Re: [Rd] Documentation bug?
Thanks. The note is indeed outdated since at least R 2.9.0 with NEWS
o predict.lm() now works correctly when the fit had more than
one offset (possibly specified both in the formula and as an
argument). This function is called by predict.glm(), so the
same isses are corrected there.
It has now been removed from ?lm in r83832 in the trunk (ported to
R-patched).
Sebastian Meyer
Am 14.02.23 um 09:31 schrieb GILLIBERT, Andre via R-devel:
Dead R developers,
In R-devel 2023-02-11 and older R versions, there is a note in the "lm
{stats}" help page specifying that:
Offsets specified by offset will not be included in predictions by
predict.lm, whereas those
specified by an offset term in the formula will be.
However, the source code as well as basic tests seem to show that both types of
offset terms are always used in predictions.
a<-data.frame(off=1:4, outcome=4:1)
mod<-lm(data=a, outcome~1, offset=off)
coef(a) # intercept is zero
predict(mod) # returns 1:4, which uses offset
predict(mod, newdata=data.frame(off=c(3,2,5))) # returns c(3,2,5) which uses
the new offset
When looking at the history of R source code, this note seems to exist from R
1.0.0 while the source code of predict.lm already called
eval(object$call$offset, newdata)
https://github.com/SurajGupta/r-source/blob/1.0.0/src/library/base/R/lm.R
https://github.com/SurajGupta/r-source/blob/1.0.0/src/library/base/man/lm.Rd
Version 0.99.0 did not contain the note, but already had the call to
eval(object$call$offset, newdata)
https://github.com/SurajGupta/r-source/blob/0.99.0/src/library/base/man/lm.Rd
https://github.com/SurajGupta/r-source/blob/0.99.0/src/library/base/R/lm.R
The actual behavior of R seems to be sane to me, but unless I miss something,
this looks like a documentation bug.
It seems to have bugged someone before:
https://stackoverflow.com/questions/71264495/why-is-predict-not-ignoring-my-offset-from-a-poisson-model-in-r-no-matter-how-i
Digging deeper in R history, it seems that this note was also found in "glm {stats}" in R
1.0.0 but was removed in R 1.4.1. Maybe somebody forgot to remove it in "lm {stats}" too.
--
Sincerely
Andr� GILLIBERT
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[Rd] Documentation bug?
Dead R developers,
In R-devel 2023-02-11 and older R versions, there is a note in the "lm
{stats}" help page specifying that:
> Offsets specified by offset will not be included in predictions by
> predict.lm, whereas
> those specified by an offset term in the formula will be.
However, the source code as well as basic tests seem to show that both types of
offset terms are always used in predictions.
a<-data.frame(off=1:4, outcome=4:1)
mod<-lm(data=a, outcome~1, offset=off)
coef(a) # intercept is zero
predict(mod) # returns 1:4, which uses offset
predict(mod, newdata=data.frame(off=c(3,2,5))) # returns c(3,2,5) which uses
the new offset
When looking at the history of R source code, this note seems to exist from R
1.0.0 while the source code of predict.lm already called
eval(object$call$offset, newdata)
https://github.com/SurajGupta/r-source/blob/1.0.0/src/library/base/R/lm.R
https://github.com/SurajGupta/r-source/blob/1.0.0/src/library/base/man/lm.Rd
Version 0.99.0 did not contain the note, but already had the call to
eval(object$call$offset, newdata)
https://github.com/SurajGupta/r-source/blob/0.99.0/src/library/base/man/lm.Rd
https://github.com/SurajGupta/r-source/blob/0.99.0/src/library/base/R/lm.R
The actual behavior of R seems to be sane to me, but unless I miss something,
this looks like a documentation bug.
It seems to have bugged someone before:
https://stackoverflow.com/questions/71264495/why-is-predict-not-ignoring-my-offset-from-a-poisson-model-in-r-no-matter-how-i
Digging deeper in R history, it seems that this note was also found in "glm
{stats}" in R 1.0.0 but was removed in R 1.4.1. Maybe somebody forgot to remove
it in "lm {stats}" too.
