umx_show control over parameter colors, examplesumx_scale_wide_twin accepts sibs #253 from lf-araujo/patch-6umxBrownie makes a rare steakumxSummarizeTwinData reports complete pairs for rMZ and rDZumx_as.numeric explicit drop = TRUEumxReduce ACE can skip ADE modelumxReduce output better formattedumx_check_parallel gains set optimizer, and row parallelumxEFA error reporting is more robustumx_scale betterumx_scale clarify polychoric and pairwise functionalityumxRAM Can include definition variables! h/t @lf-araujoumxRAM example a model with a def var on meansumxMR can standardize manifests.prolific_read_demog outputs a ready to paste demographics string.prolific_anonymize can delete more columns.umxReduce.MxModelACE now aware of umx_set_auto_run #241 @lf-araujoexpression instead of using uXXXXumxMatrixFree undocumented argument 'byrow'umxMRDoC sketch mode fixedfin_ticker open a stock in the browser.umxTwinMaker can manage definition variables (by @lf-araujo)umxSummary suppress duplicate pathsumxGxE_window handles target range without error once more (h/t Marla Kürten)umxMRDoC byrow misspellingumxMRDoC Direction of causation with twins! (by @lf-araujo)umxMatrixFree to help in simulations (by @lf-araujo)prolific_anonymize() remove IDs and other identifying columns: Ideal when sharing data.ggAddR helper to add R/beta to a graphumx_strings2numeric helper function to recode strings to numbersRMSEA()umxAPA gains cols to allow input checking in place of Rs…umx_strings2numeric example, handle 1 col dfprolific_read_demog handle "DATA_EXPIRED"umx_score_scale reliability works with correctAnswersumx_is_numeric works with tibble input h/t @psychelzhlibs can for package update using force.update = TRUEumxAPA cor/means output data.frame inputumxModify works with new R null behaviorumxAPA (and others) report = "html" works properly.umx_score_scale omega refsumx_read_prolific_demog -> prolific_read_demogumx_merge_randomized_columns wide-2-mingled (rather than wide2long) to unify data from people assigned to different conditions.umxDiscTwin Discordant twin test for causal effects.umxDiscTwin Graphical output for publication.umxPlot ease customized/journal-close, e.g. y~x, -> x y plot, with r^2.umxAPA t-test reporting.umx_score_scale gains error and proportion.umx_score_scale report only omega total when 1 factor extracted.umx_read_prolific_demog gains functionality.umxMR: gained `tryHard'umxGxEwindow: gained tryHard, smarter print control.umxGxEwindow: removes un-needed columns.umxGxE checks that selDefs are numeric (closes #196, h/t @salvatoj)umxRun: gained summary control.umx_read_prolific_demog more control, better defaults, and more reliable summary table.umx_score_scale cleaner output for 1 factor case with omega.xmu_twin_print_means now takes >1 covariate h/t @Eren Kafadar #201xmu_safe_run_summary now takes refModels = FALSE h/t @lf-araujo #200umxACEcov plot and summary working (needed to filter covs from DVs).xmu_twin_print_means handles more than 1 covariate and improves labeling.umx_score_scale handles NA correctly.umxPath stops when v*m* is used with firstAt or fixedAt.umxAlgebra warns that it isn't functional.umx_print call fixed where was being called with file.umxCP help .svg figure instead of `.png`` (smaller).umxMR Remove unsupported 'weights' parameter.umxDoC can take data (#ht @lf-araujo )umxDoC plot Rd figure includes specifics.umxPower search plot with fixed N has effect size on the x axis.umxGxE plot legend location works for ggplot.umx_score_scale gains omega reliability.umx_score_scale bug in handling new mapstrings.umxDoC plot.omxLocateParameters call was breaking umxSummary.xmu_safe_run_summary supports intervals parameter.umxSummary works with umxSuperModel now that paths have types.umx_make_twinData works with custom namesumx_make_twinData no longer shifts means now that mean and sd parameters are available.umxGetModel, umxGetLatents, and `umxGetManifestsumxPower can plot power search space! (beta!)noNAs() helper returning complete rows of a data.frame.umxThresholdMatrix can handle one value columnsumxPath gains v0m.umxPower parameters ==1 for power search with fixed numxPower refpower.ACE.test can run ADE modelpower.ACE.test Clarify which of power, effect, and n are fixed or being estimated.umxReduce.ACE gains tryHard (compute ACE/ADE/CE/AE, outputs a table an also AIC-based probability weights for which is the preferable model)umxReduce tests familiality (E model)umxReduce(ACE) includes the parameters of the reduced models. #ht @nick martinumxSummarizeTwinData takes an age column and notes when it can’t be foundumx_score_scale can score items with character labelsumx_score_scale gains the ability to report Cronbach alphaumx_score_scale changed default na.rm = TRUE.umxAPA gains OR output for logit modelstmx_show handles matricesumx_rename better names for deprecated parametersumxRun has tryHard (not a very useful function)umxCompare can silently return a data.frame for further modificationumxCP warning to not use correlatedACEumxAPA (invisibly) returns the standardized model for lmbucks more control for formatting moneylibs now install.packages() if not foundumx_make_TwinData shifts data to be positive if it not being scaledgrViz() in place of print(DiagrammR())` (should work better with