Recent Releases of umx

What's Changed

IMPROVED: umxCLPM refactor and corrections by @lf-araujo
IMPROVED umxSummarizeTwinData reports complete pairs for rMZ and rDZ
IMPROVED: umxRAM Can include definition variables! h/t @lf-araujo
IMPROVED: umxReduce ACE can skip ADE model
IMPROVED: umxReduce output better formatted
IMPROVED: umx_check_parallel gains set optimizer, and row parallel
IMPROVED: umx_scale_wide_twin accepts sibs #253 from lf-araujo/patch-6
IMPROVED: umx_as.numeric explicit drop = TRUE
IMPROVED: umxEFA error reporting is more robust
IMPROVED umxBrownie makes a rare steak
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.MxModelACE now aware of umx_set_auto_run #241 @lf-araujo
HELP: umx_scale better
HELP: umx_scale clarify polychoric and pairwise functionality
HELP: umxRAM example a model with a def var on means

- R
Published by tbates over 1 year ago

umx - More twins, causation, unicode and maintainance

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 -> xmuDFtomxDataTypeCov
- xmumodelneedsmeans -> xmucheckneedsmeans
- umxswapablock -> xmudataswapa_block
- umxDescribeDataWLS -> xmudescribedata_WLS
- umxcov2raw -> umxmakerawfrom_cov
- umxmakebincontpairdata -> xmumakebincontpairdata
- 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: umxsetdatavariancecheck 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 checkwindevel; 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: umxgraphvizrank, 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 removeunusedmanifests 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("umxautorun" = 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!

- R
Published by tbates over 2 years ago

umx - underline

Just removing underscore character from image names to work around old CRAN latex engine

Full Changelog: https://github.com/tbates/umx/compare/v4.15.0...v4.15.1

- R
Published by tbates over 3 years ago

umx - New features causal modeling with twins, and many smaller improvements!

umx 4.15.0

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.

- R
Published by tbates over 3 years ago

umx -

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: power.ACE.test Clarify which of power, effect, and n are fixed or being estimated.
IMPROVED: power.ACE.test can run ADE model
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 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)
BETA: umx_score_scale can score items with character labels (not working in this release!!)
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

- R
Published by tbates about 4 years ago

umx - Version: 4.9.0

NEW: umxACEv and umxACE work with nSib = 3!
BETA: umxCP correlatedACE was not being filtered out of the expectation #hat-tip @micanzach But this feature is still broken; DON'T USE IT!
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

- R
Published by tbates over 4 years ago

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.

- R
Published by tbates over 4 years ago

umx - 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 can choose between pdf, png, svg plot output (in addition to DiagrammeR and graphviz)
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
NEW: umx_lower.tri helper to get lower.tri values in 1 call
HELP: umxCP Document that correlatedA works on a, c and e, allowing factors built by these matrices 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...
IMPROVED: fin_compound_interest now outputs a table of annual returns
IMPROVED: umxAPA uses cat to improve usability of summary data
NEW: umx_set_plot_use_hrbrthemes control
NEW: plot.percent plot support for percent change questions

- R
Published by tbates about 5 years ago

umx - Bunny-Wunnies Freak Out

umx 4.2.5: 40 additional features, fixes, code and help improvements!

December 2020 R 4.0.3 (2020-12-12) (commit a2a16bbb29)
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.
NEW: geometric_mean
NEW: fin_compound_interest
NEW: fin_percent_off
IMPROVED: umxPlotGxE gains CI ribbons (closes #96)
IMPROVED: umxPlotGxE defaults to use ggplot and now returns the graphs for decoration (closes #139)
IMPROVED: umxPlotGxE can now plot user-specified moderator ranges (closes #96)
IMPROVED: umxPlotIP now relies on matrix cells, not the labels they contain (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: 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 now can install a package if not installed, as well as open the CRAN page for the package.
IMPROVED: umx_rename_file nicer user 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 handle non-df input
IMPROVED: umx_rename_file nicer user feedback about matches and files checked
IMPROVED: umx_set_table_format to markdown on load
FIXED: 'umxRAM` group option failing to pass autoRun tryHard Merge pull request #134 @khusmann
FIXED: umxRAM with a model as first parameter now doesn't demand new data. Updates data if data is provided.
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 actually 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: 'umxSummarywrapsmxRefModels` error for WLS models in tryCatch to tell user OpenMx doesn't support fit stats for WLS as yet.
BACKWARD: umxThresholdMatrix changed parameter from selDVs to fullVarNames to prevent user error.
HELP: harmonic_mean example averaging speeds across distance.
NEW: umx_read_prolific_demog to read prolific academic demographics files.

- R
Published by tbates about 5 years ago

umx - means and covariates & 68 other things!

umx 4.0.0 May 2020

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).

- R
Published by tbates almost 6 years ago

umx - umx 3.0.6

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).
umx_score_scale: implemented score = "mean" and score = "max".
umx_score_scale: better documentation.
umxGxE gains dzAr and dzCr control so ADE is possible as well as assortative mating.
xmu_twin_check works with mxData * IMPROVED: xmu_twin_starts works with mxData input.
xmu_make_top_twin works with mxData input.
xmu_twin_check support mxData (was just data.frame input).
umx_long_2_wide: help notes on processing TWINIDs into famID and twinID columns.
REPAIR: umxSummary handles std=NULL as documented (don't show parameter table).
RENAME: umx_nice_data --> umx_make_twin_data_nice.

