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* *
* 0.8 SERIES NEWS *
* *
**************************************************
CHANGES IN VGAM VERSION 0.8-4
NEW FEATURES
o VGAM family functions renamed (Ouch!):
1. 'betabinom.ab' renamed to 'betabinomial.ab'.
o Other functions renamed (Ouch!):
1. '[dpr]betabin' renamed to '[dpr]betabinom' etc.;
2. '[dpr]betabin.ab' renamed to '[dpr]betabinom.ab' etc.;
o Slot names changed (Ouch!):
1. 'link' renamed to 'linkfun' for class "vglmff";
2. 'inverse' renamed to 'linkinv' for class "vglmff".
o Extra arguments added to freund61().
o New VGAM family functions:
abbott(), zigeometric(dpqr), huber1().
o New functions: [p]polono(),
depvar() generic for the dependent (response) variable,
Qvar() and explink() for quasi-variances.
o Improved functions: [d]polono(), [dr]betabin() handles rho = 0
(suggested by Peng Yu).
o Improved family functions: normal1() handles matrix 'weights'.
o Defaults changed: [dr]betabin(rho = 0).
o New methods functions: nobs(), nvar(), depvar().
o Renaming: fitted.vlm() is now fittedvlm(),
persp.qrrvglm() is now perspqrrvglm(),
predict.qrrvglm() is now predictqrrvglm(),
predict.vglm() is now predictvglm().
o New data sets: finney44.
o VGAM now depends on R >= 2.11.1.
o Tested okay on R 2.14.0.
BUG FIXES
o zibinomial() had 2 wrong elements in the EIM,
thanks to Alan Welsh for picking this up.
o margeff() for cumulative() was faulty.
o blurb slot of binormal() was faulty.
o betabinomial() did not return the estimated rho in @misc$rho as
did betabinomial.ab().
o kumar() did not initialize well with non-integer prior weights.
o rdagum() did not handle the 'scale' argument correctly.
o codes() in s() is defunct so it has been replaced.
CHANGES IN VGAM VERSION 0.8-3
NEW FEATURES
o Argument names changed (Ouch!):
1. 'method.init' renamed to 'imethod';
2. 'k' renamed to 'size' in negbinomial(), zanegbinomial(),
posnegbinomial(), and zinegbinomial():
e.g., 'lk' renamed to 'lsize', 'ik' renamed to 'isize', etc.
o New data sets: hued, huie, huse, ugss, uscrime;
usagrain renamed to usgrain.
o The "prior.weights" slot is now a "matrix", not "numeric".
o [dpr]betabin.ab() now handles size = 0. Thanks to Robert Wolpert
for picking up this bug.
o New VGAM family functions:
[d]binormal(), [dr]huggins91() but this is not working properly,
[dpqr]explogarithmic(), polya().
o New functions: [dpqr]tobit().
o Improved family functions: tobit() implements the proper EIM for the
standard model, dcennormal1() has some new arguments [and renamed],
cennormal1(), cenrayleigh() renamed.
o VGAM now depends on R >= 2.10.0.
o Rcam(), moffset(), etc. for RCAMs have been improved and modified.
o VGAM family functions currently withdrawn: frechet3().
o Tested ok on R 2.13.0.
BUG FIXES
o tobit()@loglikelihood had omitted the constant in dnorm().
Also, tobit() uses simulated Fisher scoring (for nonstandard model).
o moffset() was buggy.
o ABO() is a little more robust.
o dirichlet()@loglikelihood miscalculated.
Ditto for gaussian()@loglikelihood (constants were omitted).
Thanks to Arne Henningsen for picking up these bugs.
o zipoissonff() did not initialize correctly and labelling was wrong
with matrix responses.
CHANGES IN VGAM VERSION 0.8-2
NEW FEATURES
o Objects of class "vglmff" have a "infos" slot to give
information about the family.
o New functions: lambertW(), rcam(), wffc.P3(),
wffc.P3star(), confint_rrnb(), confint_nb1().
o New VGAM family functions:
binom2.Rho(), [dpqr]expgeometric(),
[dpqr]genrayleigh(), [dpqr]huber(),
[dpqr]koenker(), studentt[23](), zipoissonff().
o Argument 'imethod' changed to 'method.init' for some
families, e.g., cnormal1(), tobit(), weibull().
o Improvements have been made to binom2.rho().
o Improved family functions:
negbinomial() has a new argument 'parallel',
micmen() has more initial value choices and fitting algorithms,
kumar(), studentt() and studentt2() now implement the EIM,
normal1() can handle multiple responses.
o Argument names changed:
'init.rho' renamed to 'irho' in binom2.rho(),
'a' renamed to 'scale' in rayleigh(),
'Structural.zero' renamed to 'szero' thoughout.
o zapoisson() permutes the linear/additive predictors.
o Several families such as negbinomial(), z[ai]negbinomial(),
zapoisson(), gamma2(), handle zero = c(-2, 3), say,
i.e., negative and positive values.
o New data sets: about half a dozen road crash data frames of
2009 NZ data.
o constraints(vglmfit) now has a 'type' argument that can be fed
into the original fit (type = "lm") as the constraints argument.
o vchol() takes drastic action to avoid infinite looping: it sets
the working weights to be proportional to the order-M diagonal
matrix.
o lognormal() and lognormal3() now have zero = 2 as the default
(was zero = NULL).
o Some variable names within grc() changed, e.g., Row. and not Row.
o The smartpred package within VGAM has updated poly(), ns(),
bs() and scale() for R version 2.12.0 (2010-10-15).
