'vcd' Extensions and Additions

Provides additional data sets, methods and documentation to complement the 'vcd' package for Visualizing Categorical Data and the 'gnm' package for Generalized Nonlinear Models. In particular, 'vcdExtra' extends mosaic, assoc and sieve plots from 'vcd' to handle 'glm()' and 'gnm()' models and adds a 3D version in 'mosaic3d'. Additionally, methods are provided for comparing and visualizing lists of 'glm' and 'loglm' objects. This package is now a support package for the book, "Discrete Data Analysis with R" by Michael Friendly and David Meyer.

Extensions and additions to vcd: Visualizing Categorical Data

Version 0.7-1

This package provides additional data sets, documentation, and a few functions designed to extend the vcd package for Visualizing Categorical Data and the gnm package for Generalized Nonlinear Models. In particular, vcdExtra extends mosaic, assoc and sieve plots from vcd to handle glm() and gnm() models and adds a 3D version in mosaic3d().

vcdExtra is now a support package for the book Discrete Data Analysis with R by Michael Friendly and David Meyer.

The main purpose of this package is to serve as a sandbox for introducing extensions of mosaic plots and related graphical methods that apply to loglinear models fitted using glm() and related, generalized nonlinear models fitted with gnm() in the gnm package. A related purpose is to fill in some holes in the analysis of categorical data in R, not provided in base R, vcd, or other commonly used packages.

The method mosaic.glm() extends the mosaic.loglm() method in the vcd package to this wider class of models. This method also works for the generalized nonlinear models fit with the gnm package, including models for square tables and models with multiplicative associations.
mosaic3d() introduces a 3D generalization of mosaic displays using the rgl package.
A new class, glmlist, is introduced for working with collections of glm objects, e.g., Kway() for fitting all K-way models from a basic marginal model, and LRstats() for brief statistical summaries of goodnes-of-fit for a collection of models.
For square tables with ordered factors, Crossings() supplements the specification of terms in model formulas using Symm(), Diag(), Topo(), etc. in the gnm package.
In addition, there are many new data sets, a tutorial vignette, Working with categorical data with R and the vcd package, vignette("vcd-tutorial", package = "vcdExtra"), and a few useful utility functions for manipulating categorical data sets and working with models for categorical data.

News

Version 0.7-1 (2017-09-28)

o Fixed buglet in expand.dft when table is 1-dim [Thx: Long Qu] o Added zero.test, a simple score test for zero inflation o Development has moved to https://github.com/friendly/vcdExtra

Version 0.7-0 (2016-01-27)

o Added Glass data o introduce links and references to DDAR o added mcaplot() to plot MCA solutions in DDAR style o added update.xtabs method o updated vignette to refer to DDAR

Version 0.6-12 (2015-10-06)

o Added Burt data o Fixed examples/vignette for ggplot_2.0.0

Version 0.6-11 (2015-09-14)

o bump pkg version for CRAN

Version 0.6-10 (2015-07-27)

o Added HospVisits data

Version 0.6-9 (2015-06-11)

o Added Mice data o Removed uses of summarise() and Summarise() from demos and examples, in preparation for deprecating them. o summarise() is now deprecated o Now use importsFrom() for all functions from recommended packages

Version 0.6-8 (2015-04-15)

o Fixed Title: and Description: for CRAN

Version 0.6-7 (2015-04-02)

o Removed loddsratio (now in vcd) (rev 252) o Removed print.Kappa (now in vcd) (rev 253) o Fixed bug in CMHtest: rmeans and cmeans labels were reversed (rev 254) o Fixed error in Fungicide.Rd, now that we require vcd_1.3-3 (rev 254) o Added WorkerSat data - 2 x 2 x 2 o Added AirCrash data

Version 0.6-6 (2015-02-04)

o Minor doc changes

Version 0.6-5 (2014-11-07)

o Added Cormorants data (fixed to latest) o Added LRstats, to replace Summarise. Older summarise() and Summarise() will eventually be deprecated. o Now Suggests: AER for NMES1988 data o collapse.table() now works with array objects

Version 0.6-3 (2014-10-27)

o Fixed bug in logLik.loglm when the data contain zero frequencies (rev 228) o Made Summarise generic, adding a method for "glmlist" objects (rev 230) o Added a coef() method for "glmlist" objects (thx: John Fox) o Added a Summarise.loglmlist method (rev 232) o Replaced all documentation uses of summarise() with Summarise() (rev 233) o Added cutfac(), a convenience wrapper for cut() (rev 234) o Now use rgl:: in all mosaic3d functions

