuHasSquareBrackets
xmuLabel_MATRIX_Model (not a user function)
xmuLabel_Matrix (not a user function)
xmuLabel_RAM_Model (not a user function)
xmuLabel: Add labels to a RAM model, matrix, or path
Make a deviation-based mxRAMObjective for ordinal models.
xmuMakeOneHeadedPathsFromPathList
xmuMakeTwoHeadedPathsFromPathList
xmuMaxLevels
xmuMI (not for end users)
xmuMinLevels
xmuPropagateLabels (not a user function)
xmuRAM2Ordinal
Create core of twin model for all-continuous data.
xmuTwinSuper_NoBinary
Not for end-users: Add a means model with covariates to a twin model
xmuValues: Set values in RAM model, matrix, or path
Quickly create, run, and report structural equation models, and twin models. See '?umx' for help, and umx_open_CRAN_page("umx") for NEWS. Timothy C. Bates, Michael C. Neale, Hermine H. Maes, (2019). umx: A library for Structural Equation and Twin Modelling in R. Twin Research and Human Genetics, 22, 27-41. <doi:10.1017/thg.2019.2>.