Print a money object | bucks print |
Convert Degrees to Degrees | deg2rad |
dl_from_dropbox | dl_from_dropbox |
Twin data for Direction of causation modelling | docData |
Extract AIC from MxModel | extractAIC.MxModel |
Compute the value of a principal & annual deposits at a compound interest over a number of years | fin_interest |
Justified P/E Ratio | fin_JustifiedPE |
Compute NI given annual Earnings. | fin_NI |
Compute the percent change needed to return to the original value after percent off (or on). | fin_percent |
Open a ticker in yahoo finance. | fin_ticker |
Work the valuation of a company | fin_valuation |
Weight data across time. | Fischbein_wt |
Fishers Method of combining p-values. | FishersMethod |
Geometric Mean | geometric_mean |
Twin data: General Family Functioning, divorce, and well-being. | GFF |
Add a fit statistic to a ggplot | ggAddR |
Harmonic Mean | harmonic_mean |
Install OpenMx, with choice of builds | install.OpenMx umx_update_OpenMx |
Twin data: IQ measured longitudinally across 4 ages. | iqdat |
load libraries | libs |
loadings Generic loadings function to extract factor loadings from exploratory or confirmatory factor analyses. | loadings |
Extract factor loadings from an EFA (factor analysis). | loadings.MxModel |
Succinctly select complete rows from a dataframe | noNAs |
Compute odds ratio (OR) | oddsratio |
Create and display a graphical path diagram for a LISREL model. | plot.MxLISRELModel |
Create and display a graphical path diagram for a model. | plot plot.MxModel |
Create and display a graphical path diagram for a path-based twin model. | plot.MxModelTwinMaker umxPlotMxModelTwinMaker |
Plot a percent change graph | plot.percent |
Test the power of an ACE model to detect paths of interest. | power.ACE.test |
Print a scale "oddsratio" object | print.oddsratio |
Print a percent object | print.percent |
Print a scale "reliability" object | print.reliability |
Print a RMSEA object | print.RMSEA |
Clean up a prolific file for sharing by removing anonymity-compromising columns. | prolific_anonymize |
Return PIDs in df | prolific_check_ID |
Read and optionally merge demographics file from prolific academic | prolific_read_demog |
qm | qm |
Convert Radians to Degrees | rad2deg |
Report coefficient alpha (reliability) | reliability |
Get residuals from an MxModel | residuals.MxModel |
Generic RMSEA function | RMSEA |
RMSEA function for MxModels | RMSEA.MxModel |
RMSEA function for MxModel summary | RMSEA.summary.mxmodel |
Compute an SE from a beta and p value | SE_from_p |
Graphical display of genotypic effects. | tmx_genotypic_effect |
Test if a factor model is identified | tmx_is.identified |
Show matrices of models in a easy-to-learn-from format. | tmx_show |
Show matrices of models in a easy-to-learn-from format. | tmx_show.MxMatrix |
Show matrices of RAM models in a easy-to-learn-from format. | tmx_show.MxModel |
Functions for Structural Equation Modeling in OpenMx | umx-package umx |
Convenient formula-based cross-tabs & built-in summary functions | umx_aggregate |
Round p-values according to APA guidelines | umx_APA_pval |
umx_apply | umx_apply |
Like the php array_shift function: shifts an item off the beginning of a list | umx_array_shift |
umx_as_numeric | umx_as_numeric |
umx_check | umx_check |
Check for required features in an OpenMx. | umx_check_model |
Check if a request name exists in a dataframe or related object | umx_check_names |
umx_check_OS | umx_check_OS |
Check if OpenMx is using OpenMP, test cores, and get timings | umx_check_parallel |
umx_cont_2_quantiles | umx2ord umx_cont_2_quantiles |
Report correlations and their p-values | umx_cor |
Explode a string (Like the php function 'explode') | umx_explode |
Break twin variable names (BMI_T1, BMI_T2) into base variable names (BMI, "_T", 1:2) | umx_explode_twin_names |
Read in files from pseudocons. | umx_file_load_pseudo |
umx_find_object | umx_find_object |
Summarizing functions used in umx_aggregate and for umxAPA | umx_fun_mean_sd |
Get bracket-style addresses from an mxMatrix | umx_get_bracket_addresses |
Get or set checkpointing for a model | umx_get_checkpoint |