Version 0.6-2 (2014-06-30)

o added Summarise, to replace summarise o Added HairEyePlace data - 4 x 5 x 2, Caithness and Aberdeen hair/eye color (rev 223) o Added PhdPubs data from Long (1997) - publications by PhD candidates o Allow Summarise to work with models w/o a deviance() function o Fixed bug in Summarise wrt degrees of freedom

Version 0.6-1 (2014-04-14)

o Added ICU data o Added Toxaemia data - multivariate response contingency table (rev 209) o Added Vietnam data - 2 x 5 x 4 frequency table (rev 210) o Added logLik.loglm to allow use of AIC() and BIC() for loglm models (rev 212) o Fixed loddsratio.Rd to work with revised vcd::CoalMiners data (rev 212) o Added blogits for bivariate binary response data o Added Vote1980 data (rev 214)

Version 0.6-0 (2014-03-07)

o Removed Authors: in DESCRIPTION, bumped version

Version 0.5-12 (2013-12-16)

o Added ShakeWords data set- word frequency counts from Shakespeare (rev 188) o Added Geissler data-- all family sizes for Saxony sex composition data (rev 190) o Added logseries functions for the logarithmic series distribution (rev 191) o Added Depends data -- dependencies of r packages (rev 192) o Fixed buglet in seq_loglm() not respecting arrays o Added seq_mosaic() (rev 194) o Added CyclingDeaths data (rev 196) o mosaic3d() gets an interpolate= option to control shading levels (rev 197) o Fixed bug in seq_mosaic, thx to David Meyer (rev 200) o Fixed bug in seq_loglm() when marginals != 1:nf

Version 0.5-11 (2013-07-01)

o Added mosaic.glmlist to plot mosaics (or other strucplots) for some or all models in a glmlist (rev 169) o Added loglim-utilities.R, containing a suite of functions to provide a more conceptual way to specify loglinear models by type ('joint', 'conditional', 'mutual', 'markov', 'saturated') (rev 171) o Added mosaic.loglmlist, similar to mosaic.glmlist for models fit using MASS::loglm (rev 173) o Both mosaic.glmlist and mosaic.glmlist get an explicit panel=argument; both get some more sensible default default arguments (rev 175) o Added seq_loglm to fit sequential loglm models to marginal subtables, giving a loglmlist result (rev 176) o Added Accident data (rev 178); fleshed out Accident examples (rev 180) o Fixed use of ::: for R 3.0.1 (rev 179) o Fixed various problems related to use of MASS:loglm (rev 181-183) o Added Titanicp to datasets (rev 185)

Version 0.5-8 (2013-03-06)

o Revised vcd-tutorial showing some examples of plyr; added a section on RC models o Added Donner data with example of ggplot2 plot for a binomial glm() o Added vcd-tutorial section using ggplot2 for Donner data o Enhanced datasets() to provide a maxTitle argument (rev 153) o Added doubledecker plots to Dyke.Rd (rev 156) o Added Draft1970table and Draft1970 data sets (rev 158) o Added example of doubledecker plots to vcd-tutorial vignette (rev 164)

Version 0.5-7 (2013-03-01)

o Completed CMHtest methods, adding overall tests across strata in a general way o CMHtest now gets an S3 generic with a formula interface o print Kappa gets digits= and CI= arguments

Version 0.5-6 (2012-11-30)

o Added Hosmer Lemeshow and HLtest methods, including plotting via vcd::rootogram() o Added CMHtest for general Cochran-Mantel-Haenszel tests o Revised vcd-tutorial vignette, adding a section on CMH tests; removed dependence on Z.cls

Version 0.5-3 (2012-03-07)

o Added Mammograms data (4x4, ordered factors, agreement) o Extended mosaic.glm examples o Added Alligator data (4x2x2x5, in frequency form) o Added DaytonSurvey data (5-way, 2x2x2x2x2 in frequency form) o Extended vcd-tutorial vignette with a section on collapsing over factors o Removed aperm.* now that aperm.table is in base R

