Re: [Rd] error in trunc function (PR#9782)
[EMAIL PROTECTED] wrote: Full_Name: Claudio Version: 2.5.1 OS: windows Submission from: (NULL) (157.138.120.198) the command get a wrong result trunc(2.3*100) 229 __ Not a bug, read FAQ 7.31 and the reference therein. -- 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] formula(CO2)
The formula attribute of the builtin CO2 dataset seems a bit strange: formula(CO2) Plant ~ Type + Treatment + conc + uptake What is one supposed to do with that? Certainly its not suitable for input to lm and none of the examples in ?CO2 use the above. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] formula(CO2)
On 16-Jul-07 13:28:50, Gabor Grothendieck wrote: The formula attribute of the builtin CO2 dataset seems a bit strange: formula(CO2) Plant ~ Type + Treatment + conc + uptake What is one supposed to do with that? Certainly its not suitable for input to lm and none of the examples in ?CO2 use the above. I think one is supposed to ignore it! (Or maybe be inspired to write a mail to the list ... ). I couldn't find anything that looked like the above formula from str(CO2). But I did spot that the order of terms in the formula: Plant, Type, treatment, conc, uptake, is the same as the order of the columns in the dataframe. So I tried: D-data.frame(x=(1:10),y=(1:10)) formula(D) x ~ y So, lo and behold, D has a formula! Or does it? Maybe if you give formula() a dataframe, it simply constructs one from the columns. Best wishes, Ted. E-Mail: (Ted Harding) [EMAIL PROTECTED] Fax-to-email: +44 (0)870 094 0861 Date: 16-Jul-07 Time: 14:57:28 -- XFMail -- __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] formula(CO2)
On 16-Jul-07 13:57:56, Ted Harding wrote: On 16-Jul-07 13:28:50, Gabor Grothendieck wrote: The formula attribute of the builtin CO2 dataset seems a bit strange: formula(CO2) Plant ~ Type + Treatment + conc + uptake What is one supposed to do with that? Certainly its not suitable for input to lm and none of the examples in ?CO2 use the above. I think one is supposed to ignore it! (Or maybe be inspired to write a mail to the list ... ). I couldn't find anything that looked like the above formula from str(CO2). But I did spot that the order of terms in the formula: Plant, Type, treatment, conc, uptake, is the same as the order of the columns in the dataframe. So I tried: D-data.frame(x=(1:10),y=(1:10)) formula(D) x ~ y So, lo and behold, D has a formula! Or does it? Maybe if you give formula() a dataframe, it simply constructs one from the columns. Now that I think about it, I can see a use for this phenomenon: formula(CO2) Plant ~ Type + Treatment + conc + uptake formula(CO2[,2:5]) Type ~ Treatment + conc + uptake formula(CO2[,3:5]) Treatment ~ conc + uptake formula(CO2[,4:5]) conc ~ uptake formula(CO2[,c(5,1,2,3,4)]) uptake ~ Plant + Type + Treatment + conc Could save a lot of typing! Best wishes, Ted. E-Mail: (Ted Harding) [EMAIL PROTECTED] Fax-to-email: +44 (0)870 094 0861 Date: 16-Jul-07 Time: 15:14:38 -- XFMail -- __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] formula(CO2)
Good point. It seems that the groupedData methods are all in the nlme package yet CO2 is in datasets. CO2 should probably be moved to nlme. Of course one still wonders whether the way formula currently works on data frames is really intended and desirable. Ted's point is well taken but I think formula.data.frame could still have the current default yet be user overridable via the formula attribute. On 7/16/07, Gavin Simpson [EMAIL PROTECTED] wrote: On Mon, 2007-07-16 at 14:57 +0100, [EMAIL PROTECTED] wrote: On 16-Jul-07 13:28:50, Gabor Grothendieck wrote: The formula attribute of the builtin CO2 dataset seems a bit strange: formula(CO2) Plant ~ Type + Treatment + conc + uptake What is one supposed to do with that? Certainly its not suitable for input to lm and none of the examples in ?CO2 use the above. I think one is supposed to ignore it! (Or maybe be inspired to write a mail to the list ... ). I couldn't find anything that looked like the above formula from str(CO2). But I did spot that the order of terms in the formula: Plant, Type, treatment, conc, uptake, is the same as the order of the columns in the dataframe. CO2 is a groupedData object not a data.frame per se. class(CO2) [1] nfnGroupedData nfGroupedData groupedDatadata.frame What Gabor saw was the result of formula.data.frame being applied to CO2, which, as you surmise Ted, is being produced from the columns of CO2. formula(CO2) Plant ~ Type + Treatment + conc + uptake stats:::formula.data.frame(CO2) Plant ~ Type + Treatment + conc + uptake But if we load nlme, we see that now (via a groupedData method for formula) a more useful formula is displayed. require(nlme) Loading required package: nlme [1] TRUE formula(CO2) uptake ~ conc | Plant as this can then be directly used in lme lme(CO2) Linear mixed-effects model fit by REML Data: CO2 Log-restricted-likelihood: -283.1447 Fixed: uptake ~ conc (Intercept)conc 19.50028981 0.01773059 snip / But like Gabor, I'm struggling to see where this [formula(data.frame)] might be used (useful)? G -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ UK. WC1E 6BT. [w] http://www.freshwaters.org.uk %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] formula(CO2)
Note that the formula uptake ~. will do the same thing so its not clear
how useful this facility really is.
