[R-sig-ME] Observation-level random effects

[Shahinur, Islam]

Hello Thierry,

No, they are not the replicates of the same family, but 20 different
families under Cross (Population) Farm.NA.

I am trying to see both Tank effect and family effect (possibly nested
within cross) separately, but it's giving me hard time with family.

Thank you for checking into this, and your suggestions will be much
appreciated!

Regards,

Shahin


On Fri., Apr. 9, 2021, 4:56 a.m. Thierry Onkelinx <thierry.onkelinx using inbo.be>
wrote:

> Dear Shahin,
>
> I assume that a1 to a20 are replicates of the same family "a". If that is
> the case, you need to use the name of the family ("a") instead of the
> replicate id's (a1 to a20). Currently, it looks like every observation has
> a unique value for family. That would lead to an observation level random
> effect, which you can't use with a Gaussian distribution as it confounds
> with the residuals.
>
> Best regards,
>
> ir. Thierry Onkelinx
> Statisticus / Statistician
>
> Vlaamse Overheid / Government of Flanders
> INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE AND
> FOREST
> Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance
> thierry.onkelinx using inbo.be
> Havenlaan 88 bus 73, 1000 Brussel
> www.inbo.be
>
>
> ///////////////////////////////////////////////////////////////////////////////////////////
> 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
>
> ///////////////////////////////////////////////////////////////////////////////////////////
>
> <https://www.inbo.be>
>
>
> Op do 8 apr. 2021 om 18:50 schreef Shahinur, Islam <shahinur.islam using mun.ca
> >:
>
>> Hello All,
>>
>> Thank you, Dr. Thierry, for the reply!
>>
>> I am still having the problem!- just in case, I have attached my data
>> template.
>>
>> When I am running the following code:
>> model1 <- lmer(development~ 1 +cross + egg +cross*egg + (1|Tank)+
>> (1|family) ,data=sp)
>>
>> Still getting the errors: Error: number of levels of each grouping factor
>> must be < number of observations (problems: family).
>>
>> Your suggestions will be much appreciated.
>>
>> Regards,
>>
>> Shahin
>>
>> <><><><><><><><><><><><><><><><><><><><><><><><><><>
>>
>> Shahinur S. Islam
>> PhD Candidate, Department of Ocean Sciences
>> Ocean Sciences Centre, Memorial University of Newfoundland
>> St. John's, NL  A1C 5S7, Canada
>> Cell: (+1)709-740-3324; Twitter: @EcoEvoGen
>>
>>
>> On Thu, Apr 8, 2021 at 1:35 PM Thierry Onkelinx <thierry.onkelinx using inbo.be>
>> wrote:
>>
>>> Dear Shanin,
>>>
>>> You can't use an observation level random effect with a Gaussian
>>> distribution.
>>> Please provide the number of observations, number of unique families and
>>> number of unique tanks.
>>>
>>> Best regards,
>>>
>>> Thierry
>>>
>>> ir. Thierry Onkelinx
>>> Statisticus / Statistician
>>>
>>> Vlaamse Overheid / Government of Flanders
>>> INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE
>>> AND FOREST
>>> Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance
>>> thierry.onkelinx using inbo.be
>>> Havenlaan 88 bus 73, 1000 Brussel
>>> www.inbo.be
>>>
>>>
>>> ///////////////////////////////////////////////////////////////////////////////////////////
>>> 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
>>>
>>> ///////////////////////////////////////////////////////////////////////////////////////////
>>>
>>> <https://www.inbo.be>
>>>
>>>
>>> Op do 8 apr. 2021 om 17:08 schreef Shahinur, Islam <
>>> shahinur.islam using mun.ca>:
>>>
>>>> Hello All,
>>>> I am having trouble with observation-level random effects while running
>>>> the
>>>> full model investigating two fixed covariates (one categorical and one
>>>> continuous) and two random covariates (tank and family). While I am
>>>> using
>>>> the only tank random effect, it works fine, but while I am adding
>>>> another
>>>> random covariate (family), I am getting the error message: Error:
>>>> number of
>>>> levels of each grouping factor must be < number of observations
>>>> (problems:
>>>> family).
>>>>
>>>> FYI, here is my code:
>>>> model1 <- lmer(development~ 1 +cross + egg +cross*egg + (1|Tank)+
>>>> (1|family) ,data=sp)
>>>>
>>>> I do have different family IDs (n=108) for each row, I assume it creates
>>>> the problem.
>>>>
>>>> Your suggestions will be much appreciated!
>>>>
>>>> Regards,
>>>>
>>>> Shahin
>>>>
>>>> <><><><><><><><><><><><><><><><><><><><><><><><><><>
>>>>
>>>> Shahinur S. Islam
>>>> PhD Candidate, Department of Ocean Sciences
>>>> Ocean Sciences Centre, Memorial University of Newfoundland
>>>> St. John's, NL  A1C 5S7, Canada
>>>> Cell: (+1)709-740-3324; Twitter: @EcoEvoGen
>>>>
>>>>         [[alternative HTML version deleted]]
>>>>
>>>> _______________________________________________
>>>> R-sig-mixed-models using r-project.org mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
>>>>
>>>

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