mvbutils-package {mvbutils} | R Documentation |
Package mvbutils is a collection of utilities offering the following main features:
cd
.
help
. There is also a complete automatic text-format backup system for functions. See fixr
.
mvbutils.packaging.tools
.
mlazy
.
mlocal
), display of what-calls-what (foodweb
), multiple replacement (multirep
), and numerous lower-level lower-level utility functions and operators (mvbutils.utils
and mvbutils.operators
).
To get the full features of the mvbutils package (in particular, the project organization), you need to start R in the same directory every time (your "ROOT task"), and then switch to whichever project from inside R; see cd
. Various options
always need to be set to make fixr
and the debug package work the way you want, so one advantage of the start-in-the-same directory-approach is that you can keep all your project-independent options()
, library loads, etc., in a single .First
function, called automatically when you start R. However, most features (including support for the debug package) may work even if you don't follow this suggestion.
On loading, the mvbutils package creates a new environment in the search path, called mvb.session.info
, which stores some housekeeping information. mvb.session.info
is never written to disk, and disappears when the R session finishes. [For Splus users: mvb.session.info
is similar to frame 0.] You should never change anything in mvb.session.info
by hand, but it is sometimes useful to look at some of the variables there:
.First.top.search
is the directory R started in (your ROOT task).
.Path
shows the currently-attached part of the task hierarchy.
base.xxx
is the original copy of an overwritten system function, e.g. help
fix.list
keeps track of functions being edited via fixr
session.start.time
is the value of Sys.time()
when mvbutils
was loaded
source.list
is used by source.mvb
to allow nesting of sources
r.window.handle
is used by the handy package (Windows only)
On loading, the present version of package mvbutils compulsorily overwrites a few system functions: library
, rbind.data.frame
, lockEnvironment
. By default, it also overwrites help
, savehistory
, loadhistory
, save.image
, difftime
, +.POSIXt
, and -.POSIXt
. (The original version of routine xxx
can always be obtained via base.xxx
if you really need it.) The modifications should have [almost] no side-effects, and/but I hope to be able to avoid them altogether in future versions of R. Briefly:
library
is modified so that its default pos
argument becomes a call to lib.pos()
. This means that packages get attached just below ROOT rather than always in position 2 (needed by cd
).
lockEnvironment
is modified to allow live-editing of loaded packages– no change to default behaviour.
rbind.data.frame
is modified to work better (IMO) when the first data.frame
has zero rows, to cope with a code-breaking change in R's behaviour several versions ago. Specifically, the modified version does not drop zero-row data.frames, and their column attributes are taken account of when rbind.data.frame
ing to the other args. This is useful when repeatedly adding rows to an initially-empty data.frame. To see the difference, experiment with rbind( data.frame( x=1, y=factor( "a")), data.frame( x=2, y=factor( "b"))[-1,])$y
vs base.rbind.data.frame(...)
with the same arguments. mvbutils
and debug
rely on the non-default behaviour, so the overwriting is not optional.
Optional but recommended replacements are as follows:
help
is modified so that, if system help
can't find help for a function (but not a method, dataset, or package), it will look for a doc
attribute of the function to display in a pager using dochelp
.
loadhistory
and savehistory
are modified so that they use the "R_HISTFILE" environment variable if it set. This can be set dynamically during an R session using Sys.setenv
. Standard R behaviour is to respect "R_HISTFILE" iff it is set before the R session starts. If "R_HISTFILE" is not set, then cd
will on first use set "R_HISTFILE" to "<<ROOT task>>/.RHistory", so that same the history file will be used throughout each and every session.
save.image
is modified to call Save
instead; this will behave exactly the same for workspaces not using mvbutils
task-hierarchy feature or the debug package, but otherwise will prevent problems with mtrace
d functions and mlazy
ed objects.
difftime
, +.POSIXt
, and -.POSIXt
are modified to behave more consistently and forgivingly. Results won't break code that doesn't make invalid assumptions. [This should probably be done in a different package.]
If you are certain that you don't want the optional replacements, set options(mvbutils.replacements=FALSE)
before loading mvbutils
. However, this will prevent cd
, fixr
, and the flat-documentation help from working properly. You can also set the "mvbutils.replacements" option to a character vector comprising some or all of the above names.
After mvbutils
has loaded, you can undo the modification of an individual function called xxx
with assign.to.base( "xxx", base.xxx)
.
ESS.and.'mvbutils'
For ESS users: I'm not an Emacs user and so haven't tried ESS with the mvbutils package myself, but a read-through of the ESS documentation (as of ~2005) suggests that a couple of ESS variables may need changing to get the two working optimally. Please check the ESS documentation for further details on these points. I will update this helpfile when/if I receive more feedback on what works.
cd
changes the search list, so you may need to alter "ess-change-sp-regex" in ESS.
cd
also changes the prompt, so you may need to alter "inferior-ess-prompt". Prompts have the form WORD1/WORD2/.../WORDn> where WORDx is a letter followed by zero or more letters, underscores, periods, or digits.
move
can add/remove objects in workspaces other than the top one, so if ESS relies on stored internal summaries of "what's where", these may need updating.
Display bugs: if you have a buggy Unix display where readline()
always returns the cursor to the start of the line, overwriting any prompt, then try options( cd.extra.CR=TRUE)
.
Mark Bravington
cd
, fixr
, mlazy
, flatdoc
, dochelp
, maintain.packages
, source.mvb
, mlocal
, do.in.envir
, foodweb
, mvbutils.operators
, mvbutils.utils
, package debug