On 7/16/07, Ted Harding [EMAIL PROTECTED] wrote:
On 16-Jul-07 14:16:10, Gabor Grothendieck wrote:
Following up on your comments it seems formula.data.frame just creates
a formula whose lhs is the first column name and whose rhs is made up
of the remaining column names. It ignores the formula attribute.
In fact, CO2 does have a formula attribute but its not extracted by
formula.data.frame:
[EMAIL PROTECTED]
uptake ~ conc | Plant
formula(CO2)
Plant ~ Type + Treatment + conc + uptake
Indeed! And, following up yet again on my own follow-up comment:
library(combinat)
for(j in (1:4)){
for(i in combn((1:4),j,simplify=FALSE)){
print(formula(CO2[,c(5,i)]))
}
}
uptake ~ Plant
uptake ~ Type
uptake ~ Treatment
uptake ~ conc
uptake ~ Plant + Type
uptake ~ Plant + Treatment
uptake ~ Plant + conc
uptake ~ Type + Treatment
uptake ~ Type + conc
uptake ~ Treatment + conc
uptake ~ Plant + Type + Treatment
uptake ~ Plant + Type + conc
uptake ~ Plant + Treatment + conc
uptake ~ Type + Treatment + conc
uptake ~ Plant + Type + Treatment + conc
opening the door to automated fitting of all possible models
(without interactions)!
Now if only I could find out how to do the interactions as well,
I would never need to think again!
best wishes,
Ted.
E-Mail: (Ted Harding) [EMAIL PROTECTED]
Fax-to-email: +44 (0)870 094 0861
Date: 16-Jul-07 Time: 15:40:36
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[Rd] S4 coerce
(I am not sure if this is a bug or a request for a more understandable
warning, or possible something obvious I should be posting on r-help.)
I am trying to coerce an new class object to be a DBIConnection and it
does not work the way I think it should:
R version 2.5.1 (2007-06-27) ...
