[R] help - hoslem.test
Luciane Maria Pilotto
lutipilotto at yahoo.com.br
Tue May 5 14:13:49 CEST 2015
Hi
Thanks for the help!
I used the following commands to run the test hoslem:
rl<-id3[,c("q06", "q08", "q10", "q11", "q12", "q13", "q14", "sexo", "edcat", "rendacat", "cpod",
"getario", "bwgr_et")]#select only variables of interest
dim(rl)#[1] 22843 12
attach(rl)
q131 <- as.numeric(cut(rl$q13,c(0,1.5,5)))-1
rl<-cbind(rl,q131)
rlna<-rl[complete.cases(rl),]#exclude NA
tpna <- glm(q131 ~ q11 + q10+rendacat+q12 + q08+q06 + q14,
family = binomial(link = "logit"), data=rlna)
hoslem.test(rlna$q131, fitted(tpna), g=10)
Thanks
Luciane
--------------------------------------------
Em seg, 4/5/15, PIKAL Petr <petr.pikal em precheza.cz> escreveu:
Assunto: RE: [R] help - hoslem.test
t.org" <r-help em r-project.org>
Data: Segunda-feira, 4 de Maio de 2015, 10:24
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-----
> Sent: Monday, May 04, 2015 2:46 PM
> To: r-help em 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.pikal em precheza.cz>
escreveu:
>
> Assunto: RE: [R] help - hoslem.test
"r-help em r-
> project.org" <r-help em r-project.org>
> Data: Sexta-feira, 1 de Maio de 2015, 3:59
>
> Hi
>
> > -----Original Message-----
> > Sent: Friday, May 01, 2015 12:49 AM
> > To: PIKAL Petr; r-help em 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 <jrkrideau em inbox.com>
> escreveu:
> >
> >
> Assunto: Re: [R] help - hoslem.test
> >
> Para: "PIKAL Petr" <petr.pikal em precheza.cz>,
> "Luciane Maria Pilotto"
> >
> "r-help em r-project.org"
> <r-help em 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.pikal em precheza.cz
> > > Sent: Thu, 30 Apr 2015 14:25:23
> +0000
> > r-help em r-project.org
> > > Subject: Re: [R] help -
> hoslem.test
> > >
> > > Hi
> > >
> > > I agree with John
> > >
> > > Just
> small
> > refinements in lines
> > >
> > >>
> -----Original Message-----
> >
> >>> -----Original Message-----
> > >>> Sent: Thu, 30 Apr 2015
> 04:24:32
> > -0700
> >
> >>> To: r-help em r-project.org,
> > jrkrideau em 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
> <jrkrideau em inbox.com>
> > escreveu:
> >
> >>>
> > >>> Assunto:
> RE: [R] help -
> > hoslem.test
> > >>> Para:
> > >>> r-help em 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-----
> >
> > >>> > Sent: Wed, 29
Apr
> 2015
> > 18:45:26 -0700
> > >>> > To: r-help em 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 em 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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