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Published by tbates about 6 years ago

umx - R 4.0 compatible

umx 3.0.5

December 2019 R 4.0.0 compatibility
BUGFIXED: 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.

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Published by tbates about 6 years ago

umx - Major version bump.

Over 80 new features and improvements!

Accompanies R 3.6.1 Action of the Toes

- R
Published by tbates over 6 years ago

umx - umx 2.10.0 April 201, R 3.5.3: great truth

- R
Published by tbates almost 7 years ago

umx - umx 2.9.9 Jan 2019, R 3.5.2: Compatibility

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: 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: removed deprecated suffix parameter from umx_scale_wide_twin_data

- R
Published by tbates about 7 years ago

umx - umx 2.9.0 December 2018, R 3.5.1: More love

BACKWARD INCOMPATIBLE: Support for suffix as a synonym for sep was finally removed after a 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: plot functions now have strip_zero which strips leading zeroes from estimates.
IMPROVED: umx_standardize_ACEv now working!
IMPROVED: xmu_safe_run_summary bad models are returned for the user.
IMPROVED: Omnigraffle stencil
IMPROVED: umxRAM labels paths in the case that no data are provided.
IMPROVED umxSimplex Start values flexible and robust (was hard coded for 4-times)
IMPROVED: umxAPA can use .Last.value as default input if none provided
IMPROVED: umxlong2wide now allows user to retain only desired twin IDs
HELP: diagrams in help improved - umxACE etc.

- R
Published by tbates about 7 years ago

umx - R 3.5.0: Simplex and improvements

umx 2.6.5 May 2018, R 3.5.0: Simplex and improvements

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 modelling
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 modelling.
INTERNAL: umx_make_sql improved

- R
Published by tbates almost 8 years ago

umx - Boulder Workshop edition

umx 2.4.0 March 21 2018, R 3.4.3 post Boulder Workshop edition)

NEW: umxIP nFac now allows specifying different numbers of a, c, and e factors!
NEW: umxACEv plot works (shows correlated factors)
NEW: umxEFA reports factor correlation matrix (thanks @ConorDolan)!
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 labelling of variables improved (catching more _Tn).
IMPROVED: umxEFA can return a loadings object.
IMPROVED: umx_makenow supports spelling check.
IMPROVED: umxACEv standardize mostly functional.
IMPROVED: umxACEv got major improvements to help file.
IMPROVED: umxACEv diagonal now unbounded by default (which is it's whole purpose)
IMPROVED: umxSummaryCP got ability to print to html.
IMPROVED: plot made more robust to unexpected labels (now that umxModify can make newLabels)!
MINOR: umx_names Added GFF examples.
DROPPED: deleted deprecated showStd and showMeans parameters from plot ACE.
BUGFIX: umxSummaryIP was assuming nFac = 1

- R
Published by tbates almost 8 years ago

umx - Back on CRAN

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)

- R
Published by tbates about 8 years ago

umx - Birthday release, Jan 2018

Whole bunch of new stuff!

Complex twin models and data simulation

NEW: umxSexLim multi-variate twin sex-limitation (beta)
NEW: umxGxE_biv bivariate Gene-environment interaction model (beta)
NEW: umx_make_TwinData Can now make bivariate moderated twin data.

Improving existing functions

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.

less interesting helpers

NEW: umx_stack Slightly more powerful version of base stack.
NEW: umx_array_shift Shifts an item off the beginning of a list.

future work

Beta: Beginning a umxGroup function as part of measurement invariance support.
DEPRECATED LONG ENOUGH: Dropped support for umxReRun (use umxModify)
DEPRECATED LONG ENOUGH: Dropped support for suffix in some places (use sep)

- R
Published by tbates about 8 years ago

umx - November 2017/R 3.4.2 CRAN release. first public beta of umxACEv

NEW ?umxACEv Beta1: Variance component version of ACE. Hammer on it for Boulder workshop!
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: umxSuperModel function to automate multiple-group model creation.
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/
- umxaggregate(sexT1 ~ 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 replace option to munge the names
IMPROVED: umxRAM in "sketch mode" now plots models automatically.
IMPROVED: install.OpenMx from UVa, 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

- R
Published by tbates over 8 years ago

umx - Waiting for CRAN to fix their El Capitan build process.... since june

- R
Published by tbates over 8 years ago

umx - umx 1.8.0 (August 2017)

umx 1.8.0 (July 2017, R 3.4.1 (Single Candle)