require(RMySQL) # or require(RSQLite)
Loading required package: RMySQL
Loading required package: DBI
[1] TRUE
m - dbDriver(MySQL) # or m - dbDriver(SQLite)
con - dbConnect(m, dbname=test)
dbGetQuery(con, create table zzz (
+vintage VARCHAR(20) NOT NULL,
+alias VARCHAR(20) default NULL,
+Documentation TEXT,
+PRIMARY KEY (vintage)
+);)
NULL
dbListTables(con)
[1] zzz
setClass(TSconnection, representation(con=DBIConnection,
+vintage = logical,
+panel = logical)
+)
[1] TSconnection
setAs(TSconnection, DBIConnection, def = function(from) [EMAIL
PROTECTED])
setIs(TSconnection, DBIConnection, coerce = function(x) [EMAIL
PROTECTED])
Warning messages:
1: there is no automatic definition for as(object, DBIConnection) -
value when object has class TSconnection and no 'replace' argument was
supplied; replacement will be an error in: makeExtends(class1, class2,
coerce, test, replace, by, classDef1 = classDef,
2: methods currently exist for coercing from TSconnection to
DBIConnection; they will be replaced. in:
..removePreviousCoerce(class1, class2, where, prevIs)
# (warning may be important, but I don't understand it)
setAs(TSconnection, MySQLConnection, def = function(from) [EMAIL
PROTECTED])
setIs(TSconnection, MySQLConnection, coerce = function(x) [EMAIL
PROTECTED])
Warning messages:
1: there is no automatic definition for as(object, MySQLConnection) -
value when object has class TSconnection and no 'replace' argument was
supplied; replacement will be an error in: makeExtends(class1, class2,
coerce, test, replace, by, classDef1 = classDef,
2: methods currently exist for coercing from TSconnection to
MySQLConnection; they will be replaced. in:
..removePreviousCoerce(class1, class2, where, prevIs)
# or
# setAs(TSconnection, SQLiteConnection, def = function(from)
[EMAIL PROTECTED])
# setIs(TSconnection, SQLiteConnection, coerce = function(x) [EMAIL
PROTECTED])
Tcon - new(TSconnection, con=dbConnect(m, dbname=test),
vintage=FALSE, panel=FALSE)
is(Tcon, DBIConnection)
[1] TRUE
is(Tcon, MySQLConnection)
[1] TRUE
# or is(Tcon, SQLiteConnection)
# This fails but I think it should work
dbListTables(Tcon)
Error in slot(from, Id) : no slot of name Id for this object of
class TSconnection
#these all work
dbListTables([EMAIL PROTECTED])
[1] zzz
dbListTables(as(Tcon, MySQLConnection) )
[1] zzz
dbListTables(as(Tcon, DBIConnection) )
[1] zzz
Is this a bug or am I doing something wrong?
Thanks,
Paul Gilbert
La version française suit le texte anglais.
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Re: [Rd] formula(CO2)
On 16-Jul-07 14:16:10, Gabor Grothendieck wrote:
Following up on your comments it seems formula.data.frame just creates
a formula whose lhs is the first column name and whose rhs is made up
of the remaining column names. It ignores the formula attribute.
In fact, CO2 does have a formula attribute but its not extracted by
formula.data.frame:
[EMAIL PROTECTED]
uptake ~ conc | Plant
formula(CO2)
Plant ~ Type + Treatment + conc + uptake
Indeed! And, following up yet again on my own follow-up comment:
library(combinat)
for(j in (1:4)){
for(i in combn((1:4),j,simplify=FALSE)){
print(formula(CO2[,c(5,i)]))
}
}
uptake ~ Plant
uptake ~ Type
uptake ~ Treatment
uptake ~ conc
uptake ~ Plant + Type
uptake ~ Plant + Treatment
uptake ~ Plant + conc
uptake ~ Type + Treatment
uptake ~ Type + conc
uptake ~ Treatment + conc
uptake ~ Plant + Type + Treatment
uptake ~ Plant + Type + conc
uptake ~ Plant + Treatment + conc
uptake ~ Type + Treatment + conc
uptake ~ Plant + Type + Treatment + conc
opening the door to automated fitting of all possible models
(without interactions)!
Now if only I could find out how to do the interactions as well,
I would never need to think again!
best wishes,
Ted.
E-Mail: (Ted Harding) [EMAIL PROTECTED]
Fax-to-email: +44 (0)870 094 0861
Date: 16-Jul-07 Time: 15:40:36
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Re: [Rd] formula(CO2)
Yes. That's what I was referring to.
On 7/16/07, Ted Harding [EMAIL PROTECTED] wrote:
On 16-Jul-07 14:42:19, Gabor Grothendieck wrote:
Note that the formula uptake ~. will do the same thing so its
not clear how useful this facility really is.
Hmmm... Do you mean somthing like
lm(uptake ~ . , data=CO2[,i])
where i is a subset of (1:4) as in my code below? In which case
I agree!
Ted.
On 7/16/07, Ted Harding [EMAIL PROTECTED] wrote:
On 16-Jul-07 14:16:10, Gabor Grothendieck wrote:
Following up on your comments it seems formula.data.frame just
creates
a formula whose lhs is the first column name and whose rhs is made
up
of the remaining column names. It ignores the formula attribute.
