| umx |
Functions for Structural Equation Modeling in OpenMx |
| umx2ord |
umx_cont_2_quantiles |
| umxACE |
Build and run a 2-group Cholesky ACE twin model (univariate or multivariate) |
| umxACEcov |
Run a Cholesky with covariates that are random (in the expected covariance matrix) |
| umxACEv |
Build and run 2-group uni- or multi-variate ACE models based on VARIANCE (not paths). |
| umxACE_DE |
Build a Double-Entry Censored Data ACE twin model |
| umxACE_GLM |
Cholesky ACE twin model with mxFitFunctionGLM |
| 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 models, p-values, data-frames and much more. |
| umxBrownie |
A recipe Easter-egg for umx |
| umxCI |
Add (and, optionally, run) confidence intervals to a structural model. |
| umxCI_boot |
umxCI_boot |
| umxCloud |
Run umx / OpenMx models on ephemeral Hetzner Cloud multicore nodes |
| umxCLPM |
Runs cross-lagged panel models |
| umxCompare |
Print a comparison table of two or more 'OpenMx::mxModel()'s, nicely formatted. |
| umxConfint |
Get confidence intervals from a umx model |
| umxCov2cor |
Convert a covariance matrix into a correlation matrix |
| umxCP |
umxCP: Build and run a Common Pathway twin model |
| umxDiagnose |
Diagnose problems in a model - not working! |
| umxDiffMZ |
MZ differences method for testing evidence for causality. |
| umxDiscTwin |
Intra-pair association in MZ, DZ twin models. (ALPHA quality!) |
| umxDoC |
Build and run a 2-group Direction of Causation twin models. |
| umxDoCp |
Make a direction of causation model based on umxPath statements |
| umxEFA |
FIML-based Exploratory Factor Analysis (EFA) |
| umxEquate |
umxEquate: Equate two or more paths |
| 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 'OpenMx::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 |
| umxGetLatents |
Get the latentVars from a RAM model |
| umxGetManifests |
Get the manifestVars from a RAM model |
| umxGetModel |
Used to get a RAM submodel by name |
| umxGetParameters |
Get parameters from a model, with support for pattern matching! |
| umxGSEM |
Fit genomic Structural Equation Models |
| umxGSEM_dl_tutorial_files |
Download tutorial-scale Genomic SEM files |
| umxGSEM_GWAS |
Multivariate genomic SEM GWAS (SNP on a factor or user model) |
| umxGSEM_label_ldsc |
Label or Assemble S, V, I, N into an LDSC-style covstruc list |
| umxGSEM_ldsc |
Multivariate LD score regression (OpenMx C++ engine) |
| umxGSEM_munge |
Munge Genomic SEM Summary Statistics |
| umxGSEM_sim_snps |
Simulate GWAS Summary Statistics for Genomic SEM |
| umxGSEM_std |
Standardize GSEM S and V matrices to the correlation metric via Delta Method |
| umxGSEM_sumstats |
Prepare multivariate SNP summary statistics for genomic SEM GWAS |
| umxGxE |
umxGxE: Implements ACE models with moderation of paths, e.g. by SES. |
| umxGxEbiv |
Purcell (2002) Bivariate GxE model: Suitable when 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 |
| umxJiggle |
umxJiggle |
| umxLav2RAM |
Convert lavaan string to a umxRAM model |
| umxLISREL |
Make a LISREL model analogous to umxRAM |
| umxMatrix |
Make a mxMatrix with automatic labels. Also takes name as the first parameter for more readable code. |
| umxMatrixFree |
Sets labeled matrix cells to free |
| umxMeasurementInvariance |
Test measurement invariance of a confirmatory factor analysis model |
| umxMI |
Report modifications which would improve fit. |
| umxModel |
Catches users typing umxModel instead of umxRAM. |
| umxModelNames |
Return names of models found within a model |
| umxModify |
umxModify: Add, set, or drop model paths by label. |
| umxMR |
Build a SEM implementing the instrumental variable design |
