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(math/R-statmod) Updated 1.4.36 to 1.5.0

28 Dec 2022: statmod 1.5.0

- New function expectedDeviance() to compute expected values and variances of
  unit deviances for linear exponential families, using C code written by
  Lizhong Chen. Add Lizhong Chen as package author.
- Replace NAMESPACE exportPattern() with export().
- New argument `n0` for compareGrowthCurves() and CompareTwoGrownCurves() to
  avoid permutation p-values exactly zero.
- Add link to Phipson & Smyth postprint on arXiv in help references for permp()
  and compareGrowthCurves().

12 Aug 2022: statmod 1.4.37

- Fix mathematic equations in remlscor.Rd.
- Explain simulation method of power.fisher.test() in power.Rd.
- Update http to https URLs in elda.Rd, gauss.quad.Rd and gauss.quad.prob.Rd.
- Change url to doi for reference in elda.Rd.
- Add doi for reference in fitNBP.Rd.

(math/R-statmod) Updated 1.4.32 to 1.4.36

25 Aug 2020: Statmod 1.4.35

- Fix Bug in tweedie(link.power=0) so that the resulting functions
  $linkinv() and $mu.eta() preserve the attributes of their
  arguments.

16 Feb 2020: statmod 1.4.34

- Improve the model description provided in the remlscoregamma() help
  page.

- tweedie() now checks whether `var.power` or `link.power` are
  character strings instead of numeric. If `var.power` is one of the
  standard family names ("gaussian", "poisson", "gamma" or
  "inverse.gaussian") or `link.power` is one of the standard link
  functions ("identity","log","inverse") then the argument is reset
  to the corresponding numerical value with a message, otherwise an
  informative error message is given.

- Cleaning up of internal code to avoid partial matching of function
  arguments, attributes or list component names. The automatic package
  tests are now run with the warnPartialMatchArgs,
  warnPartialMatchAttr and warnPartialMatchDollar options all set to
  TRUE.

 4 Jan 2020: statmod 1.4.33

- The components returned by mixedModel2Fit() relating to fixed
  coefficients are now documented explicitly. The help page has been
  corrected to refer to the argument `only.varcomp` instead of
  `fixed.estimates`. The vector of `reml.residuals` is no longer
  part of the output.

- The test file has been slightly revised using zapsmall() so ensure
  that the test output file remains correct for R with ATLAS BLAS.

Update all R packages to canonical form.

The canonical form [1] of an R package Makefile includes the
following:

- The first stanza includes R_PKGNAME, R_PKGVER, PKGREVISION (as
  needed), and CATEGORIES.

- HOMEPAGE is not present but defined in math/R/Makefile.extension to
  refer to the CRAN web page describing the package.  Other relevant
  web pages are often linked from there via the URL field.

This updates all current R packages to this form, which will make
regular updates _much_ easier, especially using pkgtools/R2pkg.

[1] http://mail-index.netbsd.org/tech-pkg/2019/08/02/msg021711.html

R-statmod: update to version 1.4.32.

Update to the canonical form of an R package and fix the LICENSE
field.

Remove MASTER_SITES= from individual R package Makefiles.

Each R package should include ../../math/R/Makefile.extension, which also
defines MASTER_SITES.  Consequently, it is redundant for the individual
packages to do the same.  Package-specific definitions also prevent
redefining MASTER_SITES in a single common place.

Update to 1.4.30

Upstream changes:
16 June 2017: statmod 1.4.30

- Bug fix to qinvgauss(). In some case the gamma approximation used
  for small right tail probabilities was taking the initial value
  outside the domain of convergence.

27 February 2017: statmod 1.4.29

- rinvgauss() now accurately handles large or infinite values for the
  mean or dispersion.

26 February 2017: statmod 1.4.28

- R_registerRoutines is now used to register the Fortran subroutine
  gaussq2.

- pinvgauss() and qinvgauss() now use a gamma approximation when the
  coefficient of variation is very small.

17 December 2016: statmod 1.4.27

- qinvgauss() now supports mean=Inf.

Update to 1.4.26

Upstream changes:
28 August 2016: statmod 1.4.26

- Fortran function gaussq2 updated to Fortran 77.