In fact, CO2 does have a formula attribute but its not extracted by
formula.data.frame:
[EMAIL PROTECTED]
uptake ~ conc | Plant
formula(CO2)
Plant ~ Type + Treatment + conc + uptake
Indeed! And, following up yet again on my own follow-up comment:
library(combinat)
for(j in (1:4)){
for(i in combn((1:4),j,simplify=FALSE)){
print(formula(CO2[,c(5,i)]))
}
}
uptake ~ Plant
uptake ~ Type
uptake ~ Treatment
uptake ~ conc
uptake ~ Plant + Type
uptake ~ Plant + Treatment
uptake ~ Plant + conc
uptake ~ Type + Treatment
uptake ~ Type + conc
uptake ~ Treatment + conc
uptake ~ Plant + Type + Treatment
uptake ~ Plant + Type + conc
uptake ~ Plant + Treatment + conc
uptake ~ Type + Treatment + conc
uptake ~ Plant + Type + Treatment + conc
opening the door to automated fitting of all possible models
(without interactions)!
Now if only I could find out how to do the interactions as well,
I would never need to think again!
best wishes,
Ted.
E-Mail: (Ted Harding) [EMAIL PROTECTED]
Fax-to-email: +44 (0)870 094 0861
Date: 16-Jul-07 Time: 15:40:36
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E-Mail: (Ted Harding) [EMAIL PROTECTED]
Fax-to-email: +44 (0)870 094 0861
Date: 16-Jul-07 Time: 16:13:15
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Re: [Rd] formula(CO2)
On 16-Jul-07 14:42:19, Gabor Grothendieck wrote:
Note that the formula uptake ~. will do the same thing so its
not clear how useful this facility really is.
Hmmm... Do you mean somthing like
lm(uptake ~ . , data=CO2[,i])
where i is a subset of (1:4) as in my code below? In which case
I agree!
Ted.
On 7/16/07, Ted Harding [EMAIL PROTECTED] wrote:
On 16-Jul-07 14:16:10, Gabor Grothendieck wrote:
Following up on your comments it seems formula.data.frame just
creates
a formula whose lhs is the first column name and whose rhs is made
up
of the remaining column names. It ignores the formula attribute.
In fact, CO2 does have a formula attribute but its not extracted by
formula.data.frame:
[EMAIL PROTECTED]
uptake ~ conc | Plant
formula(CO2)
Plant ~ Type + Treatment + conc + uptake
Indeed! And, following up yet again on my own follow-up comment:
library(combinat)
for(j in (1:4)){
for(i in combn((1:4),j,simplify=FALSE)){
print(formula(CO2[,c(5,i)]))
}
}
uptake ~ Plant
uptake ~ Type
uptake ~ Treatment
uptake ~ conc
uptake ~ Plant + Type
uptake ~ Plant + Treatment
uptake ~ Plant + conc
uptake ~ Type + Treatment
uptake ~ Type + conc
uptake ~ Treatment + conc
uptake ~ Plant + Type + Treatment
uptake ~ Plant + Type + conc
uptake ~ Plant + Treatment + conc
uptake ~ Type + Treatment + conc
uptake ~ Plant + Type + Treatment + conc
opening the door to automated fitting of all possible models
(without interactions)!
Now if only I could find out how to do the interactions as well,
I would never need to think again!
best wishes,
Ted.
E-Mail: (Ted Harding) [EMAIL PROTECTED]
Fax-to-email: +44 (0)870 094 0861
Date: 16-Jul-07 Time: 15:40:36
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E-Mail: (Ted Harding) [EMAIL PROTECTED]
Fax-to-email: +44 (0)870 094 0861
Date: 16-Jul-07 Time: 16:13:15
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Re: [Rd] formula(CO2)
CO2 is apparently a groupedData object; the formula attribute is described by
Pinheiro and Bates as a 'display formula'.
Perhaps reference to the nlme package's groupedData help would be informative?
Gabor Grothendieck [EMAIL PROTECTED] 16/07/2007 16:18:37
Yes. That's what I was referring to.
On 7/16/07, Ted Harding [EMAIL PROTECTED] wrote:
On 16-Jul-07 14:42:19, Gabor Grothendieck wrote:
Note that the formula uptake ~. will do the same thing so its
not clear how useful this facility really is.
