Log Message:
(math/R-psych) Updated 2.2.5 to 2.3.2

Changes in psych version 2.3.2 (2023-02-15):

  Introduction:

         * The psych package includes functions and data sets to do
           classic and modern psychometrics and to analyze personality
           and experimental psychological data sets. The psych package
           has been developed as a supplement to courses in research
           methods in psychology, personality research, and graduate
           level psychometric theory courses. The functions are a
           supplement to the text (in progress): An introduction to
           psychometric theory with applications in R. The functions
           are also written to further research in the
           Personality-Motivation-Cognition Laboratory at Northwestern
           University.

         * Additional functions are added sporadically.

         * This news file reports changes that have been made as the
           package has been developed.

         * To report bugs, send email to
           <mailto:revelle@northwestern.edu> using bug.report.

         * Version 2.3.1 is the development release of the psych
           package. It is available as a source file for Macs or PCs in
           the repository at <https://personality-project.org/r/>. The
           released version on CRAN is 2.2.9 The second digit reflects
           the year (i.e., 2023), the third set the month (i.e., 2.2.5
           was released in May of 2022) the last two digits of
           development versions reflect either an minor change or the
           day of any modifications, e.g. 1.8.3.3 was the third attempt
           to get 1.8.3 released.  1.7.8 was released in August, 2017.

         * To install this development version, use the command:
           install.packages("psych",
           repos="https://personality-project.org/r", \ 
type="source").
           Remember to restart R and library(psych) to make the new
           version active.

  Additions:

         * Modified alpha so that it returns a keys list rather than a
           vector

         * Added the smooth option to fa, fa.stats and fa.extension.
           This by default had been true.  Now allows users to specify
           that they don't want to smooth improper correlation
           matrices.  Affects just the fa.stats output.

         * Improved the documentation for irt.fa, and fa.extend

         * Change the verbiage in omega to reflect that we are finding
           sums of squared loadings rather than eigenvalues (Thanks to
           Niels Waller for this point.)

         * Added the percentage of items with their highest correlation
           on the keyed scale (as an index of scale quality) Requested
           by Asghar Minaei.

         * Added the MIMS and MIMT matrices to scoreOverlap and to
           scoreItems These matrices reflect the average item
           correlation within and between scales (MIMS) and the average
           item x scale correlation within and between scales (MIMT).
           Suggested by Asghar Minaei.

         * Added options to the correlations in cortest and also
           improved the documentation.

         * Added alpha2r to convert alpha to average r (a trivial, one
           liner, but convenient sometimes)

         * Added crossValidationBoot to do multiple derivations / cross
           validations

         * Modified factorScore so that it will give scores even in the
           case of missing data.  Scores are found from the mean of the
           non-missing items on a factor. To just get scores for
           non-missing subjects, specify impute="none"

         * Added faReg /faRegression to make use of fa.extend to find
           the regressions with dependent variables in a more
           understandable output.  Modified extend.diagram to draw
           these as well.  Although developed to use fa.extend, faReg
           will also do regressions based upon factor scores from the
           raw data.

         * Added SAPAfy to "sapafy" data matrices. (a trivial but
           useful helper function)

         * Improved examples for iclust.

         * Following a suggestion from Ethan Fosse, I have reversed the
           direction of the arrow in ICLUST to go from the items to the
           clusters.  This is now the default but the old style can
           still be drawn using iclust.diagram with the bottomup
           parameter set to FALSE.

         * Minor tweaks to corPlot allowing the fixing of trailing
           zeros and the number of digits to display.

         * Improved corPlotUpperLowerCi to find correlations (and Cis)
           if given raw data.  This improves usability, because the
           naive user would expect that behavior.

         * Added the show option to lowerCor so that it will just find
           but not display the correlations. Defaults to TRUE.

         * Added corCi and corr.test output to the objects that
           error.dots can display

         * Added eigenCi to find and plot the confidence intervals of
           eigen values.

         * Added more timings and changed the default size for bigCor

  Bugs Fixed:

         * Fixed scoreItems so that the delete=TRUE option actually
           works. (Based upon a report by Christopher Wiese ) Also
           improved the documentation about why this is needed.

         * Fixed a typo in fa with the fm=alpha method.  Reported by
           Philipp Doebler.

         * Finally fixed a bug in bestItems so that it works with raw
           data.

         * Fixed a very minor bug in polychoric that was throwing a
           warning and now is breaking.  Results do not change.
           (Reported by Goran Kardum)

         * Fixed cor.smooth so that if it is given raw data, it will
           first find the correlations.

         * Fixed minor typo in fa.Rd (thanks to Ian Buller for pointing
           this out).

         * Fixed crossValidation to work with subsets of variables.

         * Fixed autoR to handle case of single variable when grouping.
           Reported by Alex Smith and thanks to various suggestions on
           stack overflow.

