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Add to tracker ] 2024-10-27 00:06:30 by Makoto Fujiwara | Files touched by this commit (1) |  |
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().
|
| 2024-10-27 00:01:48 by Makoto Fujiwara | Files touched by this commit (2) |
Log message: (math/R-VGAM) 4 of +TEST_DEPENDS, font issue still exists |
| 2024-01-24 12:49:19 by Makoto Fujiwara | Files touched by this commit (2) |
Log message:
(math/R-VGAM) Updated 1.1.8 to 1.1.9
CHANGES IN VGAM VERSION 1.1-9
NEW FEATURES
o Soon: VGAM will require R >= 4.4.0 because plot.profile
will move from \pkg{MASS} to \pkg{stats}. Sorry!
o Yettodo: modify dgaitdlog() to be like
dgaitdpois() in terms of safeguarding against too
much deflation and inflation (to return NaN).
Ditto to dgaitdzeta() and dgaitdnbinom().
Ditto for the p-type functions.
o New family functions: gammaff.mm(), hurea(d).
o New generic and/or methods functions: cops().
o acat(), cumulative(), cratio(), propodds(), sratio() handles
argument 'thresholds' equalling 'symmetric1' and 'symmetric0'.
Note from version 1.1-8 that 'equidistant' was added.
o Tested okay on R 4.3.0.
BUG FIXES and CHANGES
o wald.stat(..., orig.SE = TRUE, values0 = values0)
assumed that values0 == 0.
o [rq]zinegbin() did not handle the case 'munb = NULL'
when 'prob' was specified. Thanks to Giuseppe D for
finding this bug.
o acat(), cumulative(), cratio(), propodds(), sratio()
must have an intercept term.
o For vglm.fit(), slot "middle" is now "middle1",
"fini" is now "fini1", and a new "start1" \
slot added.
o bigamma.mckay() moved into VGAMdata 1.1-9.
o nakagami() has a zero = "shape" argument.
o [dp]gaitdpois() have more range checking, e.g., for too
much deflation and inflation.
o For more speed, several slow-checking .Rd files
have been changed by using \dontrun{}.
o summary(posbernoulli.tb()) failed to print the confidence
interval. Thanks to Carl Schwarz for picking this up.
o DFLOAT() changed to DBLE() in some .f files.
|
| 2023-06-15 12:57:41 by Makoto Fujiwara | Files touched by this commit (2) |
Log message:
(math/R-VGAM) Updated 1.1.6 to 1.1.8
CHANGES IN VGAM VERSION 1.1-8
NEW FEATURES
o Warnings from R-devel addressed.
o acat(), cumulative(), cratio(), sratio() have arguments
'thresholds', 'Tref', 'Treverse'.
o hdeffsev() has been edited.
o margeff() works for poissonff(), negbinomial() and
posnegbinomial() objects.
o multilogit() did not handle 1-row arguments correctly when
'inverse = FALSE'. Now vglm(y, multinomial) handles a 1-row y,
as well as acat and cumulative and [cs]ratio.
o rrvglm.fit() is more robust with respect to 'one.more'.
o plot.vgam() issues an error if sm.os()/sm.ps() is used with
deriv.arg > 0.
o New data set: budworm.
BUG FIXES and CHANGES
o rainbow.sky has a new green.
o zoabetaR() handles the argument 'constraints'. Thanks
to Riccardo Lo Martire for helping to find the bug.
CHANGES IN VGAM VERSION 1.1-7
NEW FEATURES
o Slot 'rqresslot' added to VGAM family functions, for implementing
randomized quantile residuals.
Available in about 50 family functions such as poissonff() currently.
o Slot 'rqresslot' added to VGAM family functions, for implementing
o Argument 'label.it' added to model.matrixvlm().
o New generic and/or methods functions: rqresid(), rqresiduals().
o New data set: lpossums.
o Tested okay on R 4.2.1.
BUG FIXES and CHANGES
o cumulative() has been replaced by its version prior
to 2021-05. Evidently some so-called improvements
created some bugs. Thanks to Johanna Neslehova for
alerting me to this.
o bistudentt() was documented wrong; thanks to
Iago Gine Vazquez for finding this.
o fill() now deprecated; replaced by fill4().
|
| 2022-05-21 15:14:49 by Makoto Fujiwara | Files touched by this commit (2) | |
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).
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| 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) | |
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 |
New packages: