On 06/11/2015 7:36 AM, Therneau, Terry M., Ph.D. wrote:
I am currently puzzled by a seach path behavior. I have a library of a dozen
routines
getlabs(), getssn(), getecg(), ... that interface to local repositories and
pull back
patient information. All have a the first 6 arguments in common, and
immediately call a
second routine to do initial processing of these 6. The functions "joe" and
"fred" below
capture the relevant portion of them.
My puzzle is this: the last test in the "test" file works fine if these
routines are
sourced and executed at the command line, it fails if the routines are bundled
up and
loaded as a library. That test is motivated by a user who called his data set
"t", and
ended up with a match to base:::t instead of his data, resulting in a strange
error
message out of model.frame --- you can always count on the users! (There are
a few hundred.)
I'm attempting to be careful with envr and enclos arguments -- how does
base end up
earlier in the search path? Perhaps this is clearly stated in the docs and
just not
clear to me? A working solution to the dilemma is of course more than welcome.
I haven't followed through all the details in fred(), but I can answer
the last question. In package code, the search order is:
- the package environment
- the imports to the package (with base being an implicit import)
- the global environment and the rest of the search list.
In code sourced to the global environment, only the third of these is
searched. Since base is in the second one, it is found first in the
package version.
Duncan Murdoch
Terry Therneau
code:
joe <- function(id, data, subset, na.action, date1, date2, other.args) {
Call <- match.call()
if (!missing(data)) temp <- fred(Call)
temp
}
fred <- function(Call) {
# get a first copy of the id and date variables
index <- match(c("id", "date1", "date2"), names(Call), nomatch=0)
temp <- Call[c(1, index)]
temp[[1]] <- as.name("list")
pf <- parent.frame(2) # the caller of the caller
data <- eval(Call$data, envir=pf)
ldata <- eval(temp, data, enclos= pf)
date1 <- ldata$date1
date2 <- ldata$date2
# Users are allowed great flexibility with dates. Both can be given
# as length 1 parameters, both can be in the data set, or one could
# be in each place. Call model.frame with a built up formula that
# includes the id and any dates of length greater than 1. This allows
# subset and na.action to be applied in the usual way.
index <- match(c("data", "subset", "na.action"), names(Call), nomatch=0)
temp <- Call[c(1, index)]
temp[[1]] <- as.name("model.frame")
tform <- "~ id"
if (length(date1) > 1 && is.name(Call$date1))
tform <- paste(tform, "+", as.character(Call$date1))
if (length(date2) > 1 && is.name(Call$date2))
tform <- paste(tform, "+", as.character(Call$date2))
tform <- as.formula(tform)
environment(tform) <- pf
temp$formula <- tform
mf <- eval(temp, enclos=pf)
# At this point the real routine has checks for legal dates, date1 <=
date2, etc
# It returns the tidied up id, date1, date2 vectors.
list(ldata=ldata, mf=mf)
}
test:
library(puzzle)
tdata <- data.frame(id=1:10,
start=as.Date(paste0("1999/", 1:10, "/25")))
xdate <- as.Date(paste0(2001:2010, "/03/10"))
joe(id, tdata, date1= "2001/10/11", date2= xdate[2])
joe(id, tdata, date1=start, date2=xdate)
sqrt <- xdate
cos <- tdata
joe(id, cos, date1=start, date2=sqrt)
DESCRIPTION:
Title: A puzzle
Priority: optional
Package: puzzle
Version: 1.1-1
LazyLoad: Yes
LazyData: Yes
Authors@R: c(person(c("Terry", "M"), "Therneau",
email="therneau.te...@mayo.edu",
role=c("cre")))
Description: What gives with my tests?
License: GPL
NAMESPACE:
export("joe")
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