Re: [Rd] [R] aligned memory allocation in C

[christophe dutang]

Thanks for your remarks.

According to
http://www.math.sci.hiroshima-u.ac.jp/~m-mat/MT/SFMT/howto-compile.html, I
need 16 bit aligned memory when using fill_array64. So I suppose I need 8
bit aligned memory. I will test what you advise me and will come back to
R-devel list after.

Thanks again

Christophe

2008/8/13 Prof Brian Ripley <[EMAIL PROTECTED]>

> On Tue, 12 Aug 2008, Jeffrey Horner wrote:
>
>  Christophe Dutang1 wrote:
>>
>>> Hi,
>>>
>>> I'm currently R porting SF Mersenne Twister algorithm of Matsumoto and
>>> Saito. To get the full power of their code, I want to use their fonction
>>> fill_array32 which need aligned memory. That is to say I need to use the C
>>> function memalign on windows, posix_memalign on linux and classic malloc on
>>> Mac OS. In 'writing R extenstion', they recommand to use R_alloc function to
>>> allocate memory in C.
>>>
>>> Does R_alloc return a pointer to aligned memory?
>>> if not how can I do this?
>>> probably no, because R crashes when I succesively R_alloc and
>>> fill_array32 (cf below) on my macbook with R 2.7.1.
>>>
>>
>> You can still do this. Just take the address returned from R_alloc and
>> test for alignment. If it's not, then just use an aligned address beyond the
>> one returned.
>>
>
> We haven't been told what the desired alignment is (and those functions
> need to be told).  On 32-bit Mac OS X, R_alloc is definitely aligned on
> 4-byte boundaries (on 64-bit OSes it is usually 8-byte aligned).
>
>  (But then the question is, which direction beyond the one returned? How
>> does one test for that?)
>>
>
> Addresses always go upwards.  So if you want 64-byte alignment you need to
> allocate a block at least 64 bytes longer than required, and go up to the
> nearest multiple of 64.
>
> BTW, this is clearly an R-devel question -- see the posting guide.
>
>
>
>> Jeff
>>
>>  Thanks in advance
>>>
>>> Kind regards
>>>
>>> Christophe
>>>
>>>
>>> PS :
>>> http://www.math.sci.hiroshima-u.ac.jp/~m-mat/MT/SFMT/howto-compile.htmlprovides
>>>  an example of memalign.
>>>
>>> PPS : mac os report
>>>
>>
> [removed]
>
> --
> 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] extending the derivs table/fools rushing in

[Ben Bolker]

  I added "plogis" to the derivative table in the
development version of R; the patch against yesterday's
R-devel src/deriv/main.c is available at
http://www.zoology.ufl.edu/bolker/deriv_patch.txt .

  I pretty much followed the framework of the other symbols;
here was my incantation

-   } else if (CAR(expr) == PlogisSymbol) {
-   ans = simplify(TimesSymbol,
-  PP_S(TimesSymbol,
-   PP_S2(ExpSymbol,
-  PP_S2(MinusSymbol,CADR(expr))),
-   PP_S(PowerSymbol,
-PP_S(PlusSymbol,
- Constant(1.),
- PP_S2(ExpSymbol,
-PP_S2(MinusSymbol,CADR(expr,
-Constant(-2.))),
-  PP(D(CADR(expr),var)));
-   UNPROTECT(8);

It seems to work:

> D(quote(plogis(a)),"a")
exp(-a) * (1 + exp(-a))^-2
> D(quote(plogis(a+b*x)),"x")
exp(-(a + b * x)) * (1 + exp(-(a + b * x)))^-2 * b

  Any thoughts?  I'm sure there's a cleverer way to do this ...

  Ben Bolker

  PS I get a minor build error at the end of the compilation
(on Ubuntu 8.10):

make[2]: *** No rule to make target `VR.ts', needed by
`stamp-recommended'.  Stop.
make[2]: Leaving directory
`/usr/local/src/R/R-devel/src/library/Recommended'
make[1]: *** [recommended-packages] Error 2
make[1]: Leaving directory
`/usr/local/src/R/R-devel/src/library/Recommended'
make: *** [stamp-recommended] Error 2

  ... don't know if that is important or not.




