Dear R experts---I would like to write a replacement for the read.csv
function that is less general, but also more efficient.
could someone please provide me with a skeleton function that shows me
how to read the arguments and return a data frame for a call to a C
function that handles
dear R experts:
I am of course no R experts, but use it regularly. I thought I would
share some experimentation with memory use. I run a linux machine
with about 4GB of memory, and R 2.5.0.
upon startup, gc() reports
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 268755 14.4
R version 2.5.0, under gentoo linux. This may be just my ignorance
about naming conventions inside loops and subsets, but the following
appears like a bug to me.
y = c( 1963, 1963, 1964, 1964, 1965, 1965 );
r1= rnorm(6);
d= data.frame ( y=y, r1=r1 );
## note: I am not attach()ing anything
ahh...it is the silent substitution of the data frame in the subset
statement. I should have known this. (PS: this may not be desirable
behavior; maybe it would be useful to issue a warning if the same name
is defined in an upper data frame. just an opinion...)
mea misunderstanding.
/iaw
] On Behalf Of ivo welch
Sent: Thursday, May 17, 2007 11:53 AM
To: jim holtman
Cc: r-help
Subject: Re: [R] bug or feature?
ahh...it is the silent substitution of the data frame in the subset
statement. I should have known this. (PS: this may not be desirable
behavior; maybe it would
hi doug: yikes. could I have done better? Oh dear. I tried to make
my example clearer half-way through, but made it worse. I meant
set.seed(1);
fe = as.factor( as.integer( runif(100)*10 ) ); y=rnorm(100); x=rnorm(100);
print(summary(lm( y ~ x + fe)))
deleted
Coefficients:
dear R experts:
sorry, I have to ask this again. I know that the answer is in section
7.2 of S Programming, but I don't have the book (and I plan to buy
the next edition---which I hope will be titled S/R programming ;-) ).
I believe the following yields a standard fixed-effects estimation:
dear R wizards:
I am trying to replace subset() with my own version that first checks
that each name in the select statement has a corresponding name in the
data set. preferably, it would have the same syntax and semantics as
subset() otherwise.
alas, subset works in interesting ways:
Beautiful. thank you. /ivo
Try:
methods(subset)
which will point you to subset.data.frame. The latter code will answer
your questions.
HTH,
--sundar
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dear R wizards --- would it make sense for names(d$columnname) to be
columnname? I can preserve the columnname through x=subset(dataset,
select=columnname), of course, but it would seem that x=d$columnname
could also do this. No? Sincerely, /iaw
__
yes, this was what I was asking for. I had the notion that one could
tag almost anything with a name, and did not appreciate the scope for
confusion. thank you for the explanation. regards, /ivo
On 4/22/07, Duncan Murdoch [EMAIL PROTECTED] wrote:
On 4/22/2007 5:46 PM, ivo welch wrote:
dear
as to not break scripts that rely on
nothing escaping. I find it very convenient in long scripts written
in perl or C to have the ability to write blips to the terminal,
too...
sincerely,
/ivo welch
On 4/20/07, ivo welch [EMAIL PROTECTED] wrote:
thank you, peter and brian. I had not found the stderr
thank you, again. (PS: the script that I needed that does BATCH exec
in my case was /usr/lib64/R/bin/BATCH; I eliminated the 21, and now
I indeed am getting the stderr to my terminal. I also now know that
Loading required package message also go to stderr.)
best,
/ivo
Dear R wizards---I read Brian Ripley's post from 2004 which said that
it was not possible to print to STDERR. Alas, I have more modest
needs. I was wondering if it was possible to just send a string to
STDERR with cat() while in CMD BATCH mode.
Is it not possible to open STDERR in R? (Or does
thank you, peter and brian. I had not found the stderr() function.
(I had looked at the R Input/Output guide.) This is great. regards,
/ivo
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hanks, dirk. this looks a bit nicer than what I put together in the
last hour, which is a simple perl script that gives me the syntax I
most like:
$ R batch.R arg1 arg2
personally, because this has no meaning in the current invoke
syntax, I think that R should understand this as the obvious
guess is no, but since
I have a second processor lying around, I am trying to get it into the
fray.]
