[R] effect function in the effects package
John Fox
jfox at mcmaster.ca
Thu Oct 20 20:24:06 CEST 2011
Dear Xu Jun,
It's really not possible for me to know the source of the error without a complete, reproducible example, but if I had to guess, I'd guess that there's a scoping problem of some sort, with the value of yr89 coming from somewhere that you don't expect. How about fitting the original model using the data argument rather than allowing the variables in the model to be found along the search path?
Best,
John
------------------------------------------------
John Fox
Sen. William McMaster Prof. of Social Statistics
Department of Sociology
McMaster University
Hamilton, Ontario, Canada
http://socserv.mcmaster.ca/jfox/
On Thu, 20 Oct 2011 14:09:28 -0400
Xu Jun <junxu.r at gmail.com> wrote:
> Dear Professor Fox,
>
> I didn't include codes in between these two commands (polr and
> plot(effect()). I am still trying to work it out. Maybe it's related
> to how I coded some of the factor variables as I got some successful
> runs after I changed the coding for some factor variables. I will keep
> working on the codes and see if I can figure out. Again, your effects
> package, I have to say, is awesome!
>
> Jun
>
> On Thu, Oct 20, 2011 at 1:26 PM, Xu Jun <junxu.r at gmail.com> wrote:
> > Dear Professor Fox,
> >
> > Thanks a lot! That is an embarrassing error. After I cleaned up and
> > simplified my codes, and ran the following two lines:
> >
> > myologit <- polr(factor(warm) ~ yr89 + male + white + age + ed + prst,
> > + data=ordwarm2, method=c("logistic"))
> >
> > plot(effect("age", myologit, xlevels=list(age=seq(20, 80, 5))))
> >
> > I am still having trouble. See below:
> >
> >> summary(myologit)
> >
> > Re-fitting to get Hessian
> >
> > Call:
> > polr(formula = factor(warm) ~ yr89 + male + white + age + ed +
> > prst, data = ordwarm2, method = c("logistic"))
> >
> > Coefficients:
> > Value Std. Error t value
> > yr89 0.523912 0.079899 6.557
> > male -0.733309 0.078483 -9.344
> > white -0.391140 0.118381 -3.304
> > age -0.021666 0.002469 -8.777
> > ed 0.067176 0.015975 4.205
> > prst 0.006072 0.003293 1.844
> >
> > Intercepts:
> > Value Std. Error t value
> > 1|2 -2.4654 0.2389 -10.3188
> > 2|3 -0.6309 0.2333 -2.7042
> > 3|4 1.2618 0.2340 5.3919
> >
> > Residual Deviance: 5689.825
> > AIC: 5707.825
> >
> >> plot(effect("age", myologit, xlevels=list(age=seq(20, 80, 5))))
> > Error in plot(effect("age", myologit, xlevels = list(age = seq(20, 80, :
> > error in evaluating the argument 'x' in selecting a method for
> > function 'plot': Error in model.frame.default(formula = factor(warm) ~
> > yr89 + male + white + :
> > variable lengths differ (found for 'yr89')
> >
> > On Thu, Oct 20, 2011 at 11:55 AM, John Fox <jfox at mcmaster.ca> wrote:
> >> Dear Xu Jun,
> >>
> >> I'm not sure whether this is the source of the error, but it may help to spell the xlevels argument correctly (it is not "xlevles").
> >>
> >> I hope this helps,
> >> John
> >>
> >> ------------------------------------------------
> >> John Fox
> >> Sen. William McMaster Prof. of Social Statistics
> >> Department of Sociology
> >> McMaster University
> >> Hamilton, Ontario, Canada
> >> http://socserv.mcmaster.ca/jfox/
> >>
> >> On Thu, 20 Oct 2011 10:34:30 -0400
> >> Xu Jun <junxu.r at gmail.com> wrote:
> >>> Dear r-help listers,
> >>>
> >>> I am using effects to produce an effect plot after the proportional
> >>> odds logistic regression model. There is no problem for me to estimate
> >>> the model, but when it comes to the graphing, I was stuck. see the
> >>> codes below:
> >>>
> >>> ##############################################################################
> >>> myologit <- polr(factor(warm) ~ yr89 + male + white + age + ed + prst,
> >>> + data=ordwarm2, method=c("logistic"))
> >>>
> >>> require(effects)
> >>> plot(effect("age", myologit, xlevles=list(age=seq(20, 80, 5),
> >>> given.values(male=1, yr89=1))))
> >>>
> >>> ##############################################################################
> >>>
> >>> I got the following error message:
> >>>
> >>> Warning message:
> >>> package 'effects' was built under R version 2.13.2
> >>> Error in plot(effect("age", myologit, xlevles = list(age = seq(20, 80, :
> >>> error in evaluating the argument 'x' in selecting a method for
> >>> function 'plot': Error in model.frame.default(formula = factor(warm) ~
> >>> yr89 + male + white + :
> >>> variable lengths differ (found for 'yr89')
> >>>
> >>>
> >>> the full set of codes:
> >>>
> >>> > myologit <- polr(factor(warm) ~ yr89 + male + white + age + ed + prst,
> >>> + data=ordwarm2, method=c("logistic"))
> >>>
> >>> > summary(myologit)
> >>>
> >>> Re-fitting to get Hessian
> >>>
> >>> Call:
> >>> polr(formula = factor(warm) ~ yr89 + male + white + age + ed +
> >>> prst, data = ordwarm2, method = c("logistic"))
> >>>
> >>> Coefficients:
> >>> Value Std. Error t value
> >>> yr89 0.523912 0.079899 6.557
> >>> male -0.733309 0.078483 -9.344
> >>> white -0.391140 0.118381 -3.304
> >>> age -0.021666 0.002469 -8.777
> >>> ed 0.067176 0.015975 4.205
> >>> prst 0.006072 0.003293 1.844
> >>>
> >>> Intercepts:
> >>> Value Std. Error t value
> >>> 1|2 -2.4654 0.2389 -10.3188
> >>> 2|3 -0.6309 0.2333 -2.7042
> >>> 3|4 1.2618 0.2340 5.3919
> >>>
> >>> Residual Deviance: 5689.825
> >>> AIC: 5707.825
> >>>
> >>> > plot(effect("age", myologit, xlevles=list(age=seq(20, 80, 5), given.values(male=1, yr89=1))))
> >>> Warning message:
> >>> package 'effects' was built under R version 2.13.2
> >>> Error in plot(effect("age", myologit, xlevles = list(age = seq(20, 80, :
> >>> error in evaluating the argument 'x' in selecting a method for
> >>> function 'plot': Error in model.frame.default(formula = factor(warm) ~
> >>> yr89 + male + white + :
> >>> variable lengths differ (found for 'yr89')
> >>>
> >>> ______________________________________________
> >>> R-help at r-project.org mailing list
> >>> 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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