| umxMRDoC |
Extends Mendelian randomization with the twin design to test evidence of causality |
| umxParameters |
Display path estimates from a model, filtering by name and value. |
| umxParan |
A wrapper to make paran easier to use. Just automates applying 'complete.cases()' |
| umxPath |
Easier (and powerful) specification of paths in SEM. |
| umxPlot |
Quickly plot y ~ x with a regression line and R^2, and nice labels. |
| umxPlotACE |
Make a graphical display of an ACE model |
| umxPlotACEcov |
Make a graphical display of an ACE model with covariates. |
| umxPlotACEv |
Produce a graphical display of an ACE variance-components twin model |
| umxPlotACE_DE |
Plot a double-entry censored twin model (umxACE_DE) |
| umxPlotACE_GLM |
Plot a GLM ACE twin model |
| umxPlotCP |
Draw and display a graphical figure of Common Pathway model |
| umxPlotDoC |
Plot a Direction of Causation Model. |
| umxPlotFun |
Easily plot functions in R |
| 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 |
| umxPlotMxModelTwinMaker |
Create and display a graphical path diagram for a path-based twin model. |
| umxPlotPredict |
'umxPlotPredict' Take a model and plot the y against predicted(y) |
| umxPlotSexLim |
Draw and display a graphical figure of a Sex limitation model |
| umxPlotSimplex |
Draw and display a graphical figure of a simplex model |
| umxPower |
Test power to detect specified path values in a model. |
| umxPrint_double_entry_data |
Pretty-print method for double-entry censored datasets |
| umxRAM |
Build and run path-based SEM models |
| umxRAM2Lav |
Convert a RAM model to a lavaan string |
| umxRAM_DE |
Build and run path-based Double-entry SEM models including censored data |
| umxRAM_GLM |
Path-based RAM model with mxFitFunctionGLM |
| umxReduce |
Reduce models, and report the results. |
| umxReduceACE |
Reduce an ACE model. |
| umxReduceGxE |
Reduce a GxE model. |
| umxRenameMatrix |
Rename a umxMatrix (even in a model) |
| umxRotate |
Generic SEM factor model loading rotation function |
| umxRotate.MxModelCP |
Rotate a CP solution |
| umxRun |
umxRun: Run an mxModel |
| umxSetParameters |
Change or fix parameters (e.g. their values, labels, bounds, ..) in a model. |
| 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.list |
Summarize a Genomic SEM / LDSC covariance structure (covstruc) |
| umxSummary.MxDataStatic |
Summarize WLS / summary-statistic OpenMx::mxData objects |
| umxSummary.MxLISRELModel |
umxSummary.MxLISRELModel |
| 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.MxModelDoC |
Shows a compact, publication-style, summary of a umx Direction of Causation model |
| umxSummary.MxModelGLM |
Summary for a RAM model with mxFitFunctionGLM |
| umxSummary.MxModelGxE |
Summarize a GxE model |
| 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.MxModelMRDoC |
Present the results of a Mendelian Randomization Direction of Causation Model in a table |
| 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. |
| umxSummary.MxRAMModel |
Shows a compact, publication-style, summary of a RAM 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. |
| umxSummaryACE_DE |
Present results of a double-entry twin ACE model (umxACE_DE) |
| umxSummaryACE_GLM |
Summary for a GLM ACE twin model (Cholesky) |
| 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 |
| umxSummaryGxE |
Summarize a GxE model |
| umxSummaryGxEbiv |
Summarize a bivariate GxE twin model |
| umxSummaryIP |
Present the results of an independent-pathway twin model in table and graphical form |
| umxSummaryMRDoC |
Present the results of a Mendelian Randomization Direction of Causation Model in a table |
