Dear R Wizards: To bore everyone to death, below is an improved and
hopefully final version of my native.slope() function. (Thanks, Jim.)
In case you are not asleep yet reading yet another post of mine, may
I ask the experts some programming questions?
[I just saw yesterday's threat---I think it would be very, very, very nice if
R would remember from what files with what linenumbers code came from.
thus ignore below questions that mention this feature. ALAS, I understand
that this cannot be done generally. But could not function definitions at
least have a component that remembers this?]
* Is there a way that I can print an R functional backtrace? Instead
of passing my subroutine name to my function "assert()" below, it
would be nice if I could just print the whole call tree [preferably
with file names+line numbers] when I want my program to gracefully
bonk out. (PS: I think that this is also what R should print when any
user program bonks out, not just the stop message.) Actually, I just
learned about traceback(), which functions nicely AFTER the program
stops, not before. But it gives no traceback earlier---and it does
not give filename+lineno.
* is there a way to print all my user defined functions? I have an
init file, in which I am defining all sorts of useful utility
functions, and I would like to print what I have defined (for memory)
upon a read of this init file? that is, something that has
functionality like
note.all.local.definitions.now.in.vector( all.local.functions )
a <- function() { }
b <- function() { }
cat( all.local.functions ); # should print 'a' and 'b'.
* is there a string variable that gives me the name of the current
function I am in?
* SUGGESTION: can we please offer the "?:" operator ala C in addition
to ifelse()? This would make R code prettier. Similarly, perl has a
nice construct, which would be lovely, but which may not jive with the
R syntax:
condition or die("the condition", condition, "has failed");
condition and cat("my condition", condition, "is met");
I believe "or" and "and" are not defined, so this may be possible...
* has it now become possible to embed sample data sets in R code? (I
asked this a while back, but there were nly kludges, no standard
"pretty" solutions.)
* SUGGESTION: The ?"function" docs would be terrific if they had a
small example at the end that showed how to return multiple arguments,
and then pick them up. I believe this is best done through lists, but
I am not sure.
I find myself programming more and more in R, so I am beginning to see
it as my standard language, rather than as a statistical program.
Regards,
/iaw
################################################################
#### native.slope computes a suitable srt from a function around
#### a point on a function. This is useful until text() gets
#### an srt parameter that is relative to the coordinate system.
#### (Ideally, R would be able to slope along a function.)
################################################################
native.slope <- function( x, y, where.i, debug =0) {
assert <- function( condition, routine, ... ) {
if (condition) return(NULL);
cat(paste(routine,...));
stop("THIS IS A FATAL ERROR!\n");
}
subname= "native.slope"; # until I discover how to print a complete
backtrace, this is it.
assert( length(x) == length(y), subname,
"Sorry, but x and y must have equal dimensions, not ", length(x), "
and ", length(y), "\n");
## try to take a symmetric field around the point to be described
l0= ifelse( where.i<=1, 1, where.i-1);
l1= ifelse( where.i>=length(y), length(y), where.i+1);
assert( !is.na(x[l0]), subname, "Sorry, but x[",l0,"] is NaN");
assert( !is.na(x[l1]), subname, "Sorry, but x[",l1,"] is NaN");
assert( !is.na(y[l0]), subname, "Sorry, but y[",l0,"] is NaN");
assert( !is.na(y[l0]), subname, "Sorry, but y[",l1,"] is NaN");
assert( y[l1] != y[l0], subname, "Sorry, but you cannot draw a slope
on a point");
## native slope in a 1:1 coordinate system
d= ( (y[l0]-y[l1])/(x[l0]-x[l1]) );
if (is.na(d)) return(0); # we do not know how to handle an undefined
spot at a function!
## now adjust by the axis scale and size of plot area
.usr <- par('usr') # dimensions of user units
.plt <- par('plt') # percent of figure area that plot region is
d.m <- (.usr[4] - .usr[3]) / (.usr[2] - .usr[1]) * (.plt[2] -
.plt[1]) / (.plt[4] - .plt[3])
assert( !is.na(d.m), subname, "Internal Error: I do not have
sensible axis dimensions (", d.m, ")\n");
## now handle the drawing system
.fin = par('fin');
asp.ratio = .fin[1]/.fin[2];
assert( !is.na(asp.ratio), subname, "Internal Error: I do not have a
reasonable drawing aspect ratio");
net.slope= d/asp.ratio/d.m;
slope = atan(net.slope)/pi*180.0;
if (debug) {
cat("\t", subname, "debug: d=", d, " (",y[where.i-1],y[where.i+1],
x[where.i-1], x[where.i+1],")\n",
"\t\td.m=",d.m, " (", .usr, ",", .plt, ")\n",
"\t\tasp.ratio=", .fin, "\n\t\t==> slope=", net.slope, "=", slope, "deg\n");
points( x[where.i], y[where.i], pch=19 );
}
return( slope = slope );
}
srt --- slope text with function?