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Re: [Rd] extending the derivs table/fools rushing in

[Gabor Grothendieck]

While you are at it could you add { to the
table so that this works:

> # this is ok
> f <- function(x) x*x
> D(body(f), "x")
x + x

> # but not g which is same as f
> # except it has { ... } surrounding its body
> g <- function(x) { x*x }
> D(body(g), "x")
Error in D(body(g), "x") : Function '`{`' is not in the derivatives table


2008/8/14 Ben Bolker <[EMAIL PROTECTED]>:
>
>  I added "plogis" to the derivative table in the
> development version of R; the patch against yesterday's
> R-devel src/deriv/main.c is available at
> http://www.zoology.ufl.edu/bolker/deriv_patch.txt .
>
>  I pretty much followed the framework of the other symbols;
> here was my incantation
>
> -   } else if (CAR(expr) == PlogisSymbol) {
> -   ans = simplify(TimesSymbol,
> -  PP_S(TimesSymbol,
> -   PP_S2(ExpSymbol,
> -  PP_S2(MinusSymbol,CADR(expr))),
> -   PP_S(PowerSymbol,
> -PP_S(PlusSymbol,
> - Constant(1.),
> - PP_S2(ExpSymbol,
> -PP_S2(MinusSymbol,CADR(expr,
> -Constant(-2.))),
> -  PP(D(CADR(expr),var)));
> -   UNPROTECT(8);
>
> It seems to work:
>
>> D(quote(plogis(a)),"a")
> exp(-a) * (1 + exp(-a))^-2
>> D(quote(plogis(a+b*x)),"x")
> exp(-(a + b * x)) * (1 + exp(-(a + b * x)))^-2 * b
>
>  Any thoughts?  I'm sure there's a cleverer way to do this ...
>
>  Ben Bolker
>
>  PS I get a minor build error at the end of the compilation
> (on Ubuntu 8.10):
>
> make[2]: *** No rule to make target `VR.ts', needed by
> `stamp-recommended'.  Stop.
> make[2]: Leaving directory
> `/usr/local/src/R/R-devel/src/library/Recommended'
> make[1]: *** [recommended-packages] Error 2
> make[1]: Leaving directory
> `/usr/local/src/R/R-devel/src/library/Recommended'
> make: *** [stamp-recommended] Error 2
>
>  ... don't know if that is important or not.
>
>
>
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>
>

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Re: [Rd] extending the derivs table/fools rushing in

[Ben Bolker]

 http://www.zoology.ufl.edu/bolker/deriv_patch2.txt

 has this change added as well.
 However, I'm not as confident that this is the right thing
to do?  Should curly brackets even be appearing in mathematical
expressions?

  Ben

Gabor Grothendieck wrote:
> While you are at it could you add { to the
> table so that this works:
> 
>> # this is ok
>> f <- function(x) x*x
>> D(body(f), "x")
> x + x
> 
>> # but not g which is same as f
>> # except it has { ... } surrounding its body
>> g <- function(x) { x*x }
>> D(body(g), "x")
> Error in D(body(g), "x") : Function '`{`' is not in the derivatives table
> 
> 
> 2008/8/14 Ben Bolker <[EMAIL PROTECTED]>:
>>  I added "plogis" to the derivative table in the
>> development version of R; the patch against yesterday's
>> R-devel src/deriv/main.c is available at
>> http://www.zoology.ufl.edu/bolker/deriv_patch.txt .
>>
>>  I pretty much followed the framework of the other symbols;
>> here was my incantation
>>
>> -   } else if (CAR(expr) == PlogisSymbol) {
>> -   ans = simplify(TimesSymbol,
>> -  PP_S(TimesSymbol,
>> -   PP_S2(ExpSymbol,
>> -  PP_S2(MinusSymbol,CADR(expr))),
>> -   PP_S(PowerSymbol,
>> -PP_S(PlusSymbol,
>> - Constant(1.),
>> - PP_S2(ExpSymbol,
>> -PP_S2(MinusSymbol,CADR(expr,
>> -Constant(-2.))),
>> -  PP(D(CADR(expr),var)));
>> -   UNPROTECT(8);
>>
>> It seems to work:
>>
>>> D(quote(plogis(a)),"a")
>> exp(-a) * (1 + exp(-a))^-2
>>> D(quote(plogis(a+b*x)),"x")
>> exp(-(a + b * x)) * (1 + exp(-(a + b * x)))^-2 * b
>>
>>  Any thoughts?  I'm sure there's a cleverer way to do this ...
>>
>>  Ben Bolker
>>
>>  PS I get a minor build error at the end of the compilation
>> (on Ubuntu 8.10):
>>
>> make[2]: *** No rule to make target `VR.ts', needed by
>> `stamp-recommended'.  Stop.
>> make[2]: Leaving directory
>> `/usr/local/src/R/R-devel/src/library/Recommended'
>> make[1]: *** [recommended-packages] Error 2
>> make[1]: Leaving directory
>> `/usr/local/src/R/R-devel/src/library/Recommended'
>> make: *** [stamp-recommended] Error 2
>>
>>  ... don't know if that is important or not.
>>
>>
>>
>> __
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>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>
>>




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Re: [Rd] extending the derivs table/fools rushing in