A working example would be appreciated.
regards,
/ivo welch
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dear R experts:
I am often struggling with a desire of wanting to change the basic
output that R prints.
For example, a year ago, I wanted to add the mean to the summary()
statement, and eventually got help from friendly souls who showed me
how to copy the summary() routine and then modify it.
gentoo linux, version 2.4.1:
d= as.data.frame(matrix(1:20, 4, 5))
d
V1 V2 V3 V4 V5
1 1 5 9 13 17
2 2 6 10 14 18
3 3 7 11 15 19
4 4 8 12 16 20
write.csv(d, file=d1.csv);
write.csv(d, file=pipe(cat d2.csv))
write.csv(d, file=pipe(gzip -c d3.csv.gz), col.names=T)
Warning message:
dear R wizards: I have a very simple suggestion/question. Would it
be easy to change the pdf device so that it adds a BoundingBox around
its output? (Under R 2.4.1, this seems not to be the case, because
epstopdf under linux complains. Fortunately, it still works
correctly.)
This is not a big
dear r-experts---I have scrounged around in google (searching r-help)
for the really obvious, but failed. could someone please point me to
whatever function computes the standard error of a linear combination
of the coefficients?
m=lm( y ~ x1 + x2 + x3 );
t.stat= (coef(m)[2]+coef(m)[3])) /
Dear R experts: I want to learn what the practically useful memory
limits are for good work with R.
(My specific problem is that I want work with daily stock returns.
In ASCII, the data set is about 72 million returns, that would have to
go into a sparse matrix (not all stocks exist for the
Dear R wizards:
I am trying (finally) to build a function that might be useful to
others. In particular, I want to create a summary.lme (extended lm)
method that [a] adds normalized coefficients and [b] white
heteroskedasticity adjusted se's and T's. I believe I already know
how to do the
Dear R readers:
I have written a short lme.R function, which adds normalized
coefficients and White heteroskedasticity-adjusted statistics to the
standard output. Otherwise, it behaves like lm. This is of course
trivial for experts, but for me and other amateur users perhaps
helpful.
y=
, at 9:00 PM, ivo welch wrote:
I have written a short lme.R function, which adds normalized
coefficients and White heteroskedasticity-adjusted statistics to the
standard output. Otherwise, it behaves like lm.
Is it a good idea to call it lme, since there's a widely used lme()
in the nlme
dear r experts:
I know its almost surely documented. if d is a data frame
median(d) -- fails (message is need numeric data)
min(d) -- succeeds, but gives a scalar.
mean(d) -- gives a vector
I am wondering whether this could be changed into something more
consistent. most naturally, the
dear R experts:
This is just a minor, minor nuisance, but I thought I would point it out:
dataset - read.table(file=pipe(cmdline), header =T,
+ na.strings=c(NaN, C,I,M, E), sep=,,
as.is=T, nrows=);
Error: cannot allocate vector of size 781249 Kb
If I extend nrows by a
thank you, everybody. It's hard to find much fault with R, but one
feature that would be nice to have would be hooks to output functions
that make it easy to augment to the output---e.g., to add a new
statistic to summary (e.g., mean, sd, different stderrs). not a big
flaw, because one can write
dear R experts: I am trying to orient myself using nls(). so, I am
just trying to copy and adapt an example in the nls() function:
d= data.frame( y= runif(10), x= runif(10) )
nls( y ~ 1/(1+x), data = d, start= list(x=0.5,y=0.5), trace=TRUE)
Error in n%%respLength : non-numeric argument
y ~ 1/(1+x)
which does not seem to match the requirement of the help page.
What are the unknowns for which you were hoping nls would solve??
