Puzzled by eval

Duncan,
    That's helpful.  Two follow-up questions:
1. Where would I have found this information?  I had looked at eval and model.frame.
I think the best description is Luke's article on namespaces, "Name 
space management for R". Luke Tierney, R News, 3(1):2-6, June 2003. 
There's a link to it from the "Technical papers" section of the HTML 
help index.  There's also a short description of this in the R Language 
Definition manual in the "Search path" section 3.5.4.
2. What stops the following code from falling down the same rabbit hole?  Shouldn't it
find base::cos first?

     library(survival)
     cos <- lung
     coxph(Surv(time, status) ~ age, data=cos)
If that code is in a function anywhere (package or not), cos will be a 
local variable created there in the evaluation environment created when 
you evaluate the function.  If you execute it at the command line, 
you'll create a variable called "cos" in the global environment.  Local 
variables come ahead of the 3 places I listed.  (This is why Luke's 
article is good:  it doesn't oversimplify.)

There's one other twist.  Even with cos being a local variable, 
cos(theta) would find base::cos, because the evaluator knows it is 
looking for a function (since it's a function call) and will skip over 
the local dataframe named cos.

Duncan Murdoch
Terry T.

On 11/06/2015 07:51 AM, Duncan Murdoch wrote:
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
This code which I think I wrote but might have gotten from elsewhere a
long time ago shows the environments that are searched from a given
function, in this case chart.RelativePerformance in
PerformanceAnalytics package.   Try it on some of your functions in
and out of packages to help determine the sequence of environments R
searches along:

library( PerformanceAnalytics )  ## change as needed
x <- environment(chart.RelativePerformance) ## change as needed
str(x)
while (!identical(x, emptyenv())) {
    p <- parent.env(x)
    cat("---- child is above this line and parent is below ----\n")
    str(p)
    if (isBaseNamespace(p)) cat("Same as .BaseNamespaceEnv\n")
    if (identical(p, baseenv())) cat("Same as baseenv()\n")
    if (identical(p, emptyenv())) cat("Same as emptyenv()\n")
    if (identical(p, globalenv())) cat("Same as globalenv()\n")
    x <- p
}
On 06/11/2015 8:20 AM, Therneau, Terry M., Ph.D. wrote:
Duncan,
    That's helpful.  Two follow-up questions:
1. Where would I have found this information?  I had looked at eval and
model.frame.

I think the best description is Luke's article on namespaces, "Name space
management for R". Luke Tierney, R News, 3(1):2-6, June 2003. There's a link
to it from the "Technical papers" section of the HTML help index.  There's
also a short description of this in the R Language Definition manual in the
"Search path" section 3.5.4.

2. What stops the following code from falling down the same rabbit hole?
Shouldn't it
find base::cos first?

     library(survival)
     cos <- lung
     coxph(Surv(time, status) ~ age, data=cos)

If that code is in a function anywhere (package or not), cos will be a local
variable created there in the evaluation environment created when you
evaluate the function.  If you execute it at the command line, you'll create
a variable called "cos" in the global environment.  Local variables come
ahead of the 3 places I listed.  (This is why Luke's article is good:  it
doesn't oversimplify.)

There's one other twist.  Even with cos being a local variable, cos(theta)
would find base::cos, because the evaluator knows it is looking for a
function (since it's a function call) and will skip over the local dataframe
named cos.

Duncan Murdoch

Terry T.

On 11/06/2015 07:51 AM, Duncan Murdoch wrote:
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

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