knitr)fin_interest more memo/type-able parameter name for inflationumxRun defaults to tryHard= "yes"umxPower supports multiple path drop.FishersMethod Rd refumxCP ref Martin, N. G., & Eaves, L. J. (1977). The Genetical Analysis of Covariance Structure. Heredity, 38, 79-95.deg2rad Rd better in htmlumxRAM sketch mode helpumxCP more refs for RdumxACEv and umxACE work with nSib = 3!umxCP correlatedACE was not being filtered out of the expectation #hat-tip @micanzach But still working on what the right choices are here...umxCP defaults to tryHard = "yes"umxRAM deprecated parameter show after 4 years deprecationtmx_show works for M matrix, closed #163kable and kbl get format passed in at all callsumx_make_TwinData supports nSib > 2 for MZ/DZr modeumxAPA more use of cat to print (easier to read and copy)umx_open_CRAN_page printing if installed version if foundumxAPA more use of cat to print (easier to read and copy)fin_interest compute effective interestxmuTwinSuper_NoBinary update for nSib > 2kable formats (pandoc "pipe" and "simple" added, "pandoc" removed)add_footnote in place of footnote...umxPath and umxRAM helpxmuTwinUpgradeMeansToCovariateModel can handle nSib=3xmu_twin_make_def_means_mats_and_alg helperxmu_start improved closes #158umxPlot now detects and plots Pearson-Aitken selection paths (solid red headless).umxPlotFun plot functions without hassles. e.g umxPlotFun("sin(x)")umxModelNames to get model and submodel names from a model.libs as a short cut for multiple library() calls
libs("x", "y", c("a", "b"))fin_valuation uses revenue, margin, expenses and PE to compute a market cap.fin_interest shorter parameter name dinflate and other improvements.umxACEv Tables now include markdown-compatible table captions.umxAPA reports R^2 for lm (in addition to beta & CI[] for each parameter)umxSummary sorts RAM parameters by type (factor loading etc.) and can filter means and residuals for ease of use.umxSummary gives desired levels for good TLI and RMSEA.umxSuperModel checks for duplicate names in incoming model names and makes them unique.umxCompare Maintain compatibility with new OpenMx changes to mxCompare (esp. for WLS).umx_read_lower accept names for lower diag.umxCP correlatedACE leaves the covariances fixed@0.umxACE added A_std closes #151umxAPA pretty printing.umxPlotFun check for character input.xmu_summary_RAM_group_parameters sort and filter RAM model parameters for ease of understanding.umxFactor now used in all examples involving factor making.plot can output to pdf, png, svg!umx_set_plot_format adds pdf, png, svg plot output (in addition to DiagrammeR and graphviz)umx_lower.tri helper to get lower.tri values in 1 callumx_set_plot_use_hrbrthemes controlplot.percent plot support for percent change questionsumxSummary now reports algebra values when present in RAM models closes #70umxSummary tables have pandoc captions (see #145)umxCompare table output and plain-English summary printing (cat)umxCP practical workflows for correlated ACEfin_compound_interest now outputs a table of annual returnsumxAPA uses cat to improve usability of summary dataumxCP Document that correlatedA works on a, c and e, allowing factors to correlate.umxGxEbiv "lboundACE" @ 0 by defaultumxSimplex exampleumxGxEbiv fix nonfunctional lboundACE and lboundM (thanks @mcneale)umxGxEbiv selVars order was imposed on expectation dimnames but didn't match the cov matrix due to bespoke nature of expCov algebras...tmx_show display model matrices on the web, with color-coded free/false, values + roll-over labels.harmonic_mean with support for weights.harmonic_mean Example averaging speeds across distance.geometric_meanfin_compound_interestfin_percentumxPlotGxE Gains CI ribbons (closes #96)umxPlotGxE Defaults to use ggplot and now returns the graphs for further decoration (closes #139)umxPlotGxE Can now plot user-specified moderator ranges (closes #96)umxPlotIP Now relies on matrix cells, not their labels (closes #61)umxACE Returns group models invisibly #134 @khusmann.plot Now allows "ortho" "compound" and "polyline" spline control.umx_set_optimization_options Can get and set "Parallel diagnostics"tmx_show Smart about not printing NULL matrices.Gained anewlabels` parameter for the equated paths (rather than one path adopting the label of the other)umx_score_scale Supports minManifests for factor scoresumx_open_CRAN_page Can now install a package, as well as open the CRAN page for the package.umx_rename_file Better feedback about matches and files checked.umx_long2wide More resilient to zygosity column type.umxSummarizeTwinData More resilient to name of age columnplot strip_zero option works for fixed (@) parametersumx_is_class Handle non-df input.umxCI: Gains regex parameter to support adding and removing CIs on labels matching a string pattern.umx_is_class Handles non-df input.umx_set_table_format Defaults to "markdown" on load.umxPlotIP Wasn't working with threshold models (didn't ignore thresh names for plot).umx_time Was using time units for model 1 for all models... h/t @khusmannumxPlotACEv Was not displaying half the variables in an MV model as NA.umx_set_cores No longer use imxGetNumThreads which is hard-coded to not report number of threads.tmx_show Has html_font parameter in help.CatchesmxRefModels` error for WLS models and politely