On Sat, 23 Dec 2006, ivo welch wrote:
dear R experts: I am trying to orient myself using nls(). so, I am
just trying to copy and adapt
dear R experts:
I wonder whether it is possible to extend the summary method for the
lm function, so that it uses an option hccm (well, model hc0). In
my line of work, it is pretty much required in reporting of almost all
linear regressions these days, which means that it would be very nice
not
thank you. exactly what I needed.
can I add it as a suggestion for the next R version to add
an option to quit that prints only one line to stderr (or stdout, but
the real one, not the batch output one) that gives a 1-line job
summary---no error (or nothing), 5 warnings, 5 warnings, fatal
error:
the following diff to the shell script invoking R prints an error
message if R terminates with an error code:
112c112,119
exec sh ${R_HOME}/bin/Rcmd [EMAIL PROTECTED] ;;
---
sh ${R_HOME}/bin/Rcmd [EMAIL PROTECTED]
rc=$?
if [ $rc -ne 0 ]; then
shift ;
dear R wizards: sorry, I am stumped. what is the parameter to just
move the location of the x-label and y-lable (not the labels on the
ticks of the x-axis and y-axis)? probably obvious, but not to me
right now... regards, /iaw
__
dear R wizards: is it possible to instruct R to save or no-save from
inside R? or does this have to be given at invokation on the
command-line?The same question applies to --no-restore-data,
although this presumably would have to be decided in a .First()
function or something like it.
on a
hi paul: thank you. great explanation.
* what you describe seems like a fairly modest advantage of the
traditional system. I have never used the new system, but this part
of the translation should be simple: if a plot() is called, set the
current viewport. emulation done. (if the user has
I just read paul murrell's new book, R graphics.
now, I have always used the traditional graphics system. apparently,
the new (trellis?) system is an entirely separate graphics system.
after reading the book, I cannot figure out what the intrinsic
capability advantage of the old graphics system
Dear R-Wizards: does anyone know how to obtain the width of the
widest y- or x-tick label that R has drawn, so that I can leave
appropriate space between it and my overall axis text label
appropriately?
regards, /ivo welch
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Dear R experts: I have an odd question: would it be better to
calculate the location of the axis label relative to the furthest
protruding tick label? the background is that I have my y-tick labels
oriented horizontally rather than vertically. if R chooses to set a
tick mark at 2, the y label
I wonder if this is an intentional feature or an oversight. in some
column summaries or in ifelse operations, apparently I am losing the
date property of my vector.
a - c(198012, 198101, 198102)
b - a*100+31
c - as.Date( as.character(b), %Y%m%d )
summary(c)
Min. 1st Qu.
Dear R wizards: sorry to bug everyone twice in one day.
I would like to annotate my graph by putting text strings into
rectangle boxes with a little cartoon-like bubble with a lid pointing
to a specific location. I can draw some sort of bubble-with-lid using
the R primitives. (has anyone done
dear R wizards:
while extolling the virtues of R, one of my young econometrics
colleagues told me that he still wants to run ox because [a] his code
is written in it (good reason); [b] because ox seems to be faster than
R in most benchmarks (huh?).
this got me to wonder. language speed can't
I just upgraded to the latest ghostscript, AFPL 8.54. When I run the
R output through gs, I get
AFPL Ghostscript 8.54: Set UseCUEColor for UseDeviceIndependentColor
to work properly.
followed by a segfault. the resulting ghostscript file is incomplete
(no %%EOF). probably a ghostscript bug,
Hi Thomas:
One case where the vector-vector recycling rules are used is in
vector-matrix operations:
a-1:4
b-diag(4)
a+b
is this last expression intended to be intuitive and thus desirable?
if anything else, I would end up writing something like this more as
an error than by
Dear R wizards:
I just got stung by the ifelse() feature.
a - 10:15
b - 20:300
test - 1
ifelse(test,a,b)
[1] 10
I had not realized that this was the default behavior---I had expected
10:15. mea culpa. however, I wonder whether it would make sense to
replace ifelse with a different
I am amazed at the stuff Gabor knows. After I jokingly suggested R manuals
were his bedtime reading he pretty much agreed: he reads documentation and
code.