Calls to smartpredenv are now VGAM:::smartpredenv.
BUG FIXES
o VGAM:::VGAMenv is used now to avoid problems locating
this environment.
o Input of the mustart, etastart and coefstart arguments at
the solution should results in only one iteration being needed.
o binomialff() and categorical familes (e.g., multinomial) only
accept a factor or non-negative counts as the response.
This allows the 'weights' vector to have any value really.
In the past the denominator of a sample proportion was allowed
via the 'weights' argument.
o wffc.P1() had some rounding problems, e.g., with 0.280 m.
CHANGES IN VGAM VERSION 0.8-1
NEW FEATURES
o Most of the Fortran 77 code has been converted to C.
This change will be largely hidden from most users
but there may be the occasional bug not detected.
Much of the heavy work was done by Alvin Sou.
o lms.bcn()@loglikelihood incorporates the constants in
the log-likelihood.
o Also, no more F90 code! This means less portability/platform
problems.
o bivgamma.mckay, formerly mckaygamma2(), has been modified
substantially.
o Improvements have been made to simplex() and
[dr]simplex() have been written.
o Expectile functions for the uniform, normal and
exponential distributions: [dpqr]-type functions.
o cqo() has EqualTolerances = TRUE and ITolerances = FALSE as
the default now. The result is that cqo() should work without
the environmental variables being scaled.
If it is scaled then setting ITolerances = TRUE will result
in greater speed and requiring less memory.
o Families that deal with proportions, such as binomialff() and
betabinomial(), incorporate weights separately from the weights
generated by the response/counts. So the weights argument can
now have any positive values.
o rrvglm(..., Norrr = NULL) can be used so that the reduced-rank
regression is applied to every variable including the intercept.
o Renaming: ggamma() is now gengamma(), etc.
o Improved functions: negbinomial() has a few new arguments.
BUG FIXES
o Deviance.categorical.data.vgam did not handle small
fitted probabilities.
o binom2.rho() could produce small negative fitted probabilities.
o seq2binomial() did not initialize 'mvector'.
o zeta() crashed on some platforms.
o cqo() appears to be working again with the new C code.
o cao() still not working with the new C code.
o zapoisson() did not implement the elambda argument correctly.
o Tested ok on R 2.11.1.
**************************************************
* *
* 0.7 SERIES NEWS *
* *
**************************************************
CHANGES IN VGAM VERSION 0.7-10
NEW FEATURES
o Surv() renamed to Surv4(), class "SurvS4" renamed to "Surv4".
o coef(summary(vglmObject)) returns a 3-column matrix of estimates,
standard errors and Wald statistics, rather than coef(vglmObject)
in the past.
o Improved VGAM family functions: fff() uses simulated Fisher
scoring now and has slightly better initial values.
o New VGAM family functions:
propodds(reverse) is equivalent to
cumulative(parallel=TRUE, reverse=reverse) (for convenience only).
o Compatible with R 2.10.1 and the article "The VGAM package
for categorical data analysis," Journal of Statistical Software,
2010. A vignette based on this paper is included.
o Argument w.als renamed to w.aml in amlnormal().
BUG FIXES
o VGAM family functions: fff() had poor initial values.
o betabinomial()@loglikelihood required 'ycounts' to be integer.
o [dpqr]betanorm() were written but not in the NAMESPACE.
CHANGES IN VGAM VERSION 0.7-9
NEW FEATURES
o New functions: margeff() for marginal effects of a vglm()
"multinomial" or "cumulative" model.
o Almost all VGAM family functions now have a "loglikelihood"
slot that incorporates any constants in the density function.
Hence the fitted likelihood may differ by a constant from
previous results.
In particular, models such as multinomial(), cumulative()
and binom2.or() have this new feature.
o vglm() now has a modified 'xij' argument which implements
eta-specific covariates. Usage now involves the form2' argument,
and the 'xij' argument does not interfere with constraint matrices.
Documentation is supplied on the VGAM website, in particular,
http://www.stat.auckland.ac.nz/~yee/VGAM/doc/xij.pdf
o cases.names() and variable.names() methods functions
written for vglm()/vgam() objects.
o cumulative() has improved initial values, especially for
long data format, i.e., when each row of the data frame is an
observation rather than inputting a matrix of counts.
o rrvglm() handles a factor response without giving a warning.
o New data: olympic.
o testf90.f90 has been renamed to testf90.f95. This may decrease
the incidences of compiler problems on some platforms (f95 seems
more popular than f90).
o For cqo() objects: AIC(), resid() have been written.
o Improved functions: negbinomial() default initial values are
more robust to outliers in the response, betabinomial() and
betabin.ab() have better initialization and "loglikelihood"
slot matches dbetabin.ab(log=TRUE).
o Renamed VGAM family functions: alsqreg() becomes amlnormal().
o Renamed arguments: lmu replaces link.mu in zibinomial().
o dzeta(p) has changed wrt 'p'.
o The functions summary.lms() and summary.rc.exponential() are
no longer distributed to avoid a warning wrt S3 vs S4
methods dispatch.
o The VGAM family functions for genetic models have been improved,
e.g., some basic error checking.
Also some changes in the names of the parameters, e.g.,
"q" to "pB" for ABO(), plus some switching of the order of the
arguments.
BUG FIXES
o VGAM interferes much less in regard to generic functions
such as predict(), fitted(), resid(), wrt other packages and
also including base's lm(), glm(), etc.
o AIC() method for rrvglm() objects was wrong (did not account
for argument 'Structural.zero').
o dzibinom(log=TRUE) was wrong.