informs user OpenMx doesn't support fit stats for WLS yet.umxThresholdMatrix Changed parameter from selDVs to fullVarNames to prevent user error.umx_read_prolific_demog to read prolific academic demographics files.umxRAM Groups in multi-group models now independent by default (label style "path_group" )umxRAM No longer demand new data if a model is given as the first parameter. Updates data if provided.umxACE Return group models invisibly #134 @khusmannumxACEv support for covariates enabled.umx_score_scale gains the ability to return a factor score.umxEFA returns scores by default when requested (used to require user to also set return = "loadings" (thanks to user!)umx_r_test handles case of overlapping variables, i.e., compare r(ab) to r(ac)umxPlotACE uses matrix cells, not labels to draw the plot (so now labels are arbitrary)umxIP checks names of nFac for each of a, c, and eumxSimplex default sep is now "_T" instead of NULL (should do this throughout?)residuals can now suppress 0s - helpful for large tablesxmu_dot_mat2dot can cope with 1-variable name listsumxValues -> xmuValues clean up namespaceumxLabels -> xmuLabels clean up namespaceparameters: std wasn't being used.umxEFA examples.umxTwinMaker.umx_score_scale Fix a bad design decision where I was storing the reversed items in the data returned to the user. Worked for 1 run, but not repeats...umx_long2wide now looks for zygosity in more than just twin 1 h/t @nathangillespie for catching this case.m1 = umxACE(selVars = "wt", selCovs= "age", sep="_T")umxTwinMaker: Make twin models by specifying just the within-twin paths for one twin
umxSuperModel and runs it!plot() and "std= TRUE" work for any model now!umxDoCp Path-based Direction of causation model.umxSummaryACE prints a means table!
plot for umxACEv now prints model name on the diagram.plot for umxACE now uses tips for printing.FishersMethod: accepts p-values for meta-analysis in "..." argument.namez handles class(list) objects, returning $ components.parameters supports standardizing parameters (closes #92) .power.ACE.test now prints the parameter and value when testing power (closes #111).umxCompare includes Delta-AIC.umxCP plot prints model name.umxGxE code to detect mismatched moderatorsumxGxE code to include co-twin moderator in means modelumxGxE simplified algebraumxIP gains report option.umxIP plot prints model name.umxSummaryGxEbiv working, with a note that the whole function is beta. h/t @MikeNeale.umxThresholdMatrix re-implemented l_u_bound - wasn't working for some time h/t @NathanGillespie.umxThresholdMatrix supports leaving all thresholds free with method= "allFree" h/t @NathanGillespie.umx_check_names returns TRUE when no names are entered.umx_check can concatenate extra messages, and is by default polite with messages.umx_check handles ... items betterumx_is_ordered can process mxData as well as df.umx_make_TwinData has dzAr.umx_make_twin_data_nice can turn numeric zyg column into human readable "MZMM" etc.umx_print gains option to append to existing file.umx_print gains option to make tables sort-able.umx_print gains option to output content in "both" md and html.umx_print supports report to html.umx_rename now uses "from=, to=" format for renaming columns.umx_rename was using old/replace instead of from/to (and so generating a polite note).umx_residualize now prints the betas (and CIs) of the residualization it performs.umx_score_scale checks input rangesumx_score_scale tell user what the max response is for reversed items if they leave this blank.umx_score_scale Warns user if there are NAs when "score" is totals.umx_rename_file: Perl mode is TRUE (allows lookahead/behind features; default list pattern is NULL.umx_rename_file now ignores file suffix by default.umx_rot can NA the last value.umx_var upgrades input to df (e.g. if you feed it a column, it now works).xmu_data_missing can hint= to user which dataset had missingness.xmu_make_mxData handles dropping rows, alerting about variance ratios.xmu_make_mxData now handles cov matrix input (added numObs parameter).umxACE improved tutorial, more tips * IMPROVED plot for umxACE now prints model name on the diagram.umxACE covariate examplesumx_explode_twin_names links for find-abilityumxACE residualize examples matchumxRenameMatrix wrap up the multiple lines of code needed to modify a matrix in OpenMx.umx_str_chars return selected characters of a string.umxTwinUpgradeMeansToCovariateModel function to add def-based covariates to means in umx twin models.xmu_data_missing helper to drop rows with missing def vars or stop and alert the user to do this.xmu_extract_column to allow mxDataxmu_twin_add_WeightMatrices helper.xmuDefMean helperxmuDefBetas helperxmu_twin_upgrade_selDvs2SelVars helper.xmu_make_TwinSuperModel handles selCovsparallel::detectCores --> imxGetNumThreads (as OpenMx does).plot for umxTwinMaker models!!xmu_path2twin twin model helper for umxPath usersxmu_path_regex helper for making twin models for umxPath usersumx_file_load_pseudo to load and process non-transmitted genome files for the method we developed in Bates, ... Gillespie, N. A. (2018). The Nature of Nurture: Using a Virtual-Parent Design to Test Parenting Effects on Children's Educational Attainment in Genotyped Families. Twin Res Hum Genet, 21(2), 