Dear R-Help group:
I have been tinkering with how I want my personal standard library
functions to look like. They are not designed to be professional and
heavyweight, but lightweight. There are probably dozens of little bugs,
because I don't know or have not properly taken care of a variety of
internal R code issues. still, I like how this ended up, and there is no
learning curve, so I thought I would share it.
I have put all my functions into a directory ~/src/iaw/R/ . In my standard
.Rprofile, I thus first added a list of my libraries (well, I have just
one) and invoke it:
options(strict="very")
Libdirs <- c("~/src/iaw/R/")
for (libdir in Libdirs) {
source( Sys.glob(paste0(libdir, "Rprofile"))) )
}
(I prefer mnemonics to numbers. it is 2013. why is it text(..., pos="1"),
when it should be text(...,pos="east")? "East", "E" should be
abbreviations for it. Then we could also use NNW...but I am getting
distracted...)
in each of my "light" libraries, I now have an Rprofile file that looks
like this
library(compiler)
cached <- paste0(libdir, "/library.Rdata")
if (file.exists(cached) & all( file.info(cached)$mtime >
file.info(Sys.glob(paste0(libdir,"/*.R")))$mtime
) ) {
load(cached)
cat("Loaded", cached, "\n")
} else {
Rprofile <- Sys.glob(paste0(libdir, "*.R"))
for (n in Rprofile) {
source(n)
}
## libraries that I need to have in order to be able to compile
library(utils)
library(parallel)
library(stats)
library(graphics)
library(grDevices)
for (n in ls()) {
(is.function(.GlobalEnv[[n]]))%or% next
##if ((n %in% c("n", "Rprofile", "cached"))) next
cat("['", n, "']\n", sep="")
.GlobalEnv[[n]] <- cmpfun(.GlobalEnv[[n]])
}
save.image(file=cached)
cat("Saved", cached, "\n")
}
the basic organizational idea now is to stick each R function into its own
.R file. the Rprofile code makes sure that whenever I change a function in
the ~src/iaw/*.R directory, the library is rebuilt (all functions are
recompiled and then saved into an .Rdata file). this is very fast in my
case; if it were not, I could add some intelligence. all of this
could/should be stuck into a universal function
("library.light(directoryname)"), but because I only have one library for
now, it can just live in the Rprofile.
with this organization, it is now also easy to keep vignettes, latex text,
other code, etc., in the same directory. they will just be ignored because
they do not end with .R.
the actual functions follow a format that is different from existing
documentation systems, incl Hadley's oxygen, but designed to plug in
(eventually) into the standard R manual and help system.
PREAMBLE <- c(
doc = '
@TITLE lagseries
@AUTHOR ivo.we...@gmail.com
@DATE Feb 25, 2013
@DESCRIPTION
"lagseries" takes a vector and shift its contents numlags items to the
left, filling in appropriate missing values to retain the length of the
vector. If panelid is named, then lagged value from another panelid will
not be assigned to be the lag. (Usually, the panelid will be the firm id,
and the panel must be sorted by firmid. Naturally, it makes little sense to
use this unless the observations are also sorted by the time of the
observation. This is, after all, a lagseries function.)
@USAGE lagseries( seriesin, numlags =1, panelid=NULL)
@ARGUMENTS
seriesin: a numeric vector
numlags: an integer, can be negative
panelid: an optional panel id
@DETAILS
None
@SEEALSO
leadseries, chgseries, pchgseries, compoundseries
@EXAMPLES
x <- rnorm(10)
xlag <- lagseries(x,2)
lm( x ~ xlag )
d <- data.frame( x <- c( rnorm(20), runif(30), rcauchy(40) ),
who= c( rep("firm1",20), rep("firm2", 30),
rep("firm3",40)),
year= c( 1961:1980, 1971:2000, 1971:2010 ) )
lagd <- data.frame( x=lagseries(d$x, panelid=who), who=d$who,
year=lagseries(d$x, panelid=who) )
',
test = '
all( lagseries( 1:6, 2, c(1,1,2,2,2,2) ) == c(NA,NA,NA,NA,3,4),
na.rm=TRUE )
')
################################################################################################################################
lagseries <- function (seriesin, numlags = 1, panelid = NULL) {
if (!is.null(getOption("strict"))) {
(is.null(seriesin)) %and% "Looks like you are trying to calc a
lagseries from a NULL or non-existing series"
(is.vector(seriesin, mode="any")) %or% "Your series is not a vector,
but a {{class(seriesin)}}."
(length(seriesin) > 1) %or% "Need more observations than
{{length(seriesin)}}"
(is.vector(numlags, mode="numeric", length=1)) %or% "numlags must be a
simple integer, not {{numlags}}."
(is.null(panelid) | (is.vector(seriesin, mode="any",
length=length(seriesin)))) %or%
"panel id must be NULL or a vector of same length as seriesin. right
now it is {{class(panelid)}}"
}
(numlags == 0) %and% return(seriesin)
if (numlags < 0) return(leadseries(seriesin, -numlags, panelid))
rv <- c(rep(NA, numlags), seriesin[1:(length(seriesin) - numlags)])
if (is.null(panelid)) return(rv)
(all(panelid >= lagseries(panelid), na.rm = TRUE)) %or% "The panel is not
sorted upwards by panel id"
ifelse(panelid != lagseries(panelid, numlags), NA, rv)
}
I think this code looks nicer than Hadley Wickham's way of marking up the
docs, but this is obviously a matter of taste. Unlike me, Hadley knows
what he is doing. Still, I wouldn't mind if Hadley adopted a second
optional format like this in oxygen3. Writing an R function that parses
this preamble for every .R file should be easy. Writing an ESS parser with
some more intelligence to understand that any R file that begins with
preamble <- c(doc='') is documentation is probably doable as well, but
emacs hacking is way beyond me. Writing code to step through the tests is
also easy. Moreover, the preamble could hold other useful info (such as a
minimum version number) if need be.
note that, in my lagseries function, I am trying to be anal about the input
checking, but I am careless about output checking.
I wish getOption("strict") would also enable internal R checking, too, but
c'est la vis.
in case someone wants to try this out, here is the sketch of my backup
routines
## if someone from r-help wants to try it out, here are some background
routines:
original.is.vector <- is.vector
is.vector <- function( x, mode ="any", length =(-1) ) {
(original.is.vector(x, mode=mode)) %or% return(FALSE)
((length<0) | (length(x)==length)) %or% return(FALSE)
TRUE
}
## abort.estring should:
## [a] add the name of the preceding invoking function at the start of
the error message, preferably with source line number
## so, the user would see an error like
## * lagseries:52:: Need more observations than 1*
## [b] evaluate every {{ }} construct and insert output into the string
## [c] abort
"%or%" <- function (e1, e2) {
if (!e1) { if (is.character(e2)) abort.estring(e2) else eval(e2) }
}
I do not know whether it is possible to build an abort.estring function
that does what I want, but R seems flexible enough to do almost anything.
I have a sketch of [b], thanks to Neal Fultz, but not of [a].
I hope this organizational design helps some others.
regards,
/iaw
----
Ivo Welch (ivo.we...@gmail.com)
http://www.ivo-welch.info/
<http://www.ivo-welch.info/>
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