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Bill.Venables@csiro.au

2006-Jan-14 23:28 UTC

[Rd] initialize expression in 'quasi' (PR#8486)

This is not so much a bug as an infelicity in the code that can easily
be fixed.

The initialize expression in the quasi family function is, (uniformly
for all links and all variance functions):


    initialize <- expression({
        n <- rep.int(1, nobs)
        mustart <- y + 0.1 * (y == 0)
    })

This is inappropriate (and often fails) for variance function
"mu(1-mu)".  Here is a short demo to show it:
#################################################

set.seed(666)
dat <- data.frame(x = rep((-10):10, each = 5), w = rep(1:5, 21))
dat <- transform(dat, y = rbinom(x, size = w, prob = pcauchy(1 + 2*x)))

modFit <- glm(y/w ~ x, quasi(link = cauchit, variance =
"mu(1-mu)"),
              dat, weights = w, trace = T)

Deviance = 309.2785 Iterations - 1 
Deviance = 3257.501 Iterations - 2 
Deviance = 1043.455 Iterations - 3 
..
Deviance = 1733.824 Iterations - 24 
Deviance = 1665.487 Iterations - 25 
Warning message:
algorithm did not converge in: glm.fit(x = X, ...
#################################################

A comprehensive fix would involve tying the initialize expression to
both the link and the variance function, but that would involve changing
make.link(), which is probably not a good idea for other reasons (though
ultimately that might be the way to go).  There are at least three
possible work-arounds:

1) use quasibinomial for this kind of model (but that's not possible
here and an unnecessary complication if you are transferring S-PLUS
code, which is how I found the problem) but quasibinomial could be
extended to take this link as well, of course.

2) warn people in the help information that with quasi() they should
always give the algorithm a bit more help and supply an appropriate
mustart.   This works fine (even if the coefficient estimates are a bit
ropey!):

#################################################
modFit <- glm(y/w ~ x, quasi(link = cauchit, variance =
"mu(1-mu)"),
  dat, weights = w, trace = T, mustart = pmax(0.001, pmin(0.999, y/w)))

Deviance = 218.9552 Iterations - 1 
Deviance = 123.2773 Iterations - 2 
Deviance = 86.13804 Iterations - 3 
Deviance = 74.23746 Iterations - 4 
Deviance = 72.03787 Iterations - 5 
Deviance = 71.89566 Iterations - 6 
Deviance = 71.89395 Iterations - 7 
Deviance = 71.89395 Iterations - 8 
Deviance = 71.89395 Iterations - 9 > #################################################

3) change quasi() slightly to cover this case, at least, in a better
way.

I have included a minimally modified version of quasi that I think
achieves this and the demo shown above. 

With the changed version the performance, in this case, is identical to
what you get above when mustart is supplied.  The changes cannot affect
performance with any other variance functions and with this variance
function should only make things better, but it just _might_ make things
work worse in extreme and unusual cases.  I have not found one, though.

Bill Venables. 



--please do not edit the information below--

Version:
 platform = i386-pc-mingw32
 arch = i386
 os = mingw32
 system = i386, mingw32
 status = 
 major = 2
 minor = 2.1
 year = 2005
 month = 12
 day = 20
 svn rev = 36812
 language = R

Windows XP Professional (build 2600) Service Pack 2.0

Locale:
LC_COLLATE=English_Australia.1252;LC_CTYPE=English_Australia.1252;LC_MON
ETARY=English_Australia.1252;LC_NUMERIC=C;LC_TIME=English_Australia.1252

Search Path:
 .GlobalEnv, package:mgcv, package:AusNew, package:MASS, package:RODBC,
package:lattice, package:splines, package:methods, package:stats,
package:graphics, package:grDevices, package:datasets, package:RBigData,
package:mvbutils, mvb.session.info, package:tools, package:utils,
package:RBigData, package:RUtilities, package:RBigLibrary,
package:g.data, Autoloads, package:base