         * Fixed scoreItems so that it will give names to unlabeled
           data and keys (was breaking GAabbreviate)

         * Fixed crossValidationBoot for case of multiple DVs

         * Fixed reliability for the case of single item scales

         * Minor improvements to cohen.d to allow easier use of
           dictionary and sorting

         * Fixed cor.smooth to handle covariances matrices (reported by
           Douglas Otto as a problem in fa)

         * Finally fixed bug in bestScales so it will handle
           correlation matrices

         * Fixed bestScales so it will produce a keys list ordered by
           correlation for correlation input.

         * Fixed a bug in cohen.kappa for weighted Kappa.  Reported by
           Ju, Yu-Jeng.

         * Fix a bug in bigCor that was not working for polychoric
           correlations

         * changed the use of the abline(h=1) in fa.parallel to draw it
           for pc not for fa. Pointed out by George Harrison.

         * Added lmCor as an alias to setCor.  (lmCor is much more
           intuitive as it is lm for correlation matrices).

To do version 2.2.9:

        * Suggestions are welcome, but the current list includes the
          following (and has included for a long time, so lets be
          patient):

        * Add confirmatory clustering to ICLUST

        * Get cluster scores in ICLUST -- analogous to factor scores
          (requested by Ben Shalet)

        * Add the ability to create multiple groups in sim.irt
          functions

        * Find canonical loadings in setCor

        * Add omega factor extension figure option (requested by Sylia
          Wilson)

        * Add option to do subject density and item density plot to IRT
          plot.

        * add the ability to scale radar plots of raw data from min to
          max, and add a scale to radar and spider plots (e.g. circular
          histograms)

        * add the ability to add labels to lavaan.diagram

        * need to check the code in scoreIrt to make sure it is right.

        * To help those who want to simulate a bifactor model, make it
          explicit.

        * Check the bias in bootstrap resampling using cor.ci

        * add symmetric=TRUE to eigen calls, think about
          only.values=TRUE for some cases

        * Add an analysis of DIF to the irt functions (requested by
          David Condon)

        * Add some power functions.

        * Add CIs for means and skews as an option (for describe as
          well as describeBy) Requested by Aaron Wichman

        * Fix statsBy to handle the case of NULL groups.  (particularly
          for the cors=TRUE option).  I think I have done this.

        * Add a function for the Meng, Rosenthal, Rubin tests for
          multiple comparisons of correlations.

        * Clean up documentation of score.irt etc.  (partly done)

        * Add complexity to omega solution

        * Add statistic to fa to report max fa. (partly done with fm =
          minrank)

        * Parallize iterations for confidence intervals in omega

        * Probably should drop much of the stats when doing iterations
          with fa or omega

        * Find unbiased cis when doing bootstrap

        * Allow the choice between regression vs. correlation in esem
          between X and Y sets.

        * Allow for different rotation options in X and Y sets in esem,
          allow omega style hierarchical structure for x (and y)

        * Fix bug in esem.diagram for ability- bifactor 3,3
          simple=FALSE,cut=.2

        * Improve documentation for esem and cosinor

        * Add interbattery diagram to the structure diagram function.

        * Add Krippendorf's alpha?

        * Add the ability to weight factor residuals to allow WLMS

        * Add the Hull method for number of factors

        * Add an option for the correlation type in bestScales
          (requested by Lorien Elleman).

        * Change help file examples so they are cleaner for people who
          example(fn)

        * Make the main functions more "tidy" in terms of their output

        * Add testthat functionality

        * Add parse capabilities to error.bars, error.dots, spider,
          etc. so that grouping variables can be specified in formula
          mode.  Partially done (not yet for spider)

        * Possible bug in cohen.kappa confidence intervals (reported by
          Marco Fornili)

        * Need to add documentation to mediate/moderate/setCor for what
          dfs are used and why.

        * Add an n.iter option to pca (requested by Michael Wood, but I
          am not sure why)

        * There is a bug in bestItems for the case of no iterations and
          dictionary = something

        * Fix bug in fa.lookup for omega g values that are negative

        * Fix bug in bestScales that does not report items if not
          iterating

        * Adjust stats in fa.extend to report the raw and then the
          extended values

        * Improve documentation for extension diagram to clarify that
          it works with fa.results

        * Add just check variables specified for being numeric (instead
          of entire data.frame) (suggested by Fransisco Wilheim)

        * Pretty up the output from mediate (perhaps make a
          mediate2latex function)

        * Improve the print function for bassAckwards

  To do:

         * Problem with scoreIrt.1pl with keys of length 2

         * Change examples to dontrun rather than commented out

         * Check the raw df in esem

         * Add RMSEA, TFI, etc. to esem (requested by Gabe Orona )

         * Clean up the various sim functions so that they are better
           documented.  (partly done.)

         * Add formula mode to lowerCor and lowerMat (to be able to
           choose a few variables in a data set) Probably not useful

         * Need to fix bug in alpha where it finds R from cov2cor
           instead of directly (reported by Karl Ove Hufthammer )

         * Add the ability to get factor scores for higher order
           factors (requested by Brandon Vaughn). Partly done in omega,
           but there are problems associated with the entire problem of
           factor scores.

