|
Chapter 10, using lme()
|
R code & output, with brief commentary, for using lme() (package nlme) in
place of lmer() (lme4)
|
Overheads -- Talk on multilevel models
|
Overheads for a talk on multilevel models. NB: Later slides canvass heavily
technical issues.
|
Lattice & other graphics
|
These notes substantially supplement the discussions of lattice in
Sections 1.6.8 and 14.12, and the lattice code in the text. They
discuss some newer lattice features that are not covered in the book.
The playwith
package warrants more than the current very brief mention. The
latticist() function, called with a data frame as argument,
starts a GUI interface to lattice. The playwith() function
allows interactive enhancements to lattice and other R plots.
|
Least squares computation
|
Computational methods used by lm(), with notes on the direct
use of R's suite of functions (qr() and friends) for working
directly with the QR matrix decomposition. These are peripherally
relevant to chapters 6-9. [Lund]
|
Generalized Linear Models
|
Brief notes on the theory of generalized linear models, and on the comparison
with linear models. [Lund]
|
Regression in practice
|
Issues for the practical use of regression methods, supplementing the
discussion in the text. [Lund]
|
Classification
|
Notes on the theory that underpins the functions lda() and qda() in R's
MASS package. For the case of two outcome classes, comparisons are
made with logistic regression using glm().
|
Analysis of microarray data
|
The package DAAGbio has a vignette, and associated files and datasets,
that demonstrates the analysis of the two-channel microarray data
that are described in Section 4.2.2.
|
R talks to LaTeX
|
Use knitr
or Sweave
to process a document that includes R code within Sweave type markup,
to generate a LaTeX document that may include any or all of R code,
output, tables and graphs. The more flexible knitr markup may now
be preferred. For knitr, production of a Markdown html
document is an alternative.
|
[Lund] These notes were developed for use with a PhD course, conducted
under the