Bill Venables, 
CMIS, CSIRO Laboratories, 
PO Box 120, Cleveland, Qld. 4163 
AUSTRALIA 
Office Phone (email preferred): +61 7 3826 7251 
Fax (if absolutely necessary):    +61 7 3826 7304 
Mobile (rarely used):                +61 4 1963 4642 
Home Phone:                          +61 7 3286 7700 
mailto:Bill.Venables at csiro.au 
http://www.cmis.csiro.au/bill.venables/

Prof Brian Ripley

2006-Jan-16 08:28 UTC

head link

[Rd] initialize expression in 'quasi' (PR#8486)

Bill,

As you see, R-bugs does not work with encoded (binary) attachments. 
Could you please send this again to R-devel with (if possible) text 
attachments?

The source code says

# 0.1 fudge here matches poisson: S has 1/6.
     initialize <- expression({ n <- rep.int(1, nobs); mustart <- y +
0.1 * (y == 0)})

although I believe S-PLUS has diverged here.

Brian

On Sun, 15 Jan 2006 Bill.Venables at csiro.au wrote:
> This is a multi-part message in MIME format.
>
> ------_=_NextPart_001_01C61962.212F35AB
> Content-Type: text/plain;
> 	charset="us-ascii"
> Content-Transfer-Encoding: quoted-printable
>
> This is not so much a bug as an infelicity in the code that can easily
> be fixed.
>
> The initialize expression in the quasi family function is, (uniformly
> for all links and all variance functions):
>
>
>    initialize <- expression({
>        n <- rep.int(1, nobs)
>        mustart <- y + 0.1 * (y =3D=3D 0)
>    })
>
> This is inappropriate (and often fails) for variance function
> "mu(1-mu)".  Here is a short demo to show it:
> #################################################
>
> set.seed(666)
> dat <- data.frame(x =3D rep((-10):10, each =3D 5), w =3D rep(1:5, 21))
> dat <- transform(dat, y =3D rbinom(x, size =3D w, prob =3D pcauchy(1 +
> 2*x)))
>
> modFit <- glm(y/w ~ x, quasi(link =3D cauchit, variance =3D
"mu(1-mu)"),
>              dat, weights =3D w, trace =3D T)
>
> Deviance =3D 309.2785 Iterations - 1=20
> Deviance =3D 3257.501 Iterations - 2=20
> Deviance =3D 1043.455 Iterations - 3=20
> ..
> Deviance =3D 1733.824 Iterations - 24=20
> Deviance =3D 1665.487 Iterations - 25=20
> Warning message:
> algorithm did not converge in: glm.fit(x =3D X, ...
> #################################################
>
> A comprehensive fix would involve tying the initialize expression to
> both the link and the variance function, but that would involve changing
> make.link(), which is probably not a good idea for other reasons (though
> ultimately that might be the way to go).  There are at least three
> possible work-arounds:
>
> 1) use quasibinomial for this kind of model (but that's not possible
> here and an unnecessary complication if you are transferring S-PLUS
> code, which is how I found the problem) but quasibinomial could be
> extended to take this link as well, of course.
>
> 2) warn people in the help information that with quasi() they should
> always give the algorithm a bit more help and supply an appropriate