CHANGES IN VGAM VERSION 0.7-8
NEW FEATURES
o [dpqr]benf() written for Benford's distribution.
o plog() and dlog() improved.
o multinomial() now has a refLevel argument to specify the
reference or baseline level of the factor.
o binom2.or() has a new argument 'morerobust'.
o Renamed arguments in mix2normal1().
o DeLury() written.
o [dpqr]-type functions related to the negative binomial distribution
have changed wrt argument names and order.
o [pq]posnegbin(), [dpqr]zapois(), [dr]zanegbin() written.
o [dpqr]zinb() renamed to [dpqr]zinegbin().
o lms.bcn(), lms.bcg(), lms.yjn() have zero=c(1,3) as the new default.
This will increase the chances of successive convergence.
o Renamed arguments in lms.bcn(), lms.bcg(), lms.yjn(), e.g.,
link.sigma is now lsigma.
Some new arguments added too, e.g., llambda.
o Works for R 2.5.0 and later (not 2.4.0 and later).
Compatible with R 2.7.2.
o Contains Fortran 90 code (since 0.7-7, actually). This will
cause problems on older Linux machines without such a
compiler. Actually, removing the .f90 file(s) will not be too
much of a problem as there is very little F90 code in use by
the package at the moment.
o New functions: dbinom2.rho(), rbinom2.rho(), dposnegbin().
o New data: wffc, wffc.indiv, wffc.teams, wffc.nc.
o Improved functions: binom2.rho(), micmen(), negbinomial(),
poissonff(), posnegbinomial(), zanegbinomial(),
o A new form2 argument has been added to vglm().
VGAM family functions such as micmen() have the regressor inputted
using form2 now, rather than the regressor argument.
The resulting usage is a more elegant.
Fitted objects have a few more slots and formulas put in set
places on the object.
o AIC() methods functions has been modified.
BUG FIXES
o The big bug whereby vgam(... ~ s(x), ... ) did not work under
Windows was due to a single array element that was not initialized.
Evidently, Linux compilers seemed to have set it to zero.
Funny, the code has worked for decade or so...
o dposbinom() was buggy at x=0. Also it now handles size=0 and
prob=0 or prob=1.
o pzipois() was buggy at x<0.
o dbetabin.ab(log=T) was incorrect outside its support.
o zipf() did not handle 0 < s < 1.
o data(ruge) was faulty.
o summary(rrvglmObject) failed.
o persp.cao(ylim=) did not work.
o plotvgam() failed when se=TRUE and which.cf was specified.
CHANGES IN VGAM VERSION 0.7-7
NEW FEATURES
o Labelling changes: binom2.or() uses "oratio" instead of "OR" (stands
for the odds ratio).
o New VGAM family functions:
zipebcom().
o New functions: dbinom2.or(), rbinom2.or().
o binom2.or() has new arguments 'imu1, 'imu2' and 'ioratio' for
inputting optional marginal probabilities and odds ratio.
The third element of the score vector uses a new formula.
o [dpqr]zinb() has arguments prob and munb set to NULL by default.
o Compatible with R 2.7.0.
BUG FIXES
o gaussianff()@loglikelihood was buggy.
o all(trivial.constraints(Blist)) changed to
all(trivial.constraints(Blist) == 1) to avoid a warning in R 2.7.0.
Ditto for 'all(findex)' and 'any(diff(Alphavec))'.
o qtriangle(0.3, theta=0.3) used to fail.
o gharmonic() handles a negative argument s.
CHANGES IN VGAM VERSION 0.7-6
NEW FEATURES
o dpolono() has a new argument 'bigx' which implements an
approximation. It is for handling large values of x.
o vglm() and vgam() now create the response and model matrices etc.
in the same way as glm(). A consequence is that the response
does not have to be "numeric" as in lm(), e.g., a factor response
is now permitted.
o New VGAM family functions:
alaplace1(), alaplace2(), alaplace3(dpqr),
amlbinomial(), amlexponential(), amlpoisson(), amh(),
lqnorm(), mbinomial(), scumulative().
o Other VGAM family functions with argument names changed or added:
lms.yjn2().
o These VGAM family functions have been improved:
alsqreg() [parallel option, w argument can be a vector, link function
for the expectiles].
o The data set "aml" has been renamed "leukemia".
o Previously laplace(zero=NULL), now laplace(zero=2).
BUG FIXES
o deplot() applied to a "lms.yjn2" object gave an unnecessary warning.
o In the leukemia and toxop data sets 1L is replaced by 1 and 2L by 2 etc.
CHANGES IN VGAM VERSION 0.7-5
NEW FEATURES
o New VGAM family functions:
betaff(), cardioid(dpqr), cauchy(), felix(d), fnormal1(dpqr),
invbinomial(), kumar(dpqr), lms.yjn2(), mix2exp(), plackett(dpr),
riceff(dr), skellam(dr), zinegbinomial(dpqr).
o These VGAM family functions have been improved:
frank(), genpoisson(), hzeta(), mix2normal1(), mix2poisson(),
pospoisson(), studentt().
o These VGAM family functions have had their default arguments changed:
genpoisson(), mix2normal1().
o New documentation: borel.tanner(dr).
o expm1() used whenever possible.
o Renamed VGAM family functions: betaff() changed to beta.ab().
o cauchy1() now returns the location estimates as the fitted values
instead of NA (for the mean).
BUG FIXES
o cumulative(), sratio(), cratio(), acat() had response-matrix
column names which got lost.
o lms.yjn() failed if there was not enough data.