9 messages · ivo welch, Pierre Kleiber, Duncan Murdoch +4 more
I'll respond to one of your multitude of queries below. Suggest that you confine your postings to a single issue so that the subject heading is more meaningful. Cheers, Pierre ivo welch offered the following remark on 02/05/06 11:28... [...]
* is there a way to print all my user defined functions? I have an
init file, in which I am defining all sorts of useful utility
functions, and I would like to print what I have defined (for memory)
upon a read of this init file? that is, something that has
functionality like
note.all.local.definitions.now.in.vector( all.local.functions )
a <- function() { }
b <- function() { }
cat( all.local.functions ); # should print 'a' and 'b'.
The following lists the functions defined in a (default current) environment:
"lsf" <- function (pos = 1)
{
junk <- ls(pos, all.names = TRUE)
junk[sapply(junk, function(x) is.function(eval(as.symbol(x))))]
}
[...]
______________________________________________ R-help at stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
----------------------------------------------------------------- Pierre Kleiber, Ph.D Email: pierre.kleiber at noaa.gov Pacific Island Fisheries Science Center Tel: 808 983-5399 NOAA Fisheries 2570 Dole St., Honolulu, HI 96822-2396 ----------------------------------------------------------------- "God could have told Moses about galaxies and mitochondria and all. But behold... It was good enough for government work."
On 2/5/2006 4:28 PM, ivo welch wrote:
Dear R Wizards: To bore everyone to death, below is an improved and hopefully final version of my native.slope() function. (Thanks, Jim.) In case you are not asleep yet reading yet another post of mine, may I ask the experts some programming questions? [I just saw yesterday's threat---I think it would be very, very, very nice if R would remember from what files with what linenumbers code came from. thus ignore below questions that mention this feature. ALAS, I understand that this cannot be done generally. But could not function definitions at least have a component that remembers this?] * Is there a way that I can print an R functional backtrace? Instead of passing my subroutine name to my function "assert()" below, it would be nice if I could just print the whole call tree [preferably with file names+line numbers] when I want my program to gracefully bonk out. (PS: I think that this is also what R should print when any user program bonks out, not just the stop message.) Actually, I just learned about traceback(), which functions nicely AFTER the program stops, not before. But it gives no traceback earlier---and it does not give filename+lineno.
There's going to be a new section on debugging in the R 2.3.0 "Writing R Extensions" manual (written by Brian Ripley). You can see it now if you build R-devel (or download a binary build from CRAN; I put Windows builds there approximately daily). I also put together a Windows-oriented debugging page at http://www.stats.uwo.ca/faculty/murdoch/software/debuggingR/.
* is there a way to print all my user defined functions? I have an
init file, in which I am defining all sorts of useful utility
functions, and I would like to print what I have defined (for memory)
upon a read of this init file? that is, something that has
functionality like
note.all.local.definitions.now.in.vector( all.local.functions )
a <- function() { }
b <- function() { }
cat( all.local.functions ); # should print 'a' and 'b'.
ls.str() includes an option to select only functions. You could also write your own filter for ls() output.
* is there a string variable that gives me the name of the current function I am in?
I don't think so, but sys.call() gets close. Watch out though: the name you see will be the name used by the caller, which may not be the name used when the function was written. For example, in a function called from apply(), you'll see FUN, not the original name. Objects don't know their own names in general, because they keep getting passed around.
* SUGGESTION: can we please offer the "?:" operator ala C in addition
to ifelse()? This would make R code prettier. Similarly, perl has a
nice construct, which would be lovely, but which may not jive with the
R syntax:
condition or die("the condition", condition, "has failed");
condition and cat("my condition", condition, "is met");
I believe "or" and "and" are not defined, so this may be possible...
The ? operator is already used as a prefix and infix operator (for the help system), so this seems unlikely.
* has it now become possible to embed sample data sets in R code? (I asked this a while back, but there were nly kludges, no standard "pretty" solutions.)
I don't understand the question. dump() produces R code that can reconstruct a dataset; is that what you want?