73-83. doi:10.1017/thg.2018.11xmu_data_missing helper to drop rows with missing def vars or stop and alert the user to do thisxmu_make_TwinSuperModel handles selCovsumxFitIndices Many new indices! @bwiernikumxPath(v.m0 = ) now uses values (if provided) to set starts for varianceumx_check_parallel use all cores (instead of half) by defaultumxPlotACE variable labels (trimmed off _T1 like umxPlotCP doesumxDoCp bound e/es above zeroumxDoCp start with all variance as specificpower.ACE.testumxLabel 100x speedup for RAM and Matrix model labeling!xmuLabel_RAM_Model 100x speedupxmu_safe_run_summary has smarter default for std (model summary default)xmu_dot_mat2dot now accepts algebra input begin umxPlot for DoCumx_check handles ... items betterxmu_make_mxData handles dropping rows, alerting about variance ratiospower.ACE.test no longer fails when estimating power at a fixed numxSummary: Improve Rd fileumxACE covariate examplesumx_explode_twin_names links for find-abilityumxDoc example but summary and plot TODOumxRAM2Lav export umx to lavaanxmu_safe_run_summary has smarter default for std (model summary default)umx_score_scale: implemented score = "mean" and score = "max"umx_score_scale: better documentationumxGxE gains dzAr and dzCr control so ADE is possible as well as assortative matingxmu_twin_check works with mxData * IMPROVED: xmu_twin_starts works with mxDataxmu_make_top_twin works with mxDataxmu_twin_check support mxData (was just data.frame input)umx_long_2_wide: gains some notes on processing TWINID into famID and twinIDumxSummary handles std=NULL as documented (don't show parameter table)umx_nice_data --> umx_make_twin_data_nice with future improvements planned to cope with non numeric twin schemes.umx_is_ordered was broken by previous fix to support the un-tidyverse mucking with dataframes... Now fixedumxRAM supports multi-group via `group = "column"umx_score_scale now works with binary (0-1) itemsumx_time gains "lap" (report elapsed time without restarting timer)umx_time behavior with no input - now prints the current time and dateumxFactorScores can now return SEsumxFactorScores allows abbreviated type namesumx_reorder can operate without verifying data (ignore precision digits in triangles of cov matrices)residuals can re-order variables for ease of checking patterns of residualsumxPath(defn= Definition vars now auto-named if labels not given closes #107umxACEv uses default name "ADEv" (instead of "ACEv") if user sets dzCr = .25umxAPA only uses italic Beta when std = TRUEumxRAM now respects umx_set_silentumxRAM2Ordinal to xmuRAM2Ordinalumx_fix_latents and umx_fix_first_loadings to encourage user to be more explicit in their modeling.August 2019 R 3.6.1 "Action of the Toes"
This release has major new features in beta including support for lavaan syntax, AND a over 80 additional improvements clean-out/cleanup of old functions and parameters that impede getting learning and using umx: Think of it like ggplot2 version 2.
ALPHA: umxRAM lavaan string syntax support!
ALPHA: umxRAM multi-group models with group="column"!
BETA: power.ACE.test and examples. (beta)
BETA: umxPower and examples (beta).
BETA: umxRotate Rotate the factor loadings in umxCP models.
NEW: umxCP and umxIP can take data and create MZ and DZ datasets.
NEW: deg2rad rad2deg utility functions
NEW: FishersMethod To combine p-values.
NEW: oddsratio.
NEW: SE_from_p helper to get SE from b and p, or get a p from CI.
NEW: umxMendelianRandomization alias to umxTwoStage.
NEW: umx_nice_data converts your twinData to the standard format (zyg = zygosity, "_T1" , "_T2" suffixing of twin variable names).
NEW: umx_select_valid to replace values in one column with those in another, if first column is NA.
NEW: umx_set_silent preference (option) for other functions to listen too and choose how much junk to print to console. Like a global verbose.
NEW: xmu_safe_run_summary can listen to silent to turn off summary and progress from models - use when running big simulation loops.
IMPROVED: namez has a better default action (call names )
IMPROVED: oddsratio teaches about limitations; supports odds-format as input (closes #102)
IMPROVED: plot can do pathLabels = "labels" to show the labels for paths
IMPROVED: plot for umxIP supports means=TRUE
IMPROVED: power.ACE.test now reports searches with fixed n nicely
IMPROVED: umxAPA now returns its output, rather than printing it. makes for easier consumption in programmatic uses.
IMPROVED: umxAPA supports cor.test and t.test
IMPROVED: umxConfint uses smart confidence intervals (just the free standardized parameters) for umxCP models.
IMPROVED: umxEFA can suppress printing when umx_set_silent(TRUE) #103
IMPROVED: umxEFA now has an option about reporting the summary fit statistics of a model (default is FALSE) see #103
IMPROVED: umxGxE removed border from legend (obscures plot to no benefit)
IMPROVED: umxGxE supports digits (rounding for tables)
IMPROVED: umxlav2RAM catch means
IMPROVED: umxPlotCP can show (non-zero) fixed paths closes #97
IMPROVED: umxReduce.GxE Don't try and drop means moderation.
IMPROVED: umxReduceGxE gains a tryHard option
IMPROVED: umxReduceGxE more rational set of reductions - means obey principle of marginality.
IMPROVED: umxSummaryGxE prints parameter table and SEs as well as the interaction plot.