| 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 (super) model |
| umxThresholdMatrix |
Create the threshold matrix needed for modeling ordinal data. |
| umxTwinMaker |
Make a twin model from a model describing just one person |
| umxTwoStage |
Build a SEM implementing the instrumental variable design |
| umxUnexplainedCausalNexus |
umxUnexplainedCausalNexus |
| 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_check |
umx_check |
| umx_checkpoint |
Set the checkpoint status for a model or global options |
| umx_check_model |
Check for required features in an OpenMx. |
| umx_check_names |
Check if a request name exists in a dataframe or related object |
| umx_check_OS |
umx_check_OS |
| umx_check_parallel |
Check that OpenMx is using OpenMP, test cores, and get timings |
| umx_complete_dollar |
umx_complete_dollar |
| umx_cont_2_quantiles |
umx_cont_2_quantiles |
| umx_cor |
Report correlations and their p-values |
| umx_data |
Show the datasets and vignettes in umx |
| umx_detect_cores |
Detect number of CPU cores (including Performance cores) |
| umx_explode |
Explode a string (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_file_load_pseudo |
Read in files from pseudocons. |
| umx_find_object |
umx_find_object |
| umx_fun_mean_sd |
Summarizing functions used in umx_aggregate and for umxAPA |
| umx_get_bracket_addresses |
Get bracket-style addresses from an mxMatrix |
| umx_get_checkpoint |
Get or set checkpointing for a model |
| umx_get_options |
Display umx options |
| umx_grep |
Search for text |
| 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_ICA_report |
Journal processing report for an ICA Scholastica export |
| umx_is_class |
Check if variables in a dataframe are in a list of classes. |
| umx_is_cov |
umx_is_cov |
| umx_is_endogenous |
List endogenous variables in a model |
| umx_is_exogenous |
umx_is_exogenous |
| umx_is_GSEM |
umx_is_GSEM |
| umx_is_LISREL |
umx_is_LISREL |
| 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_log_wide_twin_data |
Log-transform wide twin data with a positive shift |
| umx_long2wide |
Take a long twin-data file and make it wide (one family per row) |
| umx_lower.tri |
Get values from lower triangle of a matrix |
| 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_double_entry_data |
Prepare data for Double-Entry Censored Twin Models |
| umx_make_fake_data |
umx_make_fake_data |
| umx_make_GxE_data |
Simulate ground-truth Purcell GxE twin data for benchmarking umxGxE |
| umx_make_MR_data |
Simulate Mendelian Randomization data |
| umx_make_raw_from_cov |
Turn a cov matrix into raw 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 (and D) parameters |
| umx_make_twin_data_nice |
Convert a twin dataset into umx standard format. |
| umx_means |
umx_means |
| umx_merge_randomized_columns |
umx_merge_randomized_columns |
| umx_move_file |
Move files |
| umx_msg |
Print the Name and Compact Contents of a Variable |
| umx_names |
umx_names |
| umx_open |
Open a file or folder |
| umx_open_CRAN_page |
Open the CRAN page for a package |
| umx_pad |
Pad an Object with NAs |
| umx_paste_names |
Concatenate base variable names with suffixes to create wide-format variable names (i.e twin-format) |
| 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 |
Rename files |
| 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 |
Rotate a vector |
| 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_reliabilities |
Accumulate scale reliabilities and report them as a table |
| umx_scale_wide_twin_data |
Scale wide twin data |
| umx_score_scale |
Score a psychometric scale by summing normal and reversed items. |
| umx_select_valid |
