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).
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