Display umx options | umx_get_options |
Search for text | umx_grep |
umx_has_been_run | umx_has_been_run |
umx_has_CIs | umx_has_CIs |
umx_has_means | umx_has_means |
Check if a label contains square brackets | umx_has_square_brackets |
Check if variables in a dataframe are in a list of classes. | umx_is_class |
umx_is_cov | umx_is_cov |
List endogenous variables in a model | umx_is_endogenous |
umx_is_exogenous | umx_is_exogenous |
Check if an object is an mxData object | umx_is_MxData |
umx_is_MxMatrix | umx_is_MxMatrix |
umx_is_MxModel | umx_is_MxModel |
Check if variables in a dataframe are numeric | umx_is_numeric |
Test if one or more variables in a dataframe are ordered | umx_is_ordered |
umx_is_RAM | umx_is_RAM |
Take a long twin-data file and make it wide (one family per row) | umx_long2wide |
Get values from lower triangle of a matrix | umx_lower.tri |
Convert lower-only matrix data to full (or enforce symmetry on a full matrix) | umx_lower2full |
"make" the umx package using devtools: release to CRAN etc. | umx_make |
umx_make_fake_data | umx_make_fake_data |
Simulate Mendelian Randomization data | umx_make_MR_data |
Turn a cov matrix into raw data | umx_make_raw_from_cov |
Convert an excel spreadsheet in a text file on sql statements. | umx_make_sql_from_excel |
Convert a twin dataset into umx standard format. | umx_make_twin_data_nice |
Simulate twin data with control over A, C, and E parameters, as well as moderation of A. | umx_make_TwinData |
umx_means | umx_means |
umx_merge_randomized_columns | umx_merge_randomized_columns |
Move files | umx_move_file |
Print the name and compact contents of variable. | umx_msg |
umx_names | namez umx_names |
Open a file or folder | umx_open |
Open the CRAN page for a package | umx_open_CRAN_page |
Pad an Object with NAs | umx_pad |
Concatenate base variable names with suffixes to create wide-format variable names (i.e twin-format) | tvars umx_paste_names |
FIML-based polychoric, polyserial, and Pearson correlations | umx_polychoric |
FIML-based Pairwise polychoric, polyserial, and Pearson correlations | umx_polypairwise |
FIML-based trio-based polychoric, polyserial, and Pearson correlations | umx_polytriowise |
Print tables in a range of formats (markdown default, see 'umx_set_table_format()' for other formats) or as a web browser table. | umx_print |
Test the difference between correlations for significance. | umx_r_test |
Read lower-triangle of data matrix from console or file | umx_read_lower |
umx_rename | umx_rename |
Rename files | umx_rename_file |
Reorder or drop variables from a correlation/covariance matrix. | umx_reorder |
Easily residualize variables in long or wide dataframes, returning them changed in-place. | umx_residualize |
Rotate a vector | umx_rot |
umx_round | umx_round |
Scale data columns, skipping non-scalable columns | umx_scale |
Scale wide twin data | umx_scale_wide_twin_data |
Score a psychometric scale by summing normal and reversed items. | umx_score_scale |
Update NA values in one column with valid entries from another | umx_select_valid |
umx_set_auto_plot | umx_set_auto_plot |
Automatically run models? | umx_set_auto_run |
umx_set_checkpoint | umx_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 |
Set the symbol for money | umx_set_dollar_symbol |
Set options that affect optimization in OpenMx | umx_set_optimization_options |
Set the optimizer in OpenMx | umx_set_optimizer |
Set output suffix used in umx SEM diagram files saved to disk. | umx_set_plot_file_suffix |
Set output format of plots (structural diagrams) in umx | umx_set_plot_format |
Set theme system to use for plots. | umx_set_plot_use_hrbrthemes |
Set the separator | umx_set_separator |
Turn off most console and summary output from umx | umx_set_silent |
umx_set_table_format | umx_set_table_format |
Stack data like stack() does, with more control. | umx_stack |
Return a standardized version of a Structural Model | umx_standardize |
Select desired characters from a string | umx_str_chars |
Return variable name as a string | umx_str_from_object |
Convert a string to an OpenMx algebra | umx_string_to_algebra |
A wrapper to map columns of strings to numeric. | umx_strings2numeric |