[Gabor Grothendieck]

Its a valid R function.   ?"{"

On Thu, Aug 14, 2008 at 1:07 PM, Ben Bolker <[EMAIL PROTECTED]> wrote:
>  http://www.zoology.ufl.edu/bolker/deriv_patch2.txt
>
>  has this change added as well.
>  However, I'm not as confident that this is the right thing
> to do?  Should curly brackets even be appearing in mathematical
> expressions?
>
>  Ben
>
> Gabor Grothendieck wrote:
>> While you are at it could you add { to the
>> table so that this works:
>>
>>> # this is ok
>>> f <- function(x) x*x
>>> D(body(f), "x")
>> x + x
>>
>>> # but not g which is same as f
>>> # except it has { ... } surrounding its body
>>> g <- function(x) { x*x }
>>> D(body(g), "x")
>> Error in D(body(g), "x") : Function '`{`' is not in the derivatives table
>>
>>
>> 2008/8/14 Ben Bolker <[EMAIL PROTECTED]>:
>>>  I added "plogis" to the derivative table in the
>>> development version of R; the patch against yesterday's
>>> R-devel src/deriv/main.c is available at
>>> http://www.zoology.ufl.edu/bolker/deriv_patch.txt .
>>>
>>>  I pretty much followed the framework of the other symbols;
>>> here was my incantation
>>>
>>> -   } else if (CAR(expr) == PlogisSymbol) {
>>> -   ans = simplify(TimesSymbol,
>>> -  PP_S(TimesSymbol,
>>> -   PP_S2(ExpSymbol,
>>> -  PP_S2(MinusSymbol,CADR(expr))),
>>> -   PP_S(PowerSymbol,
>>> -PP_S(PlusSymbol,
>>> - Constant(1.),
>>> - PP_S2(ExpSymbol,
>>> -
>>> PP_S2(MinusSymbol,CADR(expr,
>>> -Constant(-2.))),
>>> -  PP(D(CADR(expr),var)));
>>> -   UNPROTECT(8);
>>>
>>> It seems to work:
>>>
 D(quote(plogis(a)),"a")
>>> exp(-a) * (1 + exp(-a))^-2
 D(quote(plogis(a+b*x)),"x")
>>> exp(-(a + b * x)) * (1 + exp(-(a + b * x)))^-2 * b
>>>
>>>  Any thoughts?  I'm sure there's a cleverer way to do this ...
>>>
>>>  Ben Bolker
>>>
>>>  PS I get a minor build error at the end of the compilation
>>> (on Ubuntu 8.10):
>>>
>>> make[2]: *** No rule to make target `VR.ts', needed by
>>> `stamp-recommended'.  Stop.
>>> make[2]: Leaving directory
>>> `/usr/local/src/R/R-devel/src/library/Recommended'
>>> make[1]: *** [recommended-packages] Error 2
>>> make[1]: Leaving directory
>>> `/usr/local/src/R/R-devel/src/library/Recommended'
>>> make: *** [stamp-recommended] Error 2
>>>
>>>  ... don't know if that is important or not.
>>>
>>>
>>>
>>> __
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>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>>
>>>
>
>
>

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Re: [Rd] extending the derivs table/fools rushing in

[Prof Brian Ripley]

The derivative of plogis is surely dlogis.  (And yes, there is a good 
reason why we have such a function: take a look at its C code.)


That means we would need an entry for dlogis too, I guess. I am not 
convinced that there is a real need for these (and where does this stop?) 
What would be much more useful is to make this user-extensible (as Bill 
Venables pointed out a decade ago).  [pd]norm were added in 2002 to 
support MASS, the ability to do all of MASS in R being a goal at the time.


On Thu, 14 Aug 2008, Ben Bolker wrote:



 I added "plogis" to the derivative table in the
development version of R; the patch against yesterday's
R-devel src/deriv/main.c is available at
http://www.zoology.ufl.edu/bolker/deriv_patch.txt .

 I pretty much followed the framework of the other symbols;
here was my incantation

-   } else if (CAR(expr) == PlogisSymbol) {
-   ans = simplify(TimesSymbol,
-  PP_S(TimesSymbol,
-   PP_S2(ExpSymbol,
-  PP_S2(MinusSymbol,CADR(expr))),
-   PP_S(PowerSymbol,
-PP_S(PlusSymbol,
- Constant(1.),
- PP_S2(ExpSymbol,
-PP_S2(MinusSymbol,CADR(expr,
-Constant(-2.))),
-  PP(D(CADR(expr),var)));
-   UNPROTECT(8);

It seems to work:


D(quote(plogis(a)),"a")

exp(-a) * (1 + exp(-a))^-2

D(quote(plogis(a+b*x)),"x")

exp(-(a + b * x)) * (1 + exp(-(a + b * x)))^-2 * b

 Any thoughts?  I'm sure there's a cleverer way to do this ...