CHANGES IN VGAM VERSION 0.7-4
NEW FEATURES
o weibull() does not handle any censored observations at all.
The function cenweibull(), which will handle censored
observations, is currently being written and will use Surv()
as input; it should be distributed with version 0.7-5 of VGAM.
o bisa() now implements full Fisher scoring. No numerical
integration is needed.
o Certain functions from the smartpred package are no longer
distributed with the VGAM package. These are
lm, glm, predict.lm, predict.mlm, predict.glm.
This is done because many users have found they interfere with
the VGAM package in unpredictable ways.
o The following VGAM family functions have improved initial values:
betabinomial(), cauchy1(), mccullagh89(), negbinomial(),
tpareto1(), zipoisson().
o New family functions: alsqreg(), dexpbinomial(), laplace(),
poissonp(), seq2binomial(), triangle(dpqr).
o VGAM family functions currently withdrawn:
cexpon().
o A new class called "SurvS4" has been prepared. It will be used
later to handle VGAM family functions beginning with "cen" that
use Surv() as input.
o log1p() used whenever possible.
BUG FIXES
o bisa() did not make use of ishape.
o cao(..., family=gaussianff) failed. It now works, although the
dispersion parameter is computed using a slightly different
formula.
CHANGES IN VGAM VERSION 0.7-3
NEW FEATURES
o gpd() now does not delete any data internally. The user should
use the subset argument of vglm() and vgam() in order to select
any subset of a data frame.
o zapoisson() has a zero argument, and this can be assigned
a negative value.
o "partial for" is added to the ylabel of linear terms of a vgam()
object when it is plotted.
o When a vgam() object is plotted with se=TRUE and if there are
linear terms then the mean of x is added to the plot (this makes
the standard error curves meet there).
o This package has been tested (somewhat) under R 2.5.0.
BUG FIXES
o plotvgam() did not work for vgam() objects using the subset argument.
o cao() objects would not show() or print(), at least under R 2.4.1.
o summary(vgam.object) failed if vgam.object was a totally linear
model (i.e., no s() term in the formula). Now the "R" slot is
assigned for all vgam() objects.
o preplotvgam() had a bug regarding $se.fit of an atomic pred$se.fit.
CHANGES IN VGAM VERSION 0.7-2
NEW FEATURES
o Almost all VGAM family functions now have an earg-type argument
to support each link function. This allows parameters specific
to each link to be passed in,
e.g., VGAMfamilyfunction(link="logoff", earg=list(offset=1))
o rinv.gaussian() is new.
o New VGAM family functions: morgenstern(), fgm(), gumbelIbiv(),
ordpoisson().
o New documentation: powl(), fsqrt().
BUG FIXES
o zanegbinomial()@last had wrong names in misc$link.
o summary(vgam.object) failed to print the anova table.
o summary(cao.object) failed.
CHANGES
o binom2.or() has argument names changed from "lp" to "lmu" etc.
This is partly to make it in keeping with other VGAM family
functions for binary responses.
o Other VGAM family functions with argument names changed: frank().
o lms.bcn(), lms.bcg(), lms.yjn() arguments have changed order.
o hyper() renamed to hyperg().
o plotvgam() uses ylim if it is inputted.
CHANGES IN VGAM VERSION 0.7-1
NEW FEATURES
o VGAM family functions now require full (name) specification
of parameter link functions. For example, binomialff(link=probit)
is ok, as is binomialff(link="probit"), but binomialff(link="pr")
isn't.
VGAM family functions no longer offer a fixed set of link
functions but the user can invoke any, as well as write their
own link function.
o Working residuals for vglm() objects are now the default.
They used to be deviance residuals but they are not defined
for most VGAM family functions.
In the future the default may become "pearson" residuals.
For safety, use the type argument, e.g.,
resid(vglmobject, type="response").
o ITolerances=TRUE is now the default for qrrvglm.control(),
consequently, equal tolerances CQO models are fitted. The
rationale for this change that setting ITolerances=TRUE
provides the fast computational speed as well as the easiest
interpretation of the results. Also, rcqo() matches this by
having EqualTolerances=TRUE as its default. However, having an
equal tolerances assumption should be checked.
o New VGAM family functions: tikuv(dpqr), [dpqr]naka(), [dpr]log(),
[dpqr]tpareto1(), betabinomial().
o VGAM family functions which have been renamed (and often improved):
New name Old name
-------- --------
dirmultinomial() dirmul()
negbinomial() negbin.mu()
negbinomial.ab() negbin.mn()
posnegbinomial() posnegbin.mu()
zanegbinomial() zanegbin.mu()
rposnegbin() rposnegbin.mu()
gamma2() gamma2.ab()
gamma2mu() gamma2()
o New functions: lerch(), rcqo().
o In the smartpred package smart.mode.is(mode.arg) now requires
mode.arg, if given, to be exactly one of 3 character strings.
Also, is.smart(object) handles object being a smart function
or a fitted object.
o The VGAM package comes with modified lm, predict.lm, predict.glm,
predict.mlm, glm functions---these implement smart prediction, and
are current to R version 2.3.1 (2006-06-01).
o The order of the linear/additive predictors for expexp()
have been switched.
o weibull(zero=2) is the default now.
o negbin.mu(), posnegbin.mu(), zanegbin.mu: these have a few added
arguments for further flexibility, and some arguments have changed
names, e.g., 'k.init' has been changed to 'ik' and 'link.mu' to
'lmu'.
o Negative binomial random variates are now generated using
rnbinom() in the stats package rather than rnegbin() in the MASS
package.
o binom2.or() and binom2.rho() have more choices for some arguments
such as lor and lrho.
o Initial values have been improved for logff(), zipf() and zetaff().
o This package should work for R 2.4.0 after additional tweaks to
handle changes in show().