> mustart.   This works fine (even if the coefficient estimates are a bit
> ropey!):
>
> #################################################
> modFit <- glm(y/w ~ x, quasi(link =3D cauchit, variance =3D
"mu(1-mu)"),
>  dat, weights =3D w, trace =3D T, mustart =3D pmax(0.001, pmin(0.999, >
y/w)))
>
> Deviance =3D 218.9552 Iterations - 1=20
> Deviance =3D 123.2773 Iterations - 2=20
> Deviance =3D 86.13804 Iterations - 3=20
> Deviance =3D 74.23746 Iterations - 4=20
> Deviance =3D 72.03787 Iterations - 5=20
> Deviance =3D 71.89566 Iterations - 6=20
> Deviance =3D 71.89395 Iterations - 7=20
> Deviance =3D 71.89395 Iterations - 8=20
> Deviance =3D 71.89395 Iterations - 9=20
>> =20
> #################################################
>
> 3) change quasi() slightly to cover this case, at least, in a better
> way.
>
> I have included a minimally modified version of quasi that I think
> achieves this and the demo shown above.=20
>
> With the changed version the performance, in this case, is identical to
> what you get above when mustart is supplied.  The changes cannot affect
> performance with any other variance functions and with this variance
> function should only make things better, but it just _might_ make things
> work worse in extreme and unusual cases.  I have not found one, though.
>
> Bill Venables.=20
>
>
>
> --please do not edit the information below--
>
> Version:
> platform =3D i386-pc-mingw32
> arch =3D i386
> os =3D mingw32
> system =3D i386, mingw32
> status =3D=20
> major =3D 2
> minor =3D 2.1
> year =3D 2005
> month =3D 12
> day =3D 20
> svn rev =3D 36812
> language =3D R
>
> Windows XP Professional (build 2600) Service Pack 2.0
>
> Locale:
>
LC_COLLATE=3DEnglish_Australia.1252;LC_CTYPE=3DEnglish_Australia.1252;LC_>
MON
>
ETARY=3DEnglish_Australia.1252;LC_NUMERIC=3DC;LC_TIME=3DEnglish_Australia>
.1252
>
> Search Path:
> .GlobalEnv, package:mgcv, package:AusNew, package:MASS, package:RODBC,
> package:lattice, package:splines, package:methods, package:stats,
> package:graphics, package:grDevices, package:datasets, package:RBigData,
> package:mvbutils, mvb.session.info, package:tools, package:utils,
> package:RBigData, package:RUtilities, package:RBigLibrary,
> package:g.data, Autoloads, package:base
>
> Bill Venables,=20
> CMIS, CSIRO Laboratories,=20
> PO Box 120, Cleveland, Qld. 4163=20
> AUSTRALIA=20
> Office Phone (email preferred): +61 7 3826 7251=20
> Fax (if absolutely necessary):    +61 7 3826 7304=20
> Mobile (rarely used):                +61 4 1963 4642=20
> Home Phone:                          +61 7 3286 7700=20
> mailto:Bill.Venables at csiro.au=20
> http://www.cmis.csiro.au/bill.venables/=20
>
>
>
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> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
>
-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
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, UK                Fax:  +44 1865 272595