 Ben Bolker

 PS I get a minor build error at the end of the compilation
(on Ubuntu 8.10):

make[2]: *** No rule to make target `VR.ts', needed by
`stamp-recommended'.  Stop.
make[2]: Leaving directory
`/usr/local/src/R/R-devel/src/library/Recommended'
make[1]: *** [recommended-packages] Error 2
make[1]: Leaving directory
`/usr/local/src/R/R-devel/src/library/Recommended'
make: *** [stamp-recommended] Error 2

 ... don't know if that is important or not.


A local-to-you problem.






--
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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Re: [Rd] extending the derivs table/fools rushing in

[Ben Bolker]

Prof Brian Ripley wrote:
> The derivative of plogis is surely dlogis.  (And yes, there is a good
> reason why we have such a function: take a look at its C code.)

  Doh.
> 
> That means we would need an entry for dlogis too, I guess. I am not
> convinced that there is a real need for these (and where does this
> stop?) What would be much more useful is to make this user-extensible
> (as Bill Venables pointed out a decade ago).  [pd]norm were added in
> 2002 to support MASS, the ability to do all of MASS in R being a goal at
> the time.

   I agree it would be great to make this user-extensible, but it's
probably a bit beyond me ... I found a web-reference of Venables saying

> There is a detailed example towards the end of Ch. 9 of V&R on how
> to extend D() and make.call(), which are the work horses for
> deriv(), to handle new functions. The new functions handled there
> are dnorm() and pnorm(), but I() would be even easier, of course.

http://www.math.yorku.ca/Who/Faculty/Monette/pub/s-old/0690.html

 ... but this is from 1997 therefore presumably MASS3? or MASS2? --
I can't find my copy of MASS3 at the moment, and don't own MASS2 ...

   The reason behind this is that I was trying to write a simple
analytic derivative calculator for formulae of the form (e.g.)

y ~ dbinom(prob=plogis(a+b*x),size=N)

Obviously in this case I could just tell people to write the
formula out as

y ~ dbinom(prob=1/(1+exp(-(a+b*x))),size=N)

 ...

  Ben Bolker



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Re: [Rd] extending the derivs table/fools rushing in

[Gabor Grothendieck]

You could see if Ryacas package can do what you want:

http://ryacas.googlecode.com

2008/8/14 Ben Bolker <[EMAIL PROTECTED]>:
> Prof Brian Ripley wrote:
>> The derivative of plogis is surely dlogis.  (And yes, there is a good
>> reason why we have such a function: take a look at its C code.)
>
>  Doh.
>>
>> That means we would need an entry for dlogis too, I guess. I am not
>> convinced that there is a real need for these (and where does this
>> stop?) What would be much more useful is to make this user-extensible
>> (as Bill Venables pointed out a decade ago).  [pd]norm were added in
>> 2002 to support MASS, the ability to do all of MASS in R being a goal at
>> the time.
>
>   I agree it would be great to make this user-extensible, but it's
> probably a bit beyond me ... I found a web-reference of Venables saying
>
>> There is a detailed example towards the end of Ch. 9 of V&R on how
>> to extend D() and make.call(), which are the work horses for
>> deriv(), to handle new functions. The new functions handled there
>> are dnorm() and pnorm(), but I() would be even easier, of course.
>
> http://www.math.yorku.ca/Who/Faculty/Monette/pub/s-old/0690.html
>
>  ... but this is from 1997 therefore presumably MASS3? or MASS2? --
> I can't find my copy of MASS3 at the moment, and don't own MASS2 ...
>
>   The reason behind this is that I was trying to write a simple
> analytic derivative calculator for formulae of the form (e.g.)
>
> y ~ dbinom(prob=plogis(a+b*x),size=N)
>
> Obviously in this case I could just tell people to write the
> formula out as
>
> y ~ dbinom(prob=1/(1+exp(-(a+b*x))),size=N)
>
>  ...
>
>  Ben Bolker
>
>
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[Rd] Typo in proc.time.Rd

[Stephen Weigand]

There's a small typo in proc.time.Rd:

\sQuote{system lime} should be \sQuote{system time}

Thanks,

Stephen

-- 
Rochester, Minn. USA

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Re: [Rd] Typo in proc.time.Rd

[Duncan Murdoch]

Stephen Weigand wrote:

There's a small typo in proc.time.Rd:

\sQuote{system lime} should be \sQuote{system time}

Thanks,

Stephen

  

Fixed, thanks.