BUG FIXES
o pbetabin() had a bug.
o studentt() has a mean of 0 only if df > 1.
o garma() failed for link="loge". It now works for binary
data with the "logit" link.
o Internally, wz <- matrix(NA, ...) changed to
wz <- matrix(as.numeric(NA), ...).
Ditto for rep(NA, ...) to rep(as.numeric(NA), ...).
o tobit() had a bug in the initialize slot.
o rposnegbin.mu() now calls the MASS library function rnegbin()
explicitly.
o gammaff() now works.
o Working residuals for cao() objects were wrong.
o lvplot() for cao() objects have a whichSpecies argument
which allows selective plotting of the species' curves.
o gaussianff() did not work with rrvglm(). It now has a
loglikelihood slot, and returns deviance residuals for M>1.
CHANGES
o gaussianff(), studentt() have the order of its arguments changed.
o eta2theta(), theta2eta(): if these have a matrix "theta" then it
no longer calls the VGAM link function one column at a time.
Hence VGAM link functions must handle matrix "theta" using one
value of "earg" argument.
o The earg argument has changed for many VGAM link functions. It
is now a list, with component names that are specific to each
link function.
See the online help files for the list component names.
Soon, every VGAM family function that allows a link function
will have an earg argument to match it, thus giving maximum
flexibility.
**************************************************
* *
* 0.6 SERIES NEWS *
* *
**************************************************
CHANGES IN VGAM VERSION 0.6-9
NEW FEATURES
o New VGAM family functions: lino(dpqr), recexp1(),
posnormal1(dpqr), betageometric(dpr), [dr]polono(),
[dpr]betabin(), gamma2mu(), bisa(dpqr), zipf(dp).
There is a new dirmul() (the old one is renamed to dirmul.old())
but it hasn't yet be completed.
o Renamed VGAM family functions: beta2() changed to betaff().
o Renamed VGAM functions: is.a.number() changed to is.Numeric().
o The Windows crossbuild was done under R 2.3.0.
BUG FIXES
o Family functions lognormal(), lognormal3() now include the
1/sqrt(2*pi) constant in @loglikelihood because of its use of
dnorm(..., log=TRUE) and dlnorm(..., log=TRUE).
o [dpqr]lognormal() withdrawn as they exist in R already.
o Documentation for betaff() contained mistakes.
o summary() of a betabin.ab() object used to fail.
o The assign statement has been removed from some FORTRAN code.
CHANGES IN VGAM VERSION 0.6-8
NEW FEATURES
o New VGAM family functions: recnormal1(), recexp1(),
paretoIV(dpqr), paretoIII(dpqr), paretoII(dpqr),
gammahyp(), benini(dpqr).
However, the fitted value (mean) for benini() may be faulty.
o Decommissioned VGAM family functions: gpdold(), ogev(),
zipoissonX().
o gumbel.block() renamed to gumbel(), and gumbel() renamed to egumbel().
o Argument names and defaults have changed for: gpd(), egev(), gev(),
ogev(), cgumbel(), egumbel(), gumbel(), and weibull().
Also, gpd(), gev() and egev() have some improvements done internally.
Also, rlplot() is new.
o Several family functions have been converted to a new convention
whereby ilocation, iscale, ishape arguments are used, and also
llocation, lscale, lshape arguments for the link functions etc.
o New link function: nidentity(theta) for negative-identity: -theta.
o New argument "untransform" in predict() and vcov() for VGLMs.
o For intercept-only models, Coef(fit) returns more user-friendly
labelled output.
BUG FIXES
o ppareto() had a bug.
o gpd() had an incorrect second derivative.
CHANGES IN VGAM VERSION 0.6-7
NEW FEATURES
o New VGAM family functions: bilogistic4(dpr), frechet2(),
frechet3(), freund61(), frank(dpr), mccullagh89().
o For cao(), df1.nl has a default of 2.5, changed from 2.0 before.
o For vglm(), vgam() etc., diagonal elements of the working weight
matrices that are less than .Machine$double.eps^0.75 are replaced
by this value. The arguments checkwz and wzepsilon support this
feature.
o More documentation on: fill() [re. the xij argument], cauchy1().
o logistic2() now uses Fisher scoring.
o Argument init.method changed to method.init in several family
functions.
o Any non-smart-prediction use of smartpredenv has been changed
to VGAMenv.
BUG FIXES
o rayleigh() was not in NAMESPACE.
o logistic1() and logistic2() had wrong first derivatives and
loglikelihood function.
logistic1() offers some choice of link function for the location
parameter.
CHANGES IN VGAM VERSION 0.6-6
NEW FEATURES
o New functions: zibinomial(), zibinom(dpqr), posbinom(dpqr),
mix2normal1(), mix2poisson(), dsnorm(), rsnorm(),
cexpon(), cgumbel(), cnormal1(), hyper().
o New generic functions: is.bell() works for RR-VGLMs, QRR-VGLMs
and RR-VGAMs (CLO, CQO and CAO, respectively).
o normal1() has a new (first) argument: lmean for the mean.
o Documentation for skewnormal1() and snorm(dr).
