Hi
thanks for data.
na.exclude does not excludes NA values. Actually it computes result without
considering NAs but keeps those NA values in propper positions so that the
result has the same length as input
Instead of several ifelse you can use
q131 <- as.numeric(cut(id3$q13,c(0,1.5,5)))-1
fitted values start with NA values
> fitted(tp1)
1241 1242 1243 1244 1245 1246
NA NA 2.143345e-11 2.143345e-11 2.143345e-11 2.143345e-11
1247 1248 1256 1268
2.143345e-11 2.143345e-11 2.143345e-11 2.143345e-11
which obviously hoslem.test is not adapted to.
>
> #Error in quantile.default(yhat, probs = seq(0, 1, 1/g)) :
> # missing values and NaN's not allowed if 'na.rm' is FALSE
you can use glm without na.action and your fitted values will be without NA.
> tp1 <- glm(q131 ~ q11 + q10+q12+edcat + q08+q06+ q14, family = binomial(link
> = "logit"), data=id3)
> fitted(tp1)
1243 1244 1245 1246 1247 1248
2.143345e-11 2.143345e-11 2.143345e-11 2.143345e-11 2.143345e-11 2.143345e-11
1256 1268
2.143345e-11 2.143345e-11
however
tp1$q131 does not exist
> tp1$q131
NULL
So again, test throws error.
Maybe you wanted
> hoslem.test(na.omit(id3$q131), fitted(tp1), g=10)
Hosmer and Lemeshow goodness of fit (GOF) test
data: na.omit(id3$q131), fitted(tp1)
X-squared = NaN, df = 8, p-value = NA
Warning message:
In Ops.factor(1, y) : ‘-’ not meaningful for factors
However q131 is factor (actually you changed it to factor)
If I change it to numeric
> id3$q131<-q131
> tp1 <- glm(q131 ~ q11 + q10+q12+edcat + q08+q06+ q14, family = binomial(link
> = "logit"), data=id3)
> hoslem.test(na.omit(id3$q131), fitted(tp1), g=10)
Hosmer and Lemeshow goodness of fit (GOF) test
data: na.omit(id3$q131), fitted(tp1)
X-squared = NaN, df = 8, p-value = NA
hoslem test works - at least it does not throw errors.
So best way for you would be to understand basic differences in object types
(numeric, factor, ....) by reading R intro and think about what hoslem test
needs as an input.
Cheers
Petr
> -----Original Message-----
> From: Luciane Maria Pilotto [mailto:lutipilo...@yahoo.com.br]
> Sent: Monday, May 04, 2015 2:46 PM
> To: r-help@r-project.org; PIKAL Petr
> Subject: RE: [R] help - hoslem.test
>
> Hi
>
> I'm trying to make a reproducible example using the command "dput" as
> fallows.
>
> The problem occurs when running the test of Hosmer and Lemeshow
> (hoslem.test) for residuals gives error. I'm using the command
> "na.action" to exclude the NA values.
>
> Thanks,
> Luciane
>
> ###############################################
>
> load(file.choose())#dataframe:"id3.rda"
> attach(id3)
>
<snip>
>
> #create binary outcome variable (q13) (transformando q13 em binária)
> q131<-ifelse(q13==1,0,ifelse(q13==2,1,ifelse(q13==3,1,
> ifelse(q13==4,1,ifelse(q13==5,1,NA)))))
Instead of several ifelse you can use
q131 <- as.numeric(cut(id3$q13,c(0,1.5,5)))-1
> id3<-cbind(id3,q131)
> id3$q131 <- as.factor(id3$q131)
>
> str(id3)
>
> tp1 <- glm(q131 ~ q11 + q10+q12+edcat + q08+q06+ q14, family =
> binomial(link = "logit"), data=id3, na.action="na.exclude")
> tp1
>
> library(ResourceSelection)
> hoslem.test(tp1$q131, fitted(tp1), g=10)
>
>
>
>
> --------------------------------------------
> Em sex, 1/5/15, PIKAL Petr <petr.pi...@precheza.cz> escreveu:
>
> Assunto: RE: [R] help - hoslem.test
> Para: "Luciane Maria Pilotto" <lutipilo...@yahoo.com.br>, "r-help@r-
> project.org" <r-help@r-project.org>
> Data: Sexta-feira, 1 de Maio de 2015, 3:59
>
> Hi
>
> > -----Original Message-----
> > From: Luciane Maria Pilotto [mailto:lutipilo...@yahoo.com.br]
> > Sent: Friday, May 01, 2015 12:49 AM
> > To: PIKAL Petr; r-help@r-project.org;
> John Kane
> > Subject: Re: [R] help -
> hoslem.test
> >
> > Ok, in
> dropbox link below you can download the bank.
> > (https://www.dropbox.com/s/9qrdf4mhd6tzypi/id3.rda?dl=0)
>
> No. Not everybody is alowed to
> use dropbox. Try to post result of
>
> dput(id3)
>
> directly to your post.
>
> Cheers
> Petr
>
> >
> > I change the script
> following the suggestions, but the error persists.
> > I used the the na.action command to delete
> the lost values.
> >
> >
>
> #######################################################################
> >
> >
> load("id3.rda")
> >
> attach(id3)
> >
> >
> #transformando q13 em binária (o/1)
> >
> q131<-ifelse(q13==1,0,ifelse(q13==2,1,ifelse(q13==3,1,
> > ifelse(q13==4,1,ifelse(q13==5,1,NA)))))
> > id3<-cbind(id3,q131)
> > id3$q131 <- as.factor(id3$q131)
> > str(id3)
> >
> > tp1 <- glm(q131 ~ q11 + q10+q12+edcat +
> q08+q06+ q14, family =
> > binomial(link =
> "logit"), data=id3,
> na.action="na.exclude")
> >
> tp1
> > hoslem.test(tp1$q131, fitted(tp1),
> g=10)
> >
> >
> >
> >
> --------------------------------------------
> > Em qui, 30/4/15, John Kane <jrkrid...@inbox.com>
> escreveu:
> >
> >
> Assunto: Re: [R] help - hoslem.test
> >
> Para: "PIKAL Petr" <petr.pi...@precheza.cz>,
> "Luciane Maria Pilotto"
> >
> <lutipilo...@yahoo.com.br>,
> "r-help@r-project.org"
> <r-help@r-
> > project.org>
> >
> Data: Quinta-feira, 30 de Abril de 2015, 11:51
> >
> > Kevin Thorpe
> pointed out
> > to me that there is a
> dropbox link at the very bottom of the
> > post that I missed. :(
> >
> > I
> > just downloaded it, read it in and it
> looks fine.
> >
> > John
> Kane
> > Kingston ON Canada
> >
> >
> > > -----Original
> > Message-----
> > >
> From: petr.pi...@precheza.cz
> > > Sent: Thu, 30 Apr 2015 14:25:23
> +0000
> > > To: lutipilo...@yahoo.com.br,
> > r-help@r-project.org
> > > Subject: Re: [R] help -
> hoslem.test
> > >
> > > Hi
> > >
> > > I agree with John
> > >
> > > Just
> small
> > refinements in lines
> > >
> > >>
> -----Original Message-----
> >
> >>> -----Original Message-----
> > >>> From: lutipilo...@yahoo.com.br
> > >>> Sent: Thu, 30 Apr 2015
> 04:24:32
> > -0700
> >
> >>> To: r-help@r-project.org,
> > jrkrid...@inbox.com
> > >>> Subject: RE: [R] help -
> > hoslem.test
> >
> >>>
> > >>>
> load("id3.rda")
> > >>
> And what is this?
> > >>
> > >> We do not
> > have access to your office or computer
> hard disc.
> > >>
> > >> Please read
> > http://stackoverflow.com/questions/5963269/how-to-make-a-
> > >> great-r-reproducible-example,
> see
> > ?dput for sending data?
> > >>
> > >>
> It is very unlikely anyone here can
> >
> help if we have no data.
> > >>
> > >>
> >
> >>>
> > attach(id3)
> > >
> > > Do
> > not use attach. It prevents from
> modifiyng id3.
> > >
> > >>>
> >
> >>> #transformando q13 em binária
> > >>>
> >
> q131<-ifelse(q13==1,1,ifelse(q13==2,2,ifelse(q13==3,2,
> > >>>
> >
> ifelse(q13==4,2,ifelse(q13==5,2,NA)))))
> > >
> >
> > > q131 <- as.numeric(cut(q13,
> > c(0,1.5,5)))
> >
> >
> > >>
> >
> x<-1:7
> > >> x
> > >
> > [1] 1 2 3 4
> 5 6 7
> > >> as.numeric(cut(x,
> > c(0,1.5,5)))
> > >
> [1] 1 2 2 2 2 NA
> > NA
> > >
> >
> >>>
> >
> id3<-cbind(id3,q131)
> > >
> > > rather dangerous in case id3 is
> not
> > data.frame but matrix
> > >
> > >>>
> id3$q131 <-
> > as.factor(id3$q131)
> > >>>
> >
> >>> tp1 <- glm(q131 ~ q11 +
> > q10+q12+edcat + q08+q06+ q14, family
> =
> > >>> binomial(link =
> > "logit"), data=id3)
> > >>>
> >
> tp1
> > >>>
> > >>>
> library(ResourceSelection)
> >
> >>> hoslem.test(tp1$q131, fitted(tp1),
> > g=10)
> > >
> > > hoslem.test
> >
> expects x to be a numeric vector of observations, binary
> > > (0/1).
> > >
> If I
> > understand correctly tp1$q131
> have values 1, 2 or NA.
> > >
> > > Cheers
> > >
> Petr
> > >
> >
> >>>
> > >>>
> > dataframe: https://www.dropbox.com/s/9qrdf4mhd6tzypi/id3.rda?dl=0
> > >>>
> >
> >>>
> > >>>
> >
> __________________________________________________
> > >>> Luciane Maria Pilotto
> > >>> Mestre e Doutoranda em
> Saúde
> > Bucal Coletiva - FO/UFRGS
> > >>> NDE
> >
> Odontologia - UNIVATES
> >
> >>>
> > Telefone: (51)
> 84512344
> > >>>
> > >>>
> >
> --------------------------------------------
> > >>> Em qui, 30/4/15, John Kane
> <jrkrid...@inbox.com>
> > escreveu:
> >
> >>>
> > >>> Assunto:
> RE: [R] help -
> > hoslem.test
> > >>> Para:
> > "Luciane Maria Pilotto" <lutipilo...@yahoo.com.br>,
> > >>> r-help@r-project.org
> > >>> Data: Quinta-feira, 30 de
> Abril
> > de 2015, 7:52
> > >>>
> >
> >>> http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-
> > >> reproducible-example
> > >>>
> >
> >>>
> > John Kane
> > >>> Kingston ON
> > Canada
> >
> >>>
> > >>>
> > >>>
> > >
> -----Original Message-----
> >
> >>> > From: lutipilo...@yahoo.com.br
> > >>> > Sent: Wed, 29 Apr
> 2015
> > 18:45:26 -0700
> > >>> > To: r-help@r-project.org
> > >>> > Subject: [R] help
> -
> > hoslem.test
> >
> >>> >
> > >>>
> > Hello,
> > >>> >
> > >>> > I'm working
> with
> > >>> ordinal logistic
> regression
> > model (polr) and would
> like
> > >>>
> > > to test the proportional odds
> assumption.
> > >>> For this,
> I ran the binary
> > >>> >
> logistic
> > >>> regressions
> with varying
> > cutpoints on the
> dependent
> > >>>
> > variable, as
> >
> >>> > described
> > in the
> following
> > >>> commands.
> > When running the test of Hosmer and
> > >>> > Lemeshow
> (hoslem.test) for
> > residuals gives
> > >>> error.
> > >>> >
> > >>> > Thanks,
> > >>> > Luciane
> > >>> >
> > >>> >
> > >>>
> >
> ______________________________________________
> > >>> > R-help@r-project.org
> > >>> mailing list -- To
> UNSUBSCRIBE
> > and more, see
> > >>> > https://stat.ethz.ch/mailman/listinfo/r-help
> > >>> > 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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