Duncan Murdoch

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Re: [Rd] [R] RNG Cycle and Duplication (PR#12537)

[p . dalgaard]

Shengqiao Li wrote:
> Hello all,
>
> I am generating large samples of random numbers. The RNG help page 
> says: "All the supplied uniform generators return 32-bit integer 
> values that are converted to doubles, so they take at most 2^32 
> distinct values and long runs will return duplicated values." But I 
> find that the cycles are not the same as the 32-bit integer.
>
> My test indicated that the cycles for Knuth's methods were 2^30 while 
> Wichmann-Hill's cycle was larger than 2^32! No numbers were duplicated 
> in 10M numbers generated by runif using Wichmann-Hill. The other three 
> methods had cycle length of 2^32.
>
> So, anybody can explain this? And any improvement to the 
> implementation can be made to increase the cycle length like the 
> Wichmann-Hill method?
>
What test? These are not simple linear congruential generators. Just 
because you get the same value twice, it doesn't mean that the sequence 
is repeating. Perhaps you should read the entire help page rather than 
just the note.

-- 
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  c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K
 (*) \(*) -- University of Copenhagen   Denmark  Ph:  (+45) 35327918
~~ - ([EMAIL PROTECTED])  FAX: (+45) 35327907

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Re: [Rd] [R] RNG Cycle and Duplication (PR#12538)

[murdoch]

Shengqiao Li wrote:
> Hello all,
>
> I am generating large samples of random numbers. The RNG help page says: 
> "All the supplied uniform generators return 32-bit integer values that are 
> converted to doubles, so they take at most 2^32 distinct values and long 
> runs will return duplicated values." But I find that the cycles are not 
> the same as the 32-bit integer.
>   

This is no bug.  Cycle length and the set of possible values are 
different concepts. 

And please don't cross-post.

Duncan Murdoch
> My test indicated that the cycles for Knuth's methods were 2^30 while 
> Wichmann-Hill's cycle was larger than 2^32! No numbers were duplicated in 
> 10M numbers generated by runif using Wichmann-Hill. The other three 
> methods had cycle length of 2^32.
>
> So, anybody can explain this? And any improvement to the 
> implementation can be made to increase the cycle length like the 
> Wichmann-Hill method?
>
>
> 
> Shengqiao Li
>
> Research Associate
> The Department of Statistics
> West Virginia University
> Morgantown, WV 26506-6330
>
> __
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> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
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Re: [Rd] [R] RNG Cycle and Duplication (PR#12540)

[shli]

  This message is in MIME format.  The first part should be readable text,
  while the remaining parts are likely unreadable without MIME-aware tools.

---559023410-851401618-1218751024=:15885
Content-Type: TEXT/PLAIN; charset=ISO-8859-1; format=flowed
Content-Transfer-Encoding: QUOTED-PRINTABLE


I didn't describe the problem clearly. It's about the number of distinct=20
values. So just ignore cycle issue.

My tests were:

RNGkind(kind=3D"Knuth-TAOCP");
sum(duplicated(runif(1e7))); #return 46552

RNGkind(kind=3D"Knuth-TAOCP-2002");
sum(duplicated(runif(1e7))); #return 46415

#These collision frequency suggested there were 2^30 distinct values by=20
birthday problem.


RNGkind(kind=3D"Marsaglia-Multicarry");
sum(duplicated(runif(1e7))); #return 11682

RNGkind(kind=3D"Super-Duper");
sum(duplicated(runif(1e7))); #return 11542

RNGkind(kind=3D"Mersenne-Twister");
sum(duplicated(runif(1e7))); #return 11656

#These indicated there were 2^32 distinct values, which agrees with the=20
help info.

RNGkind(kind=3D"Wichmann-Hill");
sum(duplicated(runif(1e7))); #return 0

#So for this method, there should be more than 2^32 distinct values.

You may not get the exact numbers, but they should be close. So how to=20
explain above problem?

I need generate a large sample without any ties, it seems to me=20
"Wichmann-Hill" is only choice right now.

=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
Shengqiao Li

The Department of Statistics
PO Box 6330
West Virginia University
Morgantown, WV 26506-6330
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D

On Thu, 14 Aug 2008, Peter Dalgaard wrote:

> Shengqiao Li wrote:
>> Hello all,
>>=20
>> I am generating large samples of random numbers. The RNG help page says:=
=20
>> "All the supplied uniform generators return 32-bit integer values that a=
re=20
>> converted to doubles, so they take at most 2^32 distinct values and long=
=20
>> runs will return duplicated values." But I find that the cycles are not =
the=20
>> same as the 32-bit integer.
>>=20
>> My test indicated that the cycles for Knuth's methods were 2^30 while=20
>> Wichmann-Hill's cycle was larger than 2^32! No numbers were duplicated i=
n=20
>> 10M numbers generated by runif using Wichmann-Hill. The other three meth=
ods=20
>> had cycle length of 2^32.
>>=20
>> So, anybody can explain this? And any improvement to the implementation =
can=20
>> be made to increase the cycle length like the Wichmann-Hill method?
>>=20
> What test? These are not simple linear congruential generators. Just beca=
use=20
> you get the same value twice, it doesn't mean that the sequence is repeat=
ing.=20
> Perhaps you should read the entire help page rather than just the note.
>
> --=20
>  O__   Peter Dalgaard =D8ster 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
>
>
---559023410-851401618-1218751024=:15885--

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[Rd] cryptic message of R CMD check

[Dr. Peter Ruckdeschel]

Hi R-devels,

recently, we have seen a new warning by "R CMD check"
appearing for the devel-version of our package distrEx available on
r-forge, e.g. as

*|install.packages("/distrEx/",repos="http://r-forge.r-project.org";)|*

Here is the warning:

%-
[...snip ...]

* checking for unstated dependencies in R code ... WARNING
.get_S4_methods_list(): *did* reduce list, dropping

See the information on DESCRIPTION files in the chapter 'Creating R

packages' of the 'Writing R Extensions' manual.

[...snip ...]
%---

We get the same warning under Linux and Windows (if this helps).

Unfortunately, we cannot give you very detailed information about
our R running --- it is R-2.8.0dev but somehow R.Version() failed
to give svn-details ---

>R.Version()$version.string
[1] "R version 2.8.0 Under development (unstable) (2006-00-00 r0)"

but we built this R based on the then devel-version on July 29.

Could you give us a clue in this
Thank you already

Peter

--
Dr. Peter Ruckdeschel, Abteilung Finanzmathematik, F3.17
Fraunhofer ITWM, Fraunhofer Platz 1, 67663 Kaiserslautern
Telefon:  +49 631/31600-4699
Fax:  +49 631/31600-5699
E-Mail :  [EMAIL PROTECTED]


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[Rd] RNG Cycle and Duplication (PR#12536)

[shli]

Hello all,

I am generating large samples of random numbers. The RNG help page says: 
"All the supplied uniform generators return 32-bit integer values that are 
converted to doubles, so they take at most 2^32 distinct values and long 
runs will return duplicated values." But I find that the cycles are not 
the same as the 32-bit integer.

My test indicated that the cycles for Knuth's methods were 2^30 while 
Wichmann-Hill's cycle was larger than 2^32! No numbers were duplicated in 
10M numbers generated by runif using Wichmann-Hill. The other three 
methods had cycle length of 2^32.

So, anybody can explain this? And any improvement to the 
implementation can be made to increase the cycle length like the 
Wichmann-Hill method?



Shengqiao Li

Research Associate
The Department of Statistics
West Virginia University
Morgantown, WV 26506-6330

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[Rd] Double-clicking in tk list dialogs

[Barry Rowlingson]

Am I the only one who finds himself futilely double-clicking a CRAN
mirror in the dialog for choosing a CRAN mirror? Yes, double-clicking
works in Windows, but not in the Tk-based dialog on Linux. I'm going
to wear out my mouse button.

Adding the following line to the tk_select.list function in the tcltk
package adds double-click functionality to list dialogs:

  tkbind(box, "",onOK)

 (put it in the right place though, after 'box' has been created).

 Not sure if this would be a default behaviour, or if its's worth
having a 'doubleClick=FALSE' argument that switches it on if TRUE.
Anyway, it was a little niggle that bothered me recently, and after
fixing someone else's TclTK problem recently I figured I'd have a go
at this.

 Consider it a feature request for the next version.

Barry

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Re: [Rd] [R] RNG Cycle and Duplication (PR#12540)

[Prof Brian Ripley]

Remember Wichmann-Hill is a composite generator.  Its composition does 
take more than 2^32 distinct values.


You still haven't identifed a problem here.  The note is to warn that 
runif() does repeat within a cycle, because people wrote code assuming 
otherwise.  It would be a poor use of runif() to rely on the low-order 
bits, and that's standard advice in the field.


For a large sample of uniforms use something like the normal inversion 
does, e.g. 2^(-30) * (runif(N, 0, 2^30) %% 2^30 + runif(N))


Please do leave R-bugs out of this: we already have 4 entries as a result 
of your misunderstandings and false claims.


On Thu, 14 Aug 2008, [EMAIL PROTECTED] wrote:


 This message is in MIME format.  The first part should be readable text,
 while the remaining parts are likely unreadable without MIME-aware tools.