BUG FIXES
o tobit() now implements Fisher scoring properly.
o Coef.vlm() needed to test for trivial constraints.
o skewnorm1() had a bug in it. It has been fixed and renamed to
skewnormal1().
o cao() had a problem with the variable "usethiseta" when it had
possible NAs.
o An appropriate error message is given if residuals=TRUE in the
call to @loglikelihood, for all VGAM family functions.
o Two unneeded lines in rgam.f have been removed.
CHANGES IN VGAM VERSION 0.6-5
NEW FEATURES
o New functions: guplot(), meplot(), ggamma(dpqr), fff(),
vonmises(), lgamma3ff, lgamma(dpqr), prentice74, tobit,
zipoisson(dpqr), [dpqr]pospois(), [dpqr]laplace but there is
no laplace().
o cqo() has been largely rewritten. It now sports a new algorithm
for ITolerances=TRUE. It can handle large data sets (e.g., 1000
sites with 100 species). Compared to other cqo() options, it is
the fastest. There are a few things to learn though to take full
advantage of the new algorithm, e.g., centering the variables.
o Windows version is cross built with R 2.2.0. The Linux version
has been tested with R 2.2.0.
o cao() has been largely rewritten. It now should not hang in the
the windows cross build version.
o .Init.Poisson.CQO() has been renamed .Init.Poisson.QO(), and also
improved (however, it uses more memory by default).
o Modelling functions such as vglm(), vgam() and cao() have
qr.arg=FALSE now. This means object sizes can be a lot smaller.
o The functions positive.poisson(), positive.binomial() etc. have
been renamed pospoisson(), posbinomial() etc.
o The functions [dpqr]gpd now have a location=0 argument.
o Some VGAM family functions will be adapted later to use the
BFGS quasi-Newton update for their working weight matrices.
o The link function logoff() now works, for constant offsets.
Link functions had the argument "extra"; now called "earg"
to avoid confusion with the argument "extra" used in vglm() etc.
Also, elogit() is new, which allows a parameter to lie between
two values (A,B), say.
BUG FIXES
o plotvgam() was incorrect if one of the terms (but not the first)
was "x" or a function of "x" such as bs(x).
o smart.expression now handles multiple 'arguments' by choosing
the first, which is the smart function name.
o lv(rrvglm.object) failed.
CHANGES IN VGAM VERSION 0.6-4
NEW FEATURES
o New family functions: betabin.ab(), betaprime(), dcnormal1(),
erlang(), expexp(), inv.gaussianff(), maxwell(), mckaygamma2(),
nakagami(), pareto1(), rayleigh(), wald().
Of these, Pareto, Rayleigh and Maxwell have random number
generation etc.
o If criter="coef" and trace=TRUE, then the number of
decimal places used to print the estimated coefficients at
each iteration is proportional to the control constant
epsilon.
o tanl() has been named to cauchit(), and appropriate
family functions reflect this change, i.e.,
link="cauchit" instead of link="tanl".
o size.binomial() has been improved.
o Documentation for gamma1(), gamma2().
BUG FIXES
o The documentation for the reverse argument in cumulative(),
cratio(), etc. was incorrect.
o vcov() didn't work on the windows version.
o cao() still hangs under the windows version, so hopefully
this bug will be fixed soon!
CHANGES IN VGAM VERSION 0.6-3
NEW FEATURES
o Built with R 2.1.0 for the .zip file (Windows version) and
deposited in the right directory at www.stat.auckland.ac.nz.
o More documentation, e.g., fitted(), yeo.johnson(),
dirmul().
o zeta() and zetaff() have been improved and/or corrected.
o The family functions binomial, poisson, quasibinomial,
quasipoisson, gaussian, inverse.gaussian, Gamma
have been withdrawn because of inteference with glm().
CHANGES IN VGAM VERSION 0.6-2
NEW FEATURES
o model.frame() and model.matrix() are roughly working for
objects that inherit from "vlm"s, e.g., "vglm" objects.
Both of these methods functions accept a "data"
argument etc.
Also, for these, smart prediction works.
o A methods function for the generic function weights() has
been written for VGLM objects. It returns
either the prior or working weights.
BUG FIXES
o The Crow1positive argument in cao() did not function correctly.
o The family functions dagum, fisk, lomax, invlomax, paralogistic,
invparalogistic, lognormal were not exported in the NAMESPACE
file.
o Functions in gaut.c and mux.c used "long" to represent integers.
In R, these should be "int". Although these are equivalent on
32-bit machines, they differ on 64-bit machines and crash.
The files are now renamed to gautr.c and muxr.c in R.
o summary(cao.object) failed.
CHANGES IN VGAM VERSION 0.6-1
NEW FEATURES
o New functions: cao() for "constrained additive ordination",
and uqo() for "unconstrained quadratic ordination".
Both of these are unfinished but will hopefully be
completed in the forseeable future.
o The function cgo() has been renamed to cqo(). Ouch!
CQO stands for "constrained quadratic ordination", and is
better than the old name cgo(), for
canonical Gaussian ordination.
o The inverse() link function has been renamed to reciprocal().
o More documentation: loglinb2() and loglinb3().
o zipbipp() renamed to zapoisson(), where "za" stand for
"zero-altered". This is more in line with the literature.
New families: zanegbin.mu, positive.negbin.mu.
New random variates: rposnegbin.mu, rpospois.
o negbin.mu() works now for cgo(). The subsequent methods
functions have been adapted to work on it too.
However, negbin.mu() is not recommended because maximum
likelihood estimation of the index parameter is fraught
numerically. It is better to use quasipoissonff().
o cgo() now uses the function .Init.Poisson.CGO() to obtain
initial values for the canonical coefficients, C.