umx_time | umx_time |
Trim whitespace surrounding a string. | umx_trim |
Get variances from a df that might contain some non-numeric columns | umx_var |
Change data family data from wide (2 twins per row) to long format. | umx_wide2long |
umx_write_to_clipboard | umx_write_to_clipboard |
Deprecated. May already stop() code and ask to be updated. May be dropped entirely in future. | umx-deprecated |
Build and run a 2-group Cholesky ACE twin model (univariate or multivariate) | umxACE |
Run a Cholesky with covariates that are random (in the expected covariance matrix) | umxACEcov |
Build and run 2-group uni- or multi-variate ACE models based on VARIANCE (not paths). | umxACEv |
A simple wrapper for mxAlgebra with name as the first parameter for more readable compact code. | umxAlgebra |
Creates nicely formatted journal-style summaries of models, p-values, data-frames and much more. | summaryAPA umxAPA |
A recipe Easter-egg for umx | umxBrownie |
Add (and, optionally, run) confidence intervals to a structural model. | umxCI |
umxCI_boot | umxCI_boot |
Runs cross-lagged panel models | umxCLPM |
Print a comparison table of one or more 'OpenMx::mxModel()'s, formatted nicely. | umxCompare |
Get confidence intervals from a umx model | umxConfint |
Convert a covariance matrix into a correlation matrix | umxCov2cor |
umxCP: Build and run a Common Pathway twin model | umxCP |
Diagnose problems in a model - not working! | umxDiagnose |
MZ differences method for testing evidence for causality. | umxDiffMZ |
Intra-pair association in MZ, DZ twin models. (ALPHA quality!) | umxDiscTwin |
Build and run a 2-group Direction of Causation twin models. | umxDoC |
Make a direction of causation model based on umxPath statements | umxDoCp |
FIML-based Exploratory Factor Analysis (EFA) | umxEFA umxFactanal |
umxEquate: Equate two or more paths | umxEquate |
Example code from Twin Research and Human Genetics Paper on umx | umxExampleCode_TRHGpaper umxExamples |
Get the expected vcov matrix | umxExpCov vcov.MxModel |
Extract the expected means matrix from an 'OpenMx::mxModel()' | umxExpMeans |
umxFactor | umxFactor umx_factor |
Return factor scores from a model as an easily consumable dataframe. | umxFactorScores |
Get additional fit-indices for a model with umxFitIndices | umxFitIndices |
umxFixAll: Fix all free parameters | umxFixAll |
Get the latentVars from a RAM model | umxGetLatents |
Get the manifestVars from a RAM model | umxGetManifests |
Used to get a RAM submodel by name | umxGetModel |
Get parameters from a model, with support for pattern matching! | umxGetParameters |
umxGxE: Implements ACE models with moderation of paths, e.g. by SES. | umxGxE |
Implement the moving-window form of GxE analysis. | umxGxE_window |
Purcell (2002) Bivariate GxE model: Suitable when twins differ on the moderator. | umxGxEbiv |
Create a matrix of correlations for variables of diverse types (binary, ordinal, continuous) | umxHetCor |
umxIP: Build and run an Independent Pathway twin model | umxIP |
umxJiggle | umxJiggle |
Convert lavaan string to a umxRAM model | umxLav2RAM |
Make a mxMatrix with automatic labels. Also takes name as the first parameter for more readable code. | umxMatrix |
Sets labeled matrix cells to free | umxMatrixFree |
Report modifications which would improve fit. | umxMI |
Catches users typing umxModel instead of umxRAM. | umxModel |
Return names of models found within a model | umxModelNames |
umxModify: Add, set, or drop model paths by label. | umxModify |
Extends Mendelian randomization with the twin design to test evidence of causality | umxMRDoC |
Display path estimates from a model, filtering by name and value. | parameters umxParameters |
A wrapper to make paran easier to use. Just automates applying 'complete.cases()' | umxParan |
Easier (and powerful) specification of paths in SEM. | umxPath |
Quickly plot y ~ x with a regression line and R^2, and nice labels. | umxPlot |
Make a graphical display of an ACE model | plot.MxModelACE umxPlotACE |
Make a graphical display of an ACE model with covariates. | plot.MxModelACEcov umxPlotACEcov |
