************************************************** * * * 0.7 SERIES NEWS * * * ************************************************** 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 implments 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