He is in any case an extraordinary resource, and his contributions to this
list are second to none. He has my vote of appreciation.
hi gabor: thank you very much. how do you know this stuff? I just
looked at the contributors() list, and you are not on it. may I
highly suggest that a wrapper for this become part of the R base? it
should also have a link from the commandArgs() help page to whatever
this function should be
hi gabor: is there a version of this for linux, too?
regards, /iaw
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may I ask one more item? is there an official or best way to
request that R add a standardized option that tells the user the R
script name? I understand that most of the R developers read this
group (bless them!), and the R developers may disagree about the
usefulness/effort ratio of such a
in R-intro.html.
so, how would I go about looking for where R defines functions? or
has this becomes so deeply wired into fortran/C in later versions that
it can no longer be changed?
help/advice as always appreciated.
sincerely,
/ivo welch
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to put code-1.r into a character vector?
help appreciated.
regards, /ivo welch
PS :I read the past R-help posts on the subject, but apparently
the older suggested solutions no longer work. (commandArgs() is not
the answer, either.) And I did also not see it under the FAQ in the R
, the R read functions are already smart enough to ignore the
comment lines.
help appreciated. regards, /ivo welch
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thank you, duncan. yikes. how about people on sane (sorry, mean
linux or unix) systems... ;-). regards, /iaw
On 4/2/06, Duncan Murdoch [EMAIL PROTECTED] wrote:
On 4/2/2006 9:34 PM, ivo welch wrote:
dear R group: I have the probably fairly common problem that I would
like to have one
thanks, but darn: I only own your modern applied statistics text.
I will buy the S programming book. is there a new edition coming
soon, or should I go with the existing text?
regards,
/iaw
On 3/28/06, Prof Brian Ripley [EMAIL PROTECTED] wrote:
There is a very similar example worked
example? help is, as always, highly appreciated.
sincerely,
/ivo welch
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[please indulge my semi-colons.] how should this be done? help, as
always, appreciated.
sincerely,
/ivo welch
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dear R wizards---I must be standing on the line (German
translation---this must be obvious). This is probably embarrassingly
obvious to anyone, except to me right now. maybe it is late.
I would like to run my R code in batch, but not see the R compilations
and my R source code---I just want to
hi marc: yes, this is it. I tried --slave alone, which had not been
enough. thanks. regards, /iaw
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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,
I am not an R expert, but I think the R idea of this task is to work
with a data frame (where you make a and b are columns), and then to
iterate over the rows.
data - read.table( textConnection(
a b
1 name1
2 name2
3 name3), header=TRUE) ; # just learned this one
for (i in 1:nrow(data)) print(
just a short beg for the next R 2.3 version:
I know it is easy to add the sd into summary() in the source bowels of
R---but everytime R is updated, my change disappears. :-(. I do not
believe that R has an easy extension mechanism for univariate
summaries, short of a function rewrite here.
data[ data$a == name2 ] # does not work and gives a weird result, yuck
data[data$a==name2,]
sorry about this. I believe a few versions back, one could not subset
data frames, so I did not even check what I wrote. Works now.
Look at ?order.
I know. This is why I suggested only that
Dear R Wizards: To bore everyone to death, below is an improved and
hopefully final version of my native.slope() function. (Thanks, Jim.)
In case you are not asleep yet reading yet another post of mine, may
I ask the experts some programming questions?
[I just saw yesterday's threat---I
Dear R wizards: First, thank you for all the responses to my earlier
queries. Will keep me busy tomorrow morning. Can I add one graphics
question to my ever changing set of bothering questions, please?
plot( c(0,1), c(0,1) );
crop.to.plot.off(); # what I want; does not exist
text( -0.3, 0.1,
, perhaps more embellished, to save me
the debugging effort?)
Or, is there an alternative to srt, which slopes the text relative to the
existing scale?
help appreciated.
sincerely,
/ivo welch
[[alternative HTML version deleted]]
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is the ability of
text to 'snake' itself along the line itself. I doubt that this is
easily possible, but I just wanted to ask.
help appreciated.
sincerely,
/ivo welch
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);
}
}
On 2/4/06, Duncan Murdoch [EMAIL PROTECTED] wrote:
On 2/4/2006 3:50 PM, ivo welch wrote:
[resent, plus small addition; I do not understand why gmail sent a
weird charset.]