The argument Use.Init.Poisson.CGO in qrrvglm.control()
now controls this feature.
o Lazy loading has been enabled for the VGAM package.
o Name spaces has been introduced into the VGAM package.
The consequencies of this might be far reaching for
code heavily based on the internals of the VGAM package.
o The application of name spaces means "ff" can be dropped
from certain family functions. In particular, poisson() can
be used instead of poissonff(), and binomial() instead
of binomialff(). Ditto for quasipoissonff() and
quasibinomialff().
o names.of() changed to namesof(). Many other function names
have been changed, particularly those of the S3 classes
such as coef. something, e.g., coef.vlm to coefvlm.
In general, S3 methods functions such as print.summary.vlm have
the first "." deleted, but classes such as "summary.vlm" retain the
".", and the function is printsummary.vlm.
BUG FIXES
o Some documentation regarding the negative binomial
distribution was wrong.
o The digamma function in FORTRAN was buggy.
o gumbel.block() now handles a vector response (equivalently,
a one column matrix) and the deviance has been decommissioned.
Instead, the log-likelihood is computed.
**************************************************
* *
* 0.5 SERIES NEWS *
* *
**************************************************
CHANGES IN VGAM VERSION 0.5-24
NEW FEATURES
o zipbipp() and zipoissonX() are new alternatives to yip88().
They fit a zero-inflated Poisson distribution.
Both can handle covariates for both parameters (p0 or
phi, and lambda.)
zipbipp() is recommended over the others.
zipoissonX() is experimental at this stage
and should be used with caution.
rpospois() is new.
o More documentation: rhobit and binom2.rho.
o binom2.or() now has lp1 and lp2 arguments, which allow
a different link function for each of the two marginal
probabilities.
o bratt() is a new family function. It fits the Bradley Terry
model with ties.
o flush.console() is used if it exists. This will make
Windows version more nicer for large data sets and when
trace=TRUE is used.
o wweights() extracts the working weights of an object.
Used to be called vweights().
CHANGES IN VGAM VERSION 0.5-23
NEW FEATURES
o The package works under the latest version, viz. 2.0.0.
There are fewer warning messages when checking :)
o persp() for CGO objects now handles Rank=1 models.
CHANGES IN VGAM VERSION 0.5-22
BUG FIXES
o plot.vgam(..., overlay=TRUE, which.cf=1:2) was incorrect.
NEW FEATURES
o demo files now are avaible for VGAM. These include lmsqreg,
distributions, and cgo. More will be added later.
CHANGES IN VGAM VERSION 0.5-21
BUG FIXES
o .Rd files adapted to reflect new changes in the library names.
o persp.qrrvglm() argument whichSpecies was faulty.
o gpd()@inverse returned erroneous centiles.
o Coef(cgo(..., FastAlgorithm=TRUE)) produced wrong results.
NEW FEATURES
o cgo(..., FastAlgorithm=TRUE) has been fined-tuned to give
greater speed and accuracy.
o lms.yjn() uses FORTRAN code to implement the Gauss-Legendre
algorithm. This results in greater accuracy.
o More documentation, especially for family functions for
extreme values modelling.
CHANGES IN VGAM VERSION 0.5-20
BUG FIXES
o vglm(y ~ x, binomialff(link=tanl)) used to fail.
o The CHECK command failed previously, but now it only
gives 5 warnings.
NEW FEATURES
o persp.qrrvglm() has been written to apply persp() to
a rank-2 CGO model.
o cgo(..., FastAlgorithm=TRUE) now has a logical argument
GradientFunction, which if TRUE (default), computes the
derivatives by using finite-difference approximations.
The default will cause the speed to generally increase.
CHANGES IN VGAM VERSION 0.5-19
BUG FIXES
o garma() did coerce the model matrix into the correct class
o fisherz() could not work out the inverse.
NEW FEATURES
o trplot() is a new generic function, and for objects of
class "qrrvglm" (a cgo() object), it produces a trajectory plot
for species.
o vcov.qrrvglm() now computes standard errors and returns the
variance-covariance matrix for rank-1 QRR-VGLMs.
o A new fast algorithm is implemented for cgo(..., FastAlgorithm=TRUE)
which only works under windows. It is a new undocumented algorithm.
o New family functions: lognormal(), lognormal3(), weibull().
o New family functions: genbetaII(), betaII(), sinmad(), dagum(),
lomax(), invlomax(), fisk(), invparalogistic(), paralogistic().
Additionally, d*, r* p* and q* forms of the
density/random-generation etc. functions for all of these
except for betaII and genbetaII.
o New link function for (0,1) parameters: tanl() for tan link.
It has a heavier tail and corresponds to a Cauchy distribution
(cf. probit for normal).
o New family function: brat() for the Bradley Terry model
(intercept model only).
CHANGES IN VGAM VERSION 0.5-18
NEW FEATURES
o I've changed deplot.lmscreg() so that the "at" argument is now
"y.arg", and the density is returned with name "density" instead
of "y". That is, "at" is now "y", and "y" is now "density".
o lvplot.rrvglm() and biplot.rrvglm() have been merged and are now
equivalent.
CHANGES IN VGAM VERSION 0.5-17
BUG FIXES
o Bestof argument in cgo() and rrvglm() was faulty.
o Bug in plot.vgam(type.resid) fixed.
NEW FEATURES
o Updated to work under R 1.8.1
o logLik() and AIC() methods functions supported for many VGAM objects.
o lms.bcn.control(), lms.bcg.control(), lms.yjn.control() now
have trace=TRUE because monitoring LMS quantile regression models
is a good idea.
o lms.bcn(), lms.bcg(), lms.yjn() now improved.