Version 0.5-2 (2010-11-28)

o Added loddsratio and related methods for log odds ratios, generalizing vcd::oddsratio from 2 x 2 (x strata) tables to R x C (x strata) tables o Added as.matrix.loddsratio, as.array.loddsratio methods o Added some simple plot examples to example(loddsratio), anticipating a plot method o Added data(Fungicide), a 2 x 2 x 2 x 2 table o Renamed summarize() and related methods to summarise() to avoid conflict with plyr. o Addition to vcd-tutorial vignette on use of aperm() with table objects o Updated demo(yamaguchi-xie) to correct row/col nomenclature and add plot of BIC o Added aperm() S3 generic to handle table objects o Moved tv.dat to inst/doc/extdata to avoid warnings in R 2.12+

Version 0.5-1 (2010-09-17)

o Added Yamaguchi87 data (5x5x3 three-way mobility table in frequency form) o Added demo(yamaguchi-xie) illustrating fitting and visualization of the models of homogeneous and log multiplicative layer effects fit in Xie (1992, Table 1) o Added BIC to summarize() and friends o Added Hauser79 data (two-way mobility table), plus some examples from Powers and Xie (2008) o Added Crossings() to construct interactions for Goodman 1972 crossings model. o Added datasets() to list datasets in packages o Extended description and examples of Kway() o Added meanResiduals() and extended mosaic.glm() (Heather Turner) o summarize() gets a sortby argument for glmlist and loglmlist objects

Version 0.5-0 (2010-04-28)

o Fleshed out mosaic3d, allowing display of observed or expected, internally calculated or externally supplied residuals, specifying the initial 3D shape, etc. This completes the 'top-level' work on mosaic3d(), borrowing code from vcd::strucplot. o Added initial handling for zero cells in the table to mosaic3d().
o Added center3d() for finding the mean coordinates of shape3d objects. o Added demo(mosaic-hec) comparing 2D and 3D mosaics for HairEyeColor data o Gave mosaic3d a label_edge argument, allowing labels for dimensions at minima or maxima o Made mosaic3d object oriented, giving it a loglm method o Added Kway(), fitting all 0-way, 1-way, 2-way, ... k-way models in a glm

Version 0.4-3 (2010-03-25)

o Added demo(mosaic3d-demo), a proof-of-concept for doing 3D mosaic displays o Added mosaic3d(), an initial basic version. o Factored out split3d() and gave it S3 methods

Version 0.4-2 (2010-03-09)

o Revised vignette("vcd-tutorial"): added some hints for mosaic(), corrected stuff regarding prior limitations of mosaic.glm() o Added demo(Wong3-1): three-way table, with models of conditional association o Added Suggest: effects for effects plots of glm(), multinom() and polr() models o Added demo(housing): visualize models fit in example(housing, package="MASS") using mosaic() and effect plots. o Updated demo(Wong2-3): added model comparison plots, glmlist processing o Added Suggest: VGAM o Extended package description in vcdExtra-package.Rd o Added glmlist() to facilitate processing, extraction, plotting, etc. of a collection of glm() models o Added loglmlist(), for collections of loglm() objects o Added summarize methods for glm, glmlist, loglm and loglmlist objects

Version 0.4-1 (2010-02-21)

o Added example(Caesar), illustrating structural zeros o Re-named Heckman variables to e1971, ..., e1968 (errors from loglm); began example(Heckman) o Added example(Detergent), example(Dyke) o Fixed bug with mosaic.glm when data in global environment (Heather Turner) o Added sieve.glm and assoc.glm methods (MF) o Added modFit.glm and modFit.loglm o Added demo(Wong2-3)

Version 0.4-0 (2010-02-23)

o Added new datasets: data/{Abortion, Bartlett, Caesar, Cancer, Detergent, Dyke, Gilby, Heart, Heckman, Hoyt, Mobility} from mosdata.sas via md2r.sas converter. o Fixed small documentation warnings o Switched inst/CHANGES to NEWS

Version 0.3-6 (2009-04-21)

o Added Depends: gnm o Added demo/{mental-glm, ucb-glm, vision-quasi} o Added demo/{occStatus,yaish-unidiff} o Initial release to CRAN

Version 0.3-5 (2009-3-6)

o mosaic.glm now uses object$data if available

Version 0.3-4 (2009-2-11)

o Fixed bugs in mosaic.glm, mosaic.gnm in models with terms like Diag(dest, origin) that get included in x$xlevels

Version 0.3-3 (2009-2-10)

o Fixed bugs in mosaic.gnm o Fixed print.GKgamma o Added example of GKgamma to vcd-tutorial

Version 0.3-2 (2009-2-8)

o Added more examples to mosaic.glm.Rd

Version 0.3-0 (2009-2-6)

o Fixed bugs in mosaic.glm and mosaic.gnm