[R] Help with lme
Annie Hoen
anniehoen at gmail.com
Fri Nov 9 18:55:52 CET 2012
Thank you both!! Great to know. I've posted my question to
r-sig-mixed-models.
Thanks again!
Annie
On 11/9/12 12:53 PM, "R. Michael Weylandt" <michael.weylandt at gmail.com>
wrote:
>On Fri, Nov 9, 2012 at 5:27 PM, Bert Gunter <gunter.berton at gene.com>
>wrote:
>> Well, you've posted to the wrong list!
>>
>> First off, you're almost always better off posting to an R SIG list
>> when one exists in your area of concern,as it does here:
>> r-sig-mixed-models.
>>
>> Second, this appears to be primarily a statistics question, and R-help
>> is not a statistics help list (though, I admit, the intersection is
>> nonempty, and that may be the case here). For statistics primarily
>> questions,you should generally post to a statistics help list like
>> stats.stackexchange.com.
>>
>> Otherwise, you're fine. :-)
>>
>> Cheers,
>> Bert
>>
>> On Fri, Nov 9, 2012 at 9:15 AM, Annie Hoen <anniehoen at gmail.com> wrote:
>>> Hi,
>>>
>>> This is my first time posting to the list so please forgive any
>>>breeches
>>> of etiquette!
>>> I am new to mixed-effects modeling.
>>>
>>> This is my dataset:
>>>
>>> subject treatment day replicate outcome
>>> 1 1 1 1 0.0
>>> 1 1 4 1 0.0
>>> 1 1 8 1 14.5
>>> 1 1 8 2 15.4
>>> 2 1 2 1 0.0
>>> 2 1 4 1 0.0
>>> 2 1 7 1 12.1
>>> 2 1 7 2 11.9
>>> 3 1 2 1 0.0
>>> 3 1 4 1 0.0
>>> 3 1 7 1 0.0
>>> 4 1 2 1 4.2
>>> 4 1 2 2 5.0
>>> 4 1 4 1 8.5
>>> 4 1 4 2 10.0
>>> 4 1 6 1 16.4
>>> 4 1 6 2 18.1
>>> 5 1 2 1 0.0
>>> 5 1 4 1 0.0
>>> 5 1 7 1 0.0
>>> 6 2 2 1 0.0
>>> 6 2 4 1 9.1
>>> 6 2 4 2 9.7
>>> 6 2 7 1 12.6
>>> 6 2 7 2 10.3
>>> 7 2 1 1 3.3
>>> 7 2 1 2 4.8
>>> 7 2 4 1 6.2
>>> 7 2 4 2 6.4
>>> 7 2 7 1 12.9
>>> 7 2 7 2 13.1
>>> 8 2 2 1 0.0
>>> 8 2 4 1 0.0
>>> 8 2 8 1 0.0
>>> 9 2 2 1 2.7
>>> 9 2 2 2 3.2
>>> 9 2 4 1 5.6
>>> 9 2 4 2 5.4
>>> 9 2 8 1 14.9
>>> 9 2 8 2 14.8
>>> 10 2 1 1 0.0
>>> 10 2 4 1 10.7
>>> 10 2 4 2 11.0
>>> 10 2 7 1 13.7
>>> 10 2 7 2 12.9
>>> 11 2 1 1 0.0
>>> 11 2 4 1 0.0
>>> 11 2 7 1 0.0
>>> 12 2 1 1 0.0
>>> 12 2 4 1 0.0
>>> 12 2 7 1 0.0
>>>
>>>
>>> It can be made using this:
>>>
>>> subject=c(1, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 4, 4, 4, 4, 4, 4, 5, 5, 5,
>>>6,
>>> 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 8, 8, 8, 9, 9, 9, 9, 9, 9, 10, 10, 10,
>>>10,
>>> 10, 11, 11, 11, 12, 12, 12)
>>> treatment=c(rep(1, 20), rep(2, 31))
>>> day=c(1, 4, 8, 8, 2, 4, 7, 7, 2, 4, 7, 2, 2, 4, 4, 6, 6, 2, 4, 7, 2,
>>>4, 4,
>>> 7, 7, 1, 1, 4, 4, 7, 7, 2, 4, 8, 2, 2, 4, 4, 8, 8, 1, 4, 4, 7, 7, 1,
>>>4, 7,
>>> 1, 4, 7)
>>> replicate=c(1, 1, 1, 2, 1, 1, 1, 2, 1, 1, 1, 1, 2, 1, 2, 1, 2, 1, 1,
>>>1, 1,
>>> 1, 2, 1, 2, 1, 2, 1, 2, 1, 2, 1, 1, 1, 1, 2, 1, 2, 1, 2, 1, 1, 2, 1,
>>>2, 1,
>>> 1, 1, 1, 1, 1)
>>> outcome=c(0, 0, 14.5, 15.4, 0, 0, 12.1, 11.9, 0, 0, 0, 4.2, 5.0, 8.5,
>>> 10.0, 16.4, 18.1, 0, 0, 0, 0, 9.1, 9.7, 12.6, 10.3, 3.3, 4.8, 6.2, 6.4,
>>> 12.9, 13.1, 0,0,0, 2.7,3.2, 5.6, 5.4, 14.9, 14.8, 0, 10.7, 11.0, 13.7,
>>> 12.9, 0, 0, 0, 0, 0, 0)
>>>
>>> data<-data.frame(cbind(subject, treatment, day, replicate, outcome))
>
>Seconding Bert's advice to repost to R-SIG-Mixed-models (it's a great
>mailing list with brilliant statisticians) and commending a really
>good reproducible example. The only thing I'd note is that you
>generally don't want to use constructs like:
>
>data.frame(cbind(....))
>
>cbind() will create a matrix object before data.frame() is called. The
>disadvantage of that is that a matrix can have only one sort of data,
>so cbind() will force it all to be the same (usually either numeric or
>character). You can loose information here, but, more importantly
>data.frame() doesn't know what went into cbind() so it doesn't bother
>to convert back to the original data type. Then you're left with a
>data.frame of all one data type, which more or less defeats the point
>of data.frames in the first place. :-)
>
>It's better to just call data.frame() directly with something like
>
>data.frame(subject, treatment, day, replicate, outcome)
>
>You'll also get the added bonus of R figuring out names for columns here.
>
>Of course, in your case, it doesn't hurt because your data really is
>all of the same type. But good practice and all that!
>
>Cheers and welcome!
>
>Michael
>
>
>>>
>>> I have two groups of subjects, each given a different treatment. The
>>> outcome (growth) was observed post-treatment on each of three days. If
>>> there was growth, it was measured in duplicate measurements.
>>>
>>> There are uneven numbers of subjects in my two treatment groups. Also,
>>>the
>>> outcome was always observed on 3 days, but the exact day of
>>>observation is
>>> not always consistent.
>>>
>>> I just want to know the effect of treatment on outcome.
>>>
>>> This is the model I've run:
>>>
>>> model <- lme(outcome ~ treatment * day, random = list(subject =
>>>pdDiag(~
>>> day)), data = data)
>>> summary(model)
>>>
>>>
>>> Can any experts out there let me know if I'm doing this right?
>>>Thanks!!!
>>>
>>> ______________________________________________
>>> 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.
>>
>>
>>
>> --
>>
>> Bert Gunter
>> Genentech Nonclinical Biostatistics
>>
>> Internal Contact Info:
>> Phone: 467-7374
>> Website:
>>
>>http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-bi
>>ostatistics/pdb-ncb-home.htm
>>
>> ______________________________________________
>> 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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