---559023410-851401618-1218751024=:15885
Content-Type: TEXT/PLAIN; charset=ISO-8859-1; format=flowed
Content-Transfer-Encoding: QUOTED-PRINTABLE


I didn't describe the problem clearly. It's about the number of distinct=20
values. So just ignore cycle issue.

My tests were:

RNGkind(kind=3D"Knuth-TAOCP");
sum(duplicated(runif(1e7))); #return 46552

RNGkind(kind=3D"Knuth-TAOCP-2002");
sum(duplicated(runif(1e7))); #return 46415

#These collision frequency suggested there were 2^30 distinct values by=20
birthday problem.


RNGkind(kind=3D"Marsaglia-Multicarry");
sum(duplicated(runif(1e7))); #return 11682

RNGkind(kind=3D"Super-Duper");
sum(duplicated(runif(1e7))); #return 11542

RNGkind(kind=3D"Mersenne-Twister");
sum(duplicated(runif(1e7))); #return 11656

#These indicated there were 2^32 distinct values, which agrees with the=20
help info.

RNGkind(kind=3D"Wichmann-Hill");
sum(duplicated(runif(1e7))); #return 0

#So for this method, there should be more than 2^32 distinct values.

You may not get the exact numbers, but they should be close. So how to=20
explain above problem?

I need generate a large sample without any ties, it seems to me=20
"Wichmann-Hill" is only choice right now.

=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
Shengqiao Li

The Department of Statistics
PO Box 6330
West Virginia University
Morgantown, WV 26506-6330
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D

On Thu, 14 Aug 2008, Peter Dalgaard wrote:


Shengqiao Li wrote:

Hello all,
=20
I am generating large samples of random numbers. The RNG help page says:=

=20

"All the supplied uniform generators return 32-bit integer values that a=

re=20

converted to doubles, so they take at most 2^32 distinct values and long=

=20

runs will return duplicated values." But I find that the cycles are not =

the=20

same as the 32-bit integer.
=20
My test indicated that the cycles for Knuth's methods were 2^30 while=20
Wichmann-Hill's cycle was larger than 2^32! No numbers were duplicated i=

n=20

10M numbers generated by runif using Wichmann-Hill. The other three meth=

ods=20

had cycle length of 2^32.
=20
So, anybody can explain this? And any improvement to the implementation =

can=20

be made to increase the cycle length like the Wichmann-Hill method?
=20

What test? These are not simple linear congruential generators. Just beca=

use=20

you get the same value twice, it doesn't mean that the sequence is repeat=

ing.=20

Perhaps you should read the entire help page rather than just the note.

--=20
 O__   Peter Dalgaard =D8ster 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



---559023410-851401618-1218751024=:15885--

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--
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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Re: [Rd] [R] RNG Cycle and Duplication (PR#12540)

[Duncan Murdoch]

[EMAIL PROTECTED] wrote:

  This message is in MIME format.  The first part should be readable text,
  while the remaining parts are likely unreadable without MIME-aware tools.

---559023410-851401618-1218751024=:15885
Content-Type: TEXT/PLAIN; charset=ISO-8859-1; format=flowed
Content-Transfer-Encoding: QUOTED-PRINTABLE


I didn't describe the problem clearly. It's about the number of distinct=20
values. So just ignore cycle issue.

My tests were:

RNGkind(kind=3D"Knuth-TAOCP");
sum(duplicated(runif(1e7))); #return 46552

RNGkind(kind=3D"Knuth-TAOCP-2002");
sum(duplicated(runif(1e7))); #return 46415

#These collision frequency suggested there were 2^30 distinct values by=20
birthday problem.
  


The birthday problem distribution applies to independent draws, but they 
are only pseudo-independent.  I think the only ways to know for sure if 
there are 2^30 values are to look at the code, or run through a complete 
cycle.  And you need to determine the cycle by looking at .Random.seed, 
not at the returned value.


RNGkind(kind=3D"Marsaglia-Multicarry");
sum(duplicated(runif(1e7))); #return 11682

RNGkind(kind=3D"Super-Duper");
sum(duplicated(runif(1e7))); #return 11542

RNGkind(kind=3D"Mersenne-Twister");
sum(duplicated(runif(1e7))); #return 11656

#These indicated there were 2^32 distinct values, which agrees with the=20
help info.

  


If there are 2^30 distinct values for the two generators above, that 
also agrees with the documentation.



RNGkind(kind=3D"Wichmann-Hill");
sum(duplicated(runif(1e7))); #return 0

#So for this method, there should be more than 2^32 distinct values.

You may not get the exact numbers, but they should be close. So how to=20
explain above problem?
  


You haven't demonstrated what you claim, but if you look at the source, 
you'll see that in fact the man page is wrong:  Wichmann-Hill is based 
on 3 integer values, which each take on approximately 15 bits of 
different values.  So Wichmann-Hill could take nearly 2^45 different 
values (actually 30269*30307*30323).