Produce a graphical display of an ACE variance-components twin model | plot.MxModelACEv umxPlotACEv |
Draw and display a graphical figure of Common Pathway model | plot.MxModelCP umxPlotCP |
Plot a Direction of Causation Model. | plot.MxModelDoC umxPlotDoC |
Easily plot functions in R | umxPlotFun |
Plot the results of a GxE univariate test for moderation of ACE components. | plot.MxModelGxE umxPlotGxE |
Plot the results of a GxE univariate test for moderation of ACE components. | plot.MxModelGxEbiv umxPlotGxEbiv |
Draw a graphical figure for a Independent Pathway model | plot.MxModelIP umxPlotIP |
Draw and display a graphical figure of a Sex limitation model | plot.MxModelSexLim umxPlotSexLim |
Draw and display a graphical figure of a simplex model | plot.MxModelSimplex umxPlotSimplex |
Test power to detect specified path values in a model. | umxPower |
Build and run path-based SEM models | umxRAM |
Convert a RAM model to a lavaan string | umxRAM2Lav |
Reduce models, and report the results. | umxReduce |
Reduce an ACE model. | umxReduceACE |
Reduce a GxE model. | umxReduceGxE |
Rename a umxMatrix (even in a model) | umxRenameMatrix |
Generic SEM factor model loading rotation function | umxRotate |
Rotate a CP solution | umxRotate.MxModelCP |
umxRun: Run an mxModel | umxRun |
Change or fix parameters (e.g. their values, labels, bounds, ..) in a model. | umxSetParameters |
Multivariate sex limitation twin model | umxSexLim |
Build and run a simplex twin model (not ready for use!) | umxSimplex |
Summarize twin data | umxSummarizeTwinData |
Shows a compact, publication-style, summary of umx models | umxSummary |
Shows a compact, publication-style, summary of a RAM model | umxSummary.MxModel umxSummary.MxRAMModel |
Shows a compact, publication-style, summary of a umx Cholesky ACE model | umxSummary.MxModelACE umxSummaryACE |
Present results of a twin ACE-model with covariates in table and graphical forms. | umxSummary.MxModelACEcov umxSummaryACEcov |
Shows a compact, publication-style, summary of a variance-based Cholesky ACE model. | umxSummary.MxModelACEv umxSummaryACEv |
Present the results of a Common-pathway twin model in table and graphical form | umxSummary.MxModelCP umxSummaryCP |
Shows a compact, publication-style, summary of a umx Direction of Causation model | umxSummary.MxModelDoC umxSummaryDoC |
Summarize a GxE model | umxSummary.MxModelGxE umxSummaryGxE |
Summarize a bivariate GxE twin model | umxSummary.MxModelGxEbiv umxSummaryGxEbiv |
Present the results of an independent-pathway twin model in table and graphical form | umxSummary.MxModelIP umxSummaryIP |
Present the results of a Mendelian Randomization Direction of Causation Model in a table | umxSummary.MxModelMRDoC umxSummaryMRDoC |
Shows a compact, publication-style, summary of a umx Sex Limitation model | umxSummary.MxModelSexLim umxSummarySexLim |
Shows a compact, publication-style, summary of a Simplex model. | umxSummary.MxModelSimplex umxSummarySimplex |
Make a multi-group model | umxSuperModel |
Create the threshold matrix needed for modeling ordinal data. | umxThresholdMatrix |
Make a twin model from the model describing just one person | umxTwinMaker |
Build a SEM implementing the instrumental variable design | umxMR umxTwoStage |
umxUnexplainedCausalNexus | umxUnexplainedCausalNexus |
Get or print the version of umx, along with detail from OpenMx and general system info. | umxVersion |
AIC weight-based conditional probabilities. | umxWeightedAIC |
Anthropometric data on twins | us_skinfold_data |
Convert a bracket address into an A_rXcX-style label. | xmu_bracket_address2rclabel |
Return whether a cell is in a set location of a matrix | xmu_cell_is_on |
xmu_check_levels_identical | xmu_check_levels_identical |
Check data to see if model needs means. | xmu_check_needs_means |
Check the minimum variance in data frame | xmu_check_variance |
xmu_CI_merge | xmu_CI_merge |
Stash the CI values of a model as strings in the values of the model | xmu_CI_stash |
Remove illegal characters from labels | xmu_clean_label |
Drop rows with missing definition variables | xmu_data_missing |
Data helper function to swap blocks of data from one set of columns to another. | xmu_data_swap_a_block |