IMPROVED: umx_cor quieter, more informative
IMPROVED: umx_is_class robust to being given a tibble (closes #101 Might need to re-open if there are more cases of where toggling drop from TRUE to FALSE interferes with data types)
IMPROVED: umx_make_raw_from_cov can add names to generated data
IMPROVED: umx_make_TwinData bivariate parameters (e.g., aMod) --> bivAmod for more clarity (closes #78)
IMPROVED: umx_make_TwinData can now simulate D i.e., A, C, D & E
IMPROVED: umx_make_TwinData More robust
IMPROVED: umx_move_file supports wildcards (closes #83)
IMPROVED: umx_rename examples
IMPROVED: umx_rename reorder parameters, call x-> data, deprecate grep in favor of regex for consistency,
IMPROVED: umx_scale_wide_data gains twins parameter
IMPROVED: umx_set_data_variance_check: set default minvar to .1
IMPROVED: umx_set_silent returns old value
IMPROVED: umx_var robustness + support ordinal variables.
IMPROVED: xmu_dot_move_ranks set min, max or same to "" to take these ranks out of the diagram - Aids tricky layouts. (closes #84)
IMPROVED: xmu_make_mxData drop duplicates from manifests list
IMPROVED: xmu_make_mxData handles manipulating a 1-column mxData input
IMPROVED: xmu_safe_run_summary supports digits (rounding for tables)
CHANGED: power.ACE.test now uses semantic labels ("a", "c" ) and can test a dropped after c. Better feedback for boundDiag
CHANGED: umx_show -> tmx_show.
CHANGED: umx_set_optimization_options to umx_set_mvn_optimization_options for user clarity.
CHANGED: umx_default_option to xmu_match.arg as programming aids are moved into xmu space.
CHANGE: umx_aggregate now uses df as default data.
CHANGED: showEstimates -> show across all functions: makes learning/usage more consistent.
CHANGED: umxGetParameters doesn't anchor search strings to front of label, nor suffix with digit label.
DROPPED: umx_drop_ok - orphan function - just use umxCompare
DROPPED: umxEval - broken anyway - just use mxEval
FIX: mxPath v0m0 , v.m0 now use labels (if two provided)
FIXED: umxACE standardizes model in summary
DEPRECATED: The parameter to show standardized parameters is universally std=TRUE (show = no longer works).
REMOVE: umxIPold
NAMESPACE clean up to make it easier for users to focus on functions they (rather than devs) will use
HELP: @md links
HELP plot Better explanation of graphing: can still be improved
HELP umx_as_numeric:better examples
HELP: umxMendelianRandomization nice figure
HELP: NEWS layout improved for R 3.6.0
HELP: Rd doi link, spell-check,
HELP: umxEFA notes it can use formulas, e.g. umxEFA(~v1+v2+v3, data)
HELP: NEWS updated
HELP: GxEbiv Improved help page
HELP: umxPower gains text and a nice figure
plot splines = T|F and min= , max = same= controls to layout your graphs!umxLav2RAM: detect ngroup, and a umxSuperModel of groups.plot.MxRAMModel plots multiple groups (on separate pages)!plot gains control of object clustering with max min and same.plot select whether to allow splines with spline=T\Fplot opt paths out of layout constraints!plot now labels plots with the group name.umx_time Handles stop without prior start. New now option returns current date.uxmSummary the annoying "umxSummary not defined" error should be fixed!umxSimplexumxLav2RAM: multiple group example in help.umx_set_separator allows Europeans to use ; in place of comma.xmu_lavaan_process_groupxmu_clean_labelxmu_name_from_lavaan_str helpercitation("umx") Our paper on umx is out!
?umxExamples to see the example code from Bates, Neale and Maes (2019).umxSexLim multivariate sex-limitation working.umxSexLim Gained nonlinear, linear, and homogeneity modesumxSexLim Gained examples.umxRAM supports WLS, UWLS, DWLS models!umxACE supports WLS, UWLS, DWLS models!umxPlotCP Supports CIs on the diagram!umx_make_top_twin_models increases the robustness and improve-ability of all twin scripts.xmu_dot_define_shapes builds the latents and manifest shape definitions (should be xmu_)xmu_check_variance checks data for minVar (default > 0.1) and comparable scale for variables (maxVarRatio default = 500)
umx_set_data_variance_check get/set variance tolerance.umx is checked on travisplot allows user control over splines, as well as max, min, same positioning.xmu_dot_move_ranks.xmu_dot_rank_string.namez options for collapse get easier to short-cut names.data(Fischbein_wt) weight of 66 females record over six 6-month intervals (from Fischbein (1977) weight data).umxRAM2 Beginning support for lavaan syntax strings.type (WLS) added to twin models...umxValues to work more reliably with data with no means.umx_rename Didn't give correct values when test = TRUE for non-grep searches (drop NAs)umxSexLim match.arg tryHardselVars vs. selDVs across different functions (search for "# New-style build-block" to see these changesumxSuperModel can take a list of models.tryHard - allow "yes" for default mxTryHard across all twin and RAM models.umxPlotCP revamped - now not dependent on labels! (old function now umxPlotCPold)xmu_model_needs_meansumxDescribeDataWLS to check whether the form of WLS requested will have means of not.umx_make: use check_win_devel; set working director for release; spelling