Bill.Venables@csiro.au

2006-Jan-16 22:55 UTC

head link

[Rd] initialize expression in 'quasi' (PR#8486)

My apologies, I thought it was going as a text attachement.  Looks like
Microsoft second guessing me again.

The problem is the 'mustart' value (if you are going to base it on the
variance structure and not the link as well) should not allow values to
touch the point 
where the variance becomes zero.  The fudge that is in there now obeys
this
'rule' for all but the mu(1-mu).  It is a bit too strong for the
'constant'
case, but I guess we are stuck with that now for back compatibility
reasons.


Here is my suggestion:

##############(cut
here)##################################################

quasi <- function (link = "identity", variance =
"constant")  {
    linktemp <- substitute(link)
    if (is.expression(linktemp) || is.call(linktemp)) 
        linktemp <- link
    else if (!is.character(linktemp)) 
        linktemp <- deparse(linktemp)
    if (is.character(linktemp)) 
        stats <- make.link(linktemp)
    else stats <- linktemp
    variancetemp <- substitute(variance)
    if (!is.character(variancetemp)) {
        variancetemp <- deparse(variancetemp)
        if (linktemp == "variance") 
            variancetemp <- eval(variance)
    }
    initialize <- NULL
#######change
    switch(variancetemp,
    constant = {
        variance <- function(mu) rep.int(1, length(mu))
        dev.resids <- function(y, mu, wt) wt * ((y - mu)^2)
        validmu <- function(mu) TRUE
    },
    "mu(1-mu)" = {
        variance <- function(mu) mu * (1 - mu)
        validmu <- function(mu) all(mu > 0) && all(mu < 1)
        dev.resids <- function(y, mu, wt) 2 * wt * (y * log(ifelse(y == 
            0, 1, y/mu)) + (1 - y) * log(ifelse(y == 1, 1, (1 - 
            y)/(1 - mu))))
        initialize <- expression({
#######change
          n <- rep.int(1, nobs)
#######change
          mustart <- pmax(0.001, pmin(0.999, y))	#######change
        })
#######change
    },
    mu = {
        variance <- function(mu) mu
        validmu <- function(mu) all(mu > 0)
        dev.resids <- function(y, mu, wt) 2 * wt * (y * log(ifelse(y == 
            0, 1, y/mu)) - (y - mu))
    },
    "mu^2" = {
        variance <- function(mu) mu^2
        validmu <- function(mu) all(mu > 0)
        dev.resids <- function(y, mu, wt) pmax(-2 * wt * (log(ifelse(y
== 
            0, 1, y)/mu) - (y - mu)/mu), 0)
    },
    "mu^3" = {
        variance <- function(mu) mu^3
        validmu <- function(mu) all(mu > 0)
        dev.resids <- function(y, mu, wt) wt * ((y - mu)^2)/(y * 
            mu^2)
    },
    stop(gettextf("'variance' \"%s\" is invalid: possible
values are
\"mu(1-mu)\", \"mu\", \"mu^2\", \"mu^3\"
and \"constant\"",
        variancetemp), domain = NA))
    if(is.null(initialize))
#######change
    initialize <- expression({
        n <- rep.int(1, nobs)
        mustart <- y + 0.1 * (y == 0)
    })
    aic <- function(y, n, mu, wt, dev) NA
    structure(list(family = "quasi", link = linktemp, linkfun
stats$linkfun,
        linkinv = stats$linkinv, variance = variance, dev.resids dev.resids, 
        aic = aic, mu.eta = stats$mu.eta, initialize = initialize, 
        validmu = validmu, valideta = stats$valideta, varfun variancetemp), 
        class = "family")
}

###############(cut here)##############################

Bill Venables, 
CMIS, CSIRO Laboratories, 
PO Box 120, Cleveland, Qld. 4163 
AUSTRALIA 
Office Phone (email preferred): +61 7 3826 7251 
Fax (if absolutely necessary):    +61 7 3826 7304 
Mobile (rarely used):                +61 4 1963 4642 
Home Phone:                          +61 7 3286 7700 
mailto:Bill.Venables at csiro.au 
http://www.cmis.csiro.au/bill.venables/ 



-----Original Message-----
From: Prof Brian Ripley [mailto:ripley at stats.ox.ac.uk] 
Sent: Monday, 16 January 2006 6:28 PM
To: Venables, Bill (CMIS, Cleveland)
Cc: r-devel at stat.math.ethz.ch
Subject: Re: [Rd] initialize expression in 'quasi' (PR#8486)


Bill,

As you see, R-bugs does not work with encoded (binary) attachments. 
Could you please send this again to R-devel with (if possible) text 
attachments?

The source code says

# 0.1 fudge here matches poisson: S has 1/6.
     initialize <- expression({ n <- rep.int(1, nobs); mustart <- y +
0.1 * (y == 0)})

although I believe S-PLUS has diverged here.

