NEWS.md

In tbates/umx: Structural Equation Modeling and Twin Modeling in R

dev

umx 4.20.00

• April 2024 R 4.4.3
• NEW: umxRAM Can include definition variables h/t @lf-araujo
• HELP: umxRAM example a model with a def var on means
• IMPROVED: umxMR can standardize manifests.
• IMPROVED: prolific_read_demog outputs a ready to paste demographics string.
• IMPROVED: prolific_anonymize can delete more columns.
• IMPROVED: various messages, and help improvements.
• FIXED: umxReduce.ACE now aware of umx_set_auto_run #241 @lf-araujo

umx 4.19.00

• November 2023 R 4.3.1 (2023-06-16)
• FIXED: encode unicode beta in an expression instead of using uXXXX
• IMPROVED: Move DiagrammeRsvg rsvg to Enhances
• FIXED: umxMatrixFree undocumented argument 'byrow'
• FIXED: umxMRDoC sketch mode fixed

umx 4.17.00

• Sept 2023 R 4.3.1 (2023-09-15)
• NEW: fin_ticker open a stock in the browser.
• IMPROVED: umxTwinMaker can manage definition variables (by @lf-araujo)
• IMPROVED: umxSummary suppress duplicate paths
• FIXED: umxGxE_window handles target range without error once more (h/t Marla Kürten)
• FIXED: umxMRDoC byrow misspelling

umx 4.16.00

• August 2023 R 4.3.1 (2023-06-16)
• NEW: umxMRDoC Direction of causation with twins! (by @lf-araujo)
• NEW: umxMatrixFree to help in simulations (by @lf-araujo)
• NEW: prolific_anonymize() remove IDs and other identifying columns: Ideal when sharing data.
• NEW: ggAddR helper to add R/beta to a graph
• NEW umx_strings2numeric helper function to recode strings to numbers
• IMPROVED: RMSEA()
• IMPROVED: umxAPA gains cols to allow input checking in place of Rs…
• IMPROVED: umx_strings2numeric example, handle 1 col df
• IMPROVED: prolific_read_demog handle "DATA_EXPIRED"
• IMPROVED: umx_score_scale reliability works with correctAnswers
• IMPROVED: umx_is_numeric works with tibble input h/t @psychelzh
• IMPROVED: libs can for package update using force.update = TRUE
• IMPROVED: umxAPA cor/means output data.frame input
• FIXED: umxModify works with new R null behavior
• FIXED: umxAPA (and others) report = "html" works properly.
• REFS: umx_score_scale omega refs
• RENAME: umx_read_prolific_demog -> prolific_read_demog

umx 4.15.1

• Nov 2022 R 4.2.1
• NEW: umx_merge_randomized_columns wide-2-mingled (rather than wide2long) to unify data from people assigned to different conditions.
• NEW: umxDiscTwin Discordant twin test for causal effects.
• NEW: umxDiscTwin Graphical output for publication.
• NEW: umxPlot ease customized/journal-close, e.g. y~x, -> x y plot, with r^2.
• IMPROVED: umxAPA t-test reporting.
• IMPROVED: umx_score_scale gains error and proportion.
• IMPROVED: umx_score_scale report only omega total when 1 factor extracted.
• IMPROVED: umx_read_prolific_demog gains functionality.
• IMPROVED: umxMR: gained `tryHard'
• IMPROVED: umxGxEwindow: gained tryHard, smarter print control.
• IMPROVED: umxGxEwindow: removes un-needed columns.
• IMPROVED: umxGxE checks that selDefs are numeric (closes #196, h/t @salvatoj)
• IMPROVED: umxRun: gained summary control.
• IMPROVED: umx_read_prolific_demog more control, better defaults, and more reliable summary table.
• IMPROVED: umx_score_scale cleaner output for 1 factor case with omega.
• FIXED: xmu_twin_print_means now takes >1 covariate h/t @Eren Kafadar #201
• FIXED: xmu_safe_run_summary now takes refModels = FALSE h/t @lf-araujo #200
• FIXED: umxACEcov plot and summary working (needed to filter covs from DVs).
• FIXED: xmu_twin_print_means handles more than 1 covariate and improves labeling.
• FIXED: umx_score_scale handles NA correctly.
• SAFE CODING: umxPath stops when v*m* is used with firstAt or fixedAt.
• SAFE CODING: umxAlgebra warns that it isn't functional.
• MINOR: umx_print call fixed where was being called with file.
• HELP: umxCP help .svg figure instead of `.png`` (smaller).
• HELP: umxMR Remove unsupported 'weights' parameter.
• ADMIN: copyright, tests, Rd improvements.

umx 4.10.50

• December 2021 R 4.1.1 (2021/11/30)
• IMPROVED: umxDoC can take data (#ht @lf-araujo )
• IMPROVED: umxDoC plot Rd figure includes specifics.
• IMPROVED: umxPower search plot with fixed N has effect size on the x axis.
• IMPROVED: umxGxE plot legend location works for ggplot.
• IMPROVED: umx_score_scale gains omega reliability.
• IMPROVED: CI printing more robust (e.g. when they fail).
• BUG: umx_score_scale bug in handling new mapstrings.
• FIXED: umxDoC plot.
• FIXED: omxLocateParameters call was breaking umxSummary.
• FIXED: xmu_safe_run_summary supports intervals parameter.
• FIXED: umxSummary works with umxSuperModel now that paths have types.
• FIXED: umx_make_twinData works with custom names
• FIXED: umx_make_twinData no longer shifts means now that mean and sd parameters are available.
• NEW: helpers to umxGetModel, umxGetLatents, and `umxGetManifests

umx 4.10.10

• November 2021 R 4.1.1 (2021/11/30)
• NEW: umxPower can plot power search space! (beta!)
• NEW: noNAs() helper returning complete rows of a data.frame.
• NEW: umxThresholdMatrix can handle one value columns
• IMPROVED: umxPath gains v0m.
• IMPROVED: umxPower parameters ==1 for power search with fixed n
• IMPROVED: umxPower ref
• IMPROVED: power.ACE.test can run ADE model
• IMPROVED: power.ACE.test Clarify which of power, effect, and n are fixed or being estimated.
• IMPROVED: umxReduce.ACE gains tryHard (compute ACE/ADE/CE/AE, outputs a table an also AIC-based probability weights for which is the preferable model)
• IMPROVED: umxReduce tests familiality (E model)
• IMPROVED: umxReduce(ACE) includes the parameters of the reduced models. #ht @nick martin
• IMPROVED: umxSummarizeTwinData takes an age column and notes when it can’t be found
• IMPROVED: umx_score_scale can score items with character labels
• IMPROVED: umx_score_scale gains the ability to report Cronbach alpha
• CHANGED: umx_score_scale changed default na.rm = TRUE.
• IMPROVED: umxAPA gains OR output for logit models
• IMPROVED: tmx_show handles matrices
• IMPROVED: umx_rename better names for deprecated parameters
• IMPROVED: umxRun has tryHard (not a very useful function)
• IMPROVED: umxCompare can silently return a data.frame for further modification
• IMPROVED: umxCP warning to not use correlatedACE
• IMPROVED: umxAPA (invisibly) returns the standardized model for lm
• IMPROVED: bucks more control for formatting money
• IMPROVED: libs now install.packages() if not found
• IMPROVED: umx_make_TwinData shifts data to be positive if it not being scaled
• IMPROVED: grViz() in place of print(DiagrammR())` (should work better with knitr)
• CHANGE: fin_interest more memo/type-able parameter name for inflation
• CHANGE: umxRun defaults to tryHard= "yes"
• FIX: umxPower supports multiple path drop.
• HELP: FishersMethod Rd ref
• HELP: umxCP ref Martin, N. G., & Eaves, L. J. (1977). The Genetical Analysis of Covariance Structure. Heredity, 38, 79-95.
• HELP: deg2rad Rd better in html
• HELP: umxRAM sketch mode help
• HELP: umxCP more refs for Rd
• HELP: improvements

