R help - Jan 2009 - loglm fitting

Dear all,

sorry to bother you all with this but I've been trying to use the loglm in
MASS package (v2.8.0) and cannot get any sensible output.
I'm wondering am I doing something very foolish or missing something
obvious.

For example, I tried the documentation help(loglm) example - here's the
code

         # Case 1: frequencies specified as an array.
         sapply(minn38, function(x) length(levels(x)))
         ## hs phs fol sex f
         ##  3   4   7   2 0
         minn38a <- array(0, c(3,4,7,2), lapply(minn38[, -5], levels))
         minn38a[data.matrix(minn38[,-5])] <- minn38$fol
         fm <- loglm(~1 + 2 + 3 + 4, minn38a)  # numerals as names.
         deviance(fm)
         > [1] 0

The deviance is zero.
I tried other examples as well (Laura Thompson) and get pretty much
nonsense.

E.g.

      library(MASS)
      options(contrasts=c("contr.treatment", "contr.poly"))
      tbl.8.3 = data.frame(mara
     
=factor(c("Yes","No"),levels=c("Yes","No")),
                            cig
     
=factor(c("Yes","No"),levels=c("No","Yes")),
                            alc
     
=factor(c("Yes","No"),levels=c("Yes","No")),
                            count=c(911,538,44,456,3,43,2,279) )
      fit.acm = loglm( count ~ alc*cig*mara,data=tbl.8.3, param=T, fit=T)


Any advice greatly appreciated.

Gerard


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Is le haghaidh an duine n? an eintitis ar a bhfuil s? d?rithe, agus le haghaidh
an duine n? an eintitis sin amh?in, a bhearta?tear an fhaisn?is a tarchuireadh
agus f?adfaidh s? go bhfuil ?bhar faoi r?n agus/n? faoi phribhl?id inti.
Toirmisctear aon athbhreithni?, atarchur n? leathadh a dh?anamh ar an bhfaisn?is
seo, aon ?s?id eile a bhaint aisti n? aon ghn?omh a dh?anamh ar a hiontaoibh, ag
daoine n? ag eintitis seachas an faighteoir beartaithe. M? fuair t? ? seo tr?
dhearmad, t?igh i dteagmh?il leis an seolt?ir, le do thoil, agus scrios an
t-?bhar as aon r?omhaire. Is ? beartas na Roinne Dl? agus Cirt, Comhionannais
agus Athch?irithe Dl?, agus na nOif?g? agus na nGn?omhaireachta? a ?s?ideann
seirbh?s? TF na Roinne, seoladh ?bhair chol?il a dh?chead?.
M?s rud ? go measann t? gur ?bhar col?il at? san ?bhar at? sa teachtaireacht seo
is ceart duit dul i dteagmh?il leis an seolt?ir l?ithreach agus le
mailminder[ag]justice.ie chomh maith.
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If we check the data, we see a mistake in the entry.
> tbl.8.3
  mara cig alc count
1  Yes Yes Yes   911
2   No  No  No   538
3  Yes Yes Yes    44
4   No  No  No   456
5  Yes Yes Yes     3
6   No  No  No    43
7  Yes Yes Yes     2
8   No  No  No   279

Try:

table8.3 <- read.table(textConnection("alc cig mar count
Yes Yes Yes 911
Yes Yes No  538
Yes No  Yes 44
Yes No  No  456
No  Yes Yes 3
No  Yes No  43
No  No  Yes 2
No  No  No  279"),header=TRUE)
closeAllConnections()
myglm <- glm(count ~ mar+cig+alc, family=poisson, data=table8.3)
myglm$fitted.values
> myglm$fitted.values
        1         2         3         4         5         6
7         8
539.98258 740.22612 282.09123 386.70007  90.59739 124.19392  47.32880
64.87990

This reproduces the fitted values for your example (Agresti, pg 323)

On Wed, Jan 14, 2009 at 7:23 AM, Gerard M. Keogh <GMKeogh@justice.ie>
wrote:
>
> Dear all,
>
> sorry to bother you all with this but I've been trying to use the loglm
in
> MASS package (v2.8.0) and cannot get any sensible output.
> I'm wondering am I doing something very foolish or missing something
> obvious.
>
> For example, I tried the documentation help(loglm) example - here's the
> code
>
>         # Case 1: frequencies specified as an array.
>         sapply(minn38, function(x) length(levels(x)))
>         ## hs phs fol sex f
>         ##  3   4   7   2 0
>         minn38a <- array(0, c(3,4,7,2), lapply(minn38[, -5], levels))
>         minn38a[data.matrix(minn38[,-5])] <- minn38$fol
>         fm <- loglm(~1 + 2 + 3 + 4, minn38a)  # numerals as names.
>         deviance(fm)
>         > [1] 0
>
> The deviance is zero.
> I tried other examples as well (Laura Thompson) and get pretty much
> nonsense.
>
> E.g.
>
>      library(MASS)
>      options(contrasts=c("contr.treatment",
"contr.poly"))
>      tbl.8.3 = data.frame(mara
>     
=factor(c("Yes","No"),levels=c("Yes","No")),
>                            cig
>     
=factor(c("Yes","No"),levels=c("No","Yes")),
>                            alc
>     
=factor(c("Yes","No"),levels=c("Yes","No")),
>                            count=c(911,538,44,456,3,43,2,279) )
>      fit.acm = loglm( count ~ alc*cig*mara,data=tbl.8.3, param=T, fit=T)
>
>
> Any advice greatly appreciated.
>
> Gerard
>
>
>
>
**********************************************************************************
> The information transmitted is intended only for the person or entity to
> which it is addressed and may contain confidential and/or privileged
> material. Any review, retransmission, dissemination or other use of, or
> taking of any action in reliance upon, this information by persons or
> entities other than the intended recipient is prohibited. If you received
> this in error, please contact the sender and delete the material from any
> computer.  It is the policy of the Department of Justice, Equality and Law
> Reform and the Agencies and Offices using its IT services to disallow the
> sending of offensive material.
> Should you consider that the material contained in this message is
> offensive you should contact the sender immediately and also mailminder[at]
> justice.ie.
>
> Is le haghaidh an duine nó an eintitis ar a bhfuil sí dírithe, agus le
> haghaidh an duine nó an eintitis sin amháin, a bheartaítear an fhaisnéis a
> tarchuireadh agus féadfaidh sé go bhfuil ábhar faoi rún agus/nó faoi
> phribhléid inti. Toirmisctear aon athbhreithniú, atarchur nó leathadh a
> dhéanamh ar an bhfaisnéis seo, aon úsáid eile a bhaint aisti nó aon ghníomh
> a dhéanamh ar a hiontaoibh, ag daoine nó ag eintitis seachas an faighteoir
> beartaithe. Má fuair tú é seo trí dhearmad, téigh i dteagmháil leis an
> seoltóir, le do thoil, agus scrios an t-ábhar as aon ríomhaire. Is é
beartas
> na Roinne Dlí agus Cirt, Comhionannais agus Athchóirithe Dlí, agus na
> nOifígí agus na nGníomhaireachtaí a úsáideann seirbhísí TF na Roinne,
> seoladh ábhair cholúil a dhícheadú.
> Más rud é go measann tú gur ábhar colúil atá san ábhar atá sa
> teachtaireacht seo is ceart duit dul i dteagmháil leis an seoltóir
> láithreach agus le mailminder[ag]justice.ie chomh maith.
>
>
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>
>
>
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