Determine if a dataset will need statistics for the means if used in a WLS model. | xmu_describe_data_WLS |
Convert a dataframe into a cov mxData object | xmu_DF_to_mxData_TypeCov |
Helper to make the list of vars and their shapes for a graphviz string | xmu_dot_define_shapes |
xmu_dot_make_paths (not for end users) | xmu_dot_make_paths |
xmu_dot_make_residuals (not for end users) | xmu_dot_make_residuals |
Internal umx function to help plotting graphviz | xmu_dot_maker |
Return dot code for paths in a matrix | xmu_dot_mat2dot |
xmu_dot_move_ranks (not for end users) | xmu_dot_move_ranks |
Helper to make a graphviz rank string | xmu_dot_rank |
xmu_dot_rank_str (not for end users) | xmu_dot_rank_str |
Get one or more columns from mzData or regular data.frame | xmu_extract_column |
Look up and report CIs for free parameters | xmu_get_CI |
Process table of paths to model | xmu_lavaan_process_group |
Make pairs of bin & continuous columns to represent censored data | xmu_make_bin_cont_pair_data |
Upgrade a dataframe to an mxData type. | xmu_make_mxData |
Helper to make a basic top, MZ, and DZ model. | xmu_make_TwinSuperModel |
Select first item in list of options, while being flexible about choices. | xmu_match.arg |
Find name for model | xmu_name_from_lavaan_str |
Where all data are missing for a twin, add default values for definition variables, allowing the row to be kept | xmu_PadAndPruneForDefVars |
Re-name variables umxPaths to twin versions | xmu_path_regex |
Re-name variables in umxPaths to twin versions | xmu_path2twin |
Print algebras from a umx model | xmu_print_algebras |
Convert an "A_r1c1"-style label to a bracket address. | xmu_rclabel_2_bracket_address |
Safely run and summarize a model | xmu_safe_run_summary |
Just a helper to cope with deprecated suffix lying around. | xmu_set_sep_from_suffix |
Show model logLik of model or print comparison table | xmu_show_fit_or_comparison |
Internal function to help building simplex models | xmu_simplex_corner |
xmu_standardize_ACE | xmu_standardize_ACE |
xmu_standardize_ACEcov | xmu_standardize_ACEcov |
Standardize an ACE variance components model (ACEv) | xmu_standardize_ACEv |
Function to standardize a common pathway model | xmu_standardize_CP |
non-user: Standardize an IP model | xmu_standardize_IP |
Standardize a Structural Model (not for end users) | xmu_standardize_RAM |
Standardize a SexLim model | xmu_standardize_SexLim |
Standardize a Simplex twin model | xmu_standardize_Simplex |
Make start values | xmu_start_value_list |
Helper providing boilerplate start values for means and variance in twin models | xmu_starts |
Order and group the parameters in a RAM summary | xmu_summary_RAM_group_parameters |
Add weight matrices to twin models. | xmu_twin_add_WeightMatrices |
Check basic aspects of input for twin models. | xmu_twin_check |
Not for user: pull variable names from a twin model | xmu_twin_get_var_names |
Make the matrices and algebras for definition-based means models | xmu_twin_make_def_means_mats_and_alg |
Upgrade selDVs to selVars | xmu_twin_upgrade_selDvs2SelVars |
xmuHasSquareBrackets | xmuHasSquareBrackets |
xmuLabel: Add labels to a RAM model, matrix, or path | xmuLabel |
xmuLabel_Matrix (not a user function) | xmuLabel_Matrix |
xmuLabel_MATRIX_Model (not a user function) | xmuLabel_MATRIX_Model |
xmuLabel_RAM_Model (not a user function) | xmuLabel_RAM_Model |
Make a deviation-based mxRAMObjective for ordinal models. | xmuMakeDeviationThresholdsMatrices |
xmuMakeOneHeadedPathsFromPathList | xmuMakeOneHeadedPathsFromPathList |
xmuMakeTwoHeadedPathsFromPathList | xmuMakeTwoHeadedPathsFromPathList |
xmuMaxLevels | xmuMaxLevels |
xmuMI (not for end users) | xmuMI |
xmuMinLevels | xmuMinLevels |
xmuPropagateLabels (not a user function) | xmuPropagateLabels |
xmuRAM2Ordinal | xmuRAM2Ordinal |
Create core of twin model for all-continuous data. | xmuTwinSuper_Continuous |
xmuTwinSuper_NoBinary | xmuTwinSuper_NoBinary |
Not for end-users: Add a means model with covariates to a twin model | xmuTwinUpgradeMeansToCovariateModel |
xmuValues: Set values in RAM model, matrix, or path | xmuValues |