| 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 |
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