[R-pkgs] update: rockchalk 1.8.0

Paul Johnson pauljohn at ku.edu
Tue Jul 30 16:41:18 CEST 2013

This will appear on CRAN mirrors soon. It's my update for Spring, 2013. I keep
track of R problems that arise in the regression course and try to facilitate
them. There are functions for describing data, presenting regression plots and
tables, some regression diagnostics.

Most of the usages are illustrated in the vignette "rockchalk".  That has plenty
of illustrations if you care to take a quick look.

If you did not try this before, here is why you might want to. The function that
the package was organized around originally was plotSlopes: draw predicted value
lines on the same scatterplot. Now this is generalized a bit, the moderator
variable can be numeric or factor and I have bent over backwards to make this
flexible for the end users. If you run the examples for "predictOMatic" and
"plotSlopes" and "plotCurves," you will get the idea.

The rest is details.

I started a NEWS file using Emacs org mode, here it is:

* version 1.8

This is the end of the Spring semester, so its time for the new rockchalk

** New, general, flexible framework for calculating marginal effects
   in regression models, linear or otherwise.

*** newdata function works. It can scan a regression, isolate the
   predictors, and then make a "mix and match" new data object for use
   with a predict function.  This is convenient for users but also very

*** The newdata framework is built on top of "divider" methods that can
    check whether a variable is numeric or categorical, and select
    example values according to user-specified criteria.

*** predictOMatic works dependably! Please try
    example(predictOMatic). The problem with single predictor models
    that bugged users of rockchalk 1.6.2 has been solved.

*** predictOMatic argument interval = c("none", "confidence",
    "prediction").  Guess what that is supposed to do? For glm,
    which does not provide a confidence interval, I've written code
    for an approximate Wald type CI, and hope to do better in future.

** Regression diagnostics.

*** getPartialCor: get partial correlations from a fitted model
(student convenience).

*** getDeltaRsquare: Returns the change in estimated R-square observed
    when each predictor is removed.  This is the squared semi-partial
    correlation coefficients (student convenience).

*** mcDiangose for multicollinearity diagnostics (student convenience)

** MeanCenter: add arguments to make selection of variables for
centering more convenient when users don't like the automatic
options centerOnlyInteractors.

** plotSlopes, plotCurves:
 *** Added intervals argument, for confidence and prediction intervals.

*** Added opacity argument to determine darkness of interval regions
    (which use the transparency "alpha layer.").

*** A lot of fiddling under the hood to make colors consistent when
    levels of modx are altered to compare plots of a given model.

*** Can produce a simple regression prediction plot if modx argument
    is omitted. This is a widely requested feature.

Please run example(plotSlopes) and example(plotCurves)

*** Changes under the hood. The common plotting functions of
    plotSlopes and plotCurves are abstracted into a function
    plotFancy, so now this will be eaiser for me to maintain. The
    plotting ritual is the same, why keep 2 functions, you ask?
    plotCurves tolerates more complicated regression
    formula. plotSlopes leads to testSlopes, and hence to

** addLines: communication between 2 dimensional regression plots and 3
dimensional plots from plotPlane. Run example(addLines).

** plot.testSlopes. Run testSlopes on an interactive model. For a
model with 2 ocontinuous predictors that interact, this will generate
an ABSOLUTELY EXCELLENT and highly informative plot displaying the
effect of the interaction.

** outreg: LaTeX tables from regression models.

*** Reworked with new arguments to make tables for more types
of regressions. There's quite a bit more room for users to customize
the type of diagnostics they want to report.

The wide variety of output types from regression models is very
bothersome. I refuse to write a separate outreg method for each
different regression packages. If you want to use a package
from an author who is willing to do that, consider the "texreg"

*** outreg2HTML. converts outreg to HTML markup and into a file.
Intended for importation into word processor programs.

** New vignette Rstyle. Most of the source-code files have been reformatted
to comply with my advice.

** genCorrelatedData2

*** genCorrelatedData2. For regression examples, suppose you want to
    have 6 columns of an MVN with a certain mean and covariance
    structure. And you want the regression formula to have
    interactions and squared-terms. No more hassle. This is a
    framework that works. Users set the mean, standard deviations, and
    correlation values in various ways. Run

*** To support that, there are more generally useful
    functions. lazyCor and lazyCov are flexible ways to create
    correlation and covariance matrices. As the names suggest, they
    are for lazy users who just want to specify some information and
    get the right thing.  This requires a set of transformation
    functions, to receive vech and create matrices, and so forth.
    Check genCorrelatedData.R, for vech2Corr, makeVec, makeSymmetric,
    checkPosDef. The latter, which I am surprised not to find in the
    base of R itself, imitates code in the MASS package for
    ascertaining if a matrix is positive definite.

*** Small, almost microscopic, revision of MASS package mvrnorm
    function to assure replication of MVN draws when the sample size
    is adjusted. The first rows of the resulting MVN draw will be the
    same, no matter how the "n" argument is changed. The same change
    has been made in the mvtnorm package's MVN random generator. While
    this is a very small code change, it does solve some very
    mysterious simulation results that have been obtained with MASS
    mvrnorm in our lab.

Paul E. Johnson			email: pauljohn at ku.edu
http://pj.freefaculty.org	Assoc. Director
Professor, Political Science 	Ctr for Research Methods & Data Analysis
1541 Lilac Lane, Rm 504		1425 Jayhawk Blvd.	
University of Kansas		Watson Library, Rm. 470  	
Lawrence, Kansas 66045-3129	Lawrence, Kansas 66045-7555
Ph: (785) 864-3523		Ph: (785) 864-3353

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