Releases

umx 4.9.0

• July 2021 R 4.1.0 (2021-06-27)
• NEW: umxACEv and umxACE work with nSib = 3!
• BETA: umxCP correlatedACE was not being filtered out of the expectation #hat-tip @micanzach But still working on what the right choices are here...
• CHANGED: umxCP defaults to tryHard = "yes"
• REMOVED: umxRAM deprecated parameter show after 4 years deprecation
• FIXED: tmx_show works for M matrix, closed #163
• FIXED: kable and kbl get format passed in at all calls
• IMPROVED: umx_make_TwinData supports nSib > 2 for MZ/DZr mode
• IMPROVED: umxAPA more use of cat to print (easier to read and copy)
• IMPROVED: umx_open_CRAN_page printing if installed version if found
• IMPROVED: umxAPA more use of cat to print (easier to read and copy)
• IMPROVED: fin_interest compute effective interest
• IMPROVED: xmuTwinSuper_NoBinary update for nSib > 2
• MINOR: kable formats (pandoc "pipe" and "simple" added, "pandoc" removed)
• MINOR: add_footnote in place of footnote...
• HELP: umxPath and umxRAM help
• HELP: better organization of functions/families
• xmu: xmuTwinUpgradeMeansToCovariateModel can handle nSib=3
• xmu: xmu_twin_make_def_means_mats_and_alg helper
• xmu: xmu_start improved closes #158

umx 4.8.0

• June 2021 R 4.1.0 (2021-06-01)
• NEW: umxPlot now detects and plots Pearson-Aitken selection paths (solid red headless).
• NEW: umxPlotFun plot functions without hassles. e.g umxPlotFun("sin(x)")
• NEW: umxModelNames to get model and submodel names from a model.
• NEW: libs as a short cut for multiple library() calls
• e.g. libs("x", "y", c("a", "b"))
• NEW: fin_valuation uses revenue, margin, expenses and PE to compute a market cap.
• IMPROVED: fin_interest shorter parameter name dinflate and other improvements.
• IMPROVED: umxACEv Tables now include markdown-compatible table captions.
• IMPROVED: umxAPA reports R^2 for lm (in addition to beta & CI[] for each parameter)
• IMPROVED: umxSummary sorts RAM parameters by type (factor loading etc.) and can filter means and residuals for ease of use.
• IMPROVED: umxSummary gives desired levels for good TLI and RMSEA.
• IMPROVED: umxSuperModel checks for duplicate names in incoming model names and makes them unique.
• IMPROVED: umxCompare Maintain compatibility with new OpenMx changes to mxCompare (esp. for WLS).
• IMPROVED: umx_read_lower accept names for lower diag.
• IMPROVED: umxCP correlatedACE leaves the covariances fixed@0.
• IMPROVED: umxACE added A_std closes #151
• IMPROVED: umxAPA pretty printing.
• IMPROVED: umxPlotFun check for character input.
• NEW: xmu_summary_RAM_group_parameters sort and filter RAM model parameters for ease of understanding.
• MINOR: umxFactor now used in all examples involving factor making.

umx 4.3.0

• January 2021 R 4.0.3 (2020-10-10)
• NEW plot can output to pdf, png, svg!
• NEW umx_set_plot_format adds pdf, png, svg plot output (in addition to DiagrammeR and graphviz)
• NEW: umx_lower.tri helper to get lower.tri values in 1 call
• NEW: umx_set_plot_use_hrbrthemes control
• NEW: plot.percent plot support for percent change questions
• IMPROVED: umxSummary now reports algebra values when present in RAM models closes #70
• IMPROVED: umxSummary tables have pandoc captions (see #145)
• IMPROVED: umxCompare table output and plain-English summary printing (cat)
• IMPROVED: umxCP practical workflows for correlated ACE
• IMPROVED: fin_compound_interest now outputs a table of annual returns
• IMPROVED: umxAPA uses cat to improve usability of summary data
• HELP: umxCP Document that correlatedA works on a, c and e, allowing factors to correlate.
• BETA: umxGxEbiv "lboundACE" @ 0 by default
• FIXED: umxSimplex example
• FIXED: umxGxEbiv fix nonfunctional lboundACE and lboundM (thanks @mcneale)
• FIXED: umxGxEbiv selVars order was imposed on expectation dimnames but didn't match the cov matrix due to bespoke nature of expCov algebras...

umx 4.2.5

• December 2020 R 4.0.3 (2020-10-10)
• NEW: tmx_show display model matrices on the web, with color-coded free/false, values + roll-over labels.
• NEW: harmonic_mean with support for weights.
• HELP: harmonic_mean Example averaging speeds across distance.
• NEW: geometric_mean
• NEW: fin_compound_interest
• NEW: fin_percent
• IMPROVED: umxPlotGxE Gains CI ribbons (closes #96)
• IMPROVED: umxPlotGxE Defaults to use ggplot and now returns the graphs for further decoration (closes #139)
• IMPROVED: umxPlotGxE Can now plot user-specified moderator ranges (closes #96)
• IMPROVED: umxPlotIP Now relies on matrix cells, not their labels (closes #61)
• IMPROVED: umxACE Returns group models invisibly #134 @khusmann.
• IMPROVED: plot Now allows "ortho" "compound" and "polyline" spline control.
• IMPROVED: umx_set_optimization_options Can get and set "Parallel diagnostics"
• IMPROVED: tmx_show Smart about not printing NULL matrices.
• IMPROVED: 'umxEquateGained anewlabels` parameter for the equated paths (rather than one path adopting the label of the other)
• IMPROVED: umx_score_scale Supports minManifests for factor scores
• IMPROVED: umx_open_CRAN_page Can now install a package, as well as open the CRAN page for the package.
• IMPROVED: umx_rename_file Better feedback about matches and files checked.
• IMPROVED: umx_long2wide More resilient to zygosity column type.
• IMPROVED: umxSummarizeTwinData More resilient to name of age column
• IMPROVED: plot strip_zero option works for fixed (@) parameters
• IMPROVED: umx_is_class Handle non-df input.
• IMPROVED: umxCI: Gains regex parameter to support adding and removing CIs on labels matching a string pattern.
• IMPROVED: umx_is_class Handles non-df input.
• IMPROVED: umx_set_table_format Defaults to "markdown" on load.
• FIXED: umxPlotIP Wasn't working with threshold models (didn't ignore thresh names for plot).
• FIXED: umx_time Was using time units for model 1 for all models... h/t @khusmann
• FIXED: umxPlotACEv Was not displaying half the variables in an MV model as NA.
• FIXED: umx_set_cores No longer use imxGetNumThreads which is hard-coded to not report number of threads.
• FIXED: Check for more than one named CI requested (closes #136).
• FIXED: tmx_show Has html_font parameter in help.
• WORKAROUND: 'umxSummaryCatchesmxRefModels` error for WLS models and politely informs user OpenMx doesn't support fit stats for WLS yet.
• BACKWARD: umxThresholdMatrix Changed parameter from selDVs to fullVarNames to prevent user error.
• NEW: umx_read_prolific_demog to read prolific academic demographics files.