--
Sincerely
Andr� GILLIBERT
[[alternative HTML version deleted]]
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[Rd] Documentation bug in kruskal.test (PR#10404)
Full_Name: Björn Bornkamp Version: 2.6.0 OS: Windows XP Submission from: (NULL) (129.217.207.144) The literature reference in the documentation for the function kruskal.test is: Myles Hollander & Douglas A. Wolfe (1973), Nonparametric statistical inference. New York: John Wiley & Sons. Pages 115Â120. But I believe it should be Myles Hollander & Douglas A. Wolfe (1973), Nonparametric statistical methods. New York: John Wiley & Sons. Pages 115Â120. There is a different book from Jean Gibbons called "Nonparametric statistical inference", but I believe it does not describe the corrected Kruskal Wallis test statistic, when there are ties in the data... __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] documentation bug for isoreg example (PR#10352)
> "BT" == Benjamin Tyner <[EMAIL PROTECTED]>
> on Thu, 18 Oct 2007 15:15:06 +0200 (CEST) writes:
BT> Full_Name: Benjamin Tyner
BT> Version: 2.6.0 (43063)
BT> OS: WinXP
BT> Submission from: (NULL) (171.161.224.10)
BT> At the end of the examples for isoreg, there is
BT> cat("R^2 =", formatC(sum(residuals(ir4)^2) / (9*var(y4)),
digits=2),"\n")
BT> I think this should be
BT> cat("R^2 =", formatC(1 - sum(residuals(ir4)^2) / (9*var(y4)),
digits=2),"\n"
I think so too, and I'm infinitely embarrassed because I think I
had put that example there {maybe cut & paste from somewhere,
but still...}
Martin Maechler, ETH Zurich.
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[Rd] documentation bug for isoreg example (PR#10352)
Full_Name: Benjamin Tyner
Version: 2.6.0 (43063)
OS: WinXP
Submission from: (NULL) (171.161.224.10)
At the end of the examples for isoreg, there is
cat("R^2 =", formatC(sum(residuals(ir4)^2) / (9*var(y4)), digits=2),"\n")
I think this should be
cat("R^2 =", formatC(1 - sum(residuals(ir4)^2) / (9*var(y4)), digits=2),"\n"
Thanks
Ben
platform i386-pc-mingw32
arch i386
os mingw32
system i386, mingw32
status
major 2
minor 6.0
year 2007
month 10
day03
svn rev43063
language R
version.string R version 2.6.0 (2007-10-03)
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Re: [Rd] Documentation bug: Section 3.3.2 of R-Lang. (PR#9928)
[EMAIL PROTECTED] wrote: > Full_Name: Simeon Bird > Version: 2.5.1 > OS: Linux > Submission from: (NULL) (131.111.200.200) > > > In the manual "The R Language Definition", section 3.3.2 reads: > > "3.3.2 Propagation of names > > propagation of names (first one wins, I think - also if it has no names?? —– > first one *with names* wins, recycling causes shortest to lose names)" > > I'm not really sure what this is talking about. > > __ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel > Several bits of the document have that kind of "proto-text" style and need to be rephrased in ordinary English. What that particular paragraph was meant to describe is this: > c(A=1)+c(b=2) A 3 > c(A=1)+c(b=2,c=3) b c 3 4 > c(1)+c(b=2) b 3 -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Documentation bug: Section 3.3.2 of R-Lang. (PR#9928)
Full_Name: Simeon Bird Version: 2.5.1 OS: Linux Submission from: (NULL) (131.111.200.200) In the manual "The R Language Definition", section 3.3.2 reads: "3.3.2 Propagation of names propagation of names (first one wins, I think - also if it has no names?? first one *with names* wins, recycling causes shortest to lose names)" I'm not really sure what this is talking about. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Documentation bug for sys.parent
In R-trunk version 41191, the 'Value' section of sys.parent.Rd explains
that sys.parent() returns an environment, which is wrong. The 'Details'
sections explains that it returns the number of the parent frame, etc.
Here's a fix:
Index: src/library/base/man/sys.parent.Rd
===
--- src/library/base/man/sys.parent.Rd (revision 41191)
+++ src/library/base/man/sys.parent.Rd (working copy)
@@ -81,8 +81,8 @@
}
\value{
\code{sys.call} returns a call, \code{sys.function} a function
- definition, and \code{sys.frame}, \code{sys.parent} and
- \code{parent.frame} return an environment.
+ definition, and \code{sys.frame} and \code{parent.frame} return an
+ environment.
For the other functions, see the Details section.