Hmmm... Do you mean somthing like
lm(uptake ~ . , data=CO2[,i])
where i is a subset of (1:4) as in my code below? In which case
I agree!
Ted.
On 7/16/07, Ted Harding [EMAIL PROTECTED] wrote:
On 16-Jul-07 14:16:10, Gabor Grothendieck wrote:
Following up on your comments it seems formula.data.frame just
creates
a formula whose lhs is the first column name and whose rhs is made
up
of the remaining column names. It ignores the formula attribute.
In fact, CO2 does have a formula attribute but its not extracted by
formula.data.frame:
[EMAIL PROTECTED]
uptake ~ conc | Plant
formula(CO2)
Plant ~ Type + Treatment + conc + uptake
Indeed! And, following up yet again on my own follow-up comment:
library(combinat)
for(j in (1:4)){
for(i in combn((1:4),j,simplify=FALSE)){
print(formula(CO2[,c(5,i)]))
}
}
uptake ~ Plant
uptake ~ Type
uptake ~ Treatment
uptake ~ conc
uptake ~ Plant + Type
uptake ~ Plant + Treatment
uptake ~ Plant + conc
uptake ~ Type + Treatment
uptake ~ Type + conc
uptake ~ Treatment + conc
uptake ~ Plant + Type + Treatment
uptake ~ Plant + Type + conc
uptake ~ Plant + Treatment + conc
uptake ~ Type + Treatment + conc
uptake ~ Plant + Type + Treatment + conc
opening the door to automated fitting of all possible models
(without interactions)!
Now if only I could find out how to do the interactions as well,
I would never need to think again!
best wishes,
Ted.
E-Mail: (Ted Harding) [EMAIL PROTECTED]
Fax-to-email: +44 (0)870 094 0861
Date: 16-Jul-07 Time: 15:40:36
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E-Mail: (Ted Harding) [EMAIL PROTECTED]
Fax-to-email: +44 (0)870 094 0861
Date: 16-Jul-07 Time: 16:13:15
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[Rd] Problem building R with Sun Studio Compiler
I would like to Build R-2.5.1 on OpenSUSE 10.2 using the SunStudio 12 compilers(http://developers.sun.com/sunstudio/index.jsp) R builds and passes make check fine without optimising. However, when I try to compile with optimisation turned on (-fast) the build gets stuck in an infinite loop at the following point: Sun_Studio/sunstudio12/bin/cc -m64 -shared -Kpic -m64 -fPIC -o grDevices.so chull.o devNull.o devPicTeX.o devPS.o devQuartz.o init.o mkdir -p -- ../../../../library/grDevices/libs make[5]: Leaving directory `/export/home/leonardz/ccb/HPF/support/R-2.5.1/ss12/R-2.5.1/src/library/grDevices/src' make[4]: Leaving directory `/export/home/leonardz/ccb/HPF/support/R-2.5.1/ss12/R-2.5.1/src/library/grDevices/src' R is running at this point and will run for as long as I do not kill it. If I compile without-fast the next line in the make is: make[3]: Entering directory `/export/home/leonardz/ccb/HPF/support/R-2.5.1/ss12/R-2.5.1/src/library/graphics' and the entire package builds and make check verifies correctly. Any ideas on why this is happening? The build works fine for gcc as well. -- Len Zaifman Systems Manager, Supercomputing Systems Centre for Computational Biology Hospital for Sick Children Toronto, Ont. M5G 1X8 [EMAIL PROTECTED] (416)813-5513 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] How to disable R's C stack checking
On Jul 6, 2007, at 6:57 AM, Ev Whin wrote: Hi all, I'm developing an application on Mac OS X Darwin which embeds R. However, the application always crashes due to the C stack checking. I know that R_CStackLimit can be set to -1 to disable the stack checking, but I don't know where to put the code R_CStackLimit=-1. After the call to Rf_initialize_R (and don't forget to define CSTACK_DEFNS and include Rinterface.h). Cheers, Simon __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Problem building R with Sun Studio Compiler
The R-admin manual did tell you not to do that!
When using the Sun compilers do @emph{not} specify @option{-fast}, as
this disables @acronym{IEEE} arithmetic and @command{make check} will
fail.