umx 4.1.0

• July 2020 R 4.0.0
• CHANGE: umxRAM Groups in multi-group models now independent by default (label style "path_group" )
• FIXED: 'umxRAM` Group option failing to pass autoRun tryHard Merge pull request #134 @khusmann
• FIXED: umxRAM No longer demand new data if a model is given as the first parameter. Updates data if provided.
• IMPROVED: umxACE Return group models invisibly #134 @khusmann
• IMPROVED: umxACEv support for covariates enabled.
• IMPROVED: umx_score_scale gains the ability to return a factor score.
• IMPROVED: umxEFA returns scores by default when requested (used to require user to also set return = "loadings" (thanks to user!)
• IMPROVED: umx_r_test handles case of overlapping variables, i.e., compare r(ab) to r(ac)
• IMPROVED: umxPlotACE uses matrix cells, not labels to draw the plot (so now labels are arbitrary)
• IMPROVED: umxIP checks names of nFac for each of a, c, and e
• IMPROVED: umxSimplex default sep is now "_T" instead of NULL (should do this throughout?)
• IMPROVED: residuals can now suppress 0s - helpful for large tables
• IMPROVED: xmu_dot_mat2dot can cope with 1-variable name lists
• DEVELOPER umxValues -> xmuValues clean up namespace
• DEVELOPER umxLabels -> xmuLabels clean up namespace
• FIXED: parameters: std wasn't being used.
• INFO: TLI /CFI vs. RMSEA
• HELP: umxEFA examples.
• HELP: umxTwinMaker.

umx 4.0.0

• May 2020 R 4.0.0
• FIXED: 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...
• FIXED: umx_long2wide now looks for zygosity in more than just twin 1 h/t @nathangillespie for catching this case.
• NEW: Covariates in twin models for ordinal and continuous manifests!
  • m1 = umxACE(selVars = "wt", selCovs= "age", sep="_T")
• NEW: umxTwinMaker: Make twin models by specifying just the within-twin paths for one twin
  • umxTwinMaker handles making twin2, variance components covariances, MZ and DZ groups, makes a umxSuperModel and runs it!
  • plot() and "std= TRUE" work for any model now!
• NEW: umxDoCp Path-based Direction of causation model.
• IMPROVED: umxSummaryACE prints a means table!
  • including for intercepts only, no means model, and intercepts + covariate betas.
  • All RAM and twin models gain this also.
• IMPROVED plot for umxACEv now prints model name on the diagram.
• IMPROVED plot for umxACE now uses tips for printing.
• IMPROVED: FishersMethod: accepts p-values for meta-analysis in "..." argument.
• IMPROVED: namez handles class(list) objects, returning $ components.
• IMPROVED: parameters supports standardizing parameters (closes #92) .
• IMPROVED: power.ACE.test now prints the parameter and value when testing power (closes #111).
• IMPROVED: umxCompare includes Delta-AIC.
• IMPROVED: umxCP plot prints model name.
• IMPROVED: umxGxE code to detect mismatched moderators
• IMPROVED: umxGxE code to include co-twin moderator in means model
• IMPROVED: umxGxE simplified algebra
• IMPROVED: umxIP gains report option.
• IMPROVED: umxIP plot prints model name.
• IMPROVED: umxSummaryGxEbiv working, with a note that the whole function is beta. h/t @MikeNeale.
• IMPROVED: umxThresholdMatrix re-implemented l_u_bound - wasn't working for some time h/t @NathanGillespie.
• IMPROVED: umxThresholdMatrix supports leaving all thresholds free with method= "allFree" h/t @NathanGillespie.
• IMPROVED: umx_check_names returns TRUE when no names are entered.
• IMPROVED: umx_check can concatenate extra messages, and is by default polite with messages.
• IMPROVED: umx_check handles ... items better
• IMPROVED: umx_is_ordered can process mxData as well as df.
• IMPROVED: umx_make_TwinData has dzAr.
• IMPROVED: umx_make_twin_data_nice can turn numeric zyg column into human readable "MZMM" etc.
• IMPROVED: umx_print gains option to append to existing file.
• IMPROVED: umx_print gains option to make tables sort-able.
• IMPROVED: umx_print gains option to output content in "both" md and html.
• IMPROVED: umx_print supports report to html.
• IMPROVED: umx_rename now uses "from=, to=" format for renaming columns.
• IMPROVED: umx_rename was using old/replace instead of from/to (and so generating a polite note).
• IMPROVED: umx_residualize now prints the betas (and CIs) of the residualization it performs.
• IMPROVED: umx_score_scale checks input ranges
• IMPROVED: umx_score_scale tell user what the max response is for reversed items if they leave this blank.
• IMPROVED: umx_score_scale Warns user if there are NAs when "score" is totals.
• IMPROVED: umx_rename_file: Perl mode is TRUE (allows lookahead/behind features; default list pattern is NULL.
• IMPROVED: umx_rename_file now ignores file suffix by default.
• IMPROVED: umx_rot can NA the last value.
• IMPROVED: umx_var upgrades input to df (e.g. if you feed it a column, it now works).
• IMPROVED: xmu_data_missing can hint= to user which dataset had missingness.
• IMPROVED: xmu_make_mxData handles dropping rows, alerting about variance ratios.
• IMPROVED: xmu_make_mxData now handles cov matrix input (added numObs parameter).
• IMPROVED: better labels for output tables.
• IMPROVED: standardize on expMean as name of means matrix even when it's a local algebra.
• IMPROVED: twin Models print out means now.
• HELP: umxACE improved tutorial, more tips * IMPROVED plot for umxACE now prints model name on the diagram.
• HELP: umxACE covariate examples
• HELP: umx_explode_twin_names links for find-ability
• HELP: umxACE residualize examples match
• NEW: umxRenameMatrix wrap up the multiple lines of code needed to modify a matrix in OpenMx.
• NEW: umx_str_chars return selected characters of a string.
• NEW: umxTwinUpgradeMeansToCovariateModel function to add def-based covariates to means in umx twin models.
• NEW: xmu_data_missing helper to drop rows with missing def vars or stop and alert the user to do this.
• NEW: xmu_extract_column to allow mxData
• NEW: xmu_twin_add_WeightMatrices helper.
• NEW: xmuDefMean helper
• NEW: xmuDefBetas helper
• NEW xmu_twin_upgrade_selDvs2SelVars helper.
• NEW: xmu_make_TwinSuperModel handles selCovs
• REPLACE: parallel::detectCores --> imxGetNumThreads (as OpenMx does).