Update NA values in one column with valid entries from another |
| umx_set_auto_plot |
umx_set_auto_plot |
| umx_set_auto_run |
Automatically run models? |
| umx_set_checkpoint |
Set the checkpoint status for a model or global options |
| umx_set_condensed_slots |
umx_set_condensed_slots |
| umx_set_cores |
Set the number of cores your models will use. |
| umx_set_data_variance_check |
umx_set_data_variance_check |
| umx_set_dollar_symbol |
Set the symbol for money |
| umx_set_optimization_options |
Set options that affect optimization in OpenMx |
| umx_set_optimizer |
Set the optimizer in OpenMx |
| umx_set_plot_file_suffix |
Set output suffix used in umx SEM diagram files saved to disk. |
| umx_set_plot_format |
Set output format of plots (structural diagrams) in umx |
| umx_set_separator |
Set the separator |
| umx_set_silent |
Turn off most console and summary output from umx |
| umx_set_table_format |
umx_set_table_format |
| umx_stack |
Stack data like stack() does, with more control. |
| umx_standardize |
Return a standardized version of a Structural Model |
| umx_strings2numeric |
A wrapper to map columns of strings to numeric. |
| umx_string_to_algebra |
Convert a string to an OpenMx algebra |
| umx_str_chars |
Select desired characters from a string |
| umx_str_from_object |
Return variable name as a string |
| umx_tail |
Show the n most extreme rows of a data.frame |
| umx_time |
umx_time |
| umx_trim |
Trim whitespace surrounding a string. |
| umx_tutorials |
Easily open vignettes (tutorials) for a package |
| umx_update_OpenMx |
Install OpenMx (GenomicMx binary build) |
| umx_var |
Get variances from a df that might contain some non-numeric columns |
| umx_wide2long |
umx_wide2long |
| umx_wide2longTwinData |
Change twin data from wide (2 twins per row) to long format. |
| umx_wide4lmer |
Take a long dataframe and make it wide for repeated measures and multi-level analysis |
| umx_write_to_clipboard |
umx_write_to_clipboard |
| umx_yj_wide_twin_data |
Yeo-Johnson transform wide twin data (Non-destructive) |
| us_skinfold_data |
Anthropometric data on twins |
| xgh_check_base_name |
Check branch address is valid. |
| xgh_get_current_branch |
Get the current git branch |
| xmuCalculateSRMR |
xmuCalculateSRMR |
| xmuHasSquareBrackets |
xmuHasSquareBrackets |
| xmuLabel |
xmuLabel: Add labels to a RAM model, matrix, or path |
| 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) |
| xmuMakeOneHeadedPathsFromPathList |
xmuMakeOneHeadedPathsFromPathList |
| xmuMakeTwoHeadedPathsFromPathList |
xmuMakeTwoHeadedPathsFromPathList |
| xmuMaxLevels |
xmuMaxLevels |
| xmuMI |
xmuMI (not for end users) |
| xmuMinLevels |
xmuMinLevels |
| xmuPropagateLabels |
xmuPropagateLabels (not a user function) |
| xmuRAM2Ordinal |
xmuRAM2Ordinal |
| xmuTwinSuper_Continuous |
Create core of twin model for all-continuous data. |
| xmuTwinSuper_NoBinary |
xmuTwinSuper_NoBinary |
| xmuTwinUpgradeMeansToCovariateModel |
Not for end-users: Add a means model with covariates to a twin model |
| xmuValues |
xmuValues: Set values in RAM model, matrix, or path |
| xmu_ace_de_apply_censor_thresholds |
Apply double-entry mean/variance/threshold identification (post-supermodel) |
| xmu_ace_de_parse_censor_meta |
Resolve which double-entry pairs get fixed censor thresholds |
| xmu_ace_de_parse_censor_rule |
Parse a double-entry censoring rule into cut, side, and fixable flag |
| xmu_ace_de_release_binary_v1 |
Drop selected traits from binary Vtot==1 constraint (DE known-cut ID) |
| xmu_bracket_address2rclabel |
Convert a bracket address into an A_rXcX-style label. |
| xmu_catml_df3_diagnostic |
Polycorrelation-block Jacobian rank degrees of freedom (diagnostic) |
