Re: [Rd] extending the derivs table/fools rushing in
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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Re: [Rd] extending the derivs table/fools rushing in
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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Re: [Rd] extending the derivs table/fools rushing in
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
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 VR 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 signature.asc Description: OpenPGP digital signature __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] extending the derivs table/fools rushing in
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 VR 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 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