The source is in https://svn.r-project.org/R/trunk/src/main/RNG.c if you 
want to check the others.

I need generate a large sample without any ties, it seems to me=20
"Wichmann-Hill" is only choice right now.
  


An alternative would be to construct a new value from two (or more) 
runif() values, but be careful that you don't mess up the distribution 
when you do that.


Duncan Murdoch

=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
Shengqiao Li

The Department of Statistics
PO Box 6330
West Virginia University
Morgantown, WV 26506-6330
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D

On Thu, 14 Aug 2008, Peter Dalgaard wrote:

  

Shengqiao Li wrote:


Hello all,
=20
I am generating large samples of random numbers. The RNG help page says:=
  

=20
  

"All the supplied uniform generators return 32-bit integer values that a=
  

re=20
  

converted to doubles, so they take at most 2^32 distinct values and long=
  

=20
  

runs will return duplicated values." But I find that the cycles are not =
  

the=20
  

same as the 32-bit integer.
=20
My test indicated that the cycles for Knuth's methods were 2^30 while=20
Wichmann-Hill's cycle was larger than 2^32! No numbers were duplicated i=
  

n=20
  

10M numbers generated by runif using Wichmann-Hill. The other three meth=
  

ods=20
  

had cycle length of 2^32.
=20
So, anybody can explain this? And any improvement to the implementation =
  

can=20
  

be made to increase the cycle length like the Wichmann-Hill method?
=20
  

What test? These are not simple linear congruential generators. Just beca=


use=20
  

you get the same value twice, it doesn't mean that the sequence is repeat=


ing.=20
  

Perhaps you should read the entire help page rather than just the note.

--=20
 O__   Peter Dalgaard =D8ster 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




---559023410-851401618-1218751024=:15885--

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Re: [Rd] cryptic message of R CMD check

[Prof Brian Ripley]

I've recently seen that message disappear again: July 29 is a long time 
ago in R development terms.  Please do as the posting guide asked and 
update your R *before posting*.


On Thu, 14 Aug 2008, Dr. Peter Ruckdeschel wrote:


Hi R-devels,

recently, we have seen a new warning by "R CMD check"
appearing for the devel-version of our package distrEx available on
r-forge, e.g. as

*|install.packages("/distrEx/",repos="http://r-forge.r-project.org";)|*

Here is the warning:

%-
[...snip ...]

* checking for unstated dependencies in R code ... WARNING
.get_S4_methods_list(): *did* reduce list, dropping
   See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.

[...snip ...]
%---

We get the same warning under Linux and Windows (if this helps).

Unfortunately, we cannot give you very detailed information about
our R running --- it is R-2.8.0dev but somehow R.Version() failed
to give svn-details ---


You built it from an SVN checkut on a machine without functional SVN, I 
believe.



R.Version()$version.string

[1] "R version 2.8.0 Under development (unstable) (2006-00-00 r0)"

but we built this R based on the then devel-version on July 29.

Could you give us a clue in this
Thank you already

Peter

--
Dr. Peter Ruckdeschel, Abteilung Finanzmathematik, F3.17
Fraunhofer ITWM, Fraunhofer Platz 1, 67663 Kaiserslautern
Telefon:  +49 631/31600-4699
Fax:  +49 631/31600-5699
E-Mail :  [EMAIL PROTECTED]





--
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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Re: [Rd] Double-clicking in tk list dialogs

[Prof Brian Ripley]

It does not seem to be standard practice for Tk-based interfaces (and 
indeed it was not part of GraphApp on Windows -- I added it after some 
years).


If you supply a tested patch to the R-devel sources it will be considered 
for 2.8.0.  The 'next version' is 2.7.2 and imminent, so I don't think we 
would consider it for that unless you get lots of support in the next 24 
hours.


On Thu, 14 Aug 2008, Barry Rowlingson wrote:


Am I the only one who finds himself futilely double-clicking a CRAN
mirror in the dialog for choosing a CRAN mirror? Yes, double-clicking
works in Windows, but not in the Tk-based dialog on Linux. I'm going
to wear out my mouse button.


I am surprised you have not set up a preferred CRAN mirror long ago.


Adding the following line to the tk_select.list function in the tcltk
package adds double-click functionality to list dialogs:

 tkbind(box, "",onOK)

(put it in the right place though, after 'box' has been created).

Not sure if this would be a default behaviour, or if its's worth
having a 'doubleClick=FALSE' argument that switches it on if TRUE.
Anyway, it was a little niggle that bothered me recently, and after
fixing someone else's TclTK problem recently I figured I'd have a go
at this.

Consider it a feature request for the next version.

Barry

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--
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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