Ex:environment for exercise chunks.
solution:environment for solutions to the exercises.
myincfig:macro for figure environments with three parameters:
(1) figure filename (2) figure width (3) figure caption
solfig:macro for figure environments within solution
chunks. This is necessary because LaTex doesn't allow for floats
within minipage environments.
myref:reference to other labs/chapters. For the book
this is a simplewrapper around ref ignoring the second argument, for
the labs this command is replaced in the useRlabs.sty file allowing
for referencing bbetween the individual documents.
booklab:macro for conditional text input with two
parameters. The first parameter will be used for the book while the
second will be used for the labs.
The following makros will automatically create index entries as side effect. Apart from that they do text highlighting as well.
R:the R language glyph (in sans serif font)
Rpackage:an R package (in bold font)
Rclass:an R class (in italics)
Rmethod:an R method (in small typewriter font)
Rfunction:an R function (in small typewriter font)
Implicit index terms can be generated using
indexTerm:with the optional first argument giving the
actual term and the second argument giving a string that appears in
the text. E.g. indexTerm[tree]{trees} would give you
"trees" in the text but create an index for "tree". Omitting the
optional first argument will create an index for the same string that
appears in the text.
Some more usful text markup that doesn't create indices:
Robject:an R object (in small typewriter font)
Rfunarg:the agument to an R function (in italics)
code:typewriter font
term:whatever \{emph} is set to
file:italics
reg:The registered trademark glyph
The following environments are used to structure the document and for parsing . They do not impose any layout.
chapterheader:this contains title, authors and abstract
of the chapter/lab
chapterbody:this contains the actual chapter body
chaptertrailer:this contains session info and references
for a chapter
yaa:This is a wrapper for input also setting the
graphics include path. Its first parameter is filename, second
parameter is graphics path
Color and options
BiocCaseStudies as objects
lcol1, lcol2 and lcol3 for light colors, and
dcol1, dcol2 and dcol3 for dark colors.
hideme can be used in
Sweave code chunks that should not be part of the Stangle output. This
only effects Stangle, so a "regular" Sweave will evaluate these
chunks. The intention is to have the possibility for sanity checks or
conditional code evaluation which should not confuse the users when
they work with the extracted code.