[R] Problem with effects package

[Lars Bishop]

Thanks for your quick response on this issue John!

Yes, in my real dataset I have many predictors and more observations
than in this example. I've started to remove one predictor at the time
until this one was found to be causing the problem.

Thanks again!
Lars.

On Sat, Jul 30, 2011 at 5:33 PM, John Fox <jfox at mcmaster.ca> wrote:
> Dear Lars,
>
> The problem is the ":" in the levels of var2, which confuses effect() about
> the structure of the model, since a colon indicates interaction. Try, e.g.,
> removing the colons:
>
> var2 <- as.factor(c("B=500", "B=500", "B=500", "B=500", "B=500", "B=500",
> "B=500", "B=500",
>                   "B=500", "C750-1000", "C750-1000", "B=500", "B=500",
> "B=500", "B=500"))
>
> Then,
>
>> effect("var2", glm1)
>
>  var2 effect
> var2
>    B=500 C750-1000
>  7947.932 13453.841
>
>
> (See how helpful it can be to furnish a reproducible example?)
>
> I agree, BTW, that this is a deficiency in effect(); I'll look into it when
> I have a chance.
>
> Finally, there really is no advantage to making an effect display for a
> model with a single predictor, though perhaps this isn't what you were doing
> in your actual application.
>
> Best,
>  John
>
>> -----Original Message-----
>> From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org]
>> On Behalf Of Lars Bishop
>> Sent: July-30-11 4:30 PM
>> To: jim holtman; r-help at r-project.org
>> Subject: Re: [R] Problem with effects package
>>
>> ok. Here's an example:
>>
>> R version 2.11.1
>> effects_2.0-10
>>
>> var1 <- c(25631.9392, 2521.2590,  6656.6516,  1362.5997,  6369.9818,
>> 27253.4223,  2073.1909,  9959.3792,
>>           3318.2500, 15323.8103, 11583.8717,  3054.5558,   625.6597,
>> 2500.0000, 11996.2271)
>> var2 <- as.factor(c("B:=500", "B:=500", "B:=500", "B:=500", "B:=500",
>> "B:=500", "B:=500", "B:=500",
>>                    "B:=500", "C:750-1000", "C:750-1000", "B:=500",
>> "B:=500", "B:=500", "B:=500"))
>>
>> glm1 <- glm(var1 ~ var2, family = Gamma(link = "log"))
>> summary(glm1)
>> library(effects)
>> plot(effect("var2", glm1))
>>
>> Error in apply(mod.matrix[, components], 1, prod) :
>>   subscript out of bounds
>> Error in plot(effect("var2", glm1)) :
>>   error in evaluating the argument 'x' in selecting a method for
>> function 'plot'
>> >
>>
>>
>> On Sat, Jul 30, 2011 at 3:10 PM, jim holtman <jholtman at gmail.com> wrote:
>> > PLEASE do read the posting guide
>> > http://www.R-project.org/posting-guide.html
>> > and provide commented, minimal, self-contained, reproducible code.
>> >
>> > We can not help unless we at least have the data that you are using.
>> >
>> > On Sat, Jul 30, 2011 at 3:01 PM, Lars Bishop <lars52r at gmail.com>
>> wrote:
>> >> Dear List,
>> >>
>> >> Several times I use this package I get the error message shown below.
>> >> When I work out simple examples, it turns out to be fine, but when
>> >> working with real and moderate size data sets I always get the same
>> >> error.
>> >>
>> >> Do you know what could be the cause of the problem?
>> >>
>> >>
>> >> Error in apply(mod.matrix[, components], 1, prod) :
>> >>  subscript out of bounds
>> >> Error in plot(effect("myvariable", glm.sev1)) :
>> >>  error in evaluating the argument 'x' in selecting a method for
>> >> function 'plot'
>> >>
>> >> Thanks,
>> >> Lars/
>> >>
>> >> ______________________________________________
>> >> 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.
>> >>
>> >
>> >
>> >
>> > --
>> > Jim Holtman
>> > Data Munger Guru
>> >
>> > What is the problem that you are trying to solve?
>> >
>>
>> ______________________________________________
>> 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.
>
>