[R-sig-ME] contrasts among simple effects

[Thierry Onkelinx]

Dear James,

Please keep the mailing list in cc. Most likely someone else would have
told you that the errors are due to a syntax error. You want lme(HR ~
drug*ordered(time), random =~1|person, correlation =
corAR1(form=~time|person), data = heartRate)

Best regards,

ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature and
Forest
team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance
Kliniekstraat 25
1070 Anderlecht
Belgium

To call in the statistician after the experiment is done may be no more
than asking him to perform a post-mortem examination: he may be able to say
what the experiment died of. ~ Sir Ronald Aylmer Fisher
The plural of anecdote is not data. ~ Roger Brinner
The combination of some data and an aching desire for an answer does not
ensure that a reasonable answer can be extracted from a given body of data.
~ John Tukey

2015-10-16 19:07 GMT+02:00 James Henson <jfhenson1 op gmail.com>:

> Dear Thierry,
>
> Thank you for the counsel. However, my perplexity persists.  Many
> variations of adding 'corAR1(form = ~time|person)' return an error
> message.  Some of these variations are below.
>
> model2b <- lme(HR ~ drug*ordered(time), random =~1|person, correlation
> =corAR1(, form=~1|person) =corAR1(, form=~time|person), data = heartRate)
>
> Error: unexpected '=' in "model2b <- lme(HR ~ drug*ordered(time), random
> =~1|person, correlation =corAR1(, form=~1|person) ="
>
>
>
> > model2b <- lme(HR ~ drug*ordered(time), random =~1|person, correlation
> =corAR1(, form=~1|person) corAR1(, form=~time|person), data = heartRate)
>
> Error: unexpected symbol in "model2b <- lme(HR ~ drug*ordered(time),
> random =~1|person, correlation =corAR1(, form=~1|person) corAR1"
>
>
>
> model2b <- lme(HR ~ drug*ordered(time), random =~1|person, correlation
> =corAR1(, form=~1|person), =corAR1(, form=~time|person), data = heartRate)
>
> Error: unexpected '=' in "model2b <- lme(HR ~ drug*ordered(time), random
> =~1|person, correlation =corAR1(, form=~1|person), ="
>
>
>
> model2b <- lme(HR ~ drug*ordered(time), random =~1|person, correlation
> =corAR1(, form=~time|person), data = heartRate)
>
> Error in structure(res, levels = lv, names = nm, class = "factor") :
> 'names' attribute [72] must be the same length as the vector [0]
>
>
>
> model2b <- lme(HR ~ drug*ordered(time), random =~1|person, correlation
> =corAR1(, form=~1|person, time|person), data = heartRate)
>
> Error in time | person :  operations are possible only for numeric,
> logical or complex types
>
>
>
> model2b <- lme(HR ~ drug*ordered(time), random =~1|person, correlation
> =corAR1(, form=~1|person, form=~time|person), data = heartRate)
>
> Error in corAR1(, form = ~1 | person, form = ~time | person) :  formal
> argument "form" matched by multiple actual arguments
>
>
>
> model2b <- lme(HR ~ drug*ordered(time), random =~1|person, correlation
> =corAR1(, form=~1|person), correlation= corAR1(, form=~time|person), data =
> heartRate)
>
> Error in lme(HR ~ drug * ordered(time), random = ~1 | person, correlation
> = corAR1(,  :   formal argument "correlation" matched by multiple actual
> arguments
>
>
> Hopefully, you can help.
>
> Books on my shelve show R examples from behavioral science.  Need a
> cookbook with R examples from  biology/agriculture, but have not found one.
>
>
> Best regards,
>
> James F. Henson
>
> Research Scientist
>
> Southern University
>
> Baton Rouge, USA
>
> Wisdom is knowing what you don't know. ~ Socrates
>
>
>
>
>
> On Fri, Oct 16, 2015 at 6:24 AM, Thierry Onkelinx <
> thierry.onkelinx op inbo.be> wrote:
>
>> Dear James,
>>
>> I think that you need to specify the order of the data as well.
>> corAR1(form = ~time|person). Otherwise the order of the observations as
>> present in the data is used.
>>
>> Best regards,
>>
>> ir. Thierry Onkelinx
>> Instituut voor natuur- en bosonderzoek / Research Institute for Nature
>> and Forest
>> team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance
>> Kliniekstraat 25
>> 1070 Anderlecht
>> Belgium
>>
>> To call in the statistician after the experiment is done may be no more
>> than asking him to perform a post-mortem examination: he may be able to say
>> what the experiment died of. ~ Sir Ronald Aylmer Fisher
>> The plural of anecdote is not data. ~ Roger Brinner
>> The combination of some data and an aching desire for an answer does not
>> ensure that a reasonable answer can be extracted from a given body of data.
>> ~ John Tukey
>>
>> 2015-10-14 18:46 GMT+02:00 James Henson <jfhenson1 op gmail.com>:
>>
>>> Greetings R Community
>>>
>>> Apologize for previously sending a csv file.
>>>
>>> My goal is to make orthogonal contrasts among simple effects in analysis
>>> of
>>> repeated measures data.  The SAS publication, on page 1224, shows how to
>>> make this type of contrasts in SAS.  But, my search of books about
>>> repeated
>>> measures analysis using R, and on-line has not yielded a methodology.
>>> Hopefully, someone can direct me to a book or publication that will show
>>> me
>>> a methodology.
>>>
>>> Statistical Analysis of Repeated Measures Data Using SAS Procedures
>>>
>>>
>>> http://cslras.pbworks.com/f/littell_j_anim_sci_76_4_analysis_of_repeated_measures_using_sas.pdf
>>>
>>>
>>>
>>> Attached is a txt data file (file name = heart_rate.txt).  My code for
>>> the
>>> repeated measures analysis is below.
>>>
>>> library("nlme")
>>>
>>> # with AR1 variance/covariance structure, with ordered statement
>>>
>>> heartRate$time <- factor(heartRate$time)
>>>
>>> model2a <- lme(HR ~ drug*ordered(time), random =~1|person, correlation
>>> =corAR1(, form=~1|person), data = heartRate)
>>>
>>> summary(model2a)
>>>
>>> anova(model2a)
>>>
>>> Making a new variable ‘simple’ that merges the variables drug and time
>>> will
>>> enable me to make orthogonal contrasts among the simple effects.  But,
>>> when
>>> using the variable ‘simple’ as the independent variable, the data will no
>>> longer be fitted to the AR1 variance/covariance structure.
>>>
>>> Thanks.
>>>
>>> Best regards,
>>>
>>> James F.Henson
>>>
>>> _______________________________________________
>>> R-sig-mixed-models op r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
>>>
>>>
>>
>

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