Subject: CVS commit: pkgsrc/math/R-VGAM
From: Makoto Fujiwara
Date: 2022-05-21 15:14:49
Message id: 20220521131449.9B2D0FAEB@cvs.NetBSD.org

Log Message:
(math/R-VGAM) Updated 1.1.1 to 1.1.6

                CHANGES IN VGAM VERSION 1.1-6

NEW FEATURES

    o   Most of the GAIT regression code have new arguments 'd.mlm'
        and 'd.mix' but mainly only the dpqr-type functions work!
        Some other functions should work such as gaitdpoisson() and
        dgaitplot(). Also, is.deflated() and goffset() are new.
    o   New family function: gaitdnbinomial().
    o   Upgraded family functions: gaitpoisson() becomes gaitdpoisson(),
        gaitlog() becomes gaitdlog(), gaitzeta() becomes gaitdzeta().
    o   New generic and/or methods functions: KLD(), Pheapseep().
    o   Some colours are pre-defined for GAITD regression, and the default
        colour scheme has changed.
    o   trim.constraints() has a new 'intercepts = TRUE' argument.
    o   Many family functions have a 'dpqrfun' component in the @infos slot.
        Useful to tie in the modelling function with its density, etc.
    o   binormal() has a new 'rho.arg' argument.
    o   Some link functions handle deriv = 4: e.g., loglink(), logitlink().
    o   vglmfit@misc$history gives the convergence history.
    o   Improvements to clogloglink() at the boundary 1.
    o   hdeff.vglm() has a new argument 'theta0'.
    o   wald.stat() cleaned up internally.
    o   Tested okay on R 4.1.2.

BUG FIXES and CHANGES

    o   All GAIT regression code has arguments 'alt.mlm' changed to
        'a.mlm', 'inf.mix' changed to 'i.mix', etc. Colours have changed.
        [dpqr]gaitpois() have been renamed to [dpqr]gaitdpois(),
        and gaitpoisson() to gaitdpoisson().
    o   [dpqr]zanegbin() no longer supports argument 'prob'.
    o   hdeff() makes a recursive call if any NAs are in the answer and
        fd.only == FALSE. So the answer should then be a 'proper' one.
    o   Code involving anova() for VGLMs/VGAMs changed to avoid an
        error when loading in \pkg{semTools}.
    o   spikeplot(..., use.table = TRUE) failed wrt x.use and y.use.
    o   vcov() slightly faster for "vglm" objects.  Thanks to Frank Harrell
        for comments that led to this.
    o   linkfun.vglm() changed to linkfunvglm().

                CHANGES IN VGAM VERSION 1.1-5

NEW FEATURES

    o   New functions: meangait(), spikeplot(), trim.constraints().
    o   iam(i, 1:M, M = M) now works, for selecting a whole row,
        and similarly for a column.
    o   Tested okay on R 4.0.3.

BUG FIXES and CHANGES

    o   gait[log,poisson,zeta](): arguments llambda.[ai] and lshape.[ai]
        equal llambda.p and lshape.p by default. This means only one
        argument needs be assigned in order to change them all.
    o   [dpqr]genpois[12]() has argument 'mean' changed to 'meanpar'.
    o   gait[log,zeta]() bug fixed wrt missing 'allprobs'.
    o   qfoldnorm() now uses the bisection method. Thanks to
        Mauricio Romero for a suggestion that led to this.
    o   gait[log,poisson,zeta]() compute the sandwich formula
        explicitly for the working weights; this has speed gains.
        Their @deriv avoids nested for() loops too.
        Their initial value grids have become coarser.
    o   Functions moved to VGAMdata 1.1-5: yip88, bellff(dr), tikuv(dpqr).

                CHANGES IN VGAM VERSION 1.1-4

NEW FEATURES

    o   Functions score.stat() and wald.stat() offer greater flexibility
        by some new arguments, and 'as.summary' changed to 'orig.SE'.
    o   Influence() computes the influence functions of a "vglm" object.
    o   Methods functions hdeff.matrix() and hdeff.numeric() are new.
    o   Family function slot genpoisson()@ weight was updated with
        the EIM derived by Easton Huch, and after major changes,
        genpoisson() was renamed to genpoisson0().
    o   New functions: [dpqr]gaitnbinom(), [dpqr]gaitgenpois[012](),
        [dpqr]gaitbinom(), dgaitplot(), plotdgait.vglm(), Trunc().
    o   New family functions: genpoisson[12](dpqr), gaitpoisson()
        so that gaitpoisson.mix() and gaitpoisson.mlm() were removed,
        gaitlog() so that gaitlog.mix() was removed,
        gaitzeta() so that gaitzeta.mix() was removed.
    o   Tested okay on R 4.0.3.

BUG FIXES and CHANGES

    o   Deprecated: dgenpois(), genpoisson(), [dpqr]gaitnbinom.m[ix,lm]().
        gatnbinomial.m[ix,lm](dpqr), [dpqr]gaitbinom.mlm(),
        gaitpoisson.mix(), gaitpoisson.mlm(), gabinomial.mlm(),
        gtbinomial().
    o   'lhs.prob' changed to 'cdf.max.s'.
    o   Argument changes for all GAIT code, e.g., 'alter' changed to
        'alt.mix' or 'alt.mlm', 'byrow.arg' to 'byrow.ai', etc.
    o   Functions moved to VGAMdata 1.1-4: oalog, oilog, otlog,
        oapospois, oipospois, otpospois, oazeta, oizeta, otzeta, oizipf,
        oiposbinomial(dpqr), [dpqr]posbinom, [dpqr]pospois, [dpqr]posnegbin.
    o   Pearson residuals no longer printed by default in a summary
        of a "vglm" object: presid = FALSE.
    o   Some changes made to plot(vgam()) code for changes in R 4.0.0,
        especially if the covariate is a character/factor.
        Now avoids "coercing argument of type 'double' to logical" warning.
    o   negbinomial(lmu = "nbcanlink") had an error relating to \ 
"newemu".

                CHANGES IN VGAM VERSION 1.1-3

NEW FEATURES

    o   New functions: [dpqr]gaitpois(), [dpqr]gaitlog(), [dpqr]gaitzeta(),
        dextlogF().
    o   New family functions: gatnbinomial.mix(dpqr),
        gaitlog.mix(dpqr), gaitpoisson.mix(dpqr), gaitpoisson.mlm(dpqr),
        extlogF1(d).
    o   New generic and/or methods functions: altered(),
        inflated(), truncated(), specialsvglm(),
        fix.crossing(), is.crossing().
    o   Coef.vlm() handles models with contiguous "multilogitlink"s,
        e.g., gaitpoisson.mlm().
    o   get.offset() is now defined as a generic function (returns the
        n x M matrix of offsets by default).
    o   Some .f files have been pruned of unnecessary code.
    o   New data set: V2.
    o   Tested okay on R 4.0.0.

BUG FIXES and CHANGES

    o   Another attempt to .Deprecated()  all link function names
        which do not end in "link", e.g., loglink() replaces loge(),
        logitlink() replaces logit().
    o   gatpoisson.mix() (now merged into gaitpoisson.mix())
        reorders its linear/additive predictors and now handles
        length(alter) == 0 (default, so equivalent to poissonff())
        and length(alter) == 1.
        Ditto for gatnbinomial.mlm(), etc.
    o   Three argument mismatches found in .f and .c code.
    o   qlog() and qyules() buggy wrt interval selection prior to
        applying bisection.
    o   'Rank mismatches' flagged by gfortran10 fixed, by not
        calling two subroutines.
    o   [dpqr]gaitpois.mlm() and [dpqr]gaitpois.mix() have been combined into
        [dpqr]gaitpois().

                CHANGES IN VGAM VERSION 1.1-2

NEW FEATURES

    o   New generic and/or methods functions: add1.vglm(),
        dfterms(), drop1.vglm(), extractAIC.vglm(),
        rootogram4vglm() [based on \pkg{countreg}],
        step4vglm().
    o   New family functions: gabinomial.mlm(), gatnbinomial.mlm(dpqr),
        gatpoisson.mix(dpqr), gatpoisson.mlm(dpqr).
    o   New functions: [dpqr]zipfmb(),
        [dpqr]gaitbinom.mlm(), [dpqr]gaitnbinom.mlm(),
        [dpqr]gaitpois.mlm(),  [dpqr]gaitnbinom.mix(),
        [dpqr]gaitpois.mix().
        Note that the naming conventions have changed somewhat, especially
        regarding the negative binomial distribution.
    o   Decommissioned functions:
        gapoisson(), gtpoisson(),
        [dpqr]gabinom(), [dpqr]gapois(),
        [dpqr]gibinom(), [dpqr]gipois(),
        [dpqr]gtbinom(), [dpqr]gtpois().
    o   eta2theta() should be able to handle links for, e.g.,
        gatpoisson.mlm(), gibinomial().
    o   posbernoulli.t() has a 'type.fitted' argument.
    o   gtpoisson.mlm() supports type.fitted = "Pobs.a",
        gipoisson.mlm() supports type.fitted = "Pstr.i".
    o   New data set: backPain2.
    o   Cleve Moler added to DESCRIPTION as a contributor, to reflect
        the use of LINPACK.
    o   Tested okay on R 3.6.1.

BUG FIXES and CHANGES

    o   Use of old link function names now result in a call to
        .Deprecated(), except for a selected few such as logit() and
        probitlink()---this will only be allowed for a limited time.
    o   negbinomial()@initialize bug fixed for "nbcanlink()" and
        multiple responses; thanks to Victor Miranda.
    o   cens.poisson() gave a warning upon a summary().
        Thanks to Jens Heumann for picking this up.
    o   bisection.basic() returns a warning, not an error, if
        it cannot find an interval which covers the root.
    o   Rank() has an improved implementation and documentation.
    o   anova.vglm() had some bugs---thanks to Thamron Keowmani for
        finding them.
    o   posnormal() failed when 'constraints' was inputted---thanks
        to Michael Zamo for picking this up.
    o   Improvements to yules(dq).

Files:
RevisionActionfile
1.6modifypkgsrc/math/R-VGAM/distinfo
1.6modifypkgsrc/math/R-VGAM/Makefile