}
Best,
Jeff
--
http://biostat.mc.vanderbilt.edu/JeffreyHorner
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Re: [Rd] documentation bug as S-Plus catches up (PR#8933)
> "RMH" == Richard M Heiberger <[EMAIL PROTECTED]> > on Sat, 3 Jun 2006 01:31:48 +0200 (CEST) writes: RMH> # R for Windows will not send your bug report RMH> automatically. # Please copy the bug report (after RMH> finishing it) to # your favorite email program and send RMH> it to # # [EMAIL PROTECTED] # RMH> ## RMH> The R documentation for "is.R" says "## 'which()' only RMH> exists in R:" This is no longer true. In S-Plus 8.0 >> version RMH> Enterprise Developer Version 8.0.1 Beta 1 for Microsoft RMH> Windows : 2006 RMH> both "is.R" and "which" are defined in the splus RMH> directory. Thank you, Rich, for the update. Note however that this is a *beta* version of S-plus, that I'd guess 95--99.5% of S-plus users are *not* using currently. Here, ETH has been paying a site licence for S-plus for many years, but we haven't been able to even use S-plus 7.x, because of problems that seem to make it impossible that the ETH-central licence server can continued to be used for S+7 (given the current IT infrastructure & staff). RMH> Now that coordination with R, including use of the RMH> package system, is one of the Insightful goals, I hope RMH> someone in R-core will be monitoring these changes. [who were you hoping for ? ;-)] RMH> Let me know if you want me to post these types of RMH> things in the future. I won't unless specically RMH> requested. I'd say we are thankful if you continue to do so, to R-devel typically rather than R-bugs, particularly in border cases like the current one. Martin RMH> Rich __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] documentation bug as S-Plus catches up (PR#8933)
# R for Windows will not send your bug report automatically. # Please copy the bug report (after finishing it) to # your favorite email program and send it to # # [EMAIL PROTECTED] # ## The R documentation for "is.R" says "## 'which()' only exists in R:" This is no longer true. In S-Plus 8.0 > version Enterprise Developer Version 8.0.1 Beta 1 for Microsoft Windows : 2006 both "is.R" and "which" are defined in the splus directory. Now that coordination with R, including use of the package system, is one of the Insightful goals, I hope someone in R-core will be monitoring these changes. Let me know if you want me to post these types of things in the future. I won't unless specically requested. Rich --please do not edit the information below-- Version: platform = i386-pc-mingw32 arch = i386 os = mingw32 system = i386, mingw32 status = major = 2 minor = 3.1 year = 2006 month = 06 day = 01 svn rev = 38247 language = R version.string = Version 2.3.1 (2006-06-01) Windows XP Home Edition (build 2600) Service Pack 2.0 Locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 Search Path: .GlobalEnv, package:grid, package:lattice, file:c:/HOME/rmh/h2/library/H2/.RData, file:c:/HOME/rmh/hh/splus.library/HH/.RData, package:car, package:Rcmdr, package:tcltk, package:methods, package:stats, package:graphics, package:grDevices, package:utils, package:datasets, RcmdrEnv, Autoloads, package:base __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Documentation bug in complex.Rd (PR#8218)
Dear all,
I noticed a documentation error in complex.Rd. A patch that corrects
the error is as follows:
[bossiaea:R-devel-src]$ svn diff
Index: src/library/base/man/complex.Rd
===
--- src/library/base/man/complex.Rd (revision 35935)
+++ src/library/base/man/complex.Rd (working copy)
@@ -52,7 +52,8 @@
complex values. Modulus and argument are also called the \emph{polar
coordinates}. If \eqn{z = x + i y} with real \eqn{x} and \eqn{y},
\code{Mod}\eqn{(z) = \sqrt{x^2 + y^2}}, and for
- \eqn{\phi= Arg(z)}, \eqn{x = \cos(\phi)} and \eqn{y = \sin(\phi)}.
+ \eqn{\phi= \code{Arg}(z)}, \eqn{x = \code{Mod}(z)\cos(\phi)} and
+ \eqn{y = \code{Mod}(z)\sin(\phi)}.
They are all generic functions: methods can be defined
for them individually or via the \code{\link{Complex}} group generic.
Cheers,
Berwin
--please do not edit the information below--
Version:
platform = i686-pc-linux-gnu
arch = i686
os = linux-gnu
system = i686, linux-gnu
status =
major = 2
minor = 2.0
year = 2005
month = 10
day = 06
svn rev = 35749
language = R
Locale:
C
Search Path:
.GlobalEnv, package:methods, package:stats, package:graphics,
package:grDevices, package:utils, package:datasets, Autoloads, package:base
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[Rd] Documentation bug in libPaths.Rd (PR#8050)
The Details section of the help for .Library / .libPaths has: "the library search path is set to the existing files in 'unique(new, .Library)' and this is returned." I think 'unique(new, .Library)' should be be changed to 'unique(c(new, .Library))'. Thank you, Stephen platform sparc-sun-solaris2.9 arch sparc os solaris2.9 system sparc, solaris2.9 status major2 minor1.0 year 2005 month04 day 18 language R __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
