doc: Added www/py-FxA version 0.7.7

(wiz)

www/Makefile: + py-FxA

(wiz)

www/py-FxA: import py-FxA-0.7.7

This is python library for interacting with the Firefox Accounts
ecosystem.

Eventually, it is planned to provide easy support for the following
features:

- being a direct firefox accounts authentication client
- being an FxA OAuth Service Provider
- accessing attached services
- helps interactions with Firefox Account servers wiht requests
  Authentication plugins.

(wiz)

doc: Added net/py-grequests version 0.7.0

(wiz)

net/Makefile: + py-grequests

(wiz)

net/py-grequests: import py-grequests-0.7.0

GRequests allows you to use Requests with Gevent to make asynchronous
HTTP Requests easily.

(wiz)

doc: Added www/py-BrowserID version 0.14.0

(wiz)

www/Makefile: + py-BrowserId

(wiz)

www/py-BrowserID: import py-BrowserID-0.14.0

This is a python client library for the BrowserID protocol that
underlies Mozilla Persona.

(wiz)

tex package updates

(markd)

tex-thmtools{,-doc}: update to 76

Worked around an `ntheorem` issue.

With `ntheorem`,  the theorem title cannot contain direct brackets, which may
come from the expansion of new `\MakeUppercase` or `\MakeLowercase`, starting
from LaTeX2e 2022-11-01.

(markd)

doc: Added security/py-hawkauthlib version 2.0.0

(wiz)

security/Makefile: + py-hawkauthlib

(wiz)

security/py-hawkauthlib: import py-hawkauthlib-2.0.0

This is a low-level library for implementing Hawk Access Authentication,
a simple HTTP request-signing scheme described.

To access resources using Hawk Access Authentication, the client
must have obtained a set of Hawk credentials including an id and
a secret key. They use these credentials to make signed requests
to the server.

(wiz)

tex-siunitx{,-doc}: update to 3.2.5

### Fixed
- Use of `\mathsf` for sanserif text documents

(markd)

tex-revtex{,-doc}: update to 4.2f

### Fixed
* Bug in \@fnsymbol with more than 8 authors.
* Detection of \eqnarray in newer LaTeX.

### Changed
* Use date format yyyy/mm/dd to be compatible with older LaTeX.

(markd)

doc: Updated pkgtools/url2pkg to 23.1.1

(wiz)

url2pkg: for python modules, assume Python 3

Bump version.

(wiz)

tex-repere{,-doc}: update to 23.05.b

Version:  23.05:
- Geometric transformations
- Background color
- Pixel art

Version:  23.05.b:
  A bug on rounding has been fixed

(markd)

tex-pstricks-add{,-doc}: update to 3.94

changes unknown

(markd)

tex-pstricks{,-doc}: update to 3.19

changes unknown

(markd)

tex-preview{,-doc}: update to 13.2

changes unknown

(markd)

doc: Added security/py-tokenlib version 2.0.0

(wiz)

security/Makefile: + py-tokenlib

(wiz)

security/py-tokenlib: import py-tokenlib-2.0.0

This is generic support library for doing token-based authentication.
You might use it to build a login system using bearer tokens,
two-legged oauth, or MAC Access authentication.

(wiz)

tex-polyglossia{,-doc}: update to 1.62

1.62
* \BCPdata was not fully expandable as required. Now it is.

1.61
Bug fixes
* Properly reset fonts on change to Latin-script other language
* Turn ^ shorthand off in aux file for Latin
* Fix stacking of nested languages and resulting bug in TOC language assignment
* Fix \greeknumeral{6}
* Fix (re)setting of scripts in inline language commands.

New features
* Introduce \BCPdata, a standardized way to gather localization information.