TIP: umxAPA can format lots of things for you: from effects in lm -try it out!
NEW: optimiser parameter for umxACE and other twin models: Set the optimizer in your model code!
NEW umx_long2wide: Merges long data on famID, for an unlimited number of individuals in a family (twinIDs)
NEW umx_wide2long: Takes a family (currently limited to 2) df, and returns a long-format version.
NEW forEach option in umxPath (like one.headed version of "unique.pairs").
IMPROVED: Auto run/plot for umxGxE
IMPROVED: switched umxGxE plot colors to the universal ACE -> RGB scheme
IMPROVED: umxCI supports setting interval and type
IMPROVED: twin models now print summary when autoRun
IMPROVED: models now plot by default
umxACEcov improved, but still not working well for multivariate
- older versions worked with 1 DV only, couldn't handle multivariate means, had poor start values.
IMPROVED: lound diag to 0 by default in umxACE
IMPROVED: Better default model name for umxACEcov;
IMPROVED: More helpful default core list for umxcheckparallel (1 and n-1); plus improved formating of times
IMPROVED: umxReduce does a much better job reporting automated umxGxE model reduction.
IMPROVED: umxAPA handles lme models
IMPROVED: umxPrint error messages
DOCUMENT logic.MxModel Rd page for logic.MxModel.
CHANGE: Rg is now off by default for umx twin model summaries
CHANGE: OpenMx now supports confint, so this has been dropped from umx (added alias to umxConfint)
CHANGE: OpenMx now supports anova, so this has been dropped from umx
FIXED: Removed superfluous print call from umx_MakeTwinData

- R
Published by tbates over 8 years ago

umx - R 3.3.3 companion - Another Canoe with better OpenMx 2.7x compatibility and some features

umx 1.5.5

This March 2017 release (in line with R 3.3.3 "Another Canoe") contains a couple of new mini-features:
NEW: umxwriteto_clipboard
NEW: umxrtest
NEW: autoRun option in umxModify (ht @bwiernik)

And also some and a rollback of a generic CSOLNP tolerance change introduced in 1.5.1: this just caused hassles - sorry. Instead, we just special-case the optimiser.

As ever: let me know what new features you'd like!

- R
Published by tbates almost 9 years ago

umx - 2.7.3 compatible

December 2016 feature release - IMPROVED: umxRAM returns invisibly - IMPROVED: umxaggregate 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: umxsetplotformat uses silent = TRUE internally where needed

- R
Published by tbates about 9 years ago

umx - CRAN release!

This version released for download on CRAN

- R
Published by tbates over 10 years ago

umx - Ready for general use

Feature complete for a release with OpenMx 2.0

- R
Published by tbates over 11 years ago

umx - umxCI work

All working well

- R
Published by tbates over 12 years ago

umx -

Better integration and updating of function list. Dropped file with ? in name for windows compatibility

- R
Published by tbates over 12 years ago

umx - umx countdown

Just a few steps closer to release.

- R
Published by tbates over 12 years ago

umx - closer to the target

What would you like to add?

- R
Published by tbates over 12 years ago

Recent Releases of umx

umx - v4.21.0

What's Changed

umx - More twins, causation, unicode and maintainance

umx 4.19.00

umx 4.17.00

umx 4.16.00

umx 4.15.1

umx 4.10.50

umx 4.10.10

Releases

umx 4.9.0

umx 4.8.0

umx 4.3.0

umx 4.2.5

umx 4.1.0

umx 4.0.0

umx 3.1.0

umx 3.0.6

umx 3.0.5

umx 3.0.0

umx 2.15.0

umx 2.10.0

umx 2.9.9

umx 2.9.0

umx 2.8.5

umx 2.8.2

umx 2.6.5

umx 2.4.0 Post-Boulder Workshop CRAN edition

umx 2.0.2

umx 2.0.0

umx 1.9.2

umx 1.9.1

umx 1.8.0

umx 1.7.5

umx 1.5.5

umx 1.5.1

umx 1.5.0

umx 1.4.9

umx 1.4.5

umx 1.4.0

umx 1.3.0

umx 1.2.8

umx 1.2.7

umx 1.2.5

umx 1.2.0

umx 1.1.5

umx 1.1.1

umx 1.1.0

umx 1.0.0

umx 0.50.0

umx - underline

umx - New features causal modeling with twins, and many smaller improvements!

umx 4.15.0

umx -

umx - Version: 4.9.0

umx - umx 4.8.0

umx - umx 4.3.0

umx - Bunny-Wunnies Freak Out

umx 4.2.5: 40 additional features, fixes, code and help improvements!

umx - means and covariates & 68 other things!

umx 4.0.0 May 2020

umx - umx 3.0.6

umx - R 4.0 compatible

umx 3.0.5

umx - Major version bump.

umx - umx 2.10.0 April 201, R 3.5.3: great truth

umx - umx 2.9.9 Jan 2019, R 3.5.2: Compatibility

umx - umx 2.9.0 December 2018, R 3.5.1: More love

umx - R 3.5.0: Simplex and improvements

umx 2.6.5 May 2018, R 3.5.0: Simplex and improvements

umx - Boulder Workshop edition

umx 2.4.0 March 21 2018, R 3.4.3 post Boulder Workshop edition)

umx - Back on CRAN

umx 2.0.2 (Feb 12 2018, R 3.4.3 Higher goals edition)

umx - Birthday release, Jan 2018

Whole bunch of new stuff!

Complex twin models and data simulation

Improving existing functions

less interesting helpers