 5 August 2016: statmod 1.4.25

- Add CITATION file.

- pinvgauss() now uses an asymptotic approximation to compute right
  tail probabilities for extreme large quantiles.  This allows it to
  give correct right tail probabilities for virtually any quantile.

- Fix to qinvgauss() to avoid NA values when computing extreme tail
  quantiles where the inverse Gaussian density is subject to floating
  underflow.

- Bug fix to qresiduals() and qresid.invgauss() for the inverse
  Guassian distribution.

Update to 1.4.24

Upstream changes:
 2 February 2016: statmod 1.4.24

- speedup for rinvgauss() by replacing rchisq() with rnorm() and
  rbinom() with runif().

- speedup for qinvgauss() by using qgamma as starting approximation
  for very small right tail probabilities, and inverse chisq as
  starting approximation for very small left tail probabilities.

- qinvgauss() now computes Newton step using log probabilities
  and a Taylor series expansion for small steps.  This improves
  accuracy in extreme cases.  The stopping criterion for the Newton
  iteration has been revised.

- Bug fix to dinvgauss(), pinvgauss() and qinvgauss() which were not
  preserving attributes of the first argument.

30 December 2015: statmod 1.4.23

- qinvgauss() has been improved to return best achievable machine
  accuracy.  It now checks for backtracking of the Newton iteration.

- dinvgauss() and pinvgauss() now check for a wider range of special
  cases.  This allows them to give valid results in some cases
  for infinite or missing parameter values and for x outside the
  support of the distribution.

26 October 2015: statmod 1.4.22

- Functions needed from the stats and graphics packages are now
  explicitly imported into the package NAMESPACE.

Update to 1.4.21

Upstream changes:
30 March 2015: statmod 1.4.21

- qinvgauss() now treats input arguments of different lengths or NA
  parameter values more carefully.

- elda() now gracefully removes structural zeros, i.e., rows where
  the number of cells or the number of assays is zero.

- S3 print and plot methods for "limdil" class now registered.

- Use of require("tweedie") in the qres.tweedie() code replaced by
  requireNameSpace("tweedie").

Update to 1.4.20
Update LICENSE

Upstream changes:
30 May 2014: statmod 1.4.20

- Considerable work on the inverse Gaussian functions dinvgauss(),
  pinvgauss(), qinvgauss() and rinvgauss().  The parameter arguments
  are changed to mean, shape and dispersion instead of mu and lambda.
  The functions now include arguments lower.tail and log.p, meaning
  that right-tailed probabilities can be used and probabilities can
  be specified on the log-scale.  Good numerical precision is
  maintained in these case.  The functions now respect attributes,
  so that a matrix argument for example will produce a matrix result.
  Checking is now done for missing values and invalid parameter
  values on an element-wise basis.  A technical report has been
  written to describe the methodology behind qinvgauss().

- This file has been renamed to NEWS instead of changelog.txt.

- The introductory help page previously called 1.Introduction is now
  named statmod-package.

13 April 2014: statmod 1.4.19

- qinvgauss() now uses a globally convergent Newton iteration, which
  produces accurate values for a greater range of parameter values.

- glmnb.fit() now supports weights.

Update to 1.4.18

Upstream changes:
27 September 2013: statmod 1.4.18
- Update reference for permp().
- bug fix to elda() so that it returns NA for the tests instead of
  giving an error when the Fisher information for the slope isNA.
- Exact roles of authors specified in DESCRIPTION file.
- All usage lines in help files wrapped at 90 characters to ensure
  that code is not truncated in pdf manual.

Update to 1.4.17
(No upstream changelog)

Update to 1.4.16

Update to statmod v1.4.14, add LICENSE and regularize package files.

Update to the latest version of the module along with R update

Update R-statmod to 1.3.6

Changes unknown

Whitespace cleanup, courtesy of pkglint.
Patch provided by Sergey Svishchev in private mail.

Recursive revision bump / recommended bump for gettext ABI change.

Imported R-statmod from pkgsrc-wip.

Miscellaneous biostatistical modeling functions.

Initial revision