* SUGGESTION: The ?"function" docs would be terrific if they had a small example at the end that showed how to return multiple arguments, and then pick them up. I believe this is best done through lists, but I am not sure.
I'd guess most people learn about functions from the Intro to R manual rather than the "function" man page, but this is a good suggestion. Duncan Murdoch
I find myself programming more and more in R, so I am beginning to see
it as my standard language, rather than as a statistical program.
Regards,
/iaw
################################################################
#### native.slope computes a suitable srt from a function around
#### a point on a function. This is useful until text() gets
#### an srt parameter that is relative to the coordinate system.
#### (Ideally, R would be able to slope along a function.)
################################################################
native.slope <- function( x, y, where.i, debug =0) {
assert <- function( condition, routine, ... ) {
if (condition) return(NULL);
cat(paste(routine,...));
stop("THIS IS A FATAL ERROR!\n");
}
subname= "native.slope"; # until I discover how to print a complete
backtrace, this is it.
assert( length(x) == length(y), subname,
"Sorry, but x and y must have equal dimensions, not ", length(x), "
and ", length(y), "\n");
## try to take a symmetric field around the point to be described
l0= ifelse( where.i<=1, 1, where.i-1);
l1= ifelse( where.i>=length(y), length(y), where.i+1);
assert( !is.na(x[l0]), subname, "Sorry, but x[",l0,"] is NaN");
assert( !is.na(x[l1]), subname, "Sorry, but x[",l1,"] is NaN");
assert( !is.na(y[l0]), subname, "Sorry, but y[",l0,"] is NaN");
assert( !is.na(y[l0]), subname, "Sorry, but y[",l1,"] is NaN");
assert( y[l1] != y[l0], subname, "Sorry, but you cannot draw a slope
on a point");
## native slope in a 1:1 coordinate system
d= ( (y[l0]-y[l1])/(x[l0]-x[l1]) );
if (is.na(d)) return(0); # we do not know how to handle an undefined
spot at a function!
## now adjust by the axis scale and size of plot area
.usr <- par('usr') # dimensions of user units
.plt <- par('plt') # percent of figure area that plot region is
d.m <- (.usr[4] - .usr[3]) / (.usr[2] - .usr[1]) * (.plt[2] -
.plt[1]) / (.plt[4] - .plt[3])
assert( !is.na(d.m), subname, "Internal Error: I do not have
sensible axis dimensions (", d.m, ")\n");
## now handle the drawing system
.fin = par('fin');
asp.ratio = .fin[1]/.fin[2];
assert( !is.na(asp.ratio), subname, "Internal Error: I do not have a
reasonable drawing aspect ratio");
net.slope= d/asp.ratio/d.m;
slope = atan(net.slope)/pi*180.0;
if (debug) {
cat("\t", subname, "debug: d=", d, " (",y[where.i-1],y[where.i+1],
x[where.i-1], x[where.i+1],")\n",
"\t\td.m=",d.m, " (", .usr, ",", .plt, ")\n",
"\t\tasp.ratio=", .fin, "\n\t\t==> slope=", net.slope, "=", slope, "deg\n");
points( x[where.i], y[where.i], pch=19 );
}
return( slope = slope );
}
______________________________________________ R-help at stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
On Sun, 5 Feb 2006, Pierre Kleiber wrote:
I'll respond to one of your multitude of queries below. Suggest that you confine your postings to a single issue so that the subject heading is more meaningful. Cheers, Pierre ivo welch offered the following remark on 02/05/06 11:28... [...]
* is there a way to print all my user defined functions? I have an
init file, in which I am defining all sorts of useful utility
functions, and I would like to print what I have defined (for memory)
upon a read of this init file? that is, something that has
functionality like
note.all.local.definitions.now.in.vector( all.local.functions )
a <- function() { }
b <- function() { }
cat( all.local.functions ); # should print 'a' and 'b'.