checkxmu_dot_mat2dot add model, toLabel and fromLabel + fromType & toTypexmu_dot_mat2dot examplexmu_safe_run_summary now copes with warnings in models, summary, compare etc. (as it should have)umxModify now supports find and replace labels with grep (not just find with grep and set free/value)xmu_assemble_twin_supermodel no longer take bVector (uses existence of weights instead)umxModify now obeys verbose optionumx_time reports % change between model timesumIP helpumx_make now supports quick-make as defaulttmx_show printing.umx_score_scale help and examples.umxModify now supports find and replace labels with grep (not just find with grep and set free/value).umxModify now obeys verbose.umxValues and elsewhere more robust to new data types.umx_read_lower examples and input checking.xmu_cell_is_on now has lower and upper triangle with or without diagonal includedxmu_dot_mat2dot now can get parameter values with CIsumxRAM feedback when no data providedxmu_make_top_twin lose "models" for shorter name.tmx_show (was umx_show - it is mostly a teaching functionxmu_dot_define_shapesxmu_dot_rankumx_mat2dot --> xmu_dot_mat2dotumx_APA_model_CI --> xmu_get_CIumx_add_variances old function not used and not very safe.thresholds option from several functions (always doing deviation-based, WLS isn't thresholds, and left-censored will be implemented differently)umxSummarizeTwinData to create summary tables for papers using twin Data.umxRAM: support definition variables to some extent in umxRAM.umxMatrix advice user when they specify umxMatrix("me", 1,1).umxModify nicer free-parameter report as default output with no changes requested (calls parameters).umxRAM preserve definition variables in data.plot strip_zero more reliable.plot dropped deprecated showMeans and showFixed from plot after 3 years (use means= and fixed = ).umx_scale_wide_twin_data dropped support for deprecated suffix parameter.suffix as a synonym for sep removed after 3-years of deprecation warnings.umxSummaryfor ACEv models: CI now works - (was 'a' not 'A').xmu_safe_run_summary Runs a model safely, optionally summarizing and comparing it to a base model.tryHard as a parameter!!autoRun option in more places.plot functions now have strip_zero option (default = strip leading zeroes from parameter estimates)umx_standardize_ACEv now working!xmu_safe_run_summary so even bad models are returned for the user to diagnose them.umxRAM now labels paths when no data are provided (simulation of sketch modes).umx_score_scale can cope with a single item.xmu_safe_run_summary don't error on code red non-run models.xmu_twin_check tells user how to rename selVars and sep when sep is not provided, but is enforced.umx_as_numeric allows user to select which columns to convert.umxSimplex start values now flexible and robust (was hard coded for 4-times).xmu_simplex_corner Takes a full values list (not just 1).umxAPA uses .Last.value as default input if none provided.umx_make supports what = "rhub".umxlong2wide now allows user to retain only desired twin IDs.xmu_mean_var_starts uses "expMean_" as the name for means cells (was "mean").xmu_safe_run_summary don't return bVector (already available)umxACE help diagrams improved with clearer ACE_matrix picture.umxRAM help gained an example of sketch-mode and diagram.umx_scale help file improvedxmu_make_mxData function to make mxData functions out of dataframes (and also drop variables from cov/cor dataframes.plots.umxCompare gains ability to output Weight AIC conditional model probabilities! h/t @mNivardumxReduce returns AIC weight-based probability of being best model.umxReduce.MxModelGxE returns best model (invisibly).umxReduce for GxE, don't run no-A and no-C models with moderation in place.namez given a list of models will return the names of each.namez allow global replace.umx_lower2full can now take a data.frame.umx_aggregate can now open tables in a web browser.install.OpenMx can now install a package file if selected in the Finder (MacOS only)install.OpenMx now works with windows.umx_print more robust to non table input.xmu_make_mxdata more robust to non dataframe input.umx_apply robustness.umx_simplex_corner can take a numeric to set matrix size.umx_long2wide warn if twinID (order) has too many levels; improved help; @mdumxAPA test parameter had no effect.umxSexLim now works for univariate tests (thanks to Michael Zakharin for reporting!)umxSummary Corrected Chi^2 df for RAM models.umxCP handles ordinal, continuous and binary data
umxCPoldumxCPplot re-written to allow arbitrary labels and correlated factors.umx_set_optimization_options function to set "mvnRelEps" tolerances which impact, especially, ordinal model.umx_is_class reports classes if not given a set of classes to checkumx_scale(verbose=TRUE) now lists the vars it didn't touch as well as those it didn't (also formatted better)umx_make_TwinData can set mean and SD of dataumx_simplex_corner can take a numeric to set matrix sizeumx_standardize_CP was ignoring existing CIsumxAlgebra This appears broken in some circumstances?umx_polychoric, umx_polypairwise, and umx_polytriowiseumxSimplextwin model!