umx 3.1.0

• 13 March 2020 R 4.0.0 compatibility
• BETA: plot for umxTwinMaker models!!
• NEW: data for example with direction of causation work on umxSummary for DoC
• NEW: xmu_path2twin twin model helper for umxPath users
• NEW: xmu_path_regex helper for making twin models for umxPath users
• NEW: umx_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.2018.11
• NEW: xmu_data_missing helper to drop rows with missing def vars or stop and alert the user to do this
• NEW: xmu_make_TwinSuperModel handles selCovs
• IMPROVED: umxFitIndices Many new indices! @bwiernik
• IMPROVED: umxPath(v.m0 = ) now uses values (if provided) to set starts for variance
• IMPROVED: umx_check_parallel use all cores (instead of half) by default
• IMPROVED: umxPlotACE variable labels (trimmed off _T1 like umxPlotCP does
• IMPROVED: umxDoCp bound e/es above zero
• IMPROVED: umxDoCp start with all variance as specific
• IMPROVED: power.ACE.test
• IMPROVED: umxLabel 100x speedup for RAM and Matrix model labeling!
• IMPROVED: xmuLabel_RAM_Model 100x speedup
• IMPROVED: xmu_safe_run_summary has smarter default for std (model summary default)
• IMPROVED: xmu_dot_mat2dot now accepts algebra input begin umxPlot for DoC
• IMPROVED: umx_check handles ... items better
• IMPROVED: xmu_make_mxData handles dropping rows, alerting about variance ratios
• BUGFIX: power.ACE.test no longer fails when estimating power at a fixed n
• HELP: umxSummary: Improve Rd file
• HELP: umxACE covariate examples
• HELP: umx_explode_twin_names links for find-ability

umx 3.0.6

• Feb 2020 R 4.0.0 compatibility
• BETA: umxDoc example but summary and plot TODO
• NEW: umxRAM2Lav export umx to lavaan
• IMPROVED: xmu_safe_run_summary has smarter default for std (model summary default)
• IMPROVED: umx_score_scale: implemented score = "mean" and score = "max"
• IMPROVED: umx_score_scale: better documentation
• IMPROVED: umxGxE gains dzAr and dzCr control so ADE is possible as well as assortative mating
• IMPROVED: xmu_twin_check works with mxData * IMPROVED: xmu_twin_starts works with mxData
• IMPROVED: xmu_make_top_twin works with mxData
• IMPROVED: xmu_twin_check support mxData (was just data.frame input)
• IMPROVED: umx_long_2_wide: gains some notes on processing TWINID into famID and twinID
• REPAIR: umxSummary handles std=NULL as documented (don't show parameter table)
• RENAME: umx_nice_data --> umx_make_twin_data_nice with future improvements planned to cope with non numeric twin schemes.

umx 3.0.5

• December 2019 R 4.0.0 compatibility
• BUG FIXED: umx_is_ordered was broken by previous fix to support the un-tidyverse mucking with dataframes... Now fixed
• BETA: umxRAM supports multi-group via `group = "column"
• IMPROVED: umx_score_scale now works with binary (0-1) items
• IMPROVED: umx_time gains "lap" (report elapsed time without restarting timer)
• IMPROVED: umx_time behavior with no input - now prints the current time and date
• IMPROVED: umxFactorScores can now return SEs
• IMPROVED: umxFactorScores allows abbreviated type names
• IMPROVED: umx_reorder can operate without verifying data (ignore precision digits in triangles of cov matrices)
• IMPROVED: residuals can re-order variables for ease of checking patterns of residuals
• IMPROVED: umxPath(defn= Definition vars now auto-named if labels not given closes #107
• IMPROVED: umxACEv uses default name "ADEv" (instead of "ACEv") if user sets dzCr = .25
• IMPROVED: umxAPA only uses italic Beta when std = TRUE
• IMPROVED: umxRAM now respects umx_set_silent
• CLEANUP: More removal of unused and obscure functions:
• CLEANUP: umxRAM2Ordinal to xmuRAM2Ordinal
• CLEANUP: umx_fix_latents and umx_fix_first_loadings to encourage user to be more explicit in their modeling.
• CLEANUP: Reorganized function groupings to be easier to navigate.

umx 3.0.0

• 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.
• Preparation for expansion to 5-group models.
• 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
• umxCovData -> xmu_DF_to_mxData_TypeCov
• xmu_model_needs_means -> xmu_check_needs_means
• umx_swap_a_block -> xmu_data_swap_a_block
• umxDescribeDataWLS -> xmu_describe_data_WLS
• umx_cov2raw -> umx_make_raw_from_cov
• umx_make_bin_cont_pair_data -> xmu_make_bin_cont_pair_data
• umxPadAndPruneForDefVars -> xmu_PadAndPruneForDefVars
• 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

umx 2.15.0

• May 2019, R 3.6.0 "Planting of a Tree"
• tip: Try new plot splines = T|F and min= , max = same= controls to layout your graphs!
• NEW: umxLav2RAM: detect ngroup, and a umxSuperModel of groups.
• NEW: plot.MxRAMModel plots multiple groups (on separate pages)!
• NEW: plot gains control of object clustering with max min and same.
• NEW: plot select whether to allow splines with spline=T\F
• NEW: plot opt paths out of layout constraints!
• IMPROVED: plot now labels plots with the group name.
• IMPROVED: umx_time Handles stop without prior start. New now option returns current date.
• FIX: uxmSummary the annoying "umxSummary not defined" error should be fixed!
• FIX: umxSimplex
• HELP: umxLav2RAM: multiple group example in help.
• Minor
• NEW: umx_set_separator allows Europeans to use ; in place of comma.
• NEW: xmu_lavaan_process_group
• NEW: xmu_clean_label
• NEW: xmu_name_from_lavaan_str helper

umx 2.10.0

• April 2019, R 3.5.3 "Great Truth"
• CITATION: citation("umx") Our paper on umx is out!
• Bates, Neale and Maes (2019). umx: twin and path-based structural equation modeling in R. Twin Research and Human Genetics. 22, 27-41. doi: 10.1017/thg.2019.2
• tip: Try ?umxExamples to see the example code from Bates, Neale and Maes (2019).
• NEW: umxSexLim multivariate sex-limitation working.
• NEW: umxSexLim Gained nonlinear, linear, and homogeneity modes
• NEW: umxSexLim Gained examples.
• NEW: umxRAM supports WLS, UWLS, DWLS models!
• NEW: umxACE supports WLS, UWLS, DWLS models!
• NEW: umxPlotCP Supports CIs on the diagram!
• NEW: umx_make_top_twin_models increases the robustness and improve-ability of all twin scripts.
• NEW: umx_set_data_variance_check to set the criteria for warning users about excessively small variance or divergence of variance.
• NEW: xmu_dot_define_shapes builds the latents and manifest shape definitions (should be xmu_)
• NEW: 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.
• NEW: umx is checked on travis
• NEW: github has build, doi, etc info boxes!
• NEW: plot allows user control over splines, as well as max, min, same positioning.
• NEW: xmu_dot_move_ranks.
• NEW: xmu_dot_rank_string.
• CHANGED: default for stripping zeros is reversed for plot.
• CHANGED: namez options for collapse get easier to short-cut names.
• DATA: data(Fischbein_wt) weight of 66 females record over six 6-month intervals (from Fischbein (1977) weight data).
• BETA: umxRAM2 Beginning support for lavaan syntax strings.
• BETA: Adding type (WLS) added to twin models...
• BETA: Universal weighted rows support for all twin models
• FIXED: umxValues to work more reliably with data with no means.
• FIXED: umx_rename Didn't give correct values when test = TRUE for non-grep searches (drop NAs)
• FIXED: umxSexLim match.arg tryHard
• FIXED: use of selVars vs. selDVs across different functions (search for "# New-style build-block" to see these changes
• IMPROVED: umxSuperModel can take a list of models.
• IMPROVED: tryHard - allow "yes" for default mxTryHard across all twin and RAM models.
• IMPROVED: umxPlotCP revamped - now not dependent on labels! (old function now umxPlotCPold)
• IMPROVED: xmu_model_needs_means
• IMPROVED: umxDescribeDataWLS to check whether the form of WLS requested will have means of not.
• IMPROVED: umx_make: use check_win_devel; set working director for release; spelling check
• IMPROVED: xmu_dot_mat2dot add model, toLabel and fromLabel + fromType & toType
• IMPROVED: xmu_dot_mat2dot example
• IMPROVED: xmu_safe_run_summary now copes with warnings in models, summary, compare etc. (as it should have)
• IMPROVED: umxModify now supports find and replace labels with grep (not just find with grep and set free/value)
• IMPROVED: xmu_assemble_twin_supermodel no longer take bVector (uses existence of weights instead)
• IMPROVED: umxModify now obeys verbose option
• IMPROVED: umx_time reports % change between model times
• IMPROVED: umIP help
• IMPROVED: umx_make now supports quick-make as default
• IMPROVED: tmx_show printing.
• IMPROVED: umx_score_scale help and examples.
• IMPROVED: umxModify now supports find and replace labels with grep (not just find with grep and set free/value).
• IMPROVED: umxModify now obeys verbose.
• IMPROVED: umxValues and elsewhere more robust to new data types.
• IMPROVED: umx_read_lower examples and input checking.
• IMPROVED: xmu_cell_is_on now has lower and upper triangle with or without diagonal included
• IMPROVED: xmu_dot_mat2dot now can get parameter values with CIs
• IMPROVED: umxRAM feedback when no data provided
• RENAME: xmu_make_top_twin lose "models" for shorter name.
• RENAME: tmx_show (was umx_show - it is mostly a teaching function
• RENAME: xmu_dot_define_shapes
• RENAME: xmu_dot_rank
• RENAME: umx_mat2dot --> xmu_dot_mat2dot
• RENAME: umx_APA_model_CI --> xmu_get_CI
• REMOVED: umx_add_variances old function not used and not very safe.
• CLEANUP: Removed thresholds option from several functions (always doing deviation-based, WLS isn't thresholds, and left-censored will be implemented differently)

