CVS commit: pkgsrc/math/R-VGAM

["Makoto Fujiwara" <mef%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   mef
Date:           Sat Oct 26 22:06:30 UTC 2024

Modified Files:
        pkgsrc/math/R-VGAM: Makefile

Log Message:
(math/R-VGAM) Updated 1.1.9 to 1.1.12, kind of commit log correction, sorry

        CHANGES IN VGAM VERSION 1.1-12
NEW FEATURES

    o   hdeffsev2() and DDfun() are new.
    o   Some link functions handle up to deriv = 9: e.g.,
        loglink(), logitlink().
    o   Tested okay on R 4.4.1.

BUG FIXES and CHANGES

    o   Passes stricter CHECKing, esp. with Rd
        \link{} targets that were missing package anchors.
        And R_Calloc() and R_Free() used.
    o   More \dontrun{} added to .Rd files, to quicken
        the checking.
    o   Several functions associated with the Laplace
        distribution moved to VGAMdata.
    o   VGAM now depends on R >= 4.1.0 which was released
        3 years ago.

                CHANGES IN VGAM VERSION 1.1-11
NEW FEATURES

    o   AIC() and BIC() methods function for "drrvglm" objects.
    o   simulate() works with multinomial(), cumulative(),
        and other categorical family functions.
    o   New family functions: N1binomial(dr), N1poisson(dr).
    o   Helper functions: is.Identity(), unmaskA(), is.non0().
    o   Tested okay on R 4.4.0.

BUG FIXES and CHANGES

    o   "rrvglm" and "drrvglm" objects now fitted under
        a common framework and algorithm.
    o   summary(vglmObject) no longer prints the
        Pearson residuals by default. Some other output may
        be suppressed if they are printed.
    o   Some argument shuffling in binormalcop().
        Argument 'stdze' means the mean and sd parameters
        may be estimated.
    o   Some argument shuffling in rrvglm.control(). Also,
        the following arguments are no longer supported:
        'Wmat', 'Norrr'", 'Svd.arg', 'Uncorrelated.latvar',
        'Alpha', 'scaleA'.
        Also, 'Crow1positive = NULL' for no effect.
    o   summary.rrvglm(h.step = 0.005) and
        summary.drrvglm(h.step = 0.005) are now defaults.
    o   More checking of links performed if vfl = TRUE.
    o   gaitdnbinomial() now assigns earg[[2]] (needed
        for rootogram4()).
    o   Coef(drrvglmObject)@A and summary(drrvglmObject) now agree.
    o   The handling of vglm(na.action) is more similar to lm() and
        glm().  Ditto for vgam().

                CHANGES IN VGAM VERSION 1.1-10
NEW FEATURES

    o   Doubly-constrained RRVGLMs are partially implemented.
        They have class "drrvglm". More checking
        is needed to iron out all problems.
    o   plotvgam(..., main = letters[1:3]) will work by
        having 3 different 'main's.
    o   chisq() has 'squared' for the chi distribution.
    o   New family functions: extbetabinomial(dpqr),
        gensh(dpqr).
    o   New functions: asinlink(), sqrtlink(), alogitlink(),
        sloglink(), lcalogitlink(), lcsloglink(), cloglink(),
        log1plink().
    o   Argument 'ynames = FALSE' added to multinomial(),
        acat(), [cs]ratio(), propodds() and cumulative(),
        which can make the output more readable. Thanks to
        Daniel Smith for the suggestion.
    o   New functions: CM.symm[01](), CM.equid(), CM.free(),
        CM.ones(), CM.qnorm().
    o   negbinomial(vfl = FALSE) has been added.
    o   Tested okay on R 4.3.2.

BUG FIXES and CHANGES

    o   acat(), cumulative(), cratio(), propodds(), sratio() handles
        argument 'Thresh' which can be assigned 'symm1', 'symm0',
        'free', 'qnorm', etc.
    o   All remnants of is.R() removed, for R 4.4.0.
    o   Some fortran code now avoids some warnings found by
        a Debian C compiler.
    o   dgaitdplot() stop()s when the parameters are
        outside the parameter space.
    o   demo() examples have been updated to run fully.
    o   "rrvglm" objects have new slots "A.est" and "C.est"
        which simplifies the code.
    o   "rrvglm" objects are estimated using the "alternating"
         'Algorithm' only, and the "derivative" method withdrawn.
    o   For RR-VGLMs and DRR-VGLMs, 'kill.all' changed to 'omit123'.
    o   rrvglm.control() has some of parameters changed
        (for more stringent convergence).
    o   Some argument shuffling: genpoisson[12](). That is,
        the order has been changed.
    o   summary.rrvglm() swapping of pasting block matrices
        according to 'fixA' was wrong.
    o   replace.constraints() renamed to replaceCMs().
    o   dtruncpareto1() no longer returns 0 at lower and upper.
        Thanks to Jason Li for picking this up.
    o   summaryvgam() and summarypvgam() calls
        summaryvglm(HDEtest = FALSE) to
        simplify things and avoid unnecessary complications.
    o   expected.betabin.ab renamed to Ebbin.ab.
    o   Deprecated: gordlink(),  pordlink(),
        nbordlink(),  nbord2link().


To generate a diff of this commit:
cvs rdiff -u -r1.9 -r1.10 pkgsrc/math/R-VGAM/Makefile

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

Modified files:

Index: pkgsrc/math/R-VGAM/Makefile
diff -u pkgsrc/math/R-VGAM/Makefile:1.9 pkgsrc/math/R-VGAM/Makefile:1.10
--- pkgsrc/math/R-VGAM/Makefile:1.9     Sat Oct 26 22:01:48 2024
+++ pkgsrc/math/R-VGAM/Makefile Sat Oct 26 22:06:30 2024
@@ -1,4 +1,4 @@
-# $NetBSD: Makefile,v 1.9 2024/10/26 22:01:48 mef Exp $
+# $NetBSD: Makefile,v 1.10 2024/10/26 22:06:30 mef Exp $
 
 R_PKGNAME=     VGAM
 R_PKGVER=      1.1-12
@@ -9,8 +9,6 @@ LICENSE=        gnu-gpl-v3
 
 USE_LANGUAGES= c fortran
 
-# Package suggested but not available: 'VGAMextra'
-# Package which this enhances but not available for checking: 'VGAMdata'
 TEST_DEPENDS+= R-VGAMdata-[0-9]*:../../math/R-VGAMdata
 TEST_DEPENDS+= R-VGAMextra-[0-9]*:../../math/R-VGAMextra