umxSummary for simplexiqdatlongitudinal IQ twin data for simplex modelingnamez alias for the ever-useful umx_names function.umxAlgebra (just allows name first).install.OpenMx URLs for NPSOL and travis builds of OpenMxumxSummary.MxModel.ACE instead of umxSummary.umxSummary.MxModelACE # i.e. delete the last period in the name... Sorry :-(parameters now returns helpful near-match names as suggestions on not finding actual matches.parameters now handles vectors of regular selectionsumx_print now handles vectors.umxConfint "smart" feature to request only free algebra cells for models I understand (umxCP in the first instance)namez can handle a model summary (accesses names() of the summary)umxGxE added option to control plot colorsumxPlotCP can handle >9 manifests issueumxGxE example improvedxmu_simplex_corner helper function for simplex modeling.umx_make_sql improvedumxIP nFac now allows specifying different numbers of a, c, and e factors!umxACEv plot works (shows correlated factors).umxACEv standardize mostly functional.umxEFA can now take a formula to select variables.umxIP and CP examples improved (3-variables, GFF data).umxIP reporting of as, cs, es simplified into compact stack.umxCP reporting of as, cs, es simplified into compact stack.umxPlotCP labeling of variables improved (catching more _Tn).umxEFA reports factor correlation matrix (thanks @ConorDolan)!umxEFA can return a loadings object.umx_makenot supports spelling check.umxACEv diagonal now unbounded by default (which is it's whole purpose)umxACEv got major improvements to help file.umxSummaryCP got ability to print to html.plot made more robust to unexpected labels (now that umxModify can write newlabels)!umx_names Added GFF examples.umxSummaryIP was assuming nFac = 1umxSummary works with multi-group models!
umxSuperModel)umxModify supports multiple find strings and replace strings!umxAPA supports glm, more robust input checking.umxEquate allows vectors of labels.umxGetParameters has better help.umxHetCor docs now note is will return a pos-def version if given a cov matrix.umxAPA now has t-test and glm examplesumx_install_OpenMx (use install.OpenMx)umxSexLim multivariate twin sex-limitation.umxGxE_biv bivariate Gene-environment interaction model.umx_make_TwinData Can now make bivariate moderated twin data.umxGroup function as part of measurement invariance support.umx_stack Slightly more powerful version of base stack.umx_array_shift Shifts an item off the beginning of a list.umxRAM can take lists of paths as input (contributed by @bwiernik).umxModify can write newlabels.umxAPA can back-out an SE if given b and CI.umxReRun (use umxModify)suffix parameter (use sep instead)umx_parameters(model, "below", .1)tmx_genotypic_effect Part of a suite of teaching functions for biometric genetics!?umxRAM has a sketch mode. just set data to a list of manifest variable names.umxSuperModel function to automate multiple-group model creation.?umxACEv Variance component version of ACE. (beta)?umxACEcov_fixed Beta1: Handles main effects of covariates in the means of continuous variables.umxModify can now equate parameters (set master = ), update is slave set of labels.
optimiser parameter for umxACE and other twin models: Set the optimizer in your model code!umx_is_numeric boolean check if variables in a dataframe are numeric.umx_is_class boolean check if variables in a dataframe match a desired class.umx_twin_check internal function for common input checks.umx_set_plot_file_suffix(c("gv", "dot") function (to control the filename used for figures)/umxACE was broken with large cov inputs h/t @NathanGillespie.umxAggregate now actually supports user functions as input...umxACEv variance components methodumxPath(Cholesky = ) method: supports labels, bounds, lbound at 0.umxPath(Cholesky = ) method: return one statement instead of a list for clarity.umxACE and umxReduce.ACE run intervalsumxReduce works better with umxACE models.umxEFA Supports minManifests.umxEFA Works better when returning a single factor score.umxParameters now supports digits.umxSummary "inline" reporting now includes AIC.umx_aggregate works with factor input/
umx_aggregate(sex_T1 ~ zyg_2grp, data = x)umx_long2wide can passalong variables.umx_wide2long much more powerfulumx_msg supports dataframesumxACE gains ability to set plot format: format = "graphviz" or "DiagrammeR"umx_set_auto_plot take TRUE/FALSE as input.umx_names: added a find and replace option for namesumxRAM in "sketch mode" now plots models automatically.install.OpenMx from University of Virginia, travis, or open travis build page.umx_cor automatically drops non-numeric columns.umxCI now supports setting interval and one- or two-sided type (h/t @Conor Dolan).R2HTML to xtableumxParameters now supports non-run models?umxAPA can format lots of things for you: from dataframes to p-values - try it out! Let me know what you'd like.?umx_parameters function, report parameter estimates, filtering by name and value!
umxParametersumx_parameters(model, "below", .1, "loading")?umx_long2wide: Merges long data on famID, for an unlimited number of individuals in a family (twinIDs).?umx_wide2long: Takes a wide df (currently limited to 2 per family), & returns a long-format version.umx_MakeTwinData.xtable (R2HTML is abandoned, strips decimals from AIC, etc.)umx_set_auto_plot(FALSE).forEach option in umxPath. This is a one.headed version of "unique.pairs".autoRun.umxGxE plot colors now use the universal ACE -> RGB scheme.umxACEcov Now tries to detect violations: Age and Sex are good examples.umxACE.umxACEcov!umxACEcov;umx_check_parallel (1 and n-1);umx_check_parallelumxReduce does a much better job reporting automated umxGxE model reduction.umxAPA handles lme models.umxPrint error messages.logic.MxModel now has an Rd page.confint. OpenMx now supports this, so I dropped it from umx (added alias to umxConfint).anova. OpenMx now supports, this so I dropped it from umx.umx_fix_first_loadings now skips latents with fixed variance.umxVersion (returns mxVersion + information on umx).umxACE start values much better for univariate models.umx_make_TwinData
varNamenThresh to threshold the created variables, and return as mxFactorsempirical parameter of mvrnormnDZPairs to get equal numbersumx_make_TwinData uses variance input. This was ambiguous previously.install.OpenMx can install UVA parallel, travis latest (on mac) or opening the travis list.