umx 2.9.9

• December 2018, R 3.5.2
• Compatibility with OpenMx changes.
• NEW: umxSummarizeTwinData to create summary tables for papers using twin Data.
• IMPROVED: umxRAM: support definition variables to some extent in umxRAM.
• IMPROVED: umxMatrix advice user when they specify umxMatrix("me", 1,1).
• IMPROVED: umxModify nicer free-parameter report as default output with no changes requested (calls parameters).
• IMPROVED: umxRAM preserve definition variables in data.
• IMPROVED: plot strip_zero more reliable.
• INCOMPATIBLE: plot dropped deprecated showMeans and showFixed from plot after 3 years (use means= and fixed = ).
• INCOMPATIBLE: umx_scale_wide_twin_data dropped support for deprecated suffix parameter.

umx 2.9.0

• December 2018, R 3.5.1: "More love"
• INCOMPATIBLE: Support for suffix as a synonym for sep removed after 3-years of deprecation warnings.
• FIXED: umxSummaryfor ACEv models: CI now works - (was 'a' not 'A').
• NEW: xmu_safe_run_summary Runs a model safely, optionally summarizing and comparing it to a base model.
• IMPROVED: All models now support tryHard as a parameter!!
• IMPROVED: autoRun option in more places.
• IMPROVED: plot functions now have strip_zero option (default = strip leading zeroes from parameter estimates)
• IMPROVED: umx_standardize_ACEv now working!
• IMPROVED: Models use xmu_safe_run_summary so even bad models are returned for the user to diagnose them.
• IMPROVED: OmniGraffle stencil improved. Use to draw diagrams.
• IMPROVED: umxRAM now labels paths when no data are provided (simulation of sketch modes).
• IMPROVED: umx_score_scale can cope with a single item.
• IMPROVED: xmu_safe_run_summary don't error on code red non-run models.
• IMPROVED: xmu_twin_check tells user how to rename selVars and sep when sep is not provided, but is enforced.
• IMPROVED: umx_as_numeric allows user to select which columns to convert.
• IMPROVED umxSimplex start values now flexible and robust (was hard coded for 4-times).
• IMPROVED xmu_simplex_corner Takes a full values list (not just 1).
• IMPROVED: umxAPA uses .Last.value as default input if none provided.
• IMPROVED: umx_make supports what = "rhub".
• IMPROVED: umxlong2wide now allows user to retain only desired twin IDs.
• IMPROVED: Help-file model diagrams use pdf for pdf output.
• MINOR: xmu_mean_var_starts uses "expMean_" as the name for means cells (was "mean").
• MODIFY: xmu_safe_run_summary don't return bVector (already available)
• HELP: umxACE help diagrams improved with clearer ACE_matrix picture.
• HELP: umxRAM help gained an example of sketch-mode and diagram.
• HELP: umx_scale help file improved
• HELP: new pdfs for images in pdf help; remove _ from image names
• HELP: Examples cleaned up

umx 2.8.5

• October 2018, R 3.5.1: "More love"
• NEW: xmu_make_mxData function to make mxData functions out of dataframes (and also drop variables from cov/cor dataframes.
• NEW: SE style confidence information for CP and IP plots.
• IMPROVED: umxCompare gains ability to output Weight AIC conditional model probabilities! h/t @mNivard
• IMPROVED: umxReduce returns AIC weight-based probability of being best model.
• IMPROVED umxReduce.MxModelGxE returns best model (invisibly).
• IMPROVED: umxReduce for GxE, don't run no-A and no-C models with moderation in place.
• IMPROVED: namez given a list of models will return the names of each.
• IMPROVED: namez allow global replace.
• IMPROVED: umx_lower2full can now take a data.frame.
• IMPROVED: umx_aggregate can now open tables in a web browser.
• IMPROVED: install.OpenMx can now install a package file if selected in the Finder (MacOS only)
• IMPROVED: install.OpenMx now works with windows.
• IMPROVED: umx_print more robust to non table input.
• IMPROVED: xmu_make_mxdata more robust to non dataframe input.
• IMPROVED umx_apply robustness.
• IMPROVED: umx_simplex_corner can take a numeric to set matrix size.
• IMPROVED: umx_long2wide warn if twinID (order) has too many levels; improved help; @md
• BUG: umxAPA test parameter had no effect.
• HELP: Better links, text, layout, etc., umxCP/IP HELP figures.