That was for Solaris and SunStudio 11, but I presume these are basically
the same compilers. (--fast has been a no-no for as long as I have been
using R on Solaris, ca 10 years.)
On Mon, 16 Jul 2007, Len Zaifman wrote:
I would like to Build R-2.5.1 on OpenSUSE 10.2 using the SunStudio 12
compilers(http://developers.sun.com/sunstudio/index.jsp)
R builds and passes make check fine without optimising. However, when I try
to compile with optimisation turned on
(-fast) the build gets stuck in an infinite loop at the following point:
Sun_Studio/sunstudio12/bin/cc -m64 -shared -Kpic -m64 -fPIC -o
grDevices.so chull.o devNull.o devPicTeX.o devPS.o
devQuartz.o init.o
mkdir -p -- ../../../../library/grDevices/libs
make[5]: Leaving directory
`/export/home/leonardz/ccb/HPF/support/R-2.5.1/ss12/R-2.5.1/src/library/grDevices/src'
make[4]: Leaving directory
`/export/home/leonardz/ccb/HPF/support/R-2.5.1/ss12/R-2.5.1/src/library/grDevices/src'
R is running at this point and will run for as long as I do not kill it.
If I compile without -fast the next line in the make is:
make[3]: Entering directory
`/export/home/leonardz/ccb/HPF/support/R-2.5.1/ss12/R-2.5.1/src/library/graphics'
and the entire package builds and make check verifies correctly. Any
ideas on why this is happening?
The build works fine for gcc as well.
--
Brian D. Ripley, [EMAIL PROTECTED]
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, UKFax: +44 1865 272595
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[Rd] substitute and expression
Hi,
I'm trying to understand whether the use of substitute() is
appropriate/documented for plotmath annotation. The following two
calls give the same results:
plot(1:10, main = expression(alpha == 1))
do.call(plot, list(1:10, main = expression(alpha == 1)))
But not these two:
plot(1:10, main = substitute(alpha == a, list(a = 2)))
do.call(plot, list(1:10, main = substitute(alpha == a, list(a = 2
Error in as.graphicsAnnot(main) : object alpha not found
(as a consequence, xyplot(..., main = substitute(alpha)) doesn't
currently work.)
On the other hand, this works:
foo - function(x) plot(1, main = x)
foo(substitute(alpha))
I'm not sure how to interpret ?plotmath; it says
If the 'text' argument to one of the text-drawing functions
('text', 'mtext', 'axis', 'legend') in R is an expression, the
argument is interpreted as a mathematical expression...
and uses substitute() in its examples, but
is.expression(substitute(alpha == a, list(a = 1)))
[1] FALSE
-Deepayan
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Re: [Rd] substitute and expression
Deepayan Sarkar wrote:
Hi,
I'm trying to understand whether the use of substitute() is
appropriate/documented for plotmath annotation. The following two
calls give the same results:
plot(1:10, main = expression(alpha == 1))
do.call(plot, list(1:10, main = expression(alpha == 1)))
But not these two:
plot(1:10, main = substitute(alpha == a, list(a = 2)))
do.call(plot, list(1:10, main = substitute(alpha == a, list(a = 2
Error in as.graphicsAnnot(main) : object alpha not found
(as a consequence, xyplot(..., main = substitute(alpha)) doesn't
currently work.)
On the other hand, this works:
foo - function(x) plot(1, main = x)
foo(substitute(alpha))
I'm not sure how to interpret ?plotmath; it says
If the 'text' argument to one of the text-drawing functions
('text', 'mtext', 'axis', 'legend') in R is an expression, the
argument is interpreted as a mathematical expression...
and uses substitute() in its examples, but
is.expression(substitute(alpha == a, list(a = 1)))
[1] FALSE
I think you need to take plotmath out of the equation and study the
difference between objects of mode call and those of mode
expression. Consider this:
f - function(...)match.call()
do.call(f, list(1:10, main = substitute(alpha == a, list(a = 2
function(...)match.call()
(1:10, main = alpha == 2)
do.call(list, list(1:10, main = substitute(alpha == a, list(a = 2
Error in do.call(list, list(1:10, main = substitute(alpha == a, list(a =
2 :
object alpha not found
The issue is that function ends up with an argument alpha == 2 which it
proceeds to evaluate (lazily), where a direct call sees
substitute(.). It is a general problem with the do.call mechanism
that it effectively pre-evaluates the argument list, which can confuse
functions that rely on accessing the original argument expression. Try,
e.g., do.call(plot, list(airquality$Wind, airquality$Ozone)) and watch
the axis labels.