The following lists the functions defined in a (default current) environment:
"lsf" <- function (pos = 1)
{
junk <- ls(pos, all.names = TRUE)
junk[sapply(junk, function(x) is.function(eval(as.symbol(x))))]
}
I am sorry, it does not in general (since eval is not looking in that environment). See ls.str (in utils) for a more elegant way to do this via exists(mode = "function")
Brian D. Ripley, ripley at stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UK Fax: +44 1865 272595
On Sun, 5 Feb 2006, Duncan Murdoch wrote:
On 2/5/2006 4:28 PM, ivo welch wrote:
Dear R Wizards: To bore everyone to death, below is an improved and hopefully final version of my native.slope() function. (Thanks, Jim.) In case you are not asleep yet reading yet another post of mine, may I ask the experts some programming questions? [I just saw yesterday's threat---I think it would be very, very, very nice if R would remember from what files with what linenumbers code came from. thus ignore below questions that mention this feature. ALAS, I understand that this cannot be done generally. But could not function definitions at least have a component that remembers this?] * Is there a way that I can print an R functional backtrace? Instead of passing my subroutine name to my function "assert()" below, it would be nice if I could just print the whole call tree [preferably with file names+line numbers] when I want my program to gracefully bonk out. (PS: I think that this is also what R should print when any user program bonks out, not just the stop message.) Actually, I just learned about traceback(), which functions nicely AFTER the program stops, not before. But it gives no traceback earlier---and it does not give filename+lineno.
'Actually', R does what you ask it to: see options(error). But before the program stops, there is no error to report. In interactive use I see no problem in typing traceback() or using recover() (see below), but for batch use we are looking at alternatives. For example, in R 2.3.0 (modern) Unix users will get a traceback after a segfault.
There's going to be a new section on debugging in the R 2.3.0 "Writing R Extensions" manual (written by Brian Ripley). You can see it now if you build R-devel (or download a binary build from CRAN; I put Windows builds there approximately daily). I also put together a Windows-oriented debugging page at http://www.stats.uwo.ca/faculty/murdoch/software/debuggingR/.
filename+lineno makes no sense: R functions are not (in the main) from files. They can be autogenerated (and often are). And I can 'fix' them. As for the call stack, try options(error=recover) and 'where': see the chapter Duncan pointed you to.
* is there a way to print all my user defined functions? I have an
init file, in which I am defining all sorts of useful utility
functions, and I would like to print what I have defined (for memory)
upon a read of this init file? that is, something that has
functionality like
note.all.local.definitions.now.in.vector( all.local.functions )
a <- function() { }
b <- function() { }
cat( all.local.functions ); # should print 'a' and 'b'.
ls.str() includes an option to select only functions. You could also write your own filter for ls() output.
* is there a string variable that gives me the name of the current function I am in?
I don't think so, but sys.call() gets close. Watch out though: the name you see will be the name used by the caller, which may not be the name used when the function was written. For example, in a function called from apply(), you'll see FUN, not the original name. Objects don't know their own names in general, because they keep getting passed around.
In the debugging context the command 'where' tells you the sequence of
calls (which can be more helpful).
More generally, functions need not even have names (Bill Venables calls
them 'anonymous functions'), as in
r <- sapply(nms,
function(n) if (exists(n, envir = envir, mode = mode))n
else as.character(NA))
from ls.str.
Brian D. Ripley, ripley at stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UK Fax: +44 1865 272595
Duncan Murdoch <murdoch at stats.uwo.ca> writes:
On 2/5/2006 4:28 PM, ivo welch wrote:
* has it now become possible to embed sample data sets in R code? (I asked this a while back, but there were nly kludges, no standard "pretty" solutions.)
I don't understand the question. dump() produces R code that can reconstruct a dataset; is that what you want?
Or dput(). You can also read from a text connection, using constructions like data <- read.table( textConnection( "a b c d 2 1 3 5 0 2 4 1 1 2 3 4"), header=TRUE) (The quotes have to placed as shown, or you get extra blank lines).
O__ ---- Peter Dalgaard ??ster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907
Thank you, as always.
May I disagree with you and offer a suggestion?
In the best of worlds, a function should have multiple attributes. In
addition to the function name and its argument list, two mandatory
attributes should be a filename and lineno. If the function is
interactively created, perhaps we can call the filename "-" and the
lineno a count that could come from the history(). Yes, it will
*NOT* be perfect, but it would be a big improvement.
If functions can have attributes, in addition to keeping the filename
and lineno, it would be great if it could have an immediate
association with a short documentation message? This could be a neat
documentation crutch, useful, e.g., in ls.str() or a describe(). the
best syntax that I can think of just stinks, but maybe a standard
argument does the job and should be encouraged.
xyz <- function(args, doc="xyz returns 0") { return(0); }
I do not think the following syntax would work stylewise:
xyz <- function "xyz returns 0" (args) { return(0); }
but it would be nicer in noting the difference between a normal
argument and a short function descriptor.
regards,
/iaw
by traceback(), do you mean the gdb() like traceback of the R
internals? This would not be too helpful to most users. I would be
more interested in my R call stack, not my underlying C call stack.