| xmu_catml_discrepancy_at_WLS |
Evaluate catML discrepancy (XX_3) at fixed WLS estimates |
| xmu_catml_eval_model |
Build correlation-matrix ML evaluation model at fixed WLS estimates |
| xmu_catml_implied_correlation |
Model-implied correlation matrix at fixed WLS estimates |
| xmu_catml_wls_v |
catML expected information matrix (V) for correlation moments |
| xmu_cell_is_on |
Return whether a cell is in a set location of a matrix |
| xmu_check_levels_identical |
xmu_check_levels_identical |
| xmu_check_needs_means |
Check data to see if model needs means. |
| xmu_check_variance |
Check the minimum variance in data frame |
| xmu_CI_merge |
xmu_CI_merge |
| xmu_CI_stash |
Stash the CI values of a model as strings in the values of the model |
| xmu_clean_label |
Remove illegal characters from labels |
| xmu_compare_constraint_note |
Lines reconciling raw free parameters with equality constraints. |
| xmu_compare_robust_ML |
xmu_compare_robust_ML |
| xmu_compare_WLS |
xmu_compare_WLS |
| xmu_custom_completer |
xmu_custom_completer |
| xmu_data_missing |
Drop rows with missing definition variables |
| xmu_data_swap_a_block |
Data helper function to swap blocks of data from one set of columns to another. |
| xmu_describe_data_WLS |
Determine if a dataset will need statistics for the means if used in a WLS model. |
| xmu_DF_to_mxData_TypeCov |
Convert a dataframe into a cov mxData object |
| xmu_dot_define_shapes |
Helper to make the list of vars and their shapes for a graphviz string |
| 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_mat2dot |
Return dot code for paths in a matrix |
| xmu_dot_move_ranks |
xmu_dot_move_ranks (not for end users) |
| xmu_dot_rank |
Helper to make a graphviz rank string |
| xmu_dot_rank_str |
xmu_dot_rank_str (not for end users) |
| xmu_equate_threshold_values |
Equate Threshold Values Across Columns in a Model |
| xmu_extract_column |
Get one or more columns from mzData or regular data.frame |
| xmu_get_CI |
Look up and report CIs for free parameters |
| xmu_gsem_expand_snp |
Expand SNP Summary Statistics into a Full Covariance Matrix |
| xmu_gsem_extract_snp_path |
Extract SNP Effect from a Fitted Model |
| xmu_gsem_subset_covstruc |
Subset a GenomicSEM Covariance Structure to Selected Traits |
| xmu_has_summary_mxData |
Check if this version of OpenMx supports modern WLS (mxData of type = "summary") |
| xmu_invert_matrix |
Invert a matrix with chol, then ginv, then solve fallbacks |
| xmu_is_ordinal_WLS |
Detect ordinal or categorical WLS models |
| xmu_is_wls |
Check if a model is a WLS model |
| xmu_lavaan_process_group |
Process table of paths to model |
| xmu_make_bin_cont_pair_data |
Make pairs of bin & continuous columns to represent censored data |
| xmu_make_mxData |
Upgrade a dataframe to an mxData type. |
| xmu_make_TwinSuperModel |
Helper to make a basic top, MZ, and DZ model. |
| xmu_match.arg |
Select first item in list of options, while being flexible about choices. |
| xmu_mxData_summary |
Create mxData(type = "summary") with an OpenMx capability guard |
| xmu_mxRefModels |
Generate reference models safely across OpenMx versions |
| xmu_name_from_lavaan_str |
Find name for model |
| xmu_openmx_engine_status |
Detect whether loaded OpenMx is a GenomicMx-capable build |
| xmu_openmx_install_message |
Canonical install recipe when GenomicMx OpenMx is required |
| xmu_PadAndPruneForDefVars |
Where all data are missing for a twin, add default values for definition variables, allowing the row to be kept |
| xmu_parse_completion_context |
xmu_parse_completion_context |
| xmu_path2twin |
Re-name variables in umxPaths to twin versions |