Does it work if you use something like
main = substitute(quote(alpha == a), list(a = 2))?
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Re: [Rd] substitute and expression
On 7/16/07, Deepayan Sarkar [EMAIL PROTECTED] wrote:
Hi,
I'm trying to understand whether the use of substitute() is
appropriate/documented for plotmath annotation. The following two
calls give the same results:
plot(1:10, main = expression(alpha == 1))
do.call(plot, list(1:10, main = expression(alpha == 1)))
But not these two:
plot(1:10, main = substitute(alpha == a, list(a = 2)))
do.call(plot, list(1:10, main = substitute(alpha == a, list(a = 2
Error in as.graphicsAnnot(main) : object alpha not found
(as a consequence, xyplot(..., main = substitute(alpha)) doesn't
currently work.)
If your question is really about do.call then use the quote = TRUE argument.
Then both of the above work:
plot(1:10, main = substitute(alpha == a, list(a = 2)))
do.call(plot, list(1:10, main = substitute(alpha == a, list(a = 2))),
quote = TRUE)
plot(1:10, main = expression(alpha == 1))
do.call(plot, list(1:10, main = expression(alpha == 1)), quote = TRUE)
Another possibility is just to make sure you are passing an expression so
that the first one would become:
plot(1:10, main = substitute(alpha == a, list(a = 2)))
do.call(plot, list(1:10, main = as.expression(substitute(alpha == a,
list(a = 2)
On the other hand, this works:
foo - function(x) plot(1, main = x)
foo(substitute(alpha))
I'm not sure how to interpret ?plotmath; it says
If the 'text' argument to one of the text-drawing functions
('text', 'mtext', 'axis', 'legend') in R is an expression, the
argument is interpreted as a mathematical expression...
and uses substitute() in its examples, but
is.expression(substitute(alpha == a, list(a = 1)))
[1] FALSE
I am not sure what examples you are referring to but if you read the
Value section in ?substitute it does say that substitute typically
returns call objects but may return a name object and in principle
can return others too so they need not be expressions.
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Re: [Rd] substitute and expression
On 7/16/07, Peter Dalgaard [EMAIL PROTECTED] wrote:
Deepayan Sarkar wrote:
Hi,
I'm trying to understand whether the use of substitute() is
appropriate/documented for plotmath annotation. The following two
calls give the same results:
plot(1:10, main = expression(alpha == 1))
do.call(plot, list(1:10, main = expression(alpha == 1)))
But not these two:
plot(1:10, main = substitute(alpha == a, list(a = 2)))
do.call(plot, list(1:10, main = substitute(alpha == a, list(a = 2
Error in as.graphicsAnnot(main) : object alpha not found
(as a consequence, xyplot(..., main = substitute(alpha)) doesn't
currently work.)
On the other hand, this works:
foo - function(x) plot(1, main = x)
foo(substitute(alpha))
I'm not sure how to interpret ?plotmath; it says
If the 'text' argument to one of the text-drawing functions
('text', 'mtext', 'axis', 'legend') in R is an expression, the
argument is interpreted as a mathematical expression...
and uses substitute() in its examples, but
is.expression(substitute(alpha == a, list(a = 1)))
[1] FALSE
I think you need to take plotmath out of the equation and study the
difference between objects of mode call and those of mode
expression. Consider this:
f - function(...)match.call()
do.call(f, list(1:10, main = substitute(alpha == a, list(a = 2
function(...)match.call()
(1:10, main = alpha == 2)
do.call(list, list(1:10, main = substitute(alpha == a, list(a = 2
Error in do.call(list, list(1:10, main = substitute(alpha == a, list(a =
2 :
object alpha not found
The issue is that function ends up with an argument alpha == 2 which it
proceeds to evaluate (lazily), where a direct call sees
substitute(.). It is a general problem with the do.call mechanism
that it effectively pre-evaluates the argument list, which can confuse
functions that rely on accessing the original argument expression. Try,
e.g., do.call(plot, list(airquality$Wind, airquality$Ozone)) and watch
the axis labels.