install.OpenMx had a broken URL, now corrected.umxRAM can now be used in "sketch" mode, to plot demos without data: just add the list of manifests as a character string to data.
m1 <- umxRAM("test", data = paste0("itemC", 1:4),
umxPath(unique.bivariate = paste0("itemC", 1:4)),
umxPath(var="X")
)
plot(m1)
umx_cont_2_quantiles now allows returning cut points, better examples, level_names
umx_cont_2_quantiles lowest threshold was emptyumxAPA now reports mode for factor dataumxLabel to rename the returned modelsep is now the preferred separator (synonym for suffix in umxACE, umxCP, umxIP)umxPath docsumx_cov_diag to umx_varumx_write_to_clipboardumx_r_testumxCP example for improved compatibility with OpenMx 2.7umxPathconfint()umxAPA table outputumx_makeumxPath(a, forms= , arrows = 2) bugumxRAM returns invisiblyumx_aggregate can summarize multiple DVs in a tableumx_aggregate can return a formatted table (kable = TRUE)umxAPA returns lower-triangle of data.frame correlations (by default)umxSE now included in OpenMx 2.7.0!umx_set_plot_format uses silent = TRUE internally where neededumx_make_TwinData fix bug in DZ moderator code and A+C computationumx_set functions now show legal options by defaultumx_set functions have silent optionumxFitIndices RMR and SRMR (h/t Brenton Wiernik!)umxMatrix with default labels and name as 1st parameterumxPath(defn = "def", labels = "data.age")umxEquate supports autoRun and compareumx_names can, as a convenience, take string vectorsumxGetOpenMx aliased to install.OpenMx or umx_install_OpenMxumxFitIndices additional fit-indices and now automatically computes reference models if needed.umxRAM remove_unused_manifests no longer updates manifestVars + leaves variable in data by default.plot "showFixed" deprecated in favor of easier to type "fixed"umxPath allows unique.pairs connectionumxRAM handles suffix labels
umxSummary to show parameters from first model in multi-group
umx_show_options to umx_get_options
umx_check_parallel typoplot calls from summaryumxRAM can now build and run Joint Continuous Ordinal models!!umx_show_options function to help users learn the options availableumxACE can now implement a form of left-censoring.umxThresholdMatrix can now implement a form of left-censoring.umxRAM & umxRAM2Ordinal can turn off reference models computation with refModels = FALSE;umx_show can show thresholdsumx_is_MxModel can take a list: listOK optionumx_check_parallel options for row-wise parallel and number of subjectsumx_time and umx_check_parallel to work with new S4 list deprecationumxTwoStage shorter run-time on 2-stage least squaresumxTwoStage FIML-based Instrumental variable and Mendelian Randomization (beta)umx_make_MR_data to simulate SNP-based Mendelian randomization data (beta)umx_set_condensed_slots(TRUE|FALSE): Get and set matrix compressionumx_get_OpenMx (download OpenMP/parallel version of OpenMx with NPSOL)umx_cont_2_quantiles(x, nlevels = )umx_factor alias to umxFactorplot(resid = "none") was not suppressing plotting residualsumxFactor now handles dataframes and allows non-ordered outputumx_CI more flexible, now allows removing CIs
umx_time handling of no input argumentsumx_pb_note better feedback and setupumxModify - if free is a string, it will be used as input and the found paths will be freed.umxModify - show summary as well when comparison = TRUEplot defaults for std and showFixed changed h/t @MikeNealeumx_scale_wide_twin_data argument names for consistency: "suffix" "data"umx_residualize ditto.umxStandardizeACEplot using DiagrammeR!umx_set_plot_format("DiagrammeR")umx_set_plot_format("graphviz")umx_set_table_format("markdown")umx_set_table_format("latex")umx_set_auto_plot(TRUE)umxEFA (beta!)loadings() support for umxEFAumx_print, umx_show, umxCompareplot now works on Windows and Unix as well as OS X! (h/t @mhunter)umxReRun to umxModify (h/t @hmaes)plot should generate pdfs for Windows and Unix users nowumxACEcov support for ACE with covariatesumx_make_TwinData added to support simulation studiesumx_check_parallel now returns timing informationumx_time now supports "start" and "stop")umxAPA can format more objects in APA style, inc just a p-value)summaryAPA can now summarize a data.frame with mean, sd, and correlationsumxLabel now preserves existing labels in umxRAM models: labels = is now savedvcov() addedumxRAM can take existing model as input (very useful)umxRAM reports model fit and comparison (if old model exists)umxPath now lbounds var@0 for v.m.umx_residualize can now take multiple DVsumxMI enhanced to cope with more situationsumxSummary more resilient with missing CIs (#ht Nathan Gillespie!)summaryAPA now handles data as well as lmumx_print resilient to 0-row inputumx_fun_mean_sd)umxCP twin models! + plot(), umxSummary()umxIP twin models! + plot(), umxSummary()umxGxE twin models! + plot(), umxSummary()umxPath limitation where "to" was not being set.umx_lower2fullconfint(); plot() etc functions implemented