CHANGES IN VGAM VERSION 0.5-16
BUG FIXES
o biplot.rrvglm() had a internal bug with @C.
o Runs under R 1.8.0 now, having a fix with "qr" slot.
o etastart, coefstart, mustart arguments were not functional in vgam().
o vchol() did not replace the correct elements; sometimes the index
was out of subscript range.
o residuals.vlm() tried to evaluate a deviance slot in a "vglmff" object
even when it was empty.
o Documentation links to functions in other packages now work.
NEW FEATURES
o lvplot.qrrvglm() has been renamed biplot.qrrvglm().
Argument Equal.tolerances changed to EqualTolerances.
Argument Circular changed to ITolerances.
rrvglm.control() now split into qrrvglm.control() and itself.
o cgo() now performs canonical Gaussian ordination.
CHANGES IN VGAM VERSION 0.5-15
BUG FIXES
o Coef.qrrvglm() failed wrt Equal.tolerances and Circular when
Rank>2.
NEW FEATURES
o gco() is now an easier interface for fitting Gaussian canonical
ordination models. gco(...) is essentially rrvglm(..., Quadratic=TRUE).
o Documentation for deplot.lmscreg(), qtplot.lmscreg(), cdf.lmscreg()
and related functions. Also for positive.poisson(),
positive.binomial() and yip88().
o lvplot.qrrvglm() improved to handle non-diagonal tolerance matrices,
and a new Rotate option is available for QRR-VGLMs.
o By default, QRR-VGLMs now have the constraint that the latent
variables are uncorrelated and have unit variances, i.e.,
their variance-covariance matrix is diag(Rank).
Also, the Crow1positive argument allows ordinations to be reflected
across axes.
CHANGES IN VGAM VERSION 0.5-14
BUG FIXES
o vgam() with s() terms and subset= used to give a bug because the
attributes of s() were lost.
o summary() of a gaussianff was faulty because control.gaussianff()
was called gaussianff.control().
NEW FEATURES
o install.packages("VGAM", CRAN="http://www.stat.auckland.ac.nz/~yee")
now works for PC and Linux/Unix, i.e., the distribution of the
VGAM package allows for this type of download.
o poissonff(), quasipoissonff(), binomialff() and
quasibinomialff() now handle multiple dispersion parameters when
mv=TRUE and onedpar=FALSE.
o Generic function predictx(), with methods function for "qrrvglm"
objects. This solves (with limited functionality) the calibration
problem.
o predict.qrrvglm() and predict.rrvglm() written (but don't work 100%)
o Coef.rrvglm() now returns an S4 object, which can be printed nicely.
o summary.qrrvglm() has been improved.
o Documentation for poissonff(), quasipoissonff(), binomialff() and
quasibinomialff().
CHANGES IN VGAM VERSION 0.5-13
BUG FIXES
o Code with T and F now use TRUE and FALSE.
NEW FEATURES
o Documentation for lms.bcn(), lms.bcg(), lms.yjn(), and bmi.
Additionally, the overall documentation has been improved
throughout.
o print.Coef.qrrvglm prints the contents of Coef(qrrvglm.object)
in a nicer format. It uses S4 features.
CHANGES IN VGAM VERSION 0.5-12
BUG FIXES
o The package now works under R 1.7.1. This includes the smart
prediction library.
o dirichlet(), skewnorm1(), geometric(), gamma2() and erlang()
had a bug that has been fixed.
NEW FEATURES
o documentation for beta2(), and dirichlet().
o Easier installation; use something like
"R CMD INSTALL -l ./myRlibs VGAM_0.5-12.tar.gz"
for a local library.
CHANGES IN VGAM VERSION 0.5-11
BUG FIXES
o The code has been upgraded to work under R 1.7.0 because
of the calls to LAPACK and object oriented features.
NEW FEATURES
o levy() added, plus grc() documentation.
o constraints added to binomialff() and poissonff() since
they both handle multivariate responses.
CHANGES IN VGAM VERSION 0.5-10
BUG FIXES
o Many univariate family functions had a faulty loglikelihood slot.
o negbin.mu() was faulty causing very slow convergence.
o Coef.vglm() had a bug due to "fit" rather than "object"
NEW FEATURES
o logff() added.
o The undocumented backchat facility now works for Splus 6.x.
This should increase the efficiency of vglm() in particular.
Thanks to Insightful and Dr J. Chambers for helping to get it
going under the S4 engine.
CHANGES IN VGAM VERSION 0.5-9
BUG FIXES
o binomialff() had a bug in @weight.
o binomialff(mv=T) used to fail.
o gev(), ogev() and egev() had @loglikelihood that was faulty.
NEW FEATURES
o .Rd documentation included for vglm(), vgam(), rrvglm(), and
associated control and class functions, plus smart prediction.
CHANGES IN VGAM VERSION 0.5-8
NEW FEATURES
o rrvglm() now has a Quadratic argument to implement the class of
Quadratic Reduced-rank VGLMs, which gives maximum likelihood
solutions to Gaussian canonical ordination problems.
Documentation is in rrvglm.pdf
CHANGES IN VGAM VERSION 0.5-7
NEW FEATURES
o vglm() now has a xij argument which implements eta-specific covariates.
Documentation is supplied on the VGAM website.
o grc() has been written for Goodman's RC association model for a
contingency table. Documentation is in rrvglm.pdf
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