Right. Lazy evaluation was the piece I was missing.
Does it work if you use something like
main = substitute(quote(alpha == a), list(a = 2))?
Not for xyplot, though I haven't figured out why. Turns out this also
doesn't work:
plot(y ~ x, data = list(x = 1:10, y = 1:10), main = substitute(alpha))
Error in as.graphicsAnnot(main) : object alpha not found
I'll take this to mean that the fact that substitute() works sometimes
(for plotmath) is an undocumented side effect of the implementation
that should not be relied upon.
-Deepayan
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[Rd] Unable to build with working iconv support on Solaris9/x86
Hi all, Have had a frustrating time trying to get R 2.5.1 running happily on Solaris9/x86, the problems seem to stem mainly from libiconv support. After a couple of hours of experimenting, I came across the following combination, note that iconv (the program, but not the library) exists in the Solaris base system, I've manually installed the full GNU distribution in /usr/local/apps/libiconv-1.11 but not in /usr/local yet. CFLAGS=-I/usr/local/apps/libiconv-1.11/include -I/usr/local/include LDFLAGS=-L/usr/local/apps/libiconv-1.11/lib -R/usr/local/apps/ libiconv-1.11/lib -L/usr/local/lib -R/usr/local/lib ./configure -- prefix=/usr/local/apps/r-2.5.1 --with-libiconv-prefix=/usr/local/apps/ libiconv-1.11 Note that the option --with-libiconv-prefix=/usr/local/apps/ libiconv-1.11 won't get me past the configure phase by itself (fails the iconv test), in fact as far as I can tell --with-libiconv-prefix has no effect at all but I've been leaving it in just in case. Anyway, with the environment variables CFLAGS and LDFLAGS set as above, the process gets through configure and make successfully, but fails 'make check' trying to do a conversion to latin1 ## x is intended to be in latin1 x - fa\xE7ile Encoding(x) [1] unknown Encoding(x) - latin1 x [1]Error: unsupported conversion Execution halted ldd -s bin/exec/R confirms that R gets it's iconv from /usr/local/ apps/libiconv-1.11/lib/libiconv.so.2 as expected ldd -s bin/exec/R [snip] find object=libiconv.so.2; required by bin/exec/R search path=/usr/local/apps/libiconv-1.11/lib:/usr/local/lib:/ usr/local/apps/gcc-3.4.5/lib/gcc/i386-pc-solaris2.9/3.4.5 (RPATH from file bin/exec/R) trying path=/usr/local/apps/libiconv-1.11/lib/libiconv.so.2 libiconv.so.2 = /usr/local/apps/libiconv-1.11/lib/ libiconv.so.2 [snip] I don't know what else to try. Anyone? Regards, -- Lucas Barbuto E: [EMAIL PROTECTED] System AdministratorT: +613 8344 1270 Department of CSSE The University of Melbourne http://www.csse.unimelb.edu.au/ __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] S4 coerce
Paul Gilbert [EMAIL PROTECTED] writes: (I am not sure if this is a bug or a request for a more understandable warning, or possible something obvious I should be posting on r-help.) I am trying to coerce an new class object to be a DBIConnection and it does not work the way I think it should: R version 2.5.1 (2007-06-27) ... require(RMySQL) # or require(RSQLite) Loading required package: RMySQL Loading required package: DBI [1] TRUE m - dbDriver(MySQL) # or m - dbDriver(SQLite) con - dbConnect(m, dbname=test) dbGetQuery(con, create table zzz ( +vintage VARCHAR(20) NOT NULL, +alias VARCHAR(20) default NULL, +Documentation TEXT, +PRIMARY KEY (vintage) +);) NULL dbListTables(con) [1] zzz setClass(TSconnection, representation(con=DBIConnection, +vintage = logical, +panel = logical) +) [1] TSconnection setAs(TSconnection, DBIConnection, def = function(from) [EMAIL PROTECTED]) I think things work as you expect up until this pint. setIs(TSconnection, DBIConnection, coerce = function(x) [EMAIL PROTECTED]) I'm confused about what you want to do here. If you want TSconnection to be a DBIConnection, why wouldn't you use inheritance? setClass(TSconnection, contains=DBIConnection, ...) + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