[and thanks again for all the other info].
regards,
/iaw
On 2/6/06, Prof Brian Ripley <ripley at stats.ox.ac.uk> wrote:
'Actually', R does what you ask it to: see options(error). But before the program stops, there is no error to report. In interactive use I see no problem in typing traceback() or using recover() (see below), but for batch use we are looking at alternatives. For example, in R 2.3.0 (modern) Unix users will get a traceback after a segfault.
There's going to be a new section on debugging in the R 2.3.0 "Writing R Extensions" manual (written by Brian Ripley). You can see it now if you build R-devel (or download a binary build from CRAN; I put Windows builds there approximately daily). I also put together a Windows-oriented debugging page at http://www.stats.uwo.ca/faculty/murdoch/software/debuggingR/.
filename+lineno makes no sense: R functions are not (in the main) from files. They can be autogenerated (and often are). And I can 'fix' them. As for the call stack, try options(error=recover) and 'where': see the chapter Duncan pointed you to.
* is there a way to print all my user defined functions? I have an
init file, in which I am defining all sorts of useful utility
functions, and I would like to print what I have defined (for memory)
upon a read of this init file? that is, something that has
functionality like
note.all.local.definitions.now.in.vector( all.local.functions )
a <- function() { }
b <- function() { }
cat( all.local.functions ); # should print 'a' and 'b'.
ls.str() includes an option to select only functions. You could also write your own filter for ls() output.
* is there a string variable that gives me the name of the current function I am in?
I don't think so, but sys.call() gets close. Watch out though: the name you see will be the name used by the caller, which may not be the name used when the function was written. For example, in a function called from apply(), you'll see FUN, not the original name. Objects don't know their own names in general, because they keep getting passed around.
In the debugging context the command 'where' tells you the sequence of
calls (which can be more helpful).
More generally, functions need not even have names (Bill Venables calls
them 'anonymous functions'), as in
r <- sapply(nms,
function(n) if (exists(n, envir = envir, mode = mode))n
else as.character(NA))
from ls.str.
--
Brian D. Ripley, ripley at stats.ox.ac.uk
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UK Fax: +44 1865 272595
5 days later
"iw" == ivo welch <ivowel at gmail.com> writes:
iw> * SUGGESTION: can we please offer the "?:" operator ala C in
iw> addition to ifelse()? This would make R code prettier.
R:
if (condition) xxx else yyy
if (condition) xxx else if (yyy) zzz else qqq
C:
condition ? xxx : yyy;
condition ? xxx : yyy ? zzz : qqq;
If this is a beauty contest, or a readability contest, I'll take R!
?: is pleasant in C because it avoids so much of the C syntactic
sugar, of which R is largely free.
As for ifelse(), for a trivial example, try running:
ifelse(array(rep(c(1,0), 50), dim=c(10,10)), "00", "99")
iw> Similarly, perl has a nice construct, which would be lovely, but
iw> which may not jive with the
iw> R syntax:
iw> condition or die("the condition", condition, "has failed");
iw> condition and cat("my condition", condition, "is met");
if (!condition) stop("the condition", condition, "has failed")
if (condition) cat("my condition", condition, "is met")
Patricia J. Hawkins Hawkins Internet Applications www.hawkinsia.com
On 2/11/06, Patricia J. Hawkins <phawkins at connact.com> wrote:
"iw" == ivo welch <ivowel at gmail.com> writes:
iw> * SUGGESTION: can we please offer the "?:" operator ala C in iw> addition to ifelse()? This would make R code prettier. R: if (condition) xxx else yyy if (condition) xxx else if (yyy) zzz else qqq C: condition ? xxx : yyy; condition ? xxx : yyy ? zzz : qqq; If this is a beauty contest, or a readability contest, I'll take R! ?: is pleasant in C because it avoids so much of the C syntactic sugar, of which R is largely free. As for ifelse(), for a trivial example, try running: ifelse(array(rep(c(1,0), 50), dim=c(10,10)), "00", "99")
Maybe this is not the point but in this particular example
we could write:
matrix(c("00", "99"), 10, 10)
iw> Similarly, perl has a nice construct, which would be lovely, but
iw> which may not jive with the
iw> R syntax:
iw> condition or die("the condition", condition, "has failed");
iw> condition and cat("my condition", condition, "is met");
if (!condition) stop("the condition", condition, "has failed")
if (condition) cat("my condition", condition, "is met")
Try this: stopifnot(condition)
-- Patricia J. Hawkins Hawkins Internet Applications www.hawkinsia.com
______________________________________________ R-help at stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html