[R] effect function in the effects package

[Xu Jun]

Dear Prof. Fox,

I just picked up R not long ago, and apologize that I am not that
familiar with some basics. I am trying to replicate what I can do with
Stata in R. Thanks for all your help!

On Thu, Oct 20, 2011 at 2:47 PM, John Fox <jfox at mcmaster.ca> wrote:
> Dear Xu Jun,
>
> On Thu, 20 Oct 2011 14:41:30 -0400
>  Xu Jun <junxu.r at gmail.com> wrote:
>> Dear Professor Fox,
>>
>> Now I got it. It all comes from my unfamiliarity with the effect
>> function. I forgot the c part in the given.values option, plus it
>> looks like plot(effect()) does not like factor(warm) in the polr
>> function. So here are the two working lines:
>>
>> ordwarm2$warm2 <- as.factor(ordwarm2$warm)
>
> Without the data, I have no idea what's going on here; the implication is that warm wasn't a factor.
>
>> myologit <- polr(warm2 ~ yr89 + male + white + age + ed + prst,
>>               data=ordwarm2, method=c("logistic"))
>> plot(effect("age", myologit, xlevels=list(age=seq(20, 80, 5)),
>> given.values=(c(male=1, yr89=1))))
>
> given.values is an argument. c() is a standard R function for combining values into a vector (or a list); it is not particular to the effects package. The parentheses around (c(male=1, yr89=1)) are entirely unnecessary, and the call to c() in  c("logistic") does nothing.
>
> Best,
>  John
>
>>
>> Again, thanks a lot for your effects package that makes graphing so much easier.
>>
>> Jun
>>
>> 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.
>> >
>> >
>> >
>> >
>
> ------------------------------------------------
> John Fox
> Sen. William McMaster Prof. of Social Statistics
> Department of Sociology
> McMaster University
> Hamilton, Ontario, Canada
> http://socserv.mcmaster.ca/jfox/
>
>