umx 2.8.2

• June 2018, R 3.5.0: Simplex or s**t sticks
• FIXED: umxSexLim now works for univariate tests (thanks to Michael Zakharin for reporting!)
• FIXED: umxSummary Corrected Chi^2 df for RAM models.
• NEW: umxCP handles ordinal, continuous and binary data
• Note: old version still available as umxCPold
• Note: new version also lower-bounds specifics at 0 by default.
• NEW: umxCPplot re-written to allow arbitrary labels and correlated factors.
• NEW helper functions: umx_graphviz_rank, umx_mat2dot
• NEW: umx_set_optimization_options function to set "mvnRelEps" tolerances which impact, especially, ordinal model.
• REFACTOR: new twin model creation helper will help ensure consistency and improve multiple twin functions
• IMPROVED: umx_is_class reports classes if not given a set of classes to check
• IMPROVED: umx_scale(verbose=TRUE) now lists the vars it didn't touch as well as those it didn't (also formatted better)
• IMPROVED: umx_make_TwinData can set mean and SD of data
• IMPROVED: umx_simplex_corner can take a numeric to set matrix size
• FIXED: umx_standardize_CP was ignoring existing CIs
• DELETED: umxAlgebra This appears broken in some circumstances?
• HELP: verbose option for twin helper; better feedback;

umx 2.6.5

• May 2018, R 3.5.0: "Poly gets a cracker"
• NEW: Beta versions of umx_polychoric, umx_polypairwise, and umx_polytriowise
• NEW: umxSimplextwin model!
• umxSummary for simplex
• `plot support for simplex
• iqdatlongitudinal IQ twin data for simplex modeling
• NEW: namez alias for the ever-useful umx_names function.
• NEW: umxAlgebra (just allows name first).
• FIX: install.OpenMx URLs for NPSOL and travis builds of OpenMx
• BREAK: Following reports of problems in RStudio, changed umx class names to remove the period character from MxModel derivative classes
• This will break hard-coded calls, for instance to umxSummary.MxModel.ACE instead of umxSummary.
• "Just" replace with umxSummary.MxModelACE # i.e. delete the last period in the name... Sorry :-(
• IMPROVED: parameters now returns helpful near-match names as suggestions on not finding actual matches.
• IMPROVED: parameters now handles vectors of regular selections
• IMPROVED: umx_print now handles vectors.
• IMPROVED: umxConfint "smart" feature to request only free algebra cells for models I understand (umxCP in the first instance)
• IMPROVED: namez can handle a model summary (accesses names() of the summary)
• IMPROVED: umxGxE added option to control plot colors
• IMPROVED: umxPlotCP can handle >9 manifests issue
• HELP: umxGxE example improved
• HELP: More related-function links in help files.
• HELP: Better error messages.
• HELP: Help titles, parameter documentation.
• INTERNAL: xmu_simplex_corner helper function for simplex modeling.
• INTERNAL: umx_make_sql improved

umx 2.4.0 Post-Boulder Workshop CRAN edition

• March 21 2018, R 3.4.4
• NEW: umxIP nFac now allows specifying different numbers of a, c, and e factors!
• NEW: umxACEv plot works (shows correlated factors).
• NEW: umxACEv standardize mostly functional.
• NEW: umxEFA can now take a formula to select variables.
• IMPROVED: umxIP and CP examples improved (3-variables, GFF data).
• IMPROVED: umxIP reporting of as, cs, es simplified into compact stack.
• IMPROVED: umxCP reporting of as, cs, es simplified into compact stack.
• IMPROVED: umxPlotCP labeling of variables improved (catching more _Tn).
• IMPROVED: umxEFA reports factor correlation matrix (thanks @ConorDolan)!
• IMPROVED: umxEFA can return a loadings object.
• IMPROVED: umx_makenot supports spelling check.
• IMPROVED: umxACEv diagonal now unbounded by default (which is it's whole purpose)
• IMPROVED: umxACEv got major improvements to help file.
• IMPROVED: umxSummaryCP got ability to print to html.
• IMPROVED: plot made more robust to unexpected labels (now that umxModify can write newlabels)!
• MINOR: umx_names Added GFF examples.
• DROPPED: deleted deprecated showStd and showMeans parameters from plot ACE.
• BUG-FIX: umxSummaryIP was assuming nFac = 1

umx 2.0.2

• Feb 12 2018, R 3.4.3 Higher goals edition
• NEW: umxSummary works with multi-group models!
  • (make these with umxSuperModel)
• NEW: umxModify supports multiple find strings and replace strings!
• IMPROVED: umxAPA supports glm, more robust input checking.
• FIXED: umxEquate allows vectors of labels.
• DOCS: umxGetParameters has better help.
• DOCS: umxHetCor docs now note is will return a pos-def version if given a cov matrix.
• DOCS: umxAPA now has t-test and glm examples
• DROPPED: umx_install_OpenMx (use install.OpenMx)

umx 2.0.0

• January 29 2018, R 3.4.3 Birthday edition
• BETA: umxSexLim multivariate twin sex-limitation.
• BETA: umxGxE_biv bivariate Gene-environment interaction model.
• BETA: umx_make_TwinData Can now make bivariate moderated twin data.
• BETA: Beginning a umxGroup function as part of measurement invariance support.
• NEW: umx_stack Slightly more powerful version of base stack.
• NEW: umx_array_shift Shifts an item off the beginning of a list.
• IMPROVED: umxRAM can take lists of paths as input (contributed by @bwiernik).
• IMPROVED: umxModify can write newlabels.
• IMPROVED: umxAPA can back-out an SE if given b and CI.
• IMPROVED: Help pages and examples improved and reorganized.
• DROPPED: umxReRun (use umxModify)
• DROPPED: support for suffix parameter (use sep instead)

umx 1.9.2

• December 2017, R 3.4.2
• TIP: Filter paths by estimated size with umx_parameters(model, "below", .1)
• NEW: tmx_genotypic_effect Part of a suite of teaching functions for biometric genetics!

umx 1.9.1

• November 2017, R 3.4.2
• TIP: ?umxRAM has a sketch mode. just set data to a list of manifest variable names.
• NEW: umxSuperModel function to automate multiple-group model creation.
• NEW ?umxACEv Variance component version of ACE. (beta)
• NEW: CIs in output tables!
• NEW ?umxACEcov_fixed Beta1: Handles main effects of covariates in the means of continuous variables.
• NEW umxModify can now equate parameters (set master = ), update is slave set of labels.
  • As a result, umxEquate now doesn't autoRun by default. Let me know if this is a pain.
• NEW: Dataset on general family functioning in twins. ?GFF
• NEW: optimiser parameter for umxACE and other twin models: Set the optimizer in your model code!
• NEW: umx_is_numeric boolean check if variables in a dataframe are numeric.
• NEW: umx_is_class boolean check if variables in a dataframe match a desired class.
• NEW: umx_twin_check internal function for common input checks.
• NEW: umx_set_plot_file_suffix(c("gv", "dot") function (to control the filename used for figures)/
• FIXED: umxACE was broken with large cov inputs h/t @NathanGillespie.
• FIXED: umxAggregate now actually supports user functions as input...
• BEGINNING: to add umxACEv variance components method
• IMPROVED: umxPath(Cholesky = ) method: supports labels, bounds, lbound at 0.
• IMPROVED: umxPath(Cholesky = ) method: return one statement instead of a list for clarity.
• IMPROVED: umxACE and umxReduce.ACE run intervals
• IMPROVED: umxReduce works better with umxACE models.
• IMPROVED: umxEFA Supports minManifests.
• IMPROVED: umxEFA Works better when returning a single factor score.
• IMPROVED: umxParameters now supports digits.
• IMPROVED: umxSummary "inline" reporting now includes AIC.
• IMPROVED: umx_aggregate works with factor input/
  • umx_aggregate(sex_T1 ~ zyg_2grp, data = x)
• IMPROVED: umx_long2wide can passalong variables.
• IMPROVED: umx_wide2long much more powerful
• IMPROVED: umx_msg supports dataframes
• IMPROVED: umxACE gains ability to set plot format: format = "graphviz" or "DiagrammeR"
• IMPROVED: umx_set_auto_plot take TRUE/FALSE as input.
• IMPROVED: umx_names: added a find and replace option for names
• IMPROVED: umxRAM in "sketch mode" now plots models automatically.
• IMPROVED: install.OpenMx from University of Virginia, travis, or open travis build page.
• IMPROVED: umx_cor automatically drops non-numeric columns.
• IMPROVED: umxCI now supports setting interval and one- or two-sided type (h/t @Conor Dolan).
• INTERNAL: Switch from R2HTML to xtable
• MINOR: umxParameters now supports non-run models

