[R-sig-ME] Conceptual doubts on how to define my random effects

[Poe, John]

This is (more or less) a chapter from Jim Hodges' book called Richly
Parameterized Linear Models: Additive, Time Series, and Spatial Models
Using Random Effects. The chapter goes through the classical interpretation
of a random effect in an experimental setting and then more modern
interpretations. It is VERY in line with Richard McElreath's general
interpretation of random effects in his statistical rethinking book.

http://www.biostat.umn.edu/~hodges/PubH8492/Hodges-ClaytonREONsubToStatSci.pdf

On Tue, Oct 9, 2018 at 5:45 AM Mario Garrido <gaadio using post.bgu.ac.il> wrote:

> Dear lme4users,
> I have some conceptual doubts on understanding the meaning of some random
> factors.
>
> Briefly, I am checking the dynamics of infection by bacteria on individuals
> from 3 different species of hosts. I am trying to fit my data to a
> generalized linear model with repeated measures. My data consists on the
> amount
> of bacterial colonies  (Myc.qPCR) at different time points (day) fin the
> blood of the 33 individual hosts (exp.ID), belonging to 3 different
> species  (sp). At time zero all the values are 0 cause the indivuals were
> still not infected.
> As I want to check whether the dynamics in the three species are different
> I included in my first model day*sp as fixed factor
>
> I am trying to fit the random effect but I have some problems with the
> interpretation. Any reading recommendations for Ecologists that we are not
> experts in statistics to understand the ecological meaning of random
> effects?
>
> I know for use that I want to control  for variance at individual level so,
> |exp.ID is needed, I also want to 'force the intercept to be zero (since at
> day zero amount of bacteria is zero) , and I also wonder whether I have to
> nest the individuals within day.
> Thus, my model would be
>
>
>
> lme(lg(Myc.qPCR)~day*sp,random=?,method="ML")
>
> And I have doubts on how to define my random effect, cause, indeed, I do
> not know what is the exact meaning of them under lme4. I understand that as
> I have a Mixed-effects model with temporal pseudoreplication I hould use
> day in the random factor, but how to include that intercept is zero?
> (1|exp.ID)
> (day|exp.ID)
> (0+day|exp.ID)
> +(1|exp.ID)+(0+day|exp.ID)
>
> Thanks!
>
> --
> Mario Garrido Escudero, PhD
> Dr. Hadas Hawlena Lab
> Mitrani Department of Desert Ecology
> Jacob Blaustein Institutes for Desert Research
> Ben-Gurion University of the Negev
> Midreshet Ben-Gurion 84990 ISRAEL
>
> gaiarrido using gmail.com; gaadio using post.bgu.ac.il
> phone: (+972) 08-659-6854
>
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>
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>


-- 




Thanks,
John


John Poe, Ph.D.
Postdoctoral Scholar / Research Methodologist
Center for Public Health Services & Systems Research
University of Kentucky
www.johndavidpoe.com

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