         * Fix a bug in alpha when finding average R (need to use cor
           rather than cov2cor when treating missing data)

         * Add weight option to statsBy (but the question is how to
           handle missing data)

         * Modify lavaan.diagram so that it handles cfa output better

         * Fix the mediate output so that it matches the summary

         * Adjust the se for correlations (in bestScales) to take into
           account the pairwise count, rather than the n.obs

         * Give model fit in setCor?

         * Improve documentation for thurstone.  Would help if we had
           an example of scaling.

         * scoreIrt.2pl needs to be able to adjust for group
           differences correctly

         * scoreIrt does not work unless keys are specified for nf > 1
           (reported by Andrew Olney)

         * Add the ability to return the true scores for subjects when
           simulating structures.  This will help fitting reliability
           models This is now done for sim and sim.minor,
           sim.hierarchical, others are in process.

         * Possible problem in pooled correlations for statsBy

         * Think about improvements in itemLookup to show means if
           desired

         * Fix bug in polychoric where it doesn't handle empty cells
           very well. (reported by Bj<c3><b6>rn \ 
B<c3><bc>denbender)

         * Fix bug in mediate for multiple dependent variables
           (reported by Martin Zeschke)

         * scoreItem should find the mean item correlation with
           na.rm=TRUE (Liz D)

         * create a scoreFastBy

         * improve the help menu for sim.multi and return the latent
           values

         * think about linking person scores to item difficulty scores
           in IRT

         * Left justify content in lookupItems (not sure how to do
           this)

         * Consider using the Jennrich approach to standard errors of
           rotated loadings

         * Still need to fix mediate to handle more than 1 DVs

         * Possible problem with the use of try in several functions.

         * Need to fix omega so that alpha is correctly calculated in
           case of no general factor

         * It would be nice to add an option to display confidence
           intervals of correlations in error.dots

Changes in psych version 2.2.12 (2022-12-14):

  Additions:

         * Modified alpha so that it returns a keys list rather than a
           vector

         * Added the smooth option to fa, fa.stats and fa.extension.
           This by default had been true.  Now allows users to specify
           that they don't want to smooth improper correlation
           matrices.  Affects just the fa.stats output.

         * Improved the documentation for irt.fa, and fa.extend

         * Change the verbiage in omega to reflect that we are finding
           sums of squared loadings rather than eigenvalues (Thanks to
           Niels Waller for this point.)

         * Added the percentage of items with their highest correlation
           on the keyed scale (as an index of scale quality) Requested
           by Asghar Minaei.

         * Added the MIMS and MIMT matrices to scoreOverlap and to
           scoreItems These matrices reflect the average item
           correlation within and between scales (MIMS) and the average
           item x scale correlation within and between scales (MIMT).
           Suggested by Asghar Minaei.

         * Added options to the correlations in cortest and also
           improved the documentation.

         * Added crossValidationBoot to do multiple derivations / cross
           validations

         * Modified factorScore so that it will give scores even in the
           case of missing data.  Scores are found from the mean of the
           non-missing items on a factor. To just get scores for
           non-missing subjects, specify impute="none"

         * Added faReg /faRegression to make use of fa.extend to find
           the regressions with dependent variables in a more
           understandable output.  Modified extend.diagram to draw
           these as well.  Although developed to use fa.extend, faReg
           will also do regressions based upon factor scores from the
           raw data.

         * Added SAPAfy to "sapafy" data matrices. (a trivial but
           useful helper function)

         * Added minor factors as an option to sim.congeneric.

         * Improveds the documentation for sim.minor to reflect the
           MacCallum paper.  Improved the code so that it screens for
           impossible models.

         * Added/improved documentation for iclust.

         * Added the order object to iclust to allow for sorting
           matrices by cluster structure.

         * Added a sqrt option to VSS.scree and fa.parallel output
           (thanks to Marco Del Giudice for the suggestion)

         * Added a coefficients object for setCor and mediate

  Bugs Fixed:

         * Fixed scoreItems so that the delete=TRUE option actually
           works. (Based upon a report by Christopher Wiese ) Also
           improved the documentation about why this is needed.

         * Fixed a typo in fa with the fm=alpha method.  Reported by
           Philipp Doebler.

         * Finally fixed a bug in bestItems so that it works with raw
           data.

         * Fixed a very minor bug in polychoric that was throwing a
           warning and now is breaking.  Results do not change.
           (Reported by Goran Kardum)

         * Fixed cor.smooth so that if it is given raw data, it will
           first find the correlations.

         * Fixed minor typo in fa.Rd (thansks to Ian Buller for
           pointing this out).

         * Fixed crossValidation to work with subsets of variables.

         * Fixed autoR to handle case of single variable when grouping.
           Reported by Alex Smith and thanks to various suggestions on
           stack overflow.

         * Fixed scoreItems so that it will give names to unlabeled
           data and keys (was breaking GAabbreviate)

         * Added the valid object to the pca function (to match the
           help file.)  Reported by Tomosumi Haitani)