umx 1.8.0

• September 2017, R 3.4.1 "Single Candle"
• TIP: ?umxAPA can format lots of things for you: from dataframes to p-values - try it out! Let me know what you'd like.
• NEW ?umx_parameters function, report parameter estimates, filtering by name and value!
  • aliased as umxParameters
  • umx_parameters(model, "below", .1, "loading")
• NEW ?umx_long2wide: Merges long data on famID, for an unlimited number of individuals in a family (twinIDs).
• NEW ?umx_wide2long: Takes a wide df (currently limited to 2 per family), & returns a long-format version.
• FIXED: Removed superfluous print call from umx_MakeTwinData.
• IMPROVED: html tables by switching to xtable (R2HTML is abandoned, strips decimals from AIC, etc.)
• IMPROVED: Plotting: Models now plot by default. Turn off with umx_set_auto_plot(FALSE).
• IMPROVED forEach option in umxPath. This is a one.headed version of "unique.pairs".
• IMPROVED: Output: Twin models now show summary when autoRun.
• IMPROVED: Graphics: umxGxE plot colors now use the universal ACE -> RGB scheme.
• IMPROVED: umxACEcov Now tries to detect violations: Age and Sex are good examples.
• IMPROVED: Stability: bound diag to 0 by default in umxACE.
• IMPROVED: Stability: Stop on covs that are identical across twins in umxACEcov!
• IMPROVED: Better default model name for umxACEcov;
• IMPROVED: More helpful default core list for umx_check_parallel (1 and n-1);
• IMPROVED: Output formatting of times in umx_check_parallel
• IMPROVED: umxReduce does a much better job reporting automated umxGxE model reduction.
• IMPROVED: umxAPA handles lme models.
• IMPROVED: umxPrint error messages.
• DOCUMENT logic.MxModel now has an Rd page.
• CHANGE: Showing Rg (genetic correlation) table is now off by default for umx twin model summaries.
• CHANGE: confint. OpenMx now supports this, so I dropped it from umx (added alias to umxConfint).
• CHANGE: anova. OpenMx now supports, this so I dropped it from umx.
• CHANGE: umx_fix_first_loadings now skips latents with fixed variance.

umx 1.7.5

• April 04 2017, R 3.3.3 "Another Canoe"
• TIP: In twin models, mzData and dzData can contain unused variables (umx removes them for you!)
• NEW: umxVersion (returns mxVersion + information on umx).
• IMPROVED: umxACE start values much better for univariate models.
• NEW: umx_make_TwinData
  • Use variance input
  • Option to set seed
  • SetvarName
  • nThresh to threshold the created variables, and return as mxFactors
  • Surface the empirical parameter of mvrnorm
  • More flexible: Leave out any one of A, C, or E.
  • omit nDZPairs to get equal numbers
  • Option to allow A+C+E ≠ 1
  • Full set of examples
  • NOTE: umx_make_TwinData uses variance input. This was ambiguous previously.
  • Docs much improved.
• NEW: install.OpenMx can install UVA parallel, travis latest (on mac) or opening the travis list.
  • BUG-FIX: install.OpenMx had a broken URL, now corrected.
• NEW: 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. splus m1 <- umxRAM("test", data = paste0("itemC", 1:4), umxPath(unique.bivariate = paste0("itemC", 1:4)), umxPath(var="X") ) plot(m1)
• NEW: umx_cont_2_quantiles now allows returning cut points, better examples, level_names
  • BUG-FIX: umx_cont_2_quantiles lowest threshold was empty
• NEW: umxAPA now reports mode for factor data
• NEW: Allow umxLabel to rename the returned model
• IMPROVED: sep is now the preferred separator (synonym for suffix in umxACE, umxCP, umxIP)
• DOCUMENT: Examples use zygosity string from twinData instead of numeric code
• DOCUMENT: Fix typo in umxPath docs
• INCOMPATIBLE: renamed umx_cov_diag to umx_var

umx 1.5.5

• March 20 2017, R 3.3.3 "Another Canoe"
• NEW: umx_write_to_clipboard
• NEW: umx_r_test
• IMPROVED: Add autoRun option to umxModify.
• FIXED: Switch away from CSOLNP in umxCP example.
• ROLLBACK: No longer generically alter CSOLNP tolerance.

umx 1.5.1

• March 05 2017 R 3.3.2
• IMPROVED: umxCP example for improved compatibility with OpenMx 2.7
• IMPROVED: umx twin models now set a better (less likely to fail) precision for CSOLNP
• IMPROVED: improved help files; document forms parameter for umxPath
• IMPROVED: handling list inputs
• IMPROVED: behavior of confint()
• IMPROVED: formatting of umxAPA table output
• ADD: "check" option to umx_make
• FIXED: umxPath(a, forms= , arrows = 2) bug

umx 1.5.0

• December 2016
• Features + OpenMx 1.7.3 compatibility release
• IMPROVED: umxRAM returns invisibly
• IMPROVED: umx_aggregate can summarize multiple DVs in a table
• IMPROVED: umx_aggregate can return a formatted table (kable = TRUE)
• IMPROVED: umxAPA returns lower-triangle of data.frame correlations (by default)
• REMOVED: umxSE now included in OpenMx 2.7.0!
• FIXED: umx_set_plot_format uses silent = TRUE internally where needed

umx 1.4.9

• December 2016
• Bug fix
• FIXED: umx_make_TwinData fix bug in DZ moderator code and A+C computation
• IMPROVED: more functionality hints in man page titles

umx 1.4.5

• November 2016 "Usability is queen/Sincere Pumpkin Patch"
• IMPROVED: Reorganize function families to increase clarity
• IMPROVED: umx_set functions now show legal options by default
• NEW: umx_set functions have silent option
• FIX secure http URLs

umx 1.4.0

• Mid October 2016 "New features and improvements"
• BUG FIX: umxFitIndices RMR and SRMR (h/t Brenton Wiernik!)
• NEW: umxMatrix with default labels and name as 1st parameter
• NEW: Definition variable umxPath type, e.g.
  • umxPath(defn = "def", labels = "data.age")
• IMPROVED: More concise feedback
• IMPROVED: umxEquate supports autoRun and compare
• IMPROVED: umx_names can, as a convenience, take string vectors
• RENAME: umxGetOpenMx aliased to install.OpenMx or umx_install_OpenMx
• IMPROVED: umxFitIndices additional fit-indices and now automatically computes reference models if needed.
• IMPROVED: umxRAM remove_unused_manifests no longer updates manifestVars + leaves variable in data by default.
• RENAME: plot "showFixed" deprecated in favor of easier to type "fixed"

umx 1.3.0

• R 3.3.1 companion: "Bug in your Hair" August 2016
• NEW: umxPath allows unique.pairs connection
• Useful for growth curve models
• IMPROVED: umxRAM handles suffix labels
  • Useful for models embedded in multi-group
• IMPROVED: umxSummary to show parameters from first model in multi-group
  • Begin to support multi-group in umxSummary
• IMPROVED: twin model figures tweaked
• CHANGE showStd= to std= in most remaining cases
  • Might need to update your code!
• CHANGE: umx_show_options to umx_get_options
  • Might need to update your code!
• FIX: umx_check_parallel typo
• FIX: plot calls from summary
• REMOVE: dependency on non-condensed slots