Dear R wizards:
I would love to write a general function that matches the slope of a plotted
line in an xy-plot
],),
d.m=,d.m, (, ylim[2],ylim[1],xlim[2],xlim[1], ),
asp.ratio=, (par()$fin)[1], :, (par()$fin)[2], ==, net.slope,
=, slope, deg\n);
}
return( slope = slope );
}
On 2/4/06, ivo welch [EMAIL PROTECTED] wrote:
Thank you, Duncan. This led me to the info I needed. Here
thank you. I am still not sure how to get the scores in princomp, though:
ds= as.data.frame( cbind(rnorm(10),rnorm(10)) )
names(ds)=c(x1,x2)
ds[5,]=c(NA,NA)
pc= princomp( formula = ~ ds$x1 + ds$x2, na.action=na.omit)
ds$pc1 = pc$scores[,1] #-- error, scores has 9 obs, ds has 10 obs
is there an
,
/ivo welch
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dear R wizards: could you please point me into the right direction? I
would like to write a general function arrow(x1,y1,x2,y2), which
naturally draws an arrow.
the basics of writing this function are of course easy. the only
complication is that I would like the arrow not to exactly hit
Dear R Wizards:
sorry, I need more help. hopefully, it will help others in the future.
I am using R 2.2.0 Patched (2005-11-07 r36217).
[a]
# copy from the postscriptFont documentation
CMitalic - postscriptFont(ComputerModern,
c(CM_regular_10.afm, CM_boldx_10.afm,
Dear R developpment team: would it be easy to introduce a global variable (in
options()) that contains the name of the R file that is currently being
processed? (ala \jobname in latex.) if this is difficult, would it be easy to
introduce something like $0 in perl (i.e., argv[0] in C), which
.
sincerely,
/ivo welch
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wrote:
On Mon, 7 Nov 2005, ivo welch wrote:
[a] I believe that the pdf device does not yet fully support
TeXencoding. (under R-2.2.0, the pdf file created with Textext as
font encoding still dies when post-processed by ghostscript.) are
there any workarounds, or are there utilities
not specify a font encoding. (I believe I need this encoding for
the math symbols, like '=', to appear in the right places.)
is this an R (enc file) bug or another mistake of mine? as always,
help would be highly appreciated.
sincerely, /iaw
---
ivo welch
encoding error does not appear in the postscript
device driver, and it works fine. It would be nice if R gave an error
message, instead of producing corrupt .pdf files. Just a suggestion...
Regards,
/iaw
---
ivo welch
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Prof Brian Ripley wrote:
find(loadhistory)
[1] package:utils
so see the comments at the top of the NEWS for 1.9.0. You will need to
use utils::loadhistory() in .Rprofile, or a loadhook.
thank you all. sheesh, it broke in 1.9.0, not 1.9.1---I looked through
the 1.9.1 release notes, and
thanks, guys. circles might be a good candidate for a graphics
primitive in the next R version, if only because---unlike the solutions
here---I believe that postscript/pdf have scaleable primitives---though
I am no postscript expert. of course, if I knew what I was talking
about, I would
hi: thanks everyone for pointing me to the contribution page..
[a] it was not obvious to me how to find this page. if you like
contributions, please make it a bit more obvious. I would think a
button on the home page would be a good idea.
[b] any kind of trinket sale (a CD?) for money would
Thanks again for all the messages.
Is the 4% in par('usr') hardcoded? if so, may I suggest making this a
user-changeable parameter for x and y axis?
I looked at psfrag, and it seems like a great package. alas, I have
switched to pdflatex, and pdffrag does not exist. :-(
I also discovered
hi: I searched the last 2 hours for a way to enter a data frame
directly in my program. (I know how to read from a file.) that is, I
would like to say something like
d - this.is.a.data.frame( c(obs1name, 0.2, 0.3),
c(obs2name, 0.4, 1.0),
thank you, chaps. ok, so this is not as straightforward as I had
thought. perhaps the read.table() function should have the ability to
read inline (terminated, e.g., by two newlines, or a usersettable
string), rather than just from a file. this would be a nice feature.
regards, /iaw
sorry to impose again.