Brian

On Sun, 15 Jan 2006 Bill.Venables at csiro.au wrote:
> This is a multi-part message in MIME format.
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>
> This is not so much a bug as an infelicity in the code that can easily
> be fixed.
>
> The initialize expression in the quasi family function is, (uniformly
> for all links and all variance functions):
>
>
>    initialize <- expression({
>        n <- rep.int(1, nobs)
>        mustart <- y + 0.1 * (y =3D=3D 0)
>    })
>
> This is inappropriate (and often fails) for variance function
> "mu(1-mu)".  Here is a short demo to show it:
> #################################################
>
> set.seed(666)
> dat <- data.frame(x =3D rep((-10):10, each =3D 5), w =3D rep(1:5, 21))
> dat <- transform(dat, y =3D rbinom(x, size =3D w, prob =3D pcauchy(1 +
> 2*x)))
>
> modFit <- glm(y/w ~ x, quasi(link =3D cauchit, variance =3D
"mu(1-mu)"),>              dat, weights =3D w, trace =3D T)
>
> Deviance =3D 309.2785 Iterations - 1=20
> Deviance =3D 3257.501 Iterations - 2=20
> Deviance =3D 1043.455 Iterations - 3=20
> ..
> Deviance =3D 1733.824 Iterations - 24=20
> Deviance =3D 1665.487 Iterations - 25=20
> Warning message:
> algorithm did not converge in: glm.fit(x =3D X, ...
> #################################################
>
> A comprehensive fix would involve tying the initialize expression to
> both the link and the variance function, but that would involve
changing> make.link(), which is probably not a good idea for other reasons
(though> ultimately that might be the way to go).  There are at least three
> possible work-arounds:
>
> 1) use quasibinomial for this kind of model (but that's not possible
> here and an unnecessary complication if you are transferring S-PLUS
> code, which is how I found the problem) but quasibinomial could be
> extended to take this link as well, of course.
>
> 2) warn people in the help information that with quasi() they should
> always give the algorithm a bit more help and supply an appropriate
> mustart.   This works fine (even if the coefficient estimates are a
bit> ropey!):
>
> #################################################
> modFit <- glm(y/w ~ x, quasi(link =3D cauchit, variance =3D
"mu(1-mu)"),>  dat, weights =3D w, trace =3D T, mustart =3D pmax(0.001, pmin(0.999,
> y/w)))
>
> Deviance =3D 218.9552 Iterations - 1=20
> Deviance =3D 123.2773 Iterations - 2=20
> Deviance =3D 86.13804 Iterations - 3=20
> Deviance =3D 74.23746 Iterations - 4=20
> Deviance =3D 72.03787 Iterations - 5=20
> Deviance =3D 71.89566 Iterations - 6=20
> Deviance =3D 71.89395 Iterations - 7=20
> Deviance =3D 71.89395 Iterations - 8=20
> Deviance =3D 71.89395 Iterations - 9=20
>> =20
> #################################################
>
> 3) change quasi() slightly to cover this case, at least, in a better
> way.
>
> I have included a minimally modified version of quasi that I think
> achieves this and the demo shown above.=20
>
> With the changed version the performance, in this case, is identical
to> what you get above when mustart is supplied.  The changes cannot
affect> performance with any other variance functions and with this variance
> function should only make things better, but it just _might_ make
things> work worse in extreme and unusual cases.  I have not found one,
though.>
> Bill Venables.=20
>
>
>
> --please do not edit the information below--
>
> Version:
> platform =3D i386-pc-mingw32
> arch =3D i386
> os =3D mingw32
> system =3D i386, mingw32
> status =3D=20
> major =3D 2
> minor =3D 2.1
> year =3D 2005
> month =3D 12
> day =3D 20
> svn rev =3D 36812
> language =3D R
>
> Windows XP Professional (build 2600) Service Pack 2.0
>
> Locale:
>LC_COLLATE=3DEnglish_Australia.1252;LC_CTYPE=3DEnglish_Australia.1252;LC
_> MON>ETARY=3DEnglish_Australia.1252;LC_NUMERIC=3DC;LC_TIME=3DEnglish_Australi
a> .1252>
> Search Path:
> .GlobalEnv, package:mgcv, package:AusNew, package:MASS, package:RODBC,
> package:lattice, package:splines, package:methods, package:stats,
> package:graphics, package:grDevices, package:datasets,
package:RBigData,> package:mvbutils, mvb.session.info, package:tools, package:utils,
> package:RBigData, package:RUtilities, package:RBigLibrary,
> package:g.data, Autoloads, package:base
>
> Bill Venables,=20
> CMIS, CSIRO Laboratories,=20
> PO Box 120, Cleveland, Qld. 4163=20
> AUSTRALIA=20
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> http://www.cmis.csiro.au/bill.venables/=20
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>
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>
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-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
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, UK                Fax:  +44 1865 272595

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