umx 1.2.8

• R 3.3.0 companion: "Very compatible" May 2016
• NEW: umxRAM can now build and run Joint Continuous Ordinal models!!
• NEW: umx_show_options function to help users learn the options available
• BETA: umxACE can now implement a form of left-censoring.
• BETA: umxThresholdMatrix can now implement a form of left-censoring.
• IMPROVE: umxRAM & umxRAM2Ordinal can turn off reference models computation with refModels = FALSE;
• IMPROVE: umx_show can show thresholds
• IMPROVED: umx_is_MxModel can take a list: listOK option
• IMPROVED: umx_check_parallel options for row-wise parallel and number of subjects
• CHANGE: I changed "suffix" to "sep" in several places for consistency: this will break some low level code: nearly all of it mine, and fixed. But might affect some users!!
• UPDATE: umx_time and umx_check_parallel to work with new S4 list deprecation
• MINOR: umxTwoStage shorter run-time on 2-stage least squares

umx 1.2.7

• May 2016 stable release
• ADDED: umxTwoStage FIML-based Instrumental variable and Mendelian Randomization (beta)
• ADDED: umx_make_MR_data to simulate SNP-based Mendelian randomization data (beta)
• ADDED: umx_set_condensed_slots(TRUE|FALSE): Get and set matrix compression
• ADDED: umx_get_OpenMx (download OpenMP/parallel version of OpenMx with NPSOL)
• ADDED: umx_cont_2_quantiles(x, nlevels = )
• ADDED: umx_factor alias to umxFactor
• FIXED: plot(resid = "none") was not suppressing plotting residuals
• IMPROVED: umxFactor now handles dataframes and allows non-ordered output
• IMPROVED: umx_CI more flexible, now allows removing CIs
  • Old code will break: replace "add" with "which"
• IMPROVED: umx_time handling of no input arguments
• IMPROVED: umx_pb_note better feedback and setup
• IMPROVED: loadings() generic
• CHANGE: umxModify - if free is a string, it will be used as input and the found paths will be freed.
• CHANGE: umxModify - show summary as well when comparison = TRUE
• CHANGE: plot defaults for std and showFixed changed h/t @MikeNeale
• CHANGE: umx_scale_wide_twin_data argument names for consistency: "suffix" "data"
• CHANGE: umx_residualize ditto.
• UPDATE: "Read me" file.

umx 1.2.5

• April 2016 R 3.2.5 "Very, Very Secure Dishes"
• Bug fix release
• FIX: $models bug in umxStandardizeACE
• EXPAND: test suite

umx 1.2.0

• April 2016 R 3.2.4 "Very Secure Dishes"
• NEW: plot using DiagrammeR!
• NEW: Choose plot format!
  • umx_set_plot_format("DiagrammeR")
  • umx_set_plot_format("graphviz")
• NEW: Choose table format!
  • umx_set_table_format("markdown")
  • umx_set_table_format("latex")
• NEW: set plotting by default: umx_set_auto_plot(TRUE)
• NEW: Exploratory factor analysis! with umxEFA (beta!)
• NEW loadings() support for umxEFA
• CHANGE: .dot --> .gv suffix for plotting (more compatible)
• CHANGE: To $ from @ accessors for OpenMx compression compatibility
• BETTER: Help! ACECov figure, ... many other improvements
• ENHANCED: umx_print, umx_show, umxCompare
• REQUIRE knitr, DiagrammeR
• INCREASE minimum R / OpenMx to >= 3.2.0 / >= 2.5.0

umx 1.1.5

• March 2016 Boulder Workshop feedback updates
• NEW: plot now works on Windows and Unix as well as OS X! (h/t @mhunter)
• CHANGE: umxReRun to umxModify (h/t @hmaes)
• BETTER: compatibility with OpenMx 2.5.2

umx 1.1.1

• Feb 2016 R 3.2.3 Wooden Christmas Tree edition
• NEW: auto-run now the default for all models!
  • Added option to switch this: options("umx_auto_run" = TRUE)
• NEW: plot should generate pdfs for Windows and Unix users now
• NEW: umxACEcov support for ACE with covariates
• NEW: umx_make_TwinData added to support simulation studies
• BETTER: umx_check_parallel now returns timing information
• BETTER: umx_time now supports "start" and "stop")
• BETTER: umxAPA can format more objects in APA style, inc just a p-value)
• BETTER: summaryAPA can now summarize a data.frame with mean, sd, and correlations
• BETTER: umxLabel now preserves existing labels in umxRAM models: labels = is now saved
• BETTER: Help improvements (wording, see-also etc)
• DEEP: Removed dependency on formula.tools

umx 1.1.0

• December 2015, R 3.2.3 "Wooden Christmas-Tree"
• NEW: vcov() added
• NEW: Begin support for sex-lim twin models
• NEW: New data file for sex-limitation
• IMPROVED: umxRAM can take existing model as input (very useful)
• IMPROVED: umxRAM reports model fit and comparison (if old model exists)
• IMPROVED: umxPath now lbounds var@0 for v.m.
• IMPROVED: umx_residualize can now take multiple DVs
• IMPROVED: umxMI enhanced to cope with more situations
• IMPROVED: umxSummary more resilient with missing CIs (#ht Nathan Gillespie!)
• IMPROVED: summaryAPA now handles data as well as lm
• IMPROVED: Help for twin functions
• IMPROVED: Various new function features
• IMPROVED: umx_print resilient to 0-row input
• IMPROVED: summary helpers (e.g. umx_fun_mean_sd)
• IMPROVED: consistency in parameter names (minor backward incompatibility)
• DEEP: Replacing @ with $ accessor begun

umx 1.0.0

• NEW umxCP twin models! + plot(), umxSummary()
• NEW umxIP twin models! + plot(), umxSummary()
• NEW umxGxE twin models! + plot(), umxSummary()
• FIXED umxPath limitation where "to" was not being set.
• SUPPORT Circles as well as lines for residual variance.
• IMPROVE Help text. Thanks Mike Neale esp.!
• IMPROVE Organization of functions into @families in the help.
• IMPROVE Example for umx_lower2full
• DROPPED umxRAM functionality to set endogenous, exogenous, and latent traits
• DROPPED Deprecated a dozen functions.

umx 0.50.0

• March 2015 R 3.1.3, "Smooth Sidewalk"
• First CRAN release!

umx 0.49.0

• IMPROVE Edge cases work
• IMPROVE Improving help files and feedback
• IMPROVE Rationalizing function names into @families

umx 0.45-beta

• Feature complete
• Bug squashing
• Optimizing function names for memorability and typing

umx 0.40-beta

• Beta level!
• Standard confint(); plot() etc functions implemented
• Adding umxRAM() and umxPath shortcuts

umx 0.30-alpha

• Alpha release
• 90% feature complete
• Lots of name rationalization

umx 0.25-alpha

• Alpha release
• 80% feature complete
• Function prefix reflects usage:: camel-case for major functions, underscore for utility functions, "xmu" prefix, "not for end-user"

tbates/umx documentation built on Sept. 13, 2024, 9:20 a.m.