(markd)

tex-pdfcrop{,-doc}: update to 1.42

1.42
Minor update to the help text, to match options added in v1.41

1.41
* allow gswin64c in restricted mode, fix typos in messages
* add -q option
* don't print whole help msg for unknown options
* do not create two pages with xetex

(markd)

tex-newtxsf{,-doc}: update to 1.055

changes unknown

(markd)

tex-mptrees{,-doc}: update to 23.04

- Regular trees
- "Auto calculated" trees
- Macros to format nodes, leaves and probabilities

(markd)

tex-mpchess{,-doc}: update to 0.6

changes unknown

(markd)

tex-metapost{,-doc}: update to 2023

changes unknown

(markd)

tex-lineno: update to 5.3

1. Handle special value of \prevdepth=-1000pt;
  thanks to Yukai Chou and Frank Mittelbach.
2. Add package options `sep' and `width' for
  setting line number separation and width.
3. Add `twocolumn` support for `bframe` env;
  thanks to Yukai Chou.

(markd)

tex-lettrine{,-doc}: update to 2.40

Changes:
- file "lettrine.ins" deleted, "lettrine.dtx" auto-generates
  "lettrine.sty" and "lettrine.cfg";
- packages "xkeyval" and "minifp" are no longer required, kernel
  packages "ltxkeys" and "xfp" are used instead.
- The second mandatory argument of \lettrine is now printed using
  \unhcopy instead of \usebox (allows microtype action and footnote calls).

(markd)

tex-latex-firstaid-dev{,-doc}: update to 1.0z

changes unknown

(markd)

doc: Updated math/R-gsl to 2.1.8

(mef)

(math/R-gsl) Updated 2.1.7 to 2.1.8

# gsl 2.1-8

* Corrections to `configure` and `configure.ac` kindly provided by Kurt Hornik

(mef)

tex-latex-base-dev{,-doc}: update to 20230601pre3

changes unknown

(markd)

tex-lastpage{,-doc}: update to 2.0b

Bug fix: What should have been "}}{}" was "}{}}".

(markd)

tex-hyperref{,-doc}: update to 7.00y

* removed puenc-greekbasic.def and now load definitions from
  greek-fontenc instead.
* xr-hyper: unified and simplified the brace handling: all defined
  references have now five brace groups. Together with the change
  in LaTeX 2023-06-01 this will improve the combination of hyperref/
  non-hyperref documents and allow to merge with xr
* xr-hyper: changed default extension from dvi to pdf
* nameref: adapt label (re)definition to changes in LaTeX 2023-06-01

(markd)

tex-forloop{,-doc}: update to 3.0

changes unknown

(markd)

tex-footmisc{,-doc}: update to 6.0e

Fix a loading order incompatibility with marginfix package

(markd)

tex-evangelion-jfm{,-doc}: update to 1.0.4e

Add new feature `plain` for to be used in the verbatim environment.

(markd)

tex-etoc{,-doc}: update to 1.2c

changes unknown

(markd)

doc: Updated math/R-gtable to 0.3.3

(mef)

(math/R-gtable) Updated 0.3.0 to 0.3.3

# gtable 0.3.3

* Specify minimum rlang version

# gtable 0.3.2

* General upkeep

# gtable 0.3.1

* Re-documented to fix HTML issues in `.Rd`.

* gtable has been re-licensed as MIT (#85).

(mef)

tex-eso-pic{,-doc}: update to 3.0c

changes unknown

(markd)

tex-cweb{,-doc}: update to 4.3.67159

changes unknown

(markd)

doc: Updated math/R-gtools to 3.9.4

(mef)

(math/R-gtools) Updated 3.9.2 to 3.9.4

gtools 3.9.4
-------------------------

- correct `stars.pval` code/doc mismatch (GH #13)
- remove spurious `browser()` call in `lastAdd`

gtools 3.9.3 - 2022-07-08
-------------------------

- maintainer switch to Ben Bolker
- removed `assignEdgewise`/`unByteCodeAssign` (uses CRAN-deprecated
  `unlockBindings()` call)

(mef)

doc: Updated math/R-hexbin to 1.28.3

(mef)

(math/R-hexbin) Updated 1.28.2 to 1.28.3, NEWS.md unknown

(mef)

doc: Updated math/R-httpRequest to 0.0.11

(mef)

(math/R-httpRequest) Updated 0.0.10 to 0.0.11, NEWS.md unknown

(mef)

doc: Updated math/R-intervals to 0.15.3

(mef)