| xmu_path_regex |
Re-name variables umxPaths to twin versions |
| xmu_print_algebras |
Print algebras from a umx model |
| xmu_ram_de_apply_censor_thresholds |
Apply RAM DE latent-trait identification |
| xmu_ram_de_parse_censor_meta |
Parse censor cuts for single-group RAM DE |
| xmu_rclabel_2_bracket_address |
Convert an "A_r1c1"-style label to a bracket address. |
| xmu_relevel_factors |
Relabel Factor Columns in a Data Frame |
| xmu_require_summary_mxData |
Require OpenMx support for type = "summary" mxData |
| xmu_robust_ML_fit |
xmu_robust_ML_fit |
| xmu_robust_WLS_fit |
Robust WLS fit statistics: Satorra-Bentler (2010) and Savalei (2021) |
| xmu_safe_run_summary |
Safely run and summarize a model |
| xmu_savalei_fit_cfi |
Robust CFI from mean-and-variance corrected noncentrality (Savalei 2021 form) |
| xmu_savalei_fit_rmsea |
Robust RMSEA from mean-and-variance corrected noncentrality (Savalei 2021 form) |
| xmu_savalei_fit_tli |
Robust TLI from mean-and-variance corrected noncentrality (Savalei 2021 form) |
| xmu_savalei_null_scaling_factor |
Savalei (2021) independence/null scaling factor \hat{c}_{3,null} |
| xmu_savalei_polycor_blocks |
Build OpenMx-native polycorrelation blocks for the Savalei sandwich |
| xmu_savalei_scaling_factor |
Savalei (2021) target scaling factor \hat{c}_3 for ordinal WLS |
| xmu_set_sep_from_suffix |
Just a helper to cope with deprecated suffix lying around. |
| xmu_show_fit_or_comparison |
Show model logLik of model or print comparison table |
| xmu_simplex_corner |
Internal function to help building simplex models |
| xmu_standardize_ACE |
xmu_standardize_ACE |
| xmu_standardize_ACEcov |
xmu_standardize_ACEcov |
| xmu_standardize_ACEv |
Standardize an ACE variance components model (ACEv) |
| xmu_standardize_CP |
Function to standardize a common pathway model |
| xmu_standardize_IP |
non-user: Standardize an IP model |
| xmu_standardize_LISREL |
xmu_standardize_LISREL |
| xmu_standardize_RAM |
Standardize a Structural Model (not for end users) |
| xmu_standardize_SexLim |
Standardize a SexLim model |
| xmu_standardize_Simplex |
Standardize a Simplex twin model |
| xmu_starts |
Helper providing boilerplate start values for means and variance in twin models |
| xmu_start_value_list |
Make start values |
| xmu_summary_RAM_group_parameters |
Order and group the parameters in a RAM summary |
| xmu_threshold_id_RAM |
Enforce or check Mehta/binary identification for threshold RAM models |
| xmu_threshold_id_twin_check |
Verify twin-model threshold identification (means / binary Vtot constraint) |
| xmu_topo_sort |
Topologically sort a graph based on from and to paths |
| xmu_twin_add_WeightMatrices |
Add weight matrices to twin models. |
| xmu_twin_check |
Check basic aspects of input for twin models. |
| xmu_twin_get_var_names |
Not for user: pull variable names from a twin model |
| xmu_twin_make_def_means_mats_and_alg |
Make the matrices and algebras for definition-based means models |
| xmu_twin_upgrade_selDvs2SelVars |
Upgrade selDVs to selVars |
| xmu_update_covar |
Update covariates in twin data sets to 99999 if missing and corresponding twin phenotype to NA |
| xmu_WLS_align_jacobian |
Align WLS implied Jacobian to asymptotic-covariance moment order |
| xmu_WLS_align_weight |
Subset and align WLS weight matrix to common moment set |
| xmu_wls_display_chi |
Display chi-square and AFIs for a WLS model (shared by summary and compare) |
| xmu_wls_extract_WV |
Extract WLS useWeight (W) and asymCov (Gamma) from an MxModel |
| xmu_WLS_polycor_names |
Polycorrelation moment names from WLS asymptotic-covariance labels |
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