./math/R-VGAM, Vector generalized linear and additive models

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Branch: CURRENT, Version: 1.1.6, Package name: R-VGAM-1.1.6, Maintainer: mishka

Vector generalized linear and additive models, and associated models
(Reduced-Rank VGLMs, Quadratic RR-VGLMs, Reduced-Rank VGAMs). This
package fits many models and distribution by maximum likelihood
estimation (MLE) or penalized MLE. Also fits constrained ordination
models in ecology.


Required to run:
[lang/g95] [math/R]

Required to build:
[pkgtools/cwrappers]

Master sites: (Expand)


Version history: (Expand)


CVS history: (Expand)


   2022-05-21 15:14:49 by Makoto Fujiwara | Files touched by this commit (2) | Package updated
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).
   2021-10-26 12:56:13 by Nia Alarie | Files touched by this commit (458)
Log message:
math: Replace RMD160 checksums with BLAKE2s checksums

All checksums have been double-checked against existing RMD160 and
SHA512 hashes
   2021-10-07 16:28:36 by Nia Alarie | Files touched by this commit (458)
Log message:
math: Remove SHA1 hashes for distfiles
   2019-08-08 21:53:58 by Brook Milligan | Files touched by this commit (189) | Package updated
Log message:
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
   2018-07-28 16:40:53 by Brook Milligan | Files touched by this commit (126)
Log message:
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.
   2018-06-01 09:10:54 by Wen Heping | Files touched by this commit (2)
Log message:
Update to 1.0.5

Upstream changes:
CHANGES IN VGAM VERSION 1.0-5

NEW FEATURES

    o   extlogit() now handles 'deriv = 3'.
    o   Generic function hdeff() implements an analytic solution
        for the following families: borel.tanner(), felix(), lindley().
        For almost all other families, finite-difference approximations
        to derivatives means that first and second derivatives can be
        computed, even with models with 'xij' terms.
    o   Generic function wald.stat() implements Wald tests with SEs evaluated
        at the null values, not at the original MLE, so do not suffer from the
        Hauck-Donner effect.
    o   "vglm" objects have a new "charfun" slot, for the
        characteristic function.
    o   "summary.vglm" and "summary.vlm" objects have new
        "coef4lrt0", "coef4score0", "coef4wald0" \ 
slots, for
        storing the 'Wald table' equivalent of LRTs, score tests and
        modified Wald tests.
        The latter has its SEs computed at the null values with the
        other coefficients obtained by further IRLS iterations, etc.
        Function summaryvglm() has arguments 'lrt0.arg', 'score0.arg',
        'wald0.arg'.
    o   TIC() is new, for the Takeuchi's Information Criterion.
        Thanks to Khedhaouiria Dikra for suggesting this.
    o   mills.ratio() and mills.ratio2() are exported.
    o   New functions: lrt.stat(), score.stat(), wald.stat(),
        which.etas(), which.xij().
    o   cauchy1() and cauchy() handle multiple responses and have
        been modernized a bit.
    o   Tested okay on R 3.4.3.

BUG FIXES and CHANGES

    o   Setting 'deriv.arg' a positive value in plotvgam() when there
        are no s() terms results in a warning.
        Thanks to Barry Goodwin for detecting this.
    o   cens.poisson() can better handle large lambda values, at least for
        left and right censored data (but not for interval-censored data yet).
        Thanks to Eugenie Hunsicker for picking up deficiencies in the code.
    o   In multinomial.Rd, it was stated that setting parallel = TRUE
        did not make the intercepts the same. It does make them the same.
        Thanks to Stuart Coles for picking this up.
    o   binomialff(multiple.responses = TRUE) returned an incorrect deviance.
    o   bilogistic() uses SFS rather than BFGS as its algorithm.
    o   Deprecated: lrp(), normal1() [use uninormal() instead].
   2018-01-22 20:22:44 by Min Sik Kim | Files touched by this commit (3) | Package updated
Log message:
math/R-VGAM: Import version 1.0-4 from pkgsrc-wip

Vector generalized linear and additive models, and associated models
(Reduced-Rank VGLMs, Quadratic RR-VGLMs, Reduced-Rank VGAMs). This
package fits many models and distribution by maximum likelihood
estimation (MLE) or penalized MLE. Also fits constrained ordination
models in ecology.

Packaged by Mike M. Volokhov, and updated by Kamil Rytarowski and me.