tbates/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).