At the default point size, R seems very good in selecting nice xlim/ylim
parameters, and leaving a little bit of space at the edges of its
xlim/ylim. alas, I now need to create ps graphics that can only occupy
a quarter of a page, so I need to blow up the text for
thank you, marc. I will play around with these parameters tomorrow at
my real computer. yes, the idea is to just create an .eps and .pdf
file, which is then \includegraphics[0.25\textwidth]{} in pdflatex. I
need to tweak with the parameter ps.options(pointsize) because
otherwise, I end up
can we put a how to donate money to R on the R webpage? perhaps with
a paypal button?
even better, because I would like to donate some funds from my research
budget, could the R-project possibly sell some trinkets for a high price
for support? it is difficult to explain to a non-profit org
. this is of course
steeped in too much history, but a name change would help---calling it
some random 6-letter combination.
regards,
/ivo welch
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hi: would it be useful to build into R an optional mechanism that
typechecks arguments? for example,
sum.across - function ( inpmatrix : matrixtype( dim[1]1, dim[2]3
) ) : vector { }
# this would define a sum.across function that can take matrices
or data sets, but not vectors,
hi: I have a y vector and an x data frame. is it possible to use the
standard linear regression (lm, summary.lm) without having to construct
a formula, i.e., all x variables should be used.
x - data.frame( rnorm(10), rnorm(10) ); # -- well, this would
really be read from a file
y -
hi: is it possible to color areas between two functions? for example,
x- 1:100;
plot(x, x^2, type=l);
lines(x,0.5*x^2, type=l);
# better
plotwithfill(x, x^2, 0.5*x^2, color=c(yellow, red);
where the first color is used if f(x)=x^2 g(x)=0.5*x^2, and the second
for the reverse.
Hi: thanks for the polygon recommendations. these work like a charm
for me.
minor documentation bug: ?plot.default states lwd is not yet supported
for postscript, but it does seem to work.
regards,
/iaw
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hi R wizards: I think it would be a good idea for me to use basic
argument checking (type, length) in function calls via an assert() like
function. How do people usually do this? Should I define my own
assert() function (or are there some predefined assertions)? If I
write my own assert,
thank you all for all the advice. regards, /iaw
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Hi: I would like to write a function that takes as its input a formula
and outputs normalized coefficients ( coef(x)*sdv(x)/sdv(y) ). now, a
formula is an object, and I cannot see how to extract the variables for
obtaining sdv's. the intent is to write something like
my.print.lm(
hi: sorry to bother you all again. I am running a simple lm(y~x+z)
regression, in which some of the observations are missing.
Unfortunately, the residuals vector from the lm object omits all the
missing values, which means that I cannot simply do residual diagnostics
(e.g., plot(y,x)).
hi andy: mea culpa. it is the exit function in most other languages.
It would be exit(0) invocation in C (C++) and perl, for example.
regards, /iaw
Liaw, Andy wrote:
So you still have not told us what exactly what you are looking for. What
do you want some sort of stop() to do inside a
hi brian: thanks. I will put in a suggestion that the docs refer to
q() in see also for stop.
regards,
/ivo
Prof Brian Ripley wrote:
That's called q() in R.
snip
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Why does stop(we are done) print
Error in eval.with.vis(expr, envir, enclos) : ?
It would seem to me that a plain stop() is not an error, and that it
would make more sense to have an error() function that is different from
a stop(). Is there a rationale here that I am missing?
sincerely,
hi andy: yes, I know what it does. My suggestion would be to have a
different command, that is a pure stop without error condition (with
its message). A stop and an error are really two different things.
regards, /ivo
Liaw, Andy wrote:
Please do read the documentation of the functions you
Is it possible to instruct R to output a line number when an error or
warning is encountered in a source() file?
sincerely, /iaw
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