(math/R-intervals) Updated 0.15.2 to 0.15.3, NEWS.md unknown

(mef)

tex-csvsimple{,-doc}: update to 2.4.0

### Added
- New additive filter options
    - `and filter bool`
    - `and filter fp`
    - `and filter strcmp`
    - `and filter not strcmp`
    - `or filter bool`
    - `or filter fp`
    - `or filter strcmp`
    - `or filter not strcmp`
- Hook `csvsimple/csvline` added with example for
  doublequote replacement
- Option setting `separator = space`

### Changed
- The content of `range` is now expanded before processing it
- Implementation of `filter bool`, `filter fp`, `filter strcmp`,
  `filter not strcmp`

(markd)

tex-cjk-ko{,-doc}: update to 2.4

changes unknown

(markd)

tex-circuitikz{,-doc}: update to 1.6.2

Several more styling options for elements (body diodes, transformers, crossing),
a clock wedge shape for logical circuits, and documentation updates for ConTeXt,
mainly noticing the (upstream) elimination of the thin `siunitx` layer
compatibility macros.

- there is no `siunitx` support for ConTeXt, point to their `units` package
- Add styling of `transform core` lines
- Add `scale` to the bodydiode options
- Add styling of crossing vertical line
- Add `clockwedge` shape

(markd)

tex-beamer{,-doc}: update to 3.70

### Added
- making the aspect ratio available to the user via `\insertaspectratio`
- adding `title`, `author`, `institute`, `date` and `titlegraphic` templates to
  make title page easier to customise

### Changed
- smoothbars outer theme: moved the shading between headline and frametitle a
  bit down to avoid the miniframe appearing clipped off in some pdf viewers
- made top shading of Singapore theme transparent
- scale height of infolines headline with fontsize of `section in head/foot`
- calculate the head/footheight at the start of each frame instead of only at
  the start of the document
- making `\part` compatible with `\nameref`

### Fixed
- adding strut to the `frame number` and `page number` footlines to avoid
  jumping
- fixed bug in `inmargin` inner theme which would show the author indicator
  even if the author was empty

(markd)

tex-babel-greek: update to 1.13.2

Warn of unsupported (or misspelled) "modifiers"
(code contributed by Javier Bezos).

Fix upcasing of text using the Latin transliteration:
drop accents with `\DeclareUppercaseMapping` (new in LaTeX 2023).

(markd)

tex-babel{,-doc}: update to 3.89

3.89
* Deprecating \SetCase, \aliasshorthands, and 'strings' package
  option in the manual.
* The manual has been split in two documents: 'babel.pdf' is the
  user guide, and 'babel-code.pdf' is the code.
* Alternative syntax to pass 'modifiers' to babel languages.
* Code cleaned up: babel.def has been shortened dramatically,
  and babel.sty is a bit smaller.

3.88
* 37 new locale files: Abkhazian, Afar, Atsam, Baluchi, Bhojpuri,
  Blin, Corsican, Erzya, Ga, Geez, Guarani, Haryanvi, Inuktitut,
  Jju, Ligurian, Muscogee, Northern Sotho, Nyanja, N’Ko,
  Papiamento, Prussian, Rajasthani, Saho, Sicilian, Silesian,
  South Ndebele, Southern Sotho, Swati, Taroko, Tigre, Tok Pisin,
  Tsonga, Tswana, Tyap, Venda, Volapük, Wolaytta.
* Fixed a few month names in Greek locales (thanks to Günter Milde).
* New hook 'begindocument'.
* Feature preview: option 'casing' in '\babelprovide' (requires a
  future change in the LaTeX kernel).

(markd)

tex-animate{,-doc}: update to 20230515

changes unknown

(markd)

doc: Updated math/R-mapproj to 1.2.11

(mef)

(math/R-mapproj) Update 1.2.8 to 1.2.11, NEWS.md unknown

(mef)

doc: Updated math/R-modelr to 0.1.11

(mef)

(math/R-modelr) Updated 0.1.8 to 0.1.11

# modelr 0.1.11

* Fixes for R CMD check

# modelr 0.1.10

* Relax test for R-devel

# modelr 0.1.9

* Redocument to fix HTML issues in .Rd

(mef)

doc: Updated math/R-mvtnorm to 1.2.2

(mef)

(math/R-mvtnorm) Updated 1.3.1 to 1.2.2

Changes in Version 1.2-2 (2023-06-05):

  Bugfixes:
        * Fix overflow problem reported by ASAN.

