Description

umx allows you to more easily build, run, modify, and report structural models, building on the OpenMx package. All core functions are organized into families, so they are easier to find (see "families" below under See Also) Please cite as: Bates, T. C., Neale, M. C., & Maes, H. H. (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.

All the functions have full-featured and well commented examples, some even have figures, so use the help, even if you think it won't help :-) Have a look, for example at umxRAM()

Check out NEWS about new features at news(package = "umx")

Details

Introductory working examples are below. You can run all demos with demo(umx) When I have a vignette, it will be: vignette("umx", package = "umx")

There is a helpful blog at https://tbates.github.io

(Only) if you want the bleeding-edge version:

devtools::install_github("tbates/umx")

References

• Bates, T. C., Neale, M. C., & Maes, H. H. (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, https://github.com/tbates/umx, tutorial: https://tbates.github.io

See Also

Other Core Model Building Functions: umxMatrix(), umxModify(), umxPath(), umxRAM(), umxSuperModel()

Other Model Summary and Comparison: umxCompare(), umxEquate(), umxMI(), umxReduce(), umxSetParameters(), umxSummary()

Other Reporting Functions: umxAPA(), umxFactorScores(), umxGetParameters(), umxParameters(), umx_aggregate(), umx_time()

Other Super-easy helpers: umxEFA(), umxTwoStage()

Other Twin Modeling Functions: power.ACE.test(), umxACEcov(), umxACEv(), umxACE(), umxCP(), umxDoCp(), umxDoC(), umxGxE_window(), umxGxEbiv(), umxGxE(), umxIP(), umxReduceACE(), umxReduceGxE(), umxReduce(), umxRotate.MxModelCP(), umxSexLim(), umxSimplex(), umxSummarizeTwinData(), umxSummaryACEv(), umxSummaryACE(), umxSummaryDoC(), umxSummaryGxEbiv(), umxSummarySexLim(), umxSummarySimplex(), umxTwinMaker()

Other Twin Data functions: umx_long2wide(), umx_make_TwinData(), umx_make_twin_data_nice(), umx_residualize(), umx_scale_wide_twin_data(), umx_wide2long()

Other Miscellaneous Stats Functions: FishersMethod(), SE_from_p(), geometric_mean(), harmonic_mean(), oddsratio(), reliability(), umxCov2cor(), umxHetCor(), umxWeightedAIC(), umx_apply(), umx_cor(), umx_means(), umx_r_test(), umx_round(), umx_scale(), umx_var()

Other Teaching and testing Functions: tmx_genotypic_effect(), tmx_is.identified()

Other Get and set: umx_get_checkpoint(), umx_get_options(), umx_set_auto_plot(), umx_set_auto_run(), umx_set_checkpoint(), umx_set_condensed_slots(), umx_set_cores(), umx_set_data_variance_check(), umx_set_optimization_options(), umx_set_optimizer(), umx_set_plot_file_suffix(), umx_set_plot_format(), umx_set_plot_use_hrbrthemes(), umx_set_separator(), umx_set_silent(), umx_set_table_format()

Other Check or test: umx_check_names(), umx_is_class(), umx_is_endogenous(), umx_is_exogenous(), umx_is_numeric(), umx_is_ordered()

Other Plotting functions: plot.MxLISRELModel(), plot.MxModelTwinMaker(), plot.MxModel(), umxPlotACEcov(), umxPlotACEv(), umxPlotACE(), umxPlotCP(), umxPlotDoC(), umxPlotFun(), umxPlotGxEbiv(), umxPlotGxE(), umxPlotIP(), umxPlotSexLim(), umxPlotSimplex()

Other Data Functions: noNAs(), umxFactor(), umxHetCor(), umx_as_numeric(), umx_cont_2_quantiles(), umx_lower2full(), umx_make_MR_data(), umx_make_TwinData(), umx_make_fake_data(), umx_make_raw_from_cov(), umx_polychoric(), umx_polypairwise(), umx_polytriowise(), umx_read_lower(), umx_read_prolific_demog(), umx_rename(), umx_reorder(), umx_score_scale(), umx_select_valid(), umx_stack()

Other File Functions: dl_from_dropbox(), umx_file_load_pseudo(), umx_make_sql_from_excel(), umx_move_file(), umx_open(), umx_rename_file(), umx_write_to_clipboard()

Other String Functions: umx_explode_twin_names(), umx_explode(), umx_grep(), umx_names(), umx_paste_names(), umx_rot(), umx_str_chars(), umx_str_from_object(), umx_trim()

Other Miscellaneous Utility Functions: install.OpenMx(), libs(), qm(), umxLav2RAM(), umxModelNames(), umxRAM2Lav(), umxVersion(), umx_array_shift(), umx_find_object(), umx_lower.tri(), umx_msg(), umx_open_CRAN_page(), umx_pad(), umx_print()

Other datasets: Fischbein_wt, GFF, docData, iqdat, us_skinfold_data

Other Advanced Model Building Functions: umxAlgebra(), umxFixAll(), umxJiggle(), umxRun(), umxThresholdMatrix(), umxUnexplainedCausalNexus(), xmuLabel(), xmuValues()

Other xmu internal not for end user: umxModel(), umxRenameMatrix(), umx_APA_pval(), umx_fun_mean_sd(), umx_get_bracket_addresses(), umx_make(), umx_standardize(), umx_string_to_algebra(), xmuHasSquareBrackets(), xmuLabel_MATRIX_Model(), xmuLabel_Matrix(), xmuLabel_RAM_Model(), xmuMI(), xmuMakeDeviationThresholdsMatrices(), xmuMakeOneHeadedPathsFromPathList(), xmuMakeTwoHeadedPathsFromPathList(), xmuMaxLevels(), xmuMinLevels(), xmuPropagateLabels(), xmuRAM2Ordinal(), xmuTwinSuper_Continuous(), xmuTwinSuper_NoBinary(), xmuTwinUpgradeMeansToCovariateModel(), xmu_CI_merge(), xmu_CI_stash(), xmu_DF_to_mxData_TypeCov(), xmu_PadAndPruneForDefVars(), xmu_bracket_address2rclabel(), xmu_cell_is_on(), xmu_check_levels_identical(), xmu_check_needs_means(), xmu_check_variance(), xmu_clean_label(), xmu_data_missing(), xmu_data_swap_a_block(), xmu_describe_data_WLS(), xmu_dot_make_paths(), xmu_dot_make_residuals(), xmu_dot_maker(), xmu_dot_move_ranks(), xmu_dot_rank_str(), xmu_extract_column(), xmu_get_CI(), xmu_lavaan_process_group(), xmu_make_TwinSuperModel(), xmu_make_bin_cont_pair_data(), xmu_make_mxData(), xmu_match.arg(), xmu_name_from_lavaan_str(), xmu_path2twin(), xmu_path_regex(), xmu_print_algebras(), xmu_rclabel_2_bracket_address(), xmu_safe_run_summary(), xmu_set_sep_from_suffix(), xmu_show_fit_or_comparison(), xmu_simplex_corner(), xmu_standardize_ACEcov(), xmu_standardize_ACEv(), xmu_standardize_ACE(), xmu_standardize_CP(), xmu_standardize_IP(), xmu_standardize_RAM(), xmu_standardize_SexLim(), xmu_standardize_Simplex(), xmu_start_value_list(), xmu_starts(), xmu_summary_RAM_group_parameters(), xmu_twin_add_WeightMatrices(), xmu_twin_check(), xmu_twin_get_var_names(), xmu_twin_make_def_means_mats_and_alg(), xmu_twin_upgrade_selDvs2SelVars()

Examples