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

Poe, John jdpo223 @ending from g@uky@edu
Tue Oct 9 22:05:08 CEST 2018

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.


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

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