  Documentation:
        * Be even more careful inverting / computing Cholesky factors
          for hessians (M1 and macos-arm64).

Changes in Version 1.2-1 (2023-06-02):

  Bugfixes:
        * Avoid attempts to allocate zero length arrays for
          one-dimensional problems.

  Documentation:
        * Catch M1mac problems with inverting hessians.

Changes in Version 1.2-0 (2023-06-02):

        * New 'lpmvnorm' function for computing multivariate normal
          log-likelihoods for interval-censored observations.

        * New 'slpmvnorm' function for computing the corresponding
          score function for interval-censored observations.

        * New 'ldmvnorm' function for computing multivariate normal
          log-likelihoods for exact observations.

        * New 'sldmvnorm' function for computing the corresponding
          score function for exact observations.

        * New 'ldpmvnorm' function for computing multivariate normal
          log-likelihoods for a mix of exact and interval-censored
          observations.

        * New 'sldpmvnorm' function for computing the corresponding
          score function for a mix of exact and interval-censored
          observations.

        * New class 'ltMatrices' representing multiple lower triangular
          matrices, with some useful methods.

        * New package vignette 'lmvnorm_src' describing these new
          features.

        * 'pmvnorm', 'qmvnorm', 'pmvt', and 'qmvt' gain a 'seed'
          argument.

        * Regression tests were improved.

        * Internal standardization is described better in the docs,
          suggested by Chris Wymant.

        * New 'NEWS' file, the old file containing information up to
          version 1.1-3 is available as 'NEWS.old'.

(mef)

(cad/ghdl) remove  patches/patch-src_ortho_llvm6_llvm-cbindings.cpp

(mef)

doc: Updated cad/ghdl to 3.0.0

(mef)

(cad/ghdl) Updated 2.0 to 3.0

## [2023-03-08] 3.0.0

[Milestone v3.0 膈����(https://github.com/ghdl/ghdl/milestone/11?closed=1)

- Handle IEEE operators for static expressions.
- Improved support of VHDL 2008 (still!).
- Start support of VHDL 2019 (`--std=19`).
- pyGHDL:
  - Experimental support to preserve VHDL code comments for documentation
  extraction.
  - Experimental packaging with a platform-specific shared library for
  standalone installation using PIP.
  - DOM: dependency graphs, instantiation graphs (design hierarchy),
  file dependencies (compile order).
- Pre-releases are published to GitHub Releases and assets are uploaded to
  pre-releases and releases.

(mef)

doc: Updated math/R-nimble to 1.0.0

(mef)

(math/R-nimble) Updated 0.13.1 to 1.0.0

#                            CHANGES IN VERSION 1.0.0 (May 2023)

This release introduces tools for automatic differentiation in NIMBLE.

## USER LEVEL CHANGES

- Add tools for automatic differentiation. Functionality includes:

    -- The ability to differentiate nimbleFunctions with respect
    to input arguments in a flexible way.

    -- The ability to differentiate `model$calculate()` calls
    with respect to model node elements.

    -- Functionality that enables Hamiltonian Monte Carlo (provided in the
    `nimbleHMC` package).

    -- A parameter transformation system to work in unconstrained parameter
    spaces when model parameters have constrained domains.

- Add Laplace approximation algorithm, allowing a user to approximate
the marginal likelihood (integration/marginalizing over random effects/
latent process values) and find the MLE.

- Improve aspects of WAIC (PR #1256):

    -- Provide aggregate and per-chain WAIC when `perChainWAIC` is `TRUE`.

    -- Report number of `pWAIC` values greater than 0.4.

    -- Warn user if WAIC is enabled but not set to `TRUE` in `runMCMC`.

    -- Improve clarity in `help(WAIC)`.

- Reduce the default adaptation interval for the `AF_slice` sampler to 200.

- Improved control of `addSampler` method of MCMC
configuration objects (PR #1293):

    -- `expandTarget` argument controls whether nodes specified in
      `target` undergo expansion via `expandNodeNames`, adding a
      separate sampler instance for each resulting node.

    -- When `expandTarget = TRUE`, the `scalarComponents` argument is
      passed as the `returnScalarComponents` argument to `expandNodeNames`.

    -- Removed `nodes` argument as redundant.  Target nodes are
      uniquely specified using the `target` argument.

- Improve handling of resetting of scale when `adaptive=FALSE` (PR #1275).

- Allow `dcat` to have a `prob` vector of length 1 (PR #1251).

- Add error trapping for MCMC `thin` argument not positive and integer-valued
(PR #1250).

- Enhance discussion of MCMC initialization in the User Manual (issue #1247).

- Enhance discussion of indexing in loops and variables in User Manual,
including differences from JAGS.

- Rework language in `help(buildMCMC)` to improve clarity.

- Add information on predefined nimbleLists to the User Manual.

- Improve error message when user-defined distribution has incorrect dimension
for `x`.

- Improve error message when mistakenly using `T()` in deterministic rather than
  stochastic model declaration.

- Improve error-trapping when a loop index is incorrectly used in indexing
a block of a variable (PR #1289).

- Error trap use of reduction operations on scalars (PR #1281).

- Error trap some cases of incorrect return type in user-defined simulation
('r') functions (PR #1280).

- Error trap case where a variable name is also used as a loop index variable
(PR #1278).

- Error trap setting deterministic nodes as data in `setData` (PR #1269).

- Better error trap of wrong size/dimensions of in `setInits` (PR #1260).

- Export `clearCompiled`, allowing users to clear compiled objects and unload
the shared library produced during nimble's compilation process (on non-Windows
operating systems).

## BUG FIXES

- Fix bug producing integer overflow in `getDependencyPathCountOneNode`
and improve efficiency of checking maximum number of paths in conjugacy
checking (PR #1322).

- Fix long-standing memory leak in `dinvwish_chol` (PR #1320).

- Fix bug giving incorrect results for `runCrossValidate`, when using the
default MSE loss function and any user-defined loss functions,
but not the 'predictive' loss function. Also, calculate loss when using
the predictive loss using the compiled model rather than the uncompiled model.
(PRs #1298, #1299).

- Fix bug in conjugacy checking that caused incorrect identification of
conjugate relationships with subsets and supersets of multivariate nodes,
as well as inconsistent slices of multivariate nodes (PR #1290).

- Fix `runMCMC` to reset the WAIC state when rerun (PR #1256).

- Fix reset mechanism for WAIC so that one can get WAIC from all the samples
in a chain that is created by multiple calls to the MCMC `$run` method even
when `getWAIC` is called in the middle (PR #1310).

- Fix bug affecting `d=2` case in uncompiled `RW_lkj_corr_cholesky` sampler
(PR #1273).

- Fix aliasing issue arising in assignment operations such as
`nf$a <- nf$a[1:3]` (PR 1301).

- Fix assignment into a block of a model variable (PR #1300).

- Fix compilation error when using `nimSeq` with integers (PR #1282).

- Fix scoping of argument evaluation for `replaceSamplers` method (PR #1287).

- Fix a corner case where particular indexing in model code prevents model
building (PR #1279).

- Fix handling of right-hand side only nodes so not flagged as deterministic
(issue #1269).

- Error trap and fix a bug in handling particular cases in list-like subsetting
(PR #1259).

- Make optimDefaultControlList handle default values completely and with
  consistent compiled and uncompiled behavior.

- make nimOptim respect parscale control parameter.

- Update manual installation chapter and `INSTALL` links to gfortran on MacOS.

## DEVELOPER LEVEL CHANGES

- Take `nimbleCppADbaseClass` out of `libnimble.a` and instead make a
session-specific .o file from it to address AD-related crashes on some OSes. (PR
#1318)

- Remove `nimOptim_model` functionality. This fixes build warning on MacOS
  involving `nimOptim` (PR #1276).

- Update `Eigen` copyright dates.

- Fix invisible return of `NULL` in nimbleFunctions without explicit return
statements (PR #1254).

- Fix inconsistent use of offset in internal conversion functions (PR #1277).

- Remove references to unsupported `trace` (issue #1262).

#                            CHANGES IN VERSION 0.13.2 (May 2023)

## DEVELOPER LEVEL CHANGES

- Remove code triggering Windows warnings about writing bytes into region of
  size 0 by modifying `setLength`.

- Remove use of C++11 standard, per CRAN requirements. As part of this, replace
  use of `std::ptr_fun` (PR #1292).

(mef)

doc: Updated math/R-ncdf4 to 1.21

(mef)

(math/R-ncdf4) Updated 1.17 to 1.21

Release 1.21 (2023-01-05) Minor change to fix compatibility with
latest version of R (removed C lang sprintf). Another small update
to libraries linked for windows by request of Tomas Kalibera.

Release 1.20 (2022-11-30) Small warning message bug fix (thank you
to Javier Vaquero-Martinez!) and updates to windows Makefile requested by
CRAN (Tomas Kalibera).

Release 1.19 (2021-12-14) Changed as per request of R developers
to build correctly on Windows using the new R toolchain (Rtools42).
Specifically, added the supplided Makevars.ucrt to src/.

Release 1.18 (2021-11-17) Fixed a bug in the way files with
complicated nested groups were processed.

(mef)

Added math/R-pracma versioln 2.4.2

(mef)

math/R-pracma: import R-pracma-2.4.2

Provides a large number of functions from numerical analysis and
linear algebra, numerical optimization, differential equations, time
series, plus some well-known special mathematical functions. Uses
'MATLAB' function names where appropriate to simplify porting.

(mef)

doc: Updated math/R-igraph to 1.4.3

(mef)

(math/R-igraph) Updated 1.4.1 to 1.4.3

# igraph 1.4.3

## Internal

  - Fix tests for dev waldo (#779, @hadley).

  - Fix linking on Windows: gfortran needs quadmath. (#778).

## Documentation

  - Mention limitation of Pajek reader (#776).

# igraph 1.4.2

## Breaking changes

- Remove `igraph.eigen.default()` and `eigen_defaults`, introduce
  internal `eigen_defaults()` as a function (#741).

- Remove broken `nexus*()` functions (#705), and `srand()` (#701).

## C core

- Update C core.

- ARPACK-based calculations are now interruptible.

- `shortest_paths()` and `all_shortest_paths()` no longer crash when
  an invalid `from` vertex is passed and weights are being used.

See
[diff](https://github.com/igraph/igraph/compare/87c70998344a39b44218f7af903bf62b8bbf3e71...98304787bc811bf709be5aeddea7b570c370988e)
for details.

## Printing

- Use true vertex names for printing vertex sets. If a vertex set
  captures a relationship between vertices (e.g., the `father`
  component of `bfs()`), the vertex set is printed as a named vector
  (#754).

- Suggest restarting R session after fatal error (#745).

## Bug fixes

- `as_long_data_frame()` now correctly processes vertex attributes and
  works with graphs without vertex attributes (#748).

- `as.hclust(hrg.fit(g))` works again (#721).

## Documentation

- The documentation is now available at <https://igraph.org/> (#743).

- Reorganize function reference (#662).

- Replace `graph()` with `make_graph()` in examples (#738).

- Add docs for `as.hclust.igraphHRG()` (#733).

- Merged man page of `hub_score()` and `authority_score()` (#698).

- Refactor contributors listing (#647).

- Improve "family" titles (#679).

- Improve docs of ego/neighborhood functions.

- Improve `transitivity()` docs.

## Internal

- Introduce cpp11 package to improve error handling in the long run (#720).

- Avoid longjmp for error handling and interrupts (#751).

- `as.hclust.igraphHRG` uses `.Call()` interface (#727).

(mef)

(devel/R-testthat) Add buildlink3.mk, see wip/R-nloptr

(mef)

doc: Updated x11/vte3 to 0.72.2

(gutteridge)

vte3: update to 0.72.2

This only has one upstream change:
emulation: Fix infinite loop on non-number OSC 104 param

While here, disable the Vala API, as it isn't used by any dependants in
pkgsrc, has a large dependency footprint, and has caused build issues in
the past.

(gutteridge)

Borrow upstream gnulib commit 0814a293 to fix static_assert on
Solaris 11.4.

(schmonz)

doc: Updated math/R-psych to 2.3.3

(mef)

(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)

(mef)