News

umx 2.8.5 October 2018, R 3.5.1: More love

• NEW: umxRAM supports WLS, UWLS, DWLS models!
• NEW: xmu_make_mxData function to make mxData functions out of dataframes (and also drop variables from cov/cor dataframes.
• NEW: SEstyle 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 noC 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 lowerbounds 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 modelling.
• INTERNAL: umx_make_sql improved

umx 2.4.0 March 21 2018, R 3.4.4 post Boulder Workshop CRAN edition)

• 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 labelling 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 make newLabels)!
• MINOR: umx_names Added GFF examples.
• DROPPED: deleted deprecated showStd and showMeans parameters from plot ACE.
• BUGFIX: 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 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

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, ignores c(nsmall)...
• 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() + umx version).
• IMPROVED: umxACE start values much better for univariate models.
• NEWFEATURES: umx_make_TwinData
  • Use variance input
  • Option to set seed
  • Add varName to datasets
  • nThresh to threhold 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.
• NEWFEATURES: install.OpenMx can install UVA parallel, travis latest (on mac) or opening the travis list.
  • BUGFIX: install.OpenMx had a broken URL, now corrected.
• NEWFEATURES: umxRAM can now be used in "sketch" mode, to plot demos without data: just add the list of manifests as a character string to data.

  m1 <- umxRAM("test", data = paste0("itemC", 1:4),
      umxPath(unique.bivariate = paste0("itemC", 1:4)),
      umxPath(var="X")
  )
  plot(m1)

• NEWFEATURES: umx_cont_2_quantiles now allows returning cut points, better examples, level_names
  • BUGFIX: umx_cont_2_quantiles lowest threshold was empty
• NEWFEATURES: umxAPA now reports mode for factor data
• NEWFEATURES: 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 summarise 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 refModels if needed.
• IMPROVED: umxRAM remove_unused_manifests no longer updates manifestVars + leaves variable in data by default.
• RENAME: plot "showFixed" deprecated in favour 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. Ta da!!
• 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 refModel 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 rowwiseParallel and numberSubjects
• 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
• UPDATE: shorter run-time on 2sls code

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: Readme.md

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 summarise 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, seealso etc)
• DEEP: Removed dependency on formula.tools

umx 1.1.0 (December 2015, R 3.2.3/Wooden Christmas-Tree update

• 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 [email protected] 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 Likely R 3.1.3 (Smooth Sidewalk) ~ 2015-03-09

• First CRAN release! WOot!

umx 0.49.0

• IMPROVE Edge cases work
• IMPROVE Improving help files and feedback
• IMPROVE Rationalising fn names into @families

umx 0.45-beta

• Feature complete
• Bug squashing
• Optimising fn 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 rationalisation

umx 0.25-alpha

• Alpha release
• 80% feature complete
• Function prefix reflects usage:: umxMajor, umx_utility_function, xmuNotForUser

Reference manual