CVS commit: wip/R-VGAM

["Mike M. Volokhov" <bubuchka%users.sourceforge.net@localhost>]

Module name:    wip
Committed by:   bubuchka
Date:           Mon Dec 31 20:12:42 UTC 2012

Modified Files:
        wip/R-VGAM: Makefile distinfo

Log Message:
Update VGAM to version 0.9.0.

New features:

    o   Major change: VGAM family functions no longer have
        arguments such as earg, escale, eshape, etc. Arguments such
        as offset that used to be passed in via those arguments can
        be done directly through the link function. For example,
        gev(lshape = "logoff", eshape = list(offset = 0.5)) is
        replaced by gev(lshape = logoff(offset = 0.5)). The @misc
        slot retains the $link and $earg components, however,
        the latter is in a different format. Functions such as
        dtheta.deta(), d2theta.deta2(), eta2theta(), theta2eta()
        have been modified. Link functions have been simplified
        somewhat.  The casual user will probably not be affected,
        but programmers will. Sorry about this!
    o   New VGAM family functions:
        [dpqr]gompertz(), [dpqr]gumbelII(), [dpr]lindley(),
        [dpqr]makeham(), [dpqr]perks().
    o   df.residual() supports a new formula/equation for 'type = "lm"'.
    o   garma("reciprocal") supported.
    o   is.parallel() for constraint matrices summary.
    o   Improved family functions:
        these can handle multiple responses:
        benini(), chisq(), erlang(), exponential(), gamma1(), geometric(),
        gpd(), inv.gaussianff(), logff(), maxwell(), rayleigh(),
        yulesimon(), zetaff().
    o   New data set: hormone
        [http://www.stat.tamu.edu/~carroll/data/hormone_data.txt].
    o   If a factor response is not ordered then a warning
        is issued for acat(), cratio(), cumulative() and sratio().
    o   New dpqr-type functions:
        [dpqr]perks(), [dpqr]mperks(), [dpqr]mbeard().
    o   Argument 'parallel' added to gamma2().
    o   New link functions: mlogit().

Bug fixes and changes:

    o   zibinomial() had 1 wrong element in the EIM; one of the
        corrections of VGAM 0.8-4 was actually incorrect.
    o   zibinomial() blurb was wrong:
        previously was "(1 - pstr0) * prob / (1 - (1 - prob)^w)" where
        prob is the mean of the ordinary binomial distribution.
        Now is "(1 - pstr0) * prob".
    o   betaff() no longer has "A" and "B" arguments; they ar
        extracted from "lmu = elogit(min = A, max = B)". 
    o   binom2.rho() has "lmu" as a new argument 2.
    o   logistic2() has has zero = -2 as default, and can handle
        multiple responses.
    o   gengamma() returned the wrong mean (picked up by Andrea Venturini):
        not b * k but b * gamma(k + 1 / d) / gamma(k).
    o   tobit.Rd nows states vector values for 'Lower' and 'Upper'
        are permitted. Also, the @misc$Lower and @misc$Upper are
        matrices of the same dimension as the response.
    o   constraints.vlm(type = c("vlm", "lm")) has been changed to
        constraints.vlm(type = c("lm", "term")) [respectively].
    o   Rcam() renamed to Rcim(), and rcam() renamed to rcim().
        Class "rcam" changed to "rcim".
    o   Days changed from "Monday" to "Mon" in all crash data frames, etc.
    o   w.wz.merge() written to handle the working weights
        for multiple responses.
        w.y.check() written to check the integrity of prior
        weights and response.
    o   Argument 'sameScale' changed to 'eq.scale',
        'quantile.probs' in negbinomial-type families changed to 'probs.y'.
    o   No more warnings: dirmultinomial().
    o   Renamed arguments: benini(earg <- eshape),
        binormal(equalmean <- eq.mean),
        binormal(equalsd <- eq.sd),
    o   dirmultinomial() can handle a 1-row response [thanks to Peng Yu].
    o   weibull() gives improved warnings re. the shape parameter wrt
        regularity conditions.
    o   The 12 most time-consuming examples have been placed in a
        \dontrun{} to save time.
    o   Argument "prob.x" renamed to "probs.x".
    o   Argument "hbw" removed from iam().
    o   Argument 'name' is passed into .C and .Fortran() [in dotC()
        and dotFortran()] is now okay because the first argument
        is unnamed.


To generate a diff of this commit:
cvs -z3 rdiff -u -r1.1 -r1.2 wip/R-VGAM/distinfo
cvs -z3 rdiff -u -r1.2 -r1.3 wip/R-VGAM/Makefile

To view a diff of this commit:
http://pkgsrc-wip.cvs.sourceforge.net/pkgsrc-wip/wip/R-VGAM/distinfo?r1=1.1&r2=1.2
http://pkgsrc-wip.cvs.sourceforge.net/pkgsrc-wip/wip/R-